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

International Nuclear Information System (INIS)

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

1988-01-01

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

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

Science.gov (United States)

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

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.

Methylation of inorganic arsenic in different mammalian species and population groups.

Science.gov (United States)

Vahter, M

1999-01-01

Thousands of people in different parts of the world are exposed to arsenic via drinking water or contaminated soil or food. The high general toxic of arsenic has been known for centuries, and research during the last decades has shown that arsenic is a potent human carcinogen. However, most experimental cancer studies have failed to demonstrate carcinogenicity in experimental animals, indicating marked variation in sensitivity towards arsenic toxicity between species. It has also been suggested that there is a variation in susceptibility among human individuals. One reason for such variability in toxic response may be variation in metabolism. Inorganic arsenic is methylated in humans as well as animals and micro-organisms, but there are considerable differences between species and individuals. In many, but not all, mammalian species, inorganic arsenic is methylated to methylarsonic acid (MMA) and dimethylarsinic acid (DMA), which are more rapidly excreted in urine than is the inorganic arsenic, especially the trivalent form (AsIII, arsenite) which is highly reactive with tissue components. Absorbed arsenate (AsV) is reduced to trivalent arsenic (AsIII) before the methyl groups are attached. It has been estimated that as much as 50-70% of absorbed AsV is rapidly reduced to AsIII, a reaction which seems to be common for most species. In most experimental animal species, DMA is the main metabolite excreted in urine. Compared to human subjects, very little MMA is produced. However, the rate of methylation varies considerably between species, and several species, e.g. the marmoset monkey and the chimpanzee have been shown not to methylate inorganic arsenic at all. In addition, the marmoset monkey accumulates arsenic in the liver. The rat, on the other hand, has an efficient methylation of arsenic but the formed DMA is to a large extent accumulated in the red blood cells. As a result, the rat shows a low rate of excretion of arsenic. In both human subjects and rodents

Dynamics and disorder of methyl group in the different phases of 2,6-dimethyl pyrazine, 4-methyl pyridine and 4-methyl pyridine N-oxide; Dynamique et desordre du groupe methyle dans les differentes phases de la 2,6-dimethyl pyrazine, 4-methyl pyridine et 4-methyl pyridine N-oxyde

Energy Technology Data Exchange (ETDEWEB)

Kaiser Morris, E

1997-12-22

The thermal and mechanical properties of organic compounds are well known to be strongly correlated with the orientational freedom of its molecules or its molecular groups such as NH{sub 3}, CH{sub 3}, CH{sub 4}... For this reason, the study of the rotational behaviour of methyl groups in the solid state as a function of temperature is of great interest. With decreasing temperature, the rotations change from classical hoping to processes where quantum mechanical rotations become important. By quantum mechanical rotations, we mean the low-temperature counterpart, for with tunneling is the dominant mode of motion. However, the interpretation of tunnelling lines is critical when it is not straightforward to relate them to specific vibrational modes and particularly so when the molecule contains crystallographically inequivalent groups. The aim of this work is to interpret such spectra (obtained from inelastic neutron scattering) from structural data. The lack of structural knowledge at low temperatures, makes therefore a limited interpretation of the spectra obtained from polycrystalline samples. In a first step it is essential to solve crystalline structure of compounds by single crystal X-rays and neutron diffraction. Indeed X-ray diffraction is necessary to locate the skeleton (C, N, O and localised H atoms). Moreover neutron diffraction is the unique tool to precise the position of H atoms of methyl groups. The exam of the nuclear density of these protons the Fourier maps allows us to evaluate the crystal potential experienced by this rotor. Inelastic neutron scattering allows on single crystals allows the complete characterizations of quantum excitations (author) 75 refs.

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

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.

Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear overhauser enhancement spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Venditti, Vincenzo; Fawzi, Nicolas L.; Clore, G. Marius, E-mail: mariusc@mail.nih.gov [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)

2011-11-15

Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to {approx}1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic relaxation enhancement (PRE), induced by nitroxide spin-labels incorporated at only a few surface-exposed engineered cysteines, provides fast, straightforward and robust access to methyl group resonance assignments, including stereoassignments for the methyl groups of leucine and valine. Neither prior assignments, including backbone assignments, for the protein, nor experiments that transfer magnetization between methyl groups and the protein backbone, are required. PRE-derived assignments are refined by 4D methyl-methyl nuclear Overhauser enhancement data, eliminating ambiguities and errors that may arise due to the high sensitivity of PREs to the potential presence of sparsely-populated transient states.

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.

Methylation-sensitive amplified polymorphism-based genome-wide analysis of cytosine methylation profiles in Nicotiana tabacum cultivars.

Science.gov (United States)

Jiao, J; Wu, J; Lv, Z; Sun, C; Gao, L; Yan, X; Cui, L; Tang, Z; Yan, B; Jia, Y

2015-11-26

This study aimed to investigate cytosine methylation profiles in different tobacco (Nicotiana tabacum) cultivars grown in China. Methylation-sensitive amplified polymorphism was used to analyze genome-wide global methylation profiles in four tobacco cultivars (Yunyan 85, NC89, K326, and Yunyan 87). Amplicons with methylated C motifs were cloned by reamplified polymerase chain reaction, sequenced, and analyzed. The results show that geographical location had a greater effect on methylation patterns in the tobacco genome than did sampling time. Analysis of the CG dinucleotide distribution in methylation-sensitive polymorphic restriction fragments suggested that a CpG dinucleotide cluster-enriched area is a possible site of cytosine methylation in the tobacco genome. The sequence alignments of the Nia1 gene (that encodes nitrate reductase) in Yunyan 87 in different regions indicate that a C-T transition might be responsible for the tobacco phenotype. T-C nucleotide replacement might also be responsible for the tobacco phenotype and may be influenced by geographical location.

Structural and Kinetic Evidence for an Extended Hydrogen-Bonding Network in Catalysis of Methyl Group Transfer

International Nuclear Information System (INIS)

Doukov, T.; Hemmi, H.; Drennan, C.; Ragsdale, S.

2007-01-01

The methyltetrahydrofolate (CH 3 -H 4 folate) corrinoid-ironsulfur protein (CFeSP) methyltransferase (MeTr) catalyzes transfer of the methyl group of CH3-H4folate to cob(I)amide. This key step in anaerobic CO and CO 2 fixation is similar to the first half-reaction in the mechanisms of other cobalamin-dependent methyltransferases. Methyl transfer requires electrophilic activation of the methyl group of CH 3 -H 4 folate, which includes proton transfer to the N5 group of the pterin ring and poises the methyl group for reaction with the Co(I) nucleophile. The structure of the binary CH 3 -H 4 folate/MeTr complex (revealed here) lacks any obvious proton donor near the N5 group. Instead, an Asn residue and water molecules are found within H-bonding distance of N5. Structural and kinetic experiments described here are consistent with the involvement of an extended H-bonding network in proton transfer to N5 of the folate that includes an Asn (Asn-199 in MeTr), a conserved Asp (Asp-160), and a water molecule. This situation is reminiscent of purine nucleoside phosphorylase, which involves protonation of the purine N7 in the transition state and is accomplished by an extended H-bond network that includes water molecules, a Glu residue, and an Asn residue (Kicska, G. A., Tyler, P. C., Evans, G. B., Furneaux, R. H., Shi, W., Fedorov, A., Lewandowicz, A., Cahill, S. M., Almo, S. C., and Schramm, V. L. (2002) Biochemistry 41, 14489-14498). In MeTr, the Asn residue swings from a distant position to within H-bonding distance of the N5 atom upon CH 3 -H 4 folate binding. An N199A variant exhibits only ∼20-fold weakened affinity for CH 3 -H 4 folate but a much more marked 20,000-40,000-fold effect on catalysis, suggesting that Asn-199 plays an important role in stabilizing a transition state or high energy intermediate for methyl transfer

Dynamics and disorder of methyl group in the different phases of 2,6-dimethyl pyrazine, 4-methyl pyridine and 4-methyl pyridine N-oxide

International Nuclear Information System (INIS)

Kaiser Morris, E.

1997-01-01

The thermal and mechanical properties of organic compounds are well known to be strongly correlated with the orientational freedom of its molecules or its molecular groups such as NH 3 , CH 3 , CH 4 ... For this reason, the study of the rotational behaviour of methyl groups in the solid state as a function of temperature is of great interest. With decreasing temperature, the rotations change from classical hoping to processes where quantum mechanical rotations become important. By quantum mechanical rotations, we mean the low-temperature counterpart, for with tunneling is the dominant mode of motion. However, the interpretation of tunnelling lines is critical when it is not straightforward to relate them to specific vibrational modes and particularly so when the molecule contains crystallographically inequivalent groups. The aim of this work is to interpret such spectra (obtained from inelastic neutron scattering) from structural data. The lack of structural knowledge at low temperatures, makes therefore a limited interpretation of the spectra obtained from polycrystalline samples. In a first step it is essential to solve crystalline structure of compounds by single crystal X-rays and neutron diffraction. Indeed X-ray diffraction is necessary to locate the skeleton (C, N, O and localised H atoms). Moreover neutron diffraction is the unique tool to precise the position of H atoms of methyl groups. The exam of the nuclear density of these protons the Fourier maps allows us to evaluate the crystal potential experienced by this rotor. Inelastic neutron scattering allows on single crystals allows the complete characterizations of quantum excitations (author)

Cost Analysis Of Replacement And Bearing Trailer Maintenance In Sugar Group Companies

OpenAIRE

Mastur, Mastur; Masyhuri, Masyhuri; Waluyati, Lestari Rahayu

2017-01-01

The purpose of this study are to understand (i) the costs and periods optimal of grease used for the replacement and maintenance bearing trailer in Sugar Group Companies (SGC), and (ii) the effect of a period and frequency of grease, lifetime bearing, frequency of replacement bearing in a year, unit trailer, brand bearing, and location of plant. The basic method used is descriptive and analytical. The location determined were in Workshop Division PT. ILP, PT. SIL, and PT. GPM. The analytical ...

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.

Identification of Differentially Methylated Sites with Weak Methylation Effects

Directory of Open Access Journals (Sweden)

Hong Tran

2018-02-01

Full Text Available Deoxyribonucleic acid (DNA methylation is an epigenetic alteration crucial for regulating stress responses. Identifying large-scale DNA methylation at single nucleotide resolution is made possible by whole genome bisulfite sequencing. An essential task following the generation of bisulfite sequencing data is to detect differentially methylated cytosines (DMCs among treatments. Most statistical methods for DMC detection do not consider the dependency of methylation patterns across the genome, thus possibly inflating type I error. Furthermore, small sample sizes and weak methylation effects among different phenotype categories make it difficult for these statistical methods to accurately detect DMCs. To address these issues, the wavelet-based functional mixed model (WFMM was introduced to detect DMCs. To further examine the performance of WFMM in detecting weak differential methylation events, we used both simulated and empirical data and compare WFMM performance to a popular DMC detection tool methylKit. Analyses of simulated data that replicated the effects of the herbicide glyphosate on DNA methylation in Arabidopsis thaliana show that WFMM results in higher sensitivity and specificity in detecting DMCs compared to methylKit, especially when the methylation differences among phenotype groups are small. Moreover, the performance of WFMM is robust with respect to small sample sizes, making it particularly attractive considering the current high costs of bisulfite sequencing. Analysis of empirical Arabidopsis thaliana data under varying glyphosate dosages, and the analysis of monozygotic (MZ twins who have different pain sensitivities—both datasets have weak methylation effects of <1%—show that WFMM can identify more relevant DMCs related to the phenotype of interest than methylKit. Differentially methylated regions (DMRs are genomic regions with different DNA methylation status across biological samples. DMRs and DMCs are essentially the same

Calculation of restricted rotational states in the methyl group

CERN Document Server

Ozaki, Y

2002-01-01

A methyl group attached to a molecule in the solid phase has a certain amount of hindrance in its rotational motion. The rotational potential can usually be expressed by the 3rd-order and the 6th-order terms of periodic functions. In the intermediate region with respect to the field strength and also the degree of mixing of two components, much variety appears in the structure of the rotational energy levels. The energy values correspond to the various molecular surroundings. The matrix elements are also derived, which yield the intensity of inelastic neutron scattering spectra. One example of calculated intensities is given. (orig.)

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

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

International Nuclear Information System (INIS)

Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

2013-01-01

Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

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.

Sequence-specific assignment of methyl groups from the neuronal SNARE complex using lanthanide-induced pseudocontact shifts

International Nuclear Information System (INIS)

Pan, Yun-Zu; Quade, Bradley; Brewer, Kyle D.; Szabo, Monika; Swarbrick, James D.; Graham, Bim; Rizo, Josep

2016-01-01

Neurotransmitter release depends critically on the neuronal SNARE complex formed by syntaxin-1, SNAP-25 and synaptobrevin, as well as on other proteins such as Munc18-1, Munc13-1 and synaptotagmin-1. Although three-dimensional structures are available for these components, it is still unclear how they are assembled between the synaptic vesicle and plasma membranes to trigger fast, Ca 2+ -dependent membrane fusion. Methyl TROSY NMR experiments provide a powerful tool to study complexes between these proteins, but assignment of the methyl groups of the SNARE complex is hindered by its limited solubility. Here we report the assignment of the isoleucine, leucine, methionine and valine methyl groups of the four SNARE motifs of syntaxin-1, SNAP-25 and synaptobrevin within the SNARE complex based solely on measurements of lanthanide-induced pseudocontact shifts. Our results illustrate the power of this approach to assign protein resonances without the need of triple resonance experiments and provide an invaluable tool for future structural studies of how the SNARE complex binds to other components of the release machinery.

Sequence-specific assignment of methyl groups from the neuronal SNARE complex using lanthanide-induced pseudocontact shifts

Energy Technology Data Exchange (ETDEWEB)

Pan, Yun-Zu; Quade, Bradley; Brewer, Kyle D. [University of Texas Southwestern Medical Center, Department of Biophysics (United States); Szabo, Monika; Swarbrick, James D.; Graham, Bim [Monash Institute of Pharmaceutical Sciences, Monash University (Australia); Rizo, Josep, E-mail: Jose.Rizo-Rey@UTSouthwestern.edu [University of Texas Southwestern Medical Center, Department of Biophysics (United States)

2016-12-15

Neurotransmitter release depends critically on the neuronal SNARE complex formed by syntaxin-1, SNAP-25 and synaptobrevin, as well as on other proteins such as Munc18-1, Munc13-1 and synaptotagmin-1. Although three-dimensional structures are available for these components, it is still unclear how they are assembled between the synaptic vesicle and plasma membranes to trigger fast, Ca{sup 2+}-dependent membrane fusion. Methyl TROSY NMR experiments provide a powerful tool to study complexes between these proteins, but assignment of the methyl groups of the SNARE complex is hindered by its limited solubility. Here we report the assignment of the isoleucine, leucine, methionine and valine methyl groups of the four SNARE motifs of syntaxin-1, SNAP-25 and synaptobrevin within the SNARE complex based solely on measurements of lanthanide-induced pseudocontact shifts. Our results illustrate the power of this approach to assign protein resonances without the need of triple resonance experiments and provide an invaluable tool for future structural studies of how the SNARE complex binds to other components of the release machinery.

Rotation of methyl side groups in polymers: A Fourier transform approach to quasielastic neutron scattering. 1: Homopolymers

International Nuclear Information System (INIS)

Arrighi, V.; Higgins, J.S.; Howells, W.S.

1995-01-01

The rotational motion of the ester methyl group in poly(methyl methacrylate) (PMMA) was investigated using quasielastic neutron scattering (QENS). A comparison between the authors results and the QENS data reported in the literature for PMMA-d 5 indicates that the amount of quasielastic broadening is highly dependent upon the energy resolution of the spectrometer. This anomalous behavior is here attributed to the method of analysis, namely, the use of a single rotational frequency. Such a procedure leads to a non-Arrhenius temperature dependence, to a temperature-dependent elastic incoherent structure factor, and to values of rotational frequency which are resolution dependent. They propose an alternative approach to the analysis of the QENS data which accounts for the existence of a distribution of rotational frequencies. The frequency data are Fourier transformed to the time domain, and the intermediate scattering function is fitted using a stretched exponential or Kohlraush-Williams-Watts function. The excellent overlap between data from different spectrometers leaves no doubt on the adequacy of their procedure. Measurements of the ether methyl group rotation in poly(vinyl methyl ether) (PVME) are also reported. The PVME data confirm that the behavior observed for PMMA-d 5 is likely to be a common feature to all polymeric systems

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.

Reorientation of the Methyl Group in MAs(III) is the Rate-Limiting Step in the ArsM As(III) S-Adenosylmethionine Methyltransferase Reaction.

Science.gov (United States)

Packianathan, Charles; Li, Jiaojiao; Kandavelu, Palani; Sankaran, Banumathi; Rosen, Barry P

2018-03-01

The most common biotransformation of trivalent inorganic arsenic (As(III)) is methylation to mono-, di-, and trimethylated species. Methylation is catalyzed by As(III) S -adenosylmethionine (SAM) methyltransferase (termed ArsM in microbes and AS3MT in animals). Methylarsenite (MAs(III)) is both the product of the first methylation step and the substrate of the second methylation step. When the rate of the overall methylation reaction was determined with As(III) as the substrate, the first methylation step was rapid, whereas the second methylation step was slow. In contrast, when MAs(III) was used as the substrate, the rate of methylation was as fast as the first methylation step when As(III) was used as the substrate. These results indicate that there is a slow conformational change between the first and second methylation steps. The structure of CmArsM from the thermophilic alga Cyanidioschyzon merolae sp. 5508 was determined with bound MAs(III) at 2.27 Å resolution. The methyl group is facing the solvent, as would be expected when MAs(III) is bound as the substrate rather than facing the SAM-binding site, as would be expected for MAs(III) as a product. We propose that the rate-limiting step in arsenic methylation is slow reorientation of the methyl group from the SAM-binding site to the solvent, which is linked to the conformation of the side chain of a conserved residue Tyr70.

Methyl group balance in brain and liver: role of choline on increased S-adenosyl methionine (SAM) demand by chronic arsenic exposure.

Science.gov (United States)

Ríos, Rosalva; Santoyo, Martha E; Cruz, Daniela; Delgado, Juan Manuel; Zarazúa, Sergio; Jiménez-Capdeville, María E

2012-11-30

Arsenic toxicity has been related to its interference with one carbon metabolism, where a high demand of S-adenosylmethionine (SAM) for arsenic methylation as well as a failure of its regeneration would compromise the availability of methyl groups for diverse cellular functions. Since exposed animals show disturbances of methylated products such as methylated arginines, myelin and axon membranes, this work investigates whether alterations of SAM, choline and phosphatidylcholine (PC) in the brain of arsenic exposed rats are associated with myelin alterations and myelin basic protein (MBP) immunoreactivity. Also these metabolites, morphologic and biochemical markers of methyl group alterations were analyzed in the liver, the main site of arsenic methylation. In adult, life-long arsenic exposed rats through drinking water (3 ppm), no changes of SAM, choline and PC concentrations where found in the brain, but SAM and PC were severely decreased in liver accompanied by a significant increase of choline. These results suggest that choline plays an important role as methyl donor in arsenic exposure, which could underlie hepatic affections observed when arsenic exposure is combined with other environmental factors. Also, important myelin and nerve fiber alterations, accompanied by a 75% decrease of MBP immunoreactivity were not associated with a SAM deficit in the brain. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Structure, function and carcinogenicity of metabolites of methylated and non-methylated polycyclic aromatic hydrocarbons: a comprehensive review.

Science.gov (United States)

Flesher, James W; Lehner, Andreas F

2016-01-01

The Unified Theory of PAH Carcinogenicity accommodates the activities of methylated and non-methylated polycyclic aromatic hydrocarbons (PAHs) and states that substitution of methyl groups on meso-methyl substituted PAHs with hydroxy, acetoxy, chloride, bromide or sulfuric acid ester groups imparts potent cancer producing properties. It incorporates specific predictions from past researchers on the mechanism of carcinogenesis by methyl-substituted hydrocarbons, including (1) requirement for metabolism to an ArCH2X type structure where X is a good leaving group and (2) biological substitution of a meso-methyl group at the most reactive center in non-methylated hydrocarbons. The Theory incorporates strong inferences of Fieser: (1) The mechanism of carcinogenesis involves a specific metabolic substitution of a hydrocarbon at its most reactive center and (2) Metabolic elimination of a carcinogen is a detoxifying process competitive with that of carcinogenesis and occurring by a different mechanism. According to this outlook, chemical or biochemical substitution of a methyl group at the reactive meso-position of non-methylated hydrocarbons is the first step in the mechanism of carcinogenesis for most, if not all, PAHs and the most potent metabolites of PAHs are to be found among the meso methyl-substituted hydrocarbons. Some PAHs and their known or potential metabolites and closely related compounds have been tested in rats for production of sarcomas at the site of subcutaneous injection and the results strongly support the specific predictions of the Unified Theory.

Methylation pathways in schizophrenia

International Nuclear Information System (INIS)

Sargent, T.W. III.

1982-01-01

Research on the biochemical causes of human psychosis concentrates on investigating whether schizophremia is linked to abnormalities in the metabolism of methyl carbon groups in the body. The metabolism of C-14 labeled methyl groups in methionine is studied in animals, normal subjects and patient volunteers

The Equivalence of the Methyl Groups in Puckered 3,3-DIMETHYL Oxetane

Science.gov (United States)

Macario, Alberto; Blanco, Susana; Lopez, Juan Carlos

2016-06-01

The spectroscopic study of molecules with large amplitude vibrations have led to reconsider the concept of molecular structure. Sometimes identifying definite bond lengths and angles is not enough to reproduce the experimental data so one must have information on the large amplitude molecular vibration potential energy function and dynamics. 3,3-dimethyloxetane (DMO) has non-planar ring equilibrium configuration and a double minimum potential function for ring-puckering with a barrier of 47 cm-1. The observation of endocyclic 13C and 18O monosubstituted isotopologues allow to conclude that the ring is puckered. However an interesting feature was observed for the 13C substitutions at the methyl carbon atoms. While two different axial and equatorial 13C-methyl groups spectra are predicted from a rigid non-planar ring DMO model, only one species was found. The observed rotational transitions appear at a frequency close to the average of the frequencies predicted for each isotopologue. The observed lines have the same intensity as that found for the 13C_α isotopomer and double that that found for the 13C_β isotopomer.^c This behaviour evidences that the two methyl groups of DMO are equivalent as could be expected for a planar ring. In this work we show how consideration of the potential function and the path for ring puckering motion to calculate the proper kinetic energy terms allow to reproduce the experimental results. Ab initio computations at the CCSD/6-311++G(d,p) level, tested on related systems, have been done for this purpose. J. A. Duckett, T. L. Smithson, and H. Wieser, J. Mol. Spectrosc. 1978, 69 , 159; J. Mol. Struct. 1979, 56, 157 J. C. López, A. G. Lesarri, R. M. Villamañán and J. L. Alonso, J. Mol. Spectrosc. 1990, 141, 231 R. Sánchez, S. Blanco, A. Lesarri, J. C. López and J. L. Alonso, Phys. Chem. Chem. Phys. 2005, 7, 1157

Knee replacement and Diagnosis-Related Groups (DRGs): patient classification and hospital reimbursement in 11 European countries.

Science.gov (United States)

Tan, Siok Swan; Chiarello, Pietro; Quentin, Wilm

2013-11-01

Researchers from 11 countries (Austria, England, Estonia, Finland, France, Germany, Ireland, Netherlands, Poland, Spain, and Sweden) compared how their Diagnosis-Related Group (DRG) systems deal with knee replacement cases. The study aims to assist knee surgeons and national authorities to optimize the grouping algorithm of their DRG systems. National or regional databases were used to identify hospital cases treated with a procedure of knee replacement. DRG classification algorithms and indicators of resource consumption were compared for those DRGs that together comprised at least 97 % of cases. Five standardized case scenarios were defined and quasi-prices according to national DRG-based hospital payment systems ascertained. Grouping algorithms for knee replacement vary widely across countries: they classify cases according to different variables (between one and five classification variables) into diverging numbers of DRGs (between one and five DRGs). Even the most expensive DRGs generally have a cost index below 2.00, implying that grouping algorithms do not adequately account for cases that are more than twice as costly as the index DRG. Quasi-prices for the most complex case vary between euro 4,920 in Estonia and euro 14,081 in Spain. Most European DRG systems were observed to insufficiently consider the most important determinants of resource consumption. Several countries' DRG system might be improved through the introduction of classification variables for revision of knee replacement or for the presence of complications or comorbidities. Ultimately, this would contribute to assuring adequate performance comparisons and fair hospital reimbursement on the basis of DRGs.

Metabolism of S-adenosylmethionine in rat hepatocytes: transfer of methyl group from S-adenosylmethionine by methyltransferase reactions

International Nuclear Information System (INIS)

Tsukada, K.; Abe, T.; Kuwahata, T.; Mitsui, K.

1985-01-01

Treatment of rats with a methionine diet leads not only to a marked increase of S-adenosylmethionine synthetase in liver, but also to the increase of glycine, guanidoacetate and betaine-homocysteine methyltransferases. The activity of tRNA methyltransferase decreased with the increased amounts of methionine in the diets. However, the activities of phospholipids and S-adenosylmethionine-homocysteine methyltransferases did not show any significant change. When hepatocarcinogenesis induced by 2-fluorenylacetamide progresses, the activities of glycine and guanidoacetate methyltransferases in rat liver decreased, and could not be detected in tumorous areas 8 months after treatment. The levels of S-adenosylmethionine in the liver also decreased to levels of one-fifth of control animals at 8 months. The uptake and metabolism of [methyl- 3 H]-methionine and -S-adenosylmethionine have been investigated by in vivo and isolated hepatocytes. The uptake of methionine and transfer of methyl group to phospholipid in the cells by methionine were remarkably higher than those by S-adenosylmethionine. These results indicate that phospholipids in hepatocytes accept methyl group from S-adenosylmethionine immediately, when it is synthesized from methionine, before mixing its pool in the cells. 39 references, 1 figure, 2 tables

Rates of hip and knee joint replacement amongst different ethnic groups in England: an analysis of National Joint Registry data.

Science.gov (United States)

Smith, M C; Ben-Shlomo, Y; Dieppe, P; Beswick, A D; Adebajo, A O; Wilkinson, J M; Blom, A W

2017-04-01

Despite a health care system that is free at the point of delivery, ethnic minorities may not always get care equitable to that of White patients in England. We examined whether ethnic differences exist in joint replacement rates and surgical practice in England. 373,613 hip and 428,936 knee National Joint Registry (NJR) primary replacement patients had coded ethnicity in Hospital Episode Statistics (HES). Age and gender adjusted observed/expected ratios of hip and knee replacements amongst ethnic groups were compared using indirect standardisation. Associations between ethnic group and type of procedure were explored and effects of demographic, clinical and hospital-related factors examined using multivariable logistic regression. Adjusted standardised observed/expected ratios were substantially lower in Blacks and Asians than Whites for hip replacement (Blacks 0.33 [95% CI, 0.31-0.35], Asians 0.20 [CI, 0.19-0.21]) and knee replacement (Blacks 0.64 [CI, 0.61-0.67], Asians 0.86 % [CI, 0.84-0.88]). Blacks were more likely to receive uncemented hip replacements (Blacks 52%, Whites 37%, Asians 44%; P replacements than Whites (men 10% vs 15%, P = 0.001; women 6% vs 14%, P replacement (OR 1.43 [CI, 1.11-1.84]). In England, hip and knee replacement rates and prosthesis type given differ amongst ethnic groups. Whether these reflect differences in clinical need or differential access to treatment requires urgent investigation. Copyright © 2017. Published by Elsevier Ltd.

Synthesis of methyl acetate from dimethyl ether using group VIII metal salts of phosphotungstic acid

Energy Technology Data Exchange (ETDEWEB)

Sardesai, A.; Lee, S.; Tartamella, T.

2002-04-01

Dimethyl ether (DME) can be produced much more efficiently in a single-stage, liquid-phase process from natural gas-based syngas as compared to the conventional process via dehydration of methanol. This process, based on dual catalysts slurried in inert oil, alleviates the chemical equilibrium limitation governing the methanol synthesis reaction and concurrently improves per-pass syngas conversion and reactor productivity. The potential, therefore, for production of methyl acetate via dimethyl ether carbonylation is of industrial importance. In the present study, conversion of dimethyl ether and carbon monoxide to methyl acetate is investigated over a variety of group VIII metal-substituted phosphotungstic acid salts. Experimental results of this catalytic reaction using rhodium, iridium, ruthenium, and palladium catalysts are evaluated and compared in terms of selectivity toward methyl acetate. The effects of active metal, support types, multiple metal loading, and feed conditions on carbonylation activity of DME are examined. Iridium metal substituted phosphotungstic acid supported on Davisil type 643 (pore size 150 A, surface area 279 m{sup 2}/g, mesh size 230-425) silica gel shows the highest activity for DME carbonylation. (author)

Integrated DNA methylation and copy-number profiling identify three clinically and biologically relevant groups of anaplastic glioma.

Science.gov (United States)

Wiestler, Benedikt; Capper, David; Sill, Martin; Jones, David T W; Hovestadt, Volker; Sturm, Dominik; Koelsche, Christian; Bertoni, Anna; Schweizer, Leonille; Korshunov, Andrey; Weiß, Elisa K; Schliesser, Maximilian G; Radbruch, Alexander; Herold-Mende, Christel; Roth, Patrick; Unterberg, Andreas; Hartmann, Christian; Pietsch, Torsten; Reifenberger, Guido; Lichter, Peter; Radlwimmer, Bernhard; Platten, Michael; Pfister, Stefan M; von Deimling, Andreas; Weller, Michael; Wick, Wolfgang

2014-10-01

The outcome of patients with anaplastic gliomas varies considerably. Whether a molecular classification of anaplastic gliomas based on large-scale genomic or epigenomic analyses is superior to histopathology for reflecting distinct biological groups, predicting outcomes and guiding therapy decisions has yet to be determined. Epigenome-wide DNA methylation analysis, using a platform which also allows the detection of copy-number aberrations, was performed in a cohort of 228 patients with anaplastic gliomas (astrocytomas, oligoastrocytomas, and oligodendrogliomas), including 115 patients of the NOA-04 trial. We further compared these tumors with a group of 55 glioblastomas. Unsupervised clustering of DNA methylation patterns revealed two main groups correlated with IDH status: CpG island methylator phenotype (CIMP) positive (77.5 %) or negative (22.5 %). CIMP(pos) (IDH mutant) tumors showed a further separation based on copy-number status of chromosome arms 1p and 19q. CIMP(neg) (IDH wild type) tumors showed hallmark copy-number alterations of glioblastomas, and clustered together with CIMP(neg) glioblastomas without forming separate groups based on WHO grade. Notably, there was no molecular evidence for a distinct biological entity representing anaplastic oligoastrocytoma. Tumor classification based on CIMP and 1p/19q status was significantly associated with survival, allowing a better prediction of outcome than the current histopathological classification: patients with CIMP(pos) tumors with 1p/19q codeletion (CIMP-codel) had the best prognosis, followed by patients with CIMP(pos) tumors but intact 1p/19q status (CIMP-non-codel). Patients with CIMP(neg) anaplastic gliomas (GBM-like) had the worst prognosis. Collectively, our data suggest that anaplastic gliomas can be grouped by IDH and 1p/19q status into three molecular groups that show clear links to underlying biology and a significant association with clinical outcome in a prospective trial cohort.

Replacement

Directory of Open Access Journals (Sweden)

S. Radhakrishnan

2014-03-01

Full Text Available The fishmeal replaced with Spirulina platensis, Chlorella vulgaris and Azolla pinnata and the formulated diet fed to Macrobrachium rosenbergii postlarvae to assess the enhancement ability of non-enzymatic antioxidants (vitamin C and E, enzymatic antioxidants (superoxide dismutase (SOD and catalase (CAT and lipid peroxidation (LPx were analysed. In the present study, the S. platensis, C. vulgaris and A. pinnata inclusion diet fed groups had significant (P < 0.05 improvement in the levels of vitamins C and E in the hepatopancreas and muscle tissue. Among all the diets, the replacement materials in 50% incorporated feed fed groups showed better performance when compared with the control group in non-enzymatic antioxidant activity. The 50% fishmeal replacement (best performance diet fed groups taken for enzymatic antioxidant study, in SOD, CAT and LPx showed no significant increases when compared with the control group. Hence, the present results revealed that the formulated feed enhanced the vitamins C and E, the result of decreased level of enzymatic antioxidants (SOD, CAT and LPx revealed that these feeds are non-toxic and do not produce any stress to postlarvae. These ingredients can be used as an alternative protein source for sustainable Macrobrachium culture.

Similarity of aberrant DNA methylation in Barrett's esophagus and esophageal adenocarcinoma

Directory of Open Access Journals (Sweden)

Gotley David C

2008-10-01

Full Text Available Abstract Background Barrett's esophagus (BE is the metaplastic replacement of squamous with columnar epithelium in the esophagus, as a result of reflux. It is the major risk factor for the development of esophageal adenocarcinoma (EAC. Methylation of CpG dinucleotides of normally unmethylated genes is associated with silencing of their expression, and is common in EAC. This study was designed to determine at what stage, in the progression from BE to EAC, methylation of key genes occurs. Results We examined nine genes (APC, CDKN2A, ID4, MGMT, RBP1, RUNX3, SFRP1, TIMP3, and TMEFF2, frequently methylated in multiple cancer types, in a panel of squamous (19 biopsies from patients without BE or EAC, 16 from patients with BE, 21 from patients with EAC, BE (40 metaplastic, seven high grade dysplastic and 37 EAC tissues. The methylation frequency, the percentage of samples that had any extent of methylation, for each of the nine genes in the EAC (95%, 59%, 76%, 57%, 70%, 73%, 95%, 74% and 83% respectively was significantly higher than in any of the squamous groups. The methylation frequency for each of the nine genes in the metaplastic BE (95%, 28%, 78%, 48%, 58%, 48%, 93%, 88% and 75% respectively was significantly higher than in the squamous samples except for CDKN2A and RBP1. The methylation frequency did not differ between BE and EAC samples, except for CDKN2A and RUNX3 which were significantly higher in EAC. The methylation extent was an estimate of both the number of methylated alleles and the density of methylation on these alleles. This was significantly greater in EAC than in metaplastic BE for all genes except APC, MGMT and TIMP3. There was no significant difference in methylation extent for any gene between high grade dysplastic BE and EAC. Conclusion We found significant methylation in metaplastic BE, which for seven of the nine genes studied did not differ in frequency from that found in EAC. This is also the first report of gene silencing

Influence of α-methyl group on molecular aggregation structure and surface physicochemical properties of fluoroalkyl side chain polymers

International Nuclear Information System (INIS)

Honda, K; Yamaguchi, H; Takahara, A; Sakata, O; Sasaki, S; Takata, M; Morita, M

2009-01-01

Influence of α-methyl group on molecular aggregation states and surface physicochemical properties of poly(fluoroalkyl acrylate)s [PFA-C y , where y is fluoromethylene number in R f group] and poly(fluoroalkykl methacrylate)s [PFMA-C y ] thin films were systematically investigated. Spin-coated PFA-C y and PFMA-C y thin films were characterized by dynamic contact angle measurements and grazing-incidence wide-angle X-ray diffraction (GIWAXD) measurements. GIWAXD data revealed that fluoroalkyl side chains of PFA-C y and PFMA-C y with y≥8 formed regular structures in the surface region as well as bulk one. However, the degree of orientation and ordering of the R f groups of PFMA-C 8 thin films was low. Also, the receding contact angle (θ r ) of PFMA-C 8 thin films was lower than that of PFA-C 8 ones. By annealing treatment, the θ r of PFMA-C 8 was increased. These results suggest that the R f groups of PFMA-C 8 were disordered due to presence of the α-methyl group. The R f groups became ordered to pack closely each other by annealing treatment, so that the water repellency was increased.

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

Science.gov (United States)

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

2013-01-01

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

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

Science.gov (United States)

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

2010-11-01

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

Solid state {sup 1}H spin-lattice relaxation and isolated-molecule and cluster electronic structure calculations in organic molecular solids: The relationship between structure and methyl group and t-butyl group rotation

Energy Technology Data Exchange (ETDEWEB)

Wang, Xianlong, E-mail: WangXianlong@uestc.edu.cn, E-mail: pbeckman@brynmawr.edu [Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, 4 North Jianshe Rd., 2nd Section, Chengdu 610054 (China); Mallory, Frank B. [Department of Chemistry, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899 (United States); Mallory, Clelia W. [Department of Chemistry, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899 (United States); Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 (United States); Odhner, Hosanna R.; Beckmann, Peter A., E-mail: WangXianlong@uestc.edu.cn, E-mail: pbeckman@brynmawr.edu [Department of Physics, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899 (United States)

2014-05-21

We report ab initio density functional theory electronic structure calculations of rotational barriers for t-butyl groups and their constituent methyl groups both in the isolated molecules and in central molecules in clusters built from the X-ray structure in four t-butyl aromatic compounds. The X-ray structures have been reported previously. We also report and interpret the temperature dependence of the solid state {sup 1}H nuclear magnetic resonance spin-lattice relaxation rate at 8.50, 22.5, and 53.0 MHz in one of the four compounds. Such experiments for the other three have been reported previously. We compare the computed barriers for methyl group and t-butyl group rotation in a central target molecule in the cluster with the activation energies determined from fitting the {sup 1}H NMR spin-lattice relaxation data. We formulate a dynamical model for the superposition of t-butyl group rotation and the rotation of the t-butyl group's constituent methyl groups. The four compounds are 2,7-di-t-butylpyrene, 1,4-di-t-butylbenzene, 2,6-di-t-butylnaphthalene, and 3-t-butylchrysene. We comment on the unusual ground state orientation of the t-butyl groups in the crystal of the pyrene and we comment on the unusually high rotational barrier of these t-butyl groups.

Damped Quantum Rotation of the Methyl Group in 9-Methyltriptycene Derivatives. The Magnitude of The Effect vs. The Activation Energy

International Nuclear Information System (INIS)

Czerski, I.; Szymanski, S.

2005-01-01

According to the damped quantum rotation (DQR) theory, hindered rotation of methyl groups, reflected in NMR spectra, is a quantum mechanical process controlled by two quantum mechanical rate constants k t and k K . The subscripts t and K, designating '' tunneling '' and '' Kramers '', refer to two specific, long-lived quantum coherence in the methyl rotor system each of which engages the space and spin coordinates of the three protons, correlated by the Pauli principle. Only in the instances where k t and k K happen to be equal, the NMR picture will be the same as for a hypothetical CH 3 group undergoing classical jumps between its three equivalent orientations, described by single rate constant k '. Departure of the ratio c = k t /k K from 1 can thus serve as a quick measure of the degree of non classicality in the stochastic dynamics of the methyl group or, in other words, of the magnitude of the DQR effect. When the Arrhenius activation energy, Ea, for k K is about 12 kJmol -1 , the non classicality factor c can exceed 5. This is an inference from our recent single-crystal NMR studies at temperatures 60 - 110 K. On an intuitive ground, there should be an inverse (but hardly linear) correlation between E a and c. Indeed, for strongly hindered methyl group in 9-methyltripticene derivatives for which the activation energies can exceed 37 kJmol -1 , the DQR effect proves to be much smaller, with the corresponding values of c not exceeding 1.20. Nonetheless, for the values of c above 1.10 it can still be clearly seen in liquid-phase NMR spectra. Here we report on our recent liquid-phase NMR experiments with a series of 9-methyltriptycene derivatives for which the values of E a for k K span the range 37.4 - 44.8 kJmol -1 while the respective, average values of c vary between 1.04 and 1.20. It comes out that, within such a narrow variability range of E a , the correlation between c and E a no longer holds. For example, for 1,2,3,4-tetrabromo-9,10-dimethyltriptycene

Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl–methyl nuclear overhauser enhancement spectroscopy

International Nuclear Information System (INIS)

Venditti, Vincenzo; Fawzi, Nicolas L.; Clore, G. Marius

2011-01-01

Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ∼1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic relaxation enhancement (PRE), induced by nitroxide spin-labels incorporated at only a few surface-exposed engineered cysteines, provides fast, straightforward and robust access to methyl group resonance assignments, including stereoassignments for the methyl groups of leucine and valine. Neither prior assignments, including backbone assignments, for the protein, nor experiments that transfer magnetization between methyl groups and the protein backbone, are required. PRE-derived assignments are refined by 4D methyl–methyl nuclear Overhauser enhancement data, eliminating ambiguities and errors that may arise due to the high sensitivity of PREs to the potential presence of sparsely-populated transient states.

Experimental vapor pressures (from 1 Pa to 100 kPa) of six saturated Fatty Acid Methyl Esters (FAMEs): Methyl hexanoate, methyl octanoate, methyl decanoate, methyl dodecanoate, methyl tetradecanoate and methyl hexadecanoate

International Nuclear Information System (INIS)

Sahraoui, Lakhdar; Khimeche, Kamel; Dahmani, Abdallah; Mokbel, Ilham; Jose, Jacques

2016-01-01

Highlight: • Vapor-liquid equilibria, Enthalpy of Vaporization, saturated Fatty Acid Methyl Ester. - Abstract: Vapor pressures of six saturated Fatty Acid Methyl Esters (FAMEs), methyl hexanoate (or methyl caproate), methyl octanoate (or methyl caprylate), Methyl decanoate (or methyl caprate), methyl dodecanoate (or methyl laurate), methyl tetradecanoate (or methyl myristate), and methyl hexadecanoate (or methyl palmitate) were measured from 1 Pa to 100 kPa and at temperature range between 262 and 453 K using a static apparatus. The experimental data (P-T) were compared with the available literature data.

Nutrient adequacy during weight loss interventions: a randomized study in women comparing the dietary intake in a meal replacement group with a traditional food group

Directory of Open Access Journals (Sweden)

Bovee Vicki

2007-06-01

Full Text Available Abstract Background Safe and effective weight control strategies are needed to stem the current obesity epidemic. The objective of this one-year study was to document and compare the macronutrient and micronutrient levels in the foods chosen by women following two different weight reduction interventions. Methods Ninety-six generally healthy overweight or obese women (ages 25–50 years; BMI 25–35 kg/m2 were randomized into a Traditional Food group (TFG or a Meal Replacement Group (MRG incorporating 1–2 meal replacement drinks or bars per day. Both groups had an energy-restricted goal of 5400 kJ/day. Dietary intake data was obtained using 3-Day Food records kept by the subjects at baseline, 6 months and one-year. For more uniform comparisons between groups, each diet intervention consisted of 18 small group sessions led by the same Registered Dietitian. Results Weight loss for the 73% (n = 70 completing this one-year study was not significantly different between the groups, but was significantly different (p ≤ .05 within each group with a mean (± standard deviation weight loss of -6.1 ± 6.7 kg (TFG, n = 35 vs -5.0 ± 4.9 kg (MRG, n = 35. Both groups had macronutrient (Carbohydrate:Protein:Fat ratios that were within the ranges recommended (50:19:31, TFG vs 55:16:29, MRG. Their reported reduced energy intake was similar (5729 ± 1424 kJ, TFG vs 5993 ± 2016 kJ, MRG. There was an improved dietary intake pattern in both groups as indicated by decreased intake of saturated fat (≤ 10%, cholesterol ( Conclusion In this one-year university-based intervention, both dietitian-led groups successfully lost weight while improving overall dietary adequacy. The group incorporating fortified meal replacements tended to have a more adequate essential nutrient intake compared to the group following a more traditional food group diet. This study supports the need to incorporate fortified foods and/or dietary supplements while following an energy

Limonene dehydrogenase hydroxylates the allylic methyl group of cyclic monoterpenes in the anaerobic terpene degradation by Castellaniella defragrans.

Science.gov (United States)

Puentes-Cala, Edinson; Liebeke, Manuel; Markert, Stephanie; Harder, Jens

2018-05-01

The enzymatic functionalization of hydrocarbons is a central step in the global carbon cycle initiating the mineralization of methane, isoprene and monoterpenes, the most abundant biologically produced hydrocarbons. Also, terpene-modifying enzymes have found many applications in the energy-economic biotechnological production of fine chemicals. Here we describe a limonene dehydrogenase that was purified from the facultatively anaerobic betaproteobacterium Castellaniella defragrans 65Phen grown on monoterpenes under denitrifying conditions in the absence of molecular oxygen. The purified limonene:ferrocenium oxidoreductase activity hydroxylated the methyl group of limonene (1-methyl-4-(1-methylethenyl)-cyclohex-1-ene) yielding perillyl alcohol ([4-(prop-1-en-2-yl)cyclohex-1-en-1-yl]methanol). The enzyme had a dithiothreitol:perillyl alcohol oxidoreductase activity yielding limonene. Mass spectrometry and molecular size determinations revealed a heterodimeric enzyme comprising CtmA and CtmB. Recently the two proteins had been identified by transposon mutagenesis and proteomics as part of the cyclic terpene metabolism ( ctm ) in Castellaniella defragrans and were annotated as FAD-dependent oxidoreductases of the protein domain family phytoene dehydrogenases and related proteins (COG1233). CtmAB is the first heterodimeric enzyme in this protein superfamily. Flavins in the purified CtmAB are oxidized by ferrocenium and are reduced by limonene. Heterologous expression of CtmA, CtmB and CtmAB in E. coli demonstrated that limonene dehydrogenase activity required both subunits carrying each a flavin cofactor. Native CtmAB oxidized a wide range of monocyclic monoterpenes containing the allylic methyl group motif (1-methyl-cyclohex-1-ene). In conclusion, we have identified CtmAB as a hydroxylating limonene dehydrogenase and the first heteromer in a family of FAD-dependent dehydrogenases acting on allylic methylene or methyl CH-bonds. We suggest a placement in EC 1

Improved labeling strategy for 13C relaxation measurements of methyl groups in proteins

International Nuclear Information System (INIS)

Lee, Andrew L.; Urbauer, Jeffrey L.; Wand, A. Joshua

1997-01-01

Selective incorporation of 13 C into the methyl groups of protein side chains is described as a means for simplifying the measurement and interpretation of 13 C relaxation parameters.High incorporation (>90%) is accomplished by using pyruvate(3- 13 C, 99%) as the sole carbon source in the growth media for protein overexpression in E. coli. This improved labeling scheme increases the sensitivity of the relaxation experiments by approximately fivefold when compared to randomly fractionally 13 C-labeled protein, allowing high-quality measurements on relatively dilute (<1 mM)protein samples at a relatively low cost

miRNAting control of DNA methylation

Indian Academy of Sciences (India)

DNA methylation is a type of epigenetic modification where a methyl group is added to the cytosine or adenine residue of a given DNA sequence. It has been observed that DNA methylation is achieved by some collaborative agglomeration of certain proteins and non-coding RNAs. The assembly of IDN2 and its ...

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

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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.

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

KAUST Repository

Guerrero Peñ a, Gerardo D.J.; Alrefaai, Mhd Maher; Yang, Seung Yeon; Raj, Abhijeet; Brito, Joaquin L.; Stephen, Samuel; Anjana, Tharalekshmy; Pillai, Vinu; Al Shoaibi, Ahmed; Chung, Suk-Ho

2016-01-01

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

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

Methylation profiling identified novel differentially methylated markers including OPCML and FLRT2 in prostate cancer.

Science.gov (United States)

Wu, Yu; Davison, Jerry; Qu, Xiaoyu; Morrissey, Colm; Storer, Barry; Brown, Lisha; Vessella, Robert; Nelson, Peter; Fang, Min

2016-04-02

To develop new methods to distinguish indolent from aggressive prostate cancers (PCa), we utilized comprehensive high-throughput array-based relative methylation (CHARM) assay to identify differentially methylated regions (DMRs) throughout the genome, including both CpG island (CGI) and non-CGI regions in PCa patients based on Gleason grade. Initially, 26 samples, including 8 each of low [Gleason score (GS) 6] and high (GS ≥7) grade PCa samples and 10 matched normal prostate tissues, were analyzed as a discovery cohort. We identified 3,567 DMRs between normal and cancer tissues, and 913 DMRs distinguishing low from high-grade cancers. Most of these DMRs were located at CGI shores. The top 5 candidate DMRs from the low vs. high Gleason comparison, including OPCML, ELAVL2, EXT1, IRX5, and FLRT2, were validated by pyrosequencing using the discovery cohort. OPCML and FLRT2 were further validated in an independent cohort consisting of 20 low-Gleason and 33 high-Gleason tissues. We then compared patients with biochemical recurrence (n=70) vs. those without (n=86) in a third cohort, and they showed no difference in methylation at these DMR loci. When GS 3+4 cases and GS 4+3 cases were compared, OPCML-DMR methylation showed a trend of lower methylation in the recurrence group (n=30) than in the no-recurrence (n=52) group. We conclude that whole-genome methylation profiling with CHARM revealed distinct patterns of differential DNA methylation between normal prostate and PCa tissues, as well as between different risk groups of PCa as defined by Gleason scores. A panel of selected DMRs may serve as novel surrogate biomarkers for Gleason score in PCa.

Rotational spectrum of 1,1-difluoroethane-argon: influence of the interaction with the Ar atom on the V 3 barrier to internal rotation of the methyl group

Science.gov (United States)

Velino, Biagio; Melandri, Sonia; Favero, Paolo G.; Dell'Erba, Adele; Caminati, Walther

2000-01-01

The free-jet millimeter-wave absorption spectrum of 1,1-difluoroethane-Ar is reported. Most of the measured lines are split due to internal rotation of the methyl group and the tunnelling motion of Ar connecting two equivalent potential energy minima. The Ar atom, close to the CHF 2 group, eclipses one of the methylic hydrogens in the symmetryless geometry of the complex, reducing in this way the barrier to the internal rotation of the methyl group with respect to isolated 1,1-difluoroethane. For high J levels the distance of Ar from the molecule increases, however, due to the centrifugal distortion, and the barrier increases towards the value for 1,1-difluoroethane.

Annotating the genome by DNA methylation.

Science.gov (United States)

Cedar, Howard; Razin, Aharon

2017-01-01

DNA methylation plays a prominent role in setting up and stabilizing the molecular design of gene regulation and by understanding this process one gains profound insight into the underlying biology of mammals. In this article, we trace the discoveries that provided the foundations of this field, starting with the mapping of methyl groups in the genome and the experiments that helped clarify how methylation patterns are maintained through cell division. We then address the basic relationship between methyl groups and gene repression, as well as the molecular rules involved in controlling this process during development in vivo. Finally, we describe ongoing work aimed at defining the role of this modification in disease and deciphering how it may serve as a mechanism for sensing the environment.

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

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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.

In vitro evaluation of N-methyl amide tripeptidomimetics as substrates for the human intestinal di-/tri-peptide transporter hPEPT1

DEFF Research Database (Denmark)

Andersen, Rikke; Nielsen, Carsten Uhd; Begtrup, Mikael

2006-01-01

application of N-methyl amide bioisosteres as peptide bond replacements in tripeptides in order to decrease degradation by peptidases and yet retain affinity for and transport via hPEPT1. Seven structurally diverse N-methyl amide tripeptidomimetics were selected based on a principal component analysis...... of structural properties of 6859 N-methyl amide tripeptidomimetics. In vitro extracellular degradation of the selected tripeptidomimetics as well as affinity for and transepithelial transport via hPEPT1 were investigated in Caco-2 cells. Decreased apparent degradation was observed for all tripeptidomimetics...... to be substrates for hPEPT1 than tripeptidomimetics with charged side chains. The results of the present study indicate that the N-methyl amide peptide bond replacement approach for increasing bioavailability of tripeptidomimetic drug candidates is not generally applicable to all tripeptides. Nevertheless...

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.)

Protein methylation in pea chloroplasts

International Nuclear Information System (INIS)

Niemi, K.J.; Adler, J.; Selman, B.R.

1990-01-01

The methylation of chloroplast proteins has been investigated by incubating intact pea (Pisum sativum) chloroplasts with [ 3 H-methyl]-S-adenosylmethionine. Incubation in the light increases the amount of methylation in both the thylakoid and stromal fractions. Numerous thylakoid proteins serve as substrates for the methyltransfer reactions. Three of these thylakoid proteins are methylated to a significantly greater extent in the light than in the dark. The primary stromal polypeptide methylated is the large subunit of ribulose bisphosphate carboxylase/oxygenase. One other stromal polypeptide is also methylated much more in the light than in the dark. Two distinct types of protein methylation occur. One methylinkage is stable to basic conditions whereas a second type is base labile. The base-stable linkage is indicative of N-methylation of amino acid residues while base-lability is suggestive of carboxymethylation of amino acid residues. Labeling in the light increases the percentage of methylation that is base labile in the thylakoid fraction while no difference is observed in the amount of base-labile methylations in light-labeled and dark-labeled stromal proteins. Also suggestive of carboxymethylation is the detection of volatile [ 3 H]methyl radioactivity which increases during the labeling period and is greater in chloroplasts labeled in the light as opposed to being labeled in the dark; this implies in vivo turnover of the [ 3 H]methyl group

Analysis of DNA Methylation of Gracilariopsis lemaneiformis Under Temperature Stress Using the Methylation Sensitive Amplification Polymorphism (MSAP) Technique

Science.gov (United States)

Peng, Chong; Sui, Zhenghong; Zhou, Wei; Hu, Yiyi; Mi, Ping; Jiang, Minjie; Li, Xiaodong; Ruan, Xudong

2018-06-01

Gracilariopsis lemaneiformis is an economically important agarophyte, which contains high quality gel and shows a high growth rate. Wild population of G. lemaneiformis displayed resident divergence, though with a low genetic diversity as was revealed by amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) analyses. In addition, different strains of G. lemaneiformis are diverse in morphology. The highly inconsistence between genetic background and physiological characteristics recommends strongly to the regulation at epigenetic level. In this study, the DNA methylation change in G. lemaneiformis among different generation branches and under different temperature stresses was assessed using methylation sensitive amplified polymorphism (MSAP) technique. It was shown that DNA methylation level among different generation branches was diverse. The full and total methylated DNA level was the lowest in the second generation branch and the highest in the third generation. The total methylation level was 61.11%, 60.88% and 64.12% at 15°C, 22°C and 26°C, respectively. Compared with the control group (22°C), the fully methylated and totally methylated ratios were increased in both experiment groups (15°C and 26°C). All of the cytosine methylation/demethylation transform (CMDT) was further analyzed. High temperature treatment could induce more CMDT than low temperature treatment did.

Minimally invasive aortic valve replacement

DEFF Research Database (Denmark)

Foghsgaard, Signe; Schmidt, Thomas Andersen; Kjaergard, Henrik K

2009-01-01

In this descriptive prospective study, we evaluate the outcomes of surgery in 98 patients who were scheduled to undergo minimally invasive aortic valve replacement. These patients were compared with a group of 50 patients who underwent scheduled aortic valve replacement through a full sternotomy...... operations were completed as mini-sternotomies, 4 died later of noncardiac causes. The aortic cross-clamp and perfusion times were significantly different across all groups (P replacement...... is an excellent operation in selected patients, but its true advantages over conventional aortic valve replacement (other than a smaller scar) await evaluation by means of randomized clinical trial. The "extended mini-aortic valve replacement" operation, on the other hand, is a risky procedure that should...

Methylation-Specific PCR Unraveled

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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.

Prediction of methyl-side Chain Dynamics in Proteins

International Nuclear Information System (INIS)

Ming Dengming; Brueschweiler, Rafael

2004-01-01

A simple analytical model is presented for the prediction of methyl-side chain dynamics in comparison with S 2 order parameters obtained by NMR relaxation spectroscopy. The model, which is an extension of the local contact model for backbone order parameter prediction, uses a static 3D protein structure as input. It expresses the methyl-group S 2 order parameters as a function of local contacts of the methyl carbon with respect to the neighboring atoms in combination with the number of consecutive mobile dihedral angles between the methyl group and the protein backbone. For six out of seven proteins the prediction results are good when compared with experimentally determined methyl-group S 2 values with an average correlation coefficient r-bar=0.65±0.14. For the unusually rigid cytochrome c 2 no significant correlation between prediction and experiment is found. The presented model provides independent support for the reliability of current side-chain relaxation methods along with their interpretation by the model-free formalism

Methyl-Analyzer--whole genome DNA methylation profiling.

Science.gov (United States)

Xin, Yurong; Ge, Yongchao; Haghighi, Fatemeh G

2011-08-15

Methyl-Analyzer is a python package that analyzes genome-wide DNA methylation data produced by the Methyl-MAPS (methylation mapping analysis by paired-end sequencing) method. Methyl-MAPS is an enzymatic-based method that uses both methylation-sensitive and -dependent enzymes covering >80% of CpG dinucleotides within mammalian genomes. It combines enzymatic-based approaches with high-throughput next-generation sequencing technology to provide whole genome DNA methylation profiles. Methyl-Analyzer processes and integrates sequencing reads from methylated and unmethylated compartments and estimates CpG methylation probabilities at single base resolution. Methyl-Analyzer is available at http://github.com/epigenomics/methylmaps. Sample dataset is available for download at http://epigenomicspub.columbia.edu/methylanalyzer_data.html. fgh3@columbia.edu Supplementary data are available at Bioinformatics online.

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.

Electronic transport in methylated fragments of DNA

International Nuclear Information System (INIS)

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

2015-01-01

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

Delirium After Transcatheter Aortic Valve Replacement.

Science.gov (United States)

Giuseffi, Jennifer L; Borges, Nyal E; Boehm, Leanne M; Wang, Li; McPherson, John A; Fredi, Joseph L; Ahmad, Rashid M; Ely, E Wesley; Pandharipande, Pratik P

2017-07-01

Postoperative delirium is associated with increased mortality. Patients undergoing transcatheter aortic valve replacement are at risk for delirium because of comorbid conditions. To compare the incidence, odds, and mortality implications of delirium between patients undergoing transcatheter replacement and patients undergoing surgical replacement. The Richmond Agitation-Sedation Scale and the Confusion Assessment Method for the Intensive Care Unit were used to assess arousal level and delirium prospectively in all patients with severe aortic stenosis who had transcatheter or surgical aortic valve replacement at an academic medical center. Multivariable logistic regression was used to determine the relationship between procedure type and occurrence of delirium. Cox regression was used to assess the association between postoperative delirium and 6-month mortality. A total of 105 patients had transcatheter replacement and 121 had surgical replacement. Patients in the transcatheter group were older (median age, 81 vs 68 years; P replacement. Delirium is less likely to develop in the transcatheter group but is associated with higher mortality in both groups. ©2017 American Association of Critical-Care Nurses.

Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes.

Science.gov (United States)

Chwialkowska, Karolina; Korotko, Urszula; Kosinska, Joanna; Szarejko, Iwona; Kwasniewski, Miroslaw

2017-01-01

Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare . However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop

Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

Directory of Open Access Journals (Sweden)

Karolina Chwialkowska

2017-11-01

Full Text Available Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq. We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation

Methyl group rotation and segmental motion in atactic polypropylene. An incoherent quasi elastic neutron scattering investigation

International Nuclear Information System (INIS)

Arrighi, V.; Triolo, A.

1999-01-01

Complete text of publication follows. Results from the analysis of recent quasielastic neutron scattering (QENS) experiments on atactic polypropylene (aPP), are presented both in the sub-T g and above T g regimes. Experiments were carried out on the IRIS (ISIS, Rutherford Appleton Laboratory, UK) and IN10 (ILL FR) spectrometers in the temperature range from 140 to 400 K. Different instrumental resolutions were used in order to cover a wide energy window. The high resolution data collected on IN10 using the fixed energy scan technique, give clear evidence of two separate dynamic processes that we attribute to methyl group rotational hopping (below T g ) and to segmental motion (above T g ), respectively. Data were fitted using a model involving a distribution of relaxation rates. The IN10 results are used in interpreting and analyzing the QENS data from the IRIS spectrometer. In order to exploit the different energy resolutions of IRIS, Fourier inversion of the experimental data was carried out. This approach to data analysis allows us to widen the energy range available for data analysis. Due to the high activation energy of the methyl group hopping in aPP, this motion overlaps with the segmental relaxation, thus making analysis of high temperature data quite complex. The IN10 results are employed in order to perform data analysis in terms of two distinct processes. (author)

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

2015-01-01

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

A DNA methylation microarray-based study identifies ERG as a gene commonly methylated in prostate cancer.

Science.gov (United States)

Schwartzman, Jacob; Mongoue-Tchokote, Solange; Gibbs, Angela; Gao, Lina; Corless, Christopher L; Jin, Jennifer; Zarour, Luai; Higano, Celestia; True, Lawrence D; Vessella, Robert L; Wilmot, Beth; Bottomly, Daniel; McWeeney, Shannon K; Bova, G Steven; Partin, Alan W; Mori, Motomi; Alumkal, Joshi

2011-10-01

DNA methylation of promoter regions is a common event in prostate cancer, one of the most common cancers in men worldwide. Because prior reports demonstrating that DNA methylation is important in prostate cancer studied a limited number of genes, we systematically quantified the DNA methylation status of 1505 CpG dinucleotides for 807 genes in 78 paraffin-embedded prostate cancer samples and three normal prostate samples. The ERG gene, commonly repressed in prostate cells in the absence of an oncogenic fusion to the TMPRSS2 gene, was one of the most commonly methylated genes, occurring in 74% of prostate cancer specimens. In an independent group of patient samples, we confirmed that ERG DNA methylation was common, occurring in 57% of specimens, and cancer-specific. The ERG promoter is marked by repressive chromatin marks mediated by polycomb proteins in both normal prostate cells and prostate cancer cells, which may explain ERG's predisposition to DNA methylation and the fact that tumors with ERG DNA methylation were more methylated, in general. These results demonstrate that bead arrays offer a high-throughput method to discover novel genes with promoter DNA methylation such as ERG, whose measurement may improve our ability to more accurately detect prostate cancer.

Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

Science.gov (United States)

Chwialkowska, Karolina; Korotko, Urszula; Kosinska, Joanna; Szarejko, Iwona; Kwasniewski, Miroslaw

2017-01-01

Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop

Protein methylation reactions in intact pea chloroplasts

International Nuclear Information System (INIS)

Niemi, K.J.

1989-01-01

Post-translational protein methylation was investigated in Pisum sativum chloroplasts. Intact pea chloroplasts were incubated with ( 3 H-methyl)-S-adenosylmethionine under various conditions. The chloroplasts were then separated into stromal and thylakoid fractions and analyzed for radioactivity transferred to protein. Light enhanced the magnitude of labeling in both fractions. One thylakoid polypeptide with an apparent molecular mass of 43 kDa was labeled only in the light. Several other thylakoid and stromal proteins were labeled in both light and dark-labeling conditions. Both base-labile methylation, carboxy-methylesters and base-stable groups, N-methylations were found. Further characterization of the methyl-transfer reactions will be presented

FKBP5 methylation as a possible marker for cortisol state and transient cortisol exposure in healthy human subjects.

Science.gov (United States)

Winkler, Britta K; Lehnert, Hendrik; Oster, Henrik; Kirchner, Henriette; Harbeck, Birgit

2017-10-01

Current glucocorticoid replacement regimens, in adrenal insufficiency, fail to mimic the physiological cortisol secretion, thereby fostering serious side effects. To experimentally evaluate the impact of CpG methylation within the FKBP5 gene as a possible short- and long-term marker for cortisol exposure in humans. An ACTH-stimulation test was carried out and methylation status of the FKBP5 gene in leukocytes was determined. A negative correlation between basal levels of methylation and serum cortisol was observed. Individual changes in FKBP5 methylation after 24 h correlated with cortisol responses. Considering previous studies conducted with murine leucocytes, FKBP5 methylation may be suitable as a long-term biomarker, rather than acute glucocorticoid exposure, also in humans.

Synthesis of DL-adrenaline (methyl C{sup 14}) (1961); Synthese de la DL-adrenaline (methyle {sup 14}C) (1961)

Energy Technology Data Exchange (ETDEWEB)

Pichat, L; Audinot, M [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1961-07-01

The sodium derivative of 5-3-4 dibenzyl oxyphenyl 2-oxazolidinone reacted with methyl iodide {sup 14}C, in stoichiometric quantity, gives rise to the corresponding N-methyl {sup 14}C derivative. The oxazolidinone ring is opened by concentrated hydrochloric acid and the benzyl groups removed by catalytic hydrogenolysis. Adrenaline methyl {sup 14}C is then purified on Dowex 50 X-12 exchange resin. Overall-yield is 45 per cent based upon methyl iodide {sup 14}C. (author) [French] Le derive sode de la (dibenzyloxy-3-4-phenyl)-5 oxazolidinone-2 traite par l'iodure de methyle {sup 14}C, en proportion stoechiometrique, fournit le derive N-methyle {sup 14}C correspondant. Apres ouverture du cycle oxazolidinone par HCL concentre et debenzylation par hydrogenation catalytique, on purifie l'adrenaline (methyle {sup 14}C) par chromatographie sur resine echangeuse Dowex 50 X-12. Le rendement est de 45 pour cent par rapport a l'iodure de methyle {sup 14}C. (auteurs)

Synthesis of DL-adrenaline (methyl C{sup 14}) (1961); Synthese de la DL-adrenaline (methyle {sup 14}C) (1961)

Energy Technology Data Exchange (ETDEWEB)

Pichat, L.; Audinot, M. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1961-07-01

The sodium derivative of 5-3-4 dibenzyl oxyphenyl 2-oxazolidinone reacted with methyl iodide {sup 14}C, in stoichiometric quantity, gives rise to the corresponding N-methyl {sup 14}C derivative. The oxazolidinone ring is opened by concentrated hydrochloric acid and the benzyl groups removed by catalytic hydrogenolysis. Adrenaline methyl {sup 14}C is then purified on Dowex 50 X-12 exchange resin. Overall-yield is 45 per cent based upon methyl iodide {sup 14}C. (author) [French] Le derive sode de la (dibenzyloxy-3-4-phenyl)-5 oxazolidinone-2 traite par l'iodure de methyle {sup 14}C, en proportion stoechiometrique, fournit le derive N-methyle {sup 14}C correspondant. Apres ouverture du cycle oxazolidinone par HCL concentre et debenzylation par hydrogenation catalytique, on purifie l'adrenaline (methyle {sup 14}C) par chromatographie sur resine echangeuse Dowex 50 X-12. Le rendement est de 45 pour cent par rapport a l'iodure de methyle {sup 14}C. (auteurs)

Irradiation as a disinfestation method - update on methyl bromide phase out, regulatory action and emerging opportunities

International Nuclear Information System (INIS)

Marcotte, Michelle

1998-01-01

Methyl bromide (MeBr), is the most widely used agricultural fumigant in the world for the control of pests and plant diseases. It is used to control pests and diseases in food, agricultural and forestry commodities after harvest, before or during storage or transportation and/or at time of import to control quarantine or storage pests. Knowing MeBr will be phased out has spurred a search for alternative treatments and products, and has placed pressure on regulatory authorities to approve alternatives. Some of methyl bromide use could be replaced with irradiation. Methyl bromide is also used for soil and structural fumigation, and although there is some use of irradiation for packaged soil or greenhouse products, in general, these uses can not be replaced by irradiation. Some radiation processing facilities have either seen increased business to disinfest commodities, or have experienced more inquiries for service. There are many other processes and products competing for this market and irradiation will not win its share of the business without an improved regulatory picture, improved marketing to methyl bromide users and improved information to answer questions from commodity sectors. The United Nations Environment Program - Methyl Bromide Technical Options Committee (MBTOC) provides a venue for the publication or information about the use and availability of irradiation as an alternative to methyl bromide. It provides the technical base to the Montreal Protocol contributing to the setting of phase out dates; this committee is actively researching and assessing all alternatives and needs information about irradiation. The author is a member of the MBTOC committee

tert-Butyl 2-methyl-2-(4-nitrobenzoylpropanoate

Directory of Open Access Journals (Sweden)

Chelsey M. Crosse

2010-02-01

Full Text Available The title compound, C15H19NO5, is bent with a dihedral angle of 61.8 (2° between the mean planes of the benzene ring and a group encompassing the ester functionality (O=C—O—C. The dihedral angle of 0.8 (2° between the mean planes of the nitro group and the benzene ring indicates near coplanarity. In the crystal, each molecule is linked to four adjacent molecules by weak C—H...O hydrogen-bonding interactions. Both benzene H atoms ortho to the ketone O atom form C—H...O hydrogen bonds with the keto O atoms of two neighboring molecules (of the keto and ester groups, respectively, and the two other interactions involve the H atoms from a methyl group of the dimethyl residue, displaying C—H...O interactions with the O atoms of the nitro groups. These four interactions for each molecule lead to the formation of two-dimensional sheets with a hydrophilic interior, held together by weak hydrogen-bonded interactions, and a hydrophobic exterior composed of protruding methyl groups which interstack with the methyl groups in adjacent sheets.

Molecular correlates with MGMT promoter methylation and silencing support CpG island methylator phenotype-low (CIMP-low) in colorectal cancer.

Science.gov (United States)

Ogino, Shuji; Kawasaki, Takako; Kirkner, Gregory J; Suemoto, Yuko; Meyerhardt, Jeffrey A; Fuchs, Charles S

2007-11-01

The CpG island methylator phenotype (CIMP or CIMP-high) with widespread promoter methylation is a distinct epigenetic phenotype in colorectal cancer. In contrast, a phenotype with less widespread promoter methylation (CIMP-low) has not been well characterised. O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation and silencing have been associated with G>A mutations and microsatellite instability-low (MSI-low). To examine molecular correlates with MGMT methylation/silencing in colorectal cancer. Utilising MethyLight technology, we quantified DNA methylation in MGMT and eight other markers (a CIMP-diagnostic panel; CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1) in 920 population-based colorectal cancers. Tumours with both MGMT methylation and loss were correlated positively with MSI-low (p = 0.02), CIMP-high (>or=6/8 methylated CIMP markers, p = 0.005), CIMP-low (1/8-5/8 methylated CIMP markers, p = 0.002, compared to CIMP-0 with 0/8 methylated markers), KRAS G>A mutation (p = 0.02), and inversely with 18q loss of heterozygosity (p = 0.0002). Tumours were classified into nine MSI/CIMP subtypes. Among the CIMP-low group, tumours with both MGMT methylation and loss were far more frequent in MSI-low tumours (67%, 12/18) than MSI-high tumours (5.6%, 1/18; p = 0.0003) and microsatellite stable (MSS) tumours (33%, 52/160; p = 0.008). However, no such relationship was observed among the CIMP-high or CIMP-0 groups. The relationship between MGMT methylation/silencing and MSI-low is limited to only CIMP-low tumours, supporting the suggestion that CIMP-low in colorectal cancer may be a different molecular phenotype from CIMP-high and CIMP-0. Our data support a molecular difference between MSI-low and MSS in colorectal cancer, and a possible link between CIMP-low, MSI-low, MGMT methylation/loss and KRAS mutation.

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.

Naturally occurring methyl salicylate glycosides.

Science.gov (United States)

Mao, Ping; Liu, Zizhen; Xie, Meng; Jiang, Rui; Liu, Weirui; Wang, Xiaohong; Meng, Shen; She, Gaimei

2014-01-01

As an important part of non steroids anti-inflammation drug (NSAIDs), salicylate has developed from natural substance salicylic acid to natrium salicylicum, to aspirin. Now, methyl salicylate glycoside, a new derivative of salicylic acid, is modified with a -COOH group integrated one methyl radical into formic ether, and a -OH linked with a monosaccharide, a disaccharide or a trisaccharide unit by glycosidic linkage. It has the similar pharmacological activities, anti-inflammatory, analgesic, antipyretic and antithrombotic as the previous salicylates' without resulting in serious side effects, particularly the gastrointestinal toxicity. Owing to the superiority of those significant bioactivities, methyl salicylate glycosides have became a hot research area in NSAIDs for several years. This paper compiles all 9 naturally occurring methyl salicylate glycosides, their distribution of the resource and pharmacological mechanism, which could contribute to the new drug discovery.

Lewis Acid Assisted Nickel-Catalyzed Cross-Coupling of Aryl Methyl Ethers by C−O Bond-Cleaving Alkylation: Prevention of Undesired β-Hydride Elimination

KAUST Repository

Liu, Xiangqian

2016-04-10

In the presence of trialkylaluminum reagents, diverse aryl methyl ethers can be transformed into valuable products by C-O bond-cleaving alkylation, for the first time without the limiting β-hydride elimination. This new nickel-catalyzed dealkoxylative alkylation method enables powerful orthogonal synthetic strategies for the transformation of a variety of naturally occurring and easily accessible anisole derivatives. The directing and/or activating properties of aromatic methoxy groups are utilized first, before they are replaced by alkyl chains in a subsequent coupling process.

Protein replacement by receptor-mediated endocytosis corrects the sensitivity of Fanconi anemia group C cells to mitomycin C

NARCIS (Netherlands)

Youssoufian, H; Kruyt, FAE; Li, XT

1999-01-01

Current methods for direct gene transfer into hematopoietic cells are inefficient. Here we show that functional complementation of Fanconi anemia (FA) group C cells by protein replacement can be as efficacious as by transfection with wild-type FAC cDNA, We expressed a chimeric protein (called

Genome-wide methylation analysis identifies differentially methylated CpG loci associated with severe obesity in childhood.

Science.gov (United States)

Huang, R C; Garratt, E S; Pan, H; Wu, Y; Davis, E A; Barton, S J; Burdge, G C; Godfrey, K M; Holbrook, J D; Lillycrop, K A

2015-01-01

Childhood obesity is a major public health issue. Here we investigated whether differential DNA methylation was associated with childhood obesity. We studied DNA methylation profiles in whole blood from 78 obese children (mean BMI Z-score: 2.6) and 71 age- and sex-matched controls (mean BMI Z-score: 0.1). DNA samples from obese and control groups were pooled and analyzed using the Infinium HumanMethylation450 BeadChip array. Comparison of the methylation profiles between obese and control subjects revealed 129 differentially methylated CpG (DMCpG) loci associated with 80 unique genes that had a greater than 10% difference in methylation (P-value obesity were validated using sodium bisulfite pyrosequencing across loci within the FYN, PIWIL4, and TAOK3 genes in individual subjects. Three CpG loci within FYN were hypermethylated in obese individuals (all P obesity was associated with lower methylation of CpG loci within PIWIL4 (P = 0.003) and TAOK3 (P = 0.001). After building logistic regression models, we determined that a 1% increase in methylation in TAOK3, multiplicatively decreased the odds of being obese by 0.91 (95% CI: 0.86 - 0.97), and an increase of 1% methylation in FYN CpG3, multiplicatively increased the odds of being obese by 1.03 (95% CI: 0.99 - 1.07). In conclusion, these findings provide evidence that childhood obesity is associated with specific DNA methylation changes in whole blood, which may have utility as biomarkers of obesity risk.

MTHFR methylation moderates the impact of smoking on DNA methylation at AHRR for African American young adults.

Science.gov (United States)

Beach, Steven R H; Lei, Man Kit; Ong, Mei Ling; Brody, Gene H; Dogan, Meeshanthini V; Philibert, Robert A

2017-09-01

Smoking has been shown to have a large, reliable, and rapid effect on demethylation of AHRR, particularly at cg05575921, suggesting that methylation may be used as an index of cigarette consumption. Because the availability of methyl donors may also influence the degree of demethylation in response to smoking, factors that affect the activity of methylene tetrahydrofolate reductase (MTHFR), a key regulator of methyl group availability, may be of interest. In the current investigation, we examined the extent to which individual differences in methylation of MTHFR moderated the association between smoking and demethylation at cg05575921 as well as at other loci on AHRR associated with a main effect of smoking. Using a discovery sample (AIM, N = 293), and a confirmatory sample (SHAPE, N = 368) of young adult African Americans, degree of methylation of loci in the first exon of MTHFR was associated with amplification of the association between smoking and AHRR demethylation at cg05575921. However, genetic variation at a commonly studied MTHFR variant, C677T, did not influence cg05575921 methylation. The significant interaction between MTHFR methylation and the smoking-induced response at cg05575921 suggests a role for individual differences in methyl cycle regulation in understanding the effects of cigarette consumption on genome wide DNA methylation. © 2017 Wiley Periodicals, Inc.

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 cat......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...

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.

Aberrant Methylation-Mediated Suppression of APAF1 in Myelodysplastic Syndrome.

Science.gov (United States)

Zaker, Farhad; Nasiri, Nahid; Amirizadeh, Naser; Razavi, Seyed Mohsen; Yaghmaie, Marjan; Teimoori-Toolabi, Ladan; Maleki, Ali; Bakhshayesh, Masoumeh

2017-04-01

Background: Myelodysplastic syndromes (MDSs) include a diverse group of clonal bone marrow disorders characterized by ineffective hematopoiesis and pancytopenia. It was found that down regulation of APAF1, a putative tumor suppressor gene (TSG), leads to resistance to chemotherapy and disease development in some cancers. In this study, we investigated the relation of APAF1 methylation status with its expression and clinicopathological factors in myelodysplastic syndrome (MDS) patients. Materials and Methods: Methylation Sensitive-High Resolution Melting Curve Analysis (MS-HRM) was employed in studying the methylation of CpG islands in the APAF1promoter region in MDS. Gene expression was analyzed by using real time RT-PCR. Results: 42.6% of patient samples were methylated in promoter region of APAF1analyzed, while methylation of the gene was not seen in controls (P<0.05). Methylation of APAF1was significantly associated with the suppression of its mRNA expression (P=0.00). The methylation status of APAF1in advanced-stage MDS patients (80%) was significantly higher than that of the early-stage MDS patients (28.2%) (P=0.001). The difference in frequency of hypermethylatedAPAF1 gene was significant between good (37.5%) and poor (85.71%) cytogenetic risk groups (P=0.043). In addition, a higher frequency of APAF1hypermethylation was observed in higher-risk MDS group (69.2%) compared to lower-risk MDS group (34.14%) (P=0.026). Conclusion: Our study indicated that APAF1hypermethylation in MDS was associated to high-risk disease classified according to the IPSS, WHO and cytogenetic risk.

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.

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

KAUST Repository

Yue, Huifeng; Zhu, Chen; Rueping, Magnus

2018-01-01

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.

Predictive value of CHFR and MLH1 methylation in human gastric cancer.

Science.gov (United States)

Li, Yazhuo; Yang, Yunsheng; Lu, Youyong; Herman, James G; Brock, Malcolm V; Zhao, Po; Guo, Mingzhou

2015-04-01

Gastric carcinoma (GC) has one of the highest mortality rates of cancer diseases and has a high incidence rate in China. Palliative chemotherapy is the main treatment for advanced gastric cancer. It is necessary to compare the effectiveness and toxicities of different regimens. This study explores the possibility of methylation of DNA damage repair genes serving as a prognostic and chemo-sensitive marker in human gastric cancer. The methylation status of five DNA damage repair genes (CHFR, FANCF, MGMT, MLH1, and RASSF1A) was detected by nested methylation-specific PCR in 102 paraffin-embedded gastric cancer samples. Chi-square or Fisher's exact tests were used to evaluate the association of methylation status and clinic-pathological factors. The Kaplan-Meier method and Cox proportional hazards models were employed to analyze the association of methylation status and chemo-sensitivity. The results indicate that CHFR, MLH1, RASSF1A, MGMT, and FANCF were methylated in 34.3% (35/102), 21.6% (22/102), 12.7% (13/102), 9.8% (10/102), and 0% (0/102) of samples, respectively. No association was found between methylation of CHFR, MLH1, RASSF1A, MGMT, or FANCF with gender, age, tumor size, tumor differentiation, lymph node metastasis, and TNM stage. In docetaxel-treated gastric cancer patients, resistance to docetaxel was found in CHFR unmethylated patients by Cox proportional hazards model (HR 0.243, 95% CI, 0.069-0.859, p = 0.028), and overall survival is longer in the CHFR methylated group compared with the CHFR unmethylated group (log-rank, p = 0.036). In oxaliplatin-treated gastric cancer patients, resistance to oxaliplatin was found in MLH1 methylated patients (HR 2.988, 95% CI, 1.064-8.394, p = 0.038), and overall survival was longer in the MLH1 unmethylated group compared with the MLH1 methylated group (log-rank, p = 0.046). CHFR is frequently methylated in human gastric cancer, and CHFR methylation may serve as a docetaxel-sensitive marker. MLH1 methylation was

Reductive methylation of insulin. Production of a biologically active tritiated insulin

Energy Technology Data Exchange (ETDEWEB)

Marsh, J W; Nahum, A; Steiner, D F [Department of Biochemistry, University of Chicago, Illinois, USA

1983-01-01

Reductive methylation of the three amino groups of porcine insulin was accomplished by incubation with formaldehyde and sodium cyanoborohydride. The two amino termini and the epsilon amino group of B29 lysine were each dimethylated within 1 h of incubation. The fully methylated insulin bound more tightly to a reverse phase column than did native insulin, had a slightly more acid isoelectric point, and maintained approximately 50% biological activity when examined with an insulin sensitive cultured cell line. Reductive methylation with sodium cyanoboro (/sup 3/H) hydride resulted in a (/sup 3/H) methylated insulin with a specific activity of 6 Ci/mmol.

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.

Mechanism and Stereochemistry of Polyketide Chain Elongation and Methyl Group Epimerization in Polyether Biosynthesis.

Science.gov (United States)

Xie, Xinqiang; Garg, Ashish; Khosla, Chaitan; Cane, David E

2017-03-01

The polyketide synthases responsible for the biosynthesis of the polyether antibiotics nanchangmycin (1) and salinomycin (4) harbor a number of redox-inactive ketoreductase (KR 0 ) domains that are implicated in the generation of C2-epimerized (2S)-2-methyl-3-ketoacyl-ACP intermediates. Evidence that the natural substrate for the polyether KR 0 domains is, as predicted, a (2R)-2-methyl-3-ketoacyl-ACP intermediate, came from a newly developed coupled ketosynthase (KS)-ketoreductase (KR) assay that established that the decarboxylative condensation of methylmalonyl-CoA with S-propionyl-N-acetylcysteamine catalyzed by the Nan[KS1][AT1] didomain from module 1 of the nanchangmycin synthase generates exclusively the corresponding (2R)-2-methyl-3-ketopentanoyl-ACP (7a) product. In tandem equilibrium isotope exchange experiments, incubation of [2- 2 H]-(2R,3S)-2-methyl-3-hydroxypentanoyl-ACP (6a) with redox-active, epimerase-inactive EryKR6 from module 6 of the 6-deoxyerythronolide B synthase and catalytic quantities of NADP + in the presence of redox-inactive, recombinant NanKR1 0 or NanKR5 0 , from modules 1 and 5 of the nanchangmycin synthase, or recombinant SalKR7 0 from module 7 of the salinomycin synthase, resulted in first-order, time-dependent washout of deuterium from 6a. Control experiments confirmed that this washout was due to KR 0 -catalyzed isotope exchange of the reversibly generated, transiently formed oxidation product [2- 2 H]-(2R)-2-methyl-3-ketopentanoyl-ACP (7a), consistent with the proposed epimerase activity of each of the KR 0 domains. Although they belong to the superfamily of short chain dehydrogenase-reductases, the epimerase-active KR 0 domains from polyether synthases lack one or both residues of the conserved Tyr-Ser dyad that has previously been implicated in KR-catalyzed epimerizations.

Melatonin-Mediated Development of Ovine Cumulus Cells, Perhaps by Regulation of DNA Methylation

Directory of Open Access Journals (Sweden)

Yi Fang

2018-02-01

Full Text Available Cumulus cells of pre-pubertal domestic animals are dysfunctional, perhaps due to age-specific epigenetic events. This study was designed to determine effects of melatonin treatment of donors on methylation modification of pre-pubertal cumulus cells. Cumulus cells from germinal vesicle stage cumulus oocyte complexes (COCs were collected from eighteen lambs which were randomly divided into control group (C and melatonin group given an 18 mg melatonin implant subcutaneous (M. Compared to the C group, the M group had higher concentrations of melatonin in plasma and follicular fluid (p < 0.05, greater superovulation, a higher proportion of fully expanded COCs, and a lower proportion of apoptotic cumulus cells (p < 0.05. Real-time PCR results showed that melatonin up-regulated expression of genes MT1, Bcl2, DNMT1, DNMT3a and DNMT3b, but down-regulated expression of genes p53, Caspase 3 and Bax (p < 0.05. Furthermore, melatonin increased FI of FITC (global methylation level on cumulus cells (p < 0.05. To understand the regulation mechanism, the DNMTs promoter methylation sequence were analyzed. Compared to the C group, although there was less methylation at two CpG sites of DNMT1 (p < 0.05 and higher methylation at two CpG sites of DNMT3a (p < 0.05, there were no significant differences in methylation of the detected DNMT1 and DNMT3a promoter regions. However, there were lower methylation levels at five CpG sites of DNMT3b, which decreased methylation of detected DNMT3b promoter region on M group (p < 0.05. In conclusion, alterations of methylation regulated by melatonin may mediate development of cumulus cells in lambs.

Migratory Insertion of Hydrogen Isocyanide in the Pentacyano(methyl)cobaltate(III) Anion

DEFF Research Database (Denmark)

Kofod, Pauli; Harris, Pernille Hanne; Larsen, Sine

2003-01-01

The preparation of the pentacyano(iminiumacetyl)cobaltate(III) anion and its N-methyl and N,N-dimethyl derivatives is reported. The iminiumacetyl group is formed by migratory insertion of cis hydrogen isocyanide in the pentacyano(methyl)cobaltate(III) anion. The new compounds have been spectrosco......The preparation of the pentacyano(iminiumacetyl)cobaltate(III) anion and its N-methyl and N,N-dimethyl derivatives is reported. The iminiumacetyl group is formed by migratory insertion of cis hydrogen isocyanide in the pentacyano(methyl)cobaltate(III) anion. The new compounds have been...

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.

Valve-sparing and valve-replacing techniques for aortic root replacement in patients with Marfan syndrome: Analysis of early outcome.

Science.gov (United States)

Volguina, Irina V; Miller, D Craig; LeMaire, Scott A; Palmero, Laura C; Wang, Xing Li; Connolly, Heidi M; Sundt, Thoralf M; Bavaria, Joseph E; Dietz, Harry C; Milewicz, Dianna M; Coselli, Joseph S

2009-05-01

A prospective, international registry study was initiated to provide contemporary comparative data on short-term clinical outcomes after aortic valve-sparing and aortic valve-replacing root operations in patients with Marfan syndrome. The purpose of this initial report is to describe the study design and to compare early outcomes in the first 151 enrolled patients. We assessed 30-day outcomes in 151 patients who met strict Ghent diagnostic criteria for Marfan syndrome and underwent aortic root replacement with either valve-replacing (n = 46) or valve-sparing techniques (n = 105) at one of 18 participating centers. In the valve replacement group, a mechanical composite valve graft was used in 39 (85%) patients and a bioprosthetic valve in 7 (15%). In the valve-sparing group, David V procedures were performed in 57 (54%) patients, David I in 38 (36%), David IV in 8 (8%), Florida sleeve in 1 (1%), and Yacoub remodeling in 1 (1%). No in-hospital or 30-day deaths occurred. Despite longer crossclamp and cardiopulmonary bypass times in the valve-sparing group, there were no significant between-group differences in postoperative complications. Thirty-day valve-related complications occurred in 2 (4%) patients undergoing valve replacement and in 3 (3%) undergoing valve-sparing procedures (P = .6). The analysis of early outcomes revealed that valve-sparing techniques were the most common approach to root replacement in patients with Marfan syndrome in these centers. The complexity of valve-sparing root replacement did not translate into any demonstrable adverse early outcomes. Subsequent analysis will compare the 3-year durability of these two surgical approaches.

Design verification for reactor head replacement

International Nuclear Information System (INIS)

Dwivedy, K.K.; Whitt, M.S.; Lee, R.

2005-01-01

This paper outlines the challenges of design verification for reactor head replacement for PWR plants and the program for qualification from the prospective of the utility design engineering group. This paper is based on the experience with the design confirmation of four reactor head replacements for two plants, and their interfacing components, parts, appurtenances, and support structures. The reactor head replacement falls under the jurisdiction of the applicable edition of the ASME Section XI code, with particular reference to repair/replacement activities. Under any repair/replacement activities, demands may be encountered in the development of program and plan for replacement due to the vintage of the original design/construction Code and the design reports governing the component qualifications. Because of the obvious importance of the reactor vessel, these challenges take on an added significance. Additional complexities are introduced to the project, when the replacement components are fabricated by vendors different from the original vendor. Specific attention is needed with respect to compatibility with the original design and construction of the part and interfacing components. The program for reactor head replacement requires evaluation of welding procedures, applicable examination, test, and acceptance criteria for material, welds, and the components. Also, the design needs to take into consideration the life of the replacement components with respect to the extended period of operation of the plant after license renewal and other plant improvements. Thus, the verification of acceptability of reactor head replacement provides challenges for development and maintenance of a program and plan, design specification, design report, manufacturer's data report and material certification, and a report of reconciliation. The technical need may also be compounded by other challenges such as widely scattered global activities and organizational barriers, which

The preference of tryptophan for membrane interfaces: insights from N-methylation of tryptophans in gramicidin channels.

Science.gov (United States)

Sun, Haiyan; Greathouse, Denise V; Andersen, Olaf S; Koeppe, Roger E

2008-08-08

To better understand the structural and functional roles of tryptophan at the membrane/water interface in membrane proteins, we examined the structural and functional consequences of Trp --> 1-methyl-tryptophan substitutions in membrane-spanning gramicidin A channels. Gramicidin A channels are miniproteins that are anchored to the interface by four Trps near the C terminus of each subunit in a membrane-spanning dimer. We masked the hydrogen bonding ability of individual or multiple Trps by 1-methylation of the indole ring and examined the structural and functional changes using circular dichroism spectroscopy, size exclusion chromatography, solid state (2)H NMR spectroscopy, and single channel analysis. N-Methylation causes distinct changes in the subunit conformational preference, channel-forming propensity, single channel conductance and lifetime, and average indole ring orientations within the membrane-spanning channels. The extent of the local ring dynamic wobble does not increase, and may decrease slightly, when the indole NH is replaced by the non-hydrogen-bonding and more bulky and hydrophobic N-CH(3) group. The changes in conformational preference, which are associated with a shift in the distribution of the aromatic residues across the bilayer, are similar to those observed previously with Trp --> Phe substitutions. We conclude that indole N-H hydrogen bonding is of major importance for the folding of gramicidin channels. The changes in ion permeability, however, are quite different for Trp --> Phe and Trp --> 1-methyl-tryptophan substitutions, indicating that the indole dipole moment and perhaps also ring size and are important for ion permeation through these channels.

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

African Journals Online (AJOL)

etchie

2013-02-20

Feb 20, 2013 ... Our method uses a single-CpG-resolution, whole-genome methylation ... Key words: Methyl-DNA immunoprecipitation, next-generation sequencing, ...... methylation is prevalent in embryonic stem cells andmaybe mediated.

The Metabolic Burden of Methyl Donor Deficiency with Focus on the Betaine Homocysteine Methyltransferase Pathway

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Rima Obeid

2013-09-01

Full Text Available Methyl groups are important for numerous cellular functions such as DNA methylation, phosphatidylcholine synthesis, and protein synthesis. The methyl group can directly be delivered by dietary methyl donors, including methionine, folate, betaine, and choline. The liver and the muscles appear to be the major organs for methyl group metabolism. Choline can be synthesized from phosphatidylcholine via the cytidine-diphosphate (CDP pathway. Low dietary choline loweres methionine formation and causes a marked increase in S-adenosylmethionine utilization in the liver. The link between choline, betaine, and energy metabolism in humans indicates novel functions for these nutrients. This function appears to goes beyond the role of the nutrients in gene methylation and epigenetic control. Studies that simulated methyl-deficient diets reported disturbances in energy metabolism and protein synthesis in the liver, fatty liver, or muscle disorders. Changes in plasma concentrations of total homocysteine (tHcy reflect one aspect of the metabolic consequences of methyl group deficiency or nutrient supplementations. Folic acid supplementation spares betaine as a methyl donor. Betaine is a significant determinant of plasma tHcy, particularly in case of folate deficiency, methionine load, or alcohol consumption. Betaine supplementation has a lowering effect on post-methionine load tHcy. Hypomethylation and tHcy elevation can be attenuated when choline or betaine is available.

Analysis of the state of posttranslational calmodulin methylation in developing pea plants

International Nuclear Information System (INIS)

Oh, Sukheung; Roberts, D.M.

1990-01-01

A specific calmodulin-N-methyltransferase was used in a radiometric assay to analyze the degree of methylation of lysine-115 in pea (Pisum sativum) plants. Calmodulin was isolated from dissected segments of developing roots of young etiolated and green pea plants and was tested for its ability to be methylated by incubation with the calmodulin methyltransferase in the presence of [ 3 H]methyl-S-adenosylmethionine. By this approach, the presence of unmethylated calmodulins were demonstrated in pea tissues, and the levels of methylation varied depending on the developmental state of the tissue tested. Calmodulin methylation levels were lower in apical root segments of both etiolated and green plants, and in the young lateral roots compared with the mature, differentiated root tissues. The incorporation of methyl groups into these calmodulin samples appears to be specific for position 115 since site-directed mutants of calmodulin with substitutions at this position competitively inhibited methyl group incorporation. The present findings, combined with previous data showing differences in the ability of methylated and unmethylated calmodulins to activate pea NAD kinase raise the possibility that posttranslational methylation of calmodulin could be another mechanism for regulating calmodulin activity

Combustion of jojoba methyl ester in an indirect injection diesel engine

Energy Technology Data Exchange (ETDEWEB)

Selim, M.Y.E. [United Arab Emirates University, Al-Ain (United Arab Emirates). Mechanical Engineering Dept.; Radwan, M.S.; Elfeky, S.M.S. [Helwan University, Cairo (Egypt). Mechanical Power Engineering Dept.

2003-07-01

An experimental investigation has been carried out to examine for the first time the performance and combustion noise of an indirect injection diesel engine running with new fuel derived from pure jojoba oil, jojoba methyl ester, and its blends with gas oil. A Ricardo E6 compression swirl diesel engine was fully instrumented for the measurement of combustion pressure and its rise rate and other operating parameters. Test parameters included the percentage of jojoba methyl ester in the blend, engine speed, load, injection timing and engine compression ratio. Results showed that the new fuel derived from jojoba is generally comparable and a good replacement to gas oil in diesel engine at most engine operating conditions, in terms of performance parameters and combustion noise produced. (author)

Effective photosensitized energy transfer of nonanuclear terbium clusters using methyl salicylate derivatives.

Science.gov (United States)

Omagari, Shun; Nakanishi, Takayuki; Seki, Tomohiro; Kitagawa, Yuichi; Takahata, Yumie; Fushimi, Koji; Ito, Hajime; Hasegawa, Yasuchika

2015-03-12

The photophysical properties of the novel nonanuclear Tb(III) clusters Tb-L1 and Tb-L2 involving the ligands methyl 4-methylsalicylate (L1) and methyl 5-methylsalicylate (L2) are reported. The position of the methyl group has an effect on their photophysical properties. The prepared nonanuclear Tb(III) clusters were identified by fast atom bombardment mass spectrometry and powder X-ray diffraction. Characteristic photophysical properties, including photoluminescence spectra, emission lifetimes, and emission quantum yields, were determined. The emission quantum yield of Tb-L1 (Φ(ππ*) = 31%) was found to be 13 times larger than that of Tb-L2 (Φ(ππ*) = 2.4%). The photophysical characterization and DFT calculations reveal the effect of the methyl group on the electronic structure of methylsalicylate ligand. In this study, the photophysical properties of the nonanuclear Tb(III) clusters are discussed in relation to the methyl group on the aromatic ring of the methylsalicylate ligand.

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

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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

Factors affecting the retention of methyl iodide by iodide-impregnated carbon

International Nuclear Information System (INIS)

Hyder, M.L.; Malstrom, R.A.

1991-01-01

This paper comprises two sets of studies of methyl iodide retention by iodide-impregnated carbon. In the first of these, the retention of the methyl iodide on the carbon surface and its subsequent evolution were observed directly by a technique of combustion and phosphorescence. In the second, the methyl iodide retention in a standard test was compared with surface area measurements and the concentration of unreacted iodine. A correlation among these parameters was identified and characterized. Carbon quality was varied through the selection of used material with differing service histories. Air from the Savannah River Site reactor buildings is vented through carbon beds for control of radioiodine before release to the atmosphere. The carbon used is North American Carbon Co. type GX-176 coconut shell carbon impregnated with 1% triethylenedimaine (TEDA) and 2% potassium iodide by weight. Replacement intervals for the carbon have been as long as thirty months. Analysis of samples withdrawn at much shorter times has shown that the TEDA is lost after a few months, and the performance of the carbon for methyl iodide retention is dependent on the iodide impregnant. Efficient methyl iodide retention is not a requirement for carbon in this service; however, methyl iodide retention as measured by the ASTM Test D3803 (method B) has been found to correlate well with other desirable properties of the carbon such as radiation stability. The studies undertaken here were intended to shed light on the changes taking place in this carbon during long-term service and to provide a basis for simpler measurements of carbon quality

Liver receptor homolog-1 is a critical determinant of methyl-pool metabolism

Science.gov (United States)

Balance of labile methyl groups (choline, methionine, betaine, and folate) is important for normal liver function. Quantitatively, a significant use of labile methyl groups is in the production of phosphatidylcholines (PCs), which are ligands for the nuclear liver receptor homolog-1 (LRH-1). We stud...

Methylation of food commodities during fumigation with methyl bromide

International Nuclear Information System (INIS)

Starratt, A.N.; Bond, E.J.

1990-01-01

Sites of methylation in several commodities (wheat, oatmeal, peanuts, almonds, apples, oranges, maize, alfalfa and potatoes) during fumigation with 14 C-methyl bromide were studied. Differences were observed in levels of the major volatiles: methanol, dimethyl sulphide and methyl mercaptan, products of O- and S-methylation, resulting from treatment of the fumigated materials with 1N sodium hydroxide. In studies of maize and wheat, histidine was the amino acid which underwent the highest level of N-methylation. (author). 24 refs, 3 tabs

In Utero Exposure to Dietary Methyl Nutrients and Breast Cancer Risk in Offspring

Science.gov (United States)

2010-09-01

distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Lipotropes (methionine, choline, folate , and vitamin B12) are dietary methyl donors and...Lipotropes are methyl group (CH3) containing essential nutrients (methionine, choline, folate , and vitamin B12) and are important methyl donors...is highly dependent on methyl donors and cofactors (11, 17). The coenzymes necessary for DNA methylation reactions include folate , vitamin B12, and

Non-Steroidal Anti-Inflammatory Drug Use and Genomic DNA Methylation in Blood.

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Lauren E Wilson

Full Text Available Non-steroidal anti-inflammatory drug (NSAID use is associated with decreased risk of some cancers. NSAID use modulates the epigenetic profile of normal colonic epithelium and may reduce risk of colon cancer through this pathway; however, the effect of NSAID use on the DNA methylation profile of other tissues including whole blood has not yet been examined.Using the Sister Study cohort, we examined the association between NSAID usage and whole genome methylation patterns in blood DNA. Blood DNA methylation status across 27,589 CpG sites was evaluated for 871 women using the Illumina Infinium HumanMethylation27 Beadchip, and in a non-overlapping replication sample of 187 women at 485,512 CpG sites using the Infinium HumanMethylation450 Beadchip. We identified a number of CpG sites that were differentially methylated in regular, long-term users of NSAIDs in the discovery group, but none of these sites were statistically significant in our replication group.We found no replicable methylation differences in blood related to NSAID usage. If NSAID use does effect blood DNA methylation patterns, differences are likely small.

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.

Comparison of group-based outpatient physiotherapy with usual care after total knee replacement: a feasibility study for a randomized controlled trial.

Science.gov (United States)

Artz, Neil; Dixon, Samantha; Wylde, Vikki; Marques, Elsa; Beswick, Andrew D; Lenguerrand, Erik; Blom, Ashley W; Gooberman-Hill, Rachael

2017-04-01

To evaluate the feasibility of conducting a randomized controlled trial comparing group-based outpatient physiotherapy with usual care in patients following total knee replacement. A feasibility study for a randomized controlled trial. One secondary-care hospital orthopaedic centre, Bristol, UK. A total of 46 participants undergoing primary total knee replacement. The intervention group were offered six group-based exercise sessions after surgery. The usual care group received standard postoperative care. Participants were not blinded to group allocation. Feasibility was assessed by recruitment, reasons for non-participation, attendance, and completion rates of study questionnaires that included the Lower Extremity Functional Scale and Knee Injury and Osteoarthritis Outcome Score. Recruitment rate was 37%. Five patients withdrew or were no longer eligible to participate. Intervention attendance was high (73%) and 84% of group participants reported they were 'very satisfied' with the exercises. Return of study questionnaires at six months was lower in the usual care (75%) than in the intervention group (100%). Mean (standard deviation) Lower Extremity Functional Scale scores at six months were 45.0 (20.8) in the usual care and 57.8 (15.2) in the intervention groups. Recruitment and retention of participants in this feasibility study was good. Group-based physiotherapy was acceptable to participants. Questionnaire return rates were lower in the usual care group, but might be enhanced by telephone follow-up. The Lower Extremity Functional Scale had high responsiveness and completion rates. Using this outcome measure, 256 participants would be required in a full-scale randomized controlled trial.

Determination of the two methyl group orientations at vapor/acetone interface with polarization null angle method in SFG vibrational spectroscopy

Science.gov (United States)

Chen, Hua; Gan, Wei; Wu, Bao-hua; Wu, Dan; Zhang, Zhen; Wang, Hong-fei

2005-06-01

We report a direct measurement of the orientation of the two CH 3 groups of acetone molecule at the vapor/acetone interface. The interfacial acetone molecule is found well-ordered, with one methyl group points away around 14.4° ± 1.9° and another into the bulk liquid around 102.8° ± 1.9° from the interface normal, and thus the C dbnd O group points into the bulk around 135.8° ± 1.9°. These results directly confirmed the highly ordered and even crystal like interfacial structure of the vapor/acetone interface from previous MD simulation. The general formulation and accurate determination of the orientational parameter D can be used to treat interfaces with complex molecular orientations.

A comparison of minimally invasive and standard aortic valve replacement.

Science.gov (United States)

Stoliński, Jarosław; Plicner, Dariusz; Grudzień, Grzegorz; Wąsowicz, Marcin; Musiał, Robert; Andres, Janusz; Kapelak, Bogusław

2016-10-01

The study objective was to compare aortic valve replacement through a right anterior minithoracotomy with aortic valve replacement through a median sternotomy. With propensity score matching, we selected 211 patients after aortic valve replacement through a right anterior minithoracotomy and 211 patients after aortic valve replacement who underwent operation between January 2010 and December 2013. Perioperative outcomes were analyzed, and multivariable logistic regression analysis of risk factors of postoperative morbidity was performed. For propensity score-matched patients, hospital mortality was 1.0% in the aortic valve replacement through a right anterior minithoracotomy group and 1.4% in the aortic valve replacement group (P = 1.000). Stroke occurred in 0.5% versus 1.4% (P = .615), myocardial infarction occurred in 1.4% versus 1.9% (P = 1.000), and new onset of atrial fibrillation occurred in 12.8% versus 24.2% (P = .003) of patients in the aortic valve replacement through a right anterior minithoracotomy and aortic valve replacement groups, respectively. Postoperative drainage was 353.5 ± 248.6 mL versus 544.3 ± 324.5 mL (P replacement through a right anterior minithoracotomy and aortic valve replacement groups, respectively. Mediastinitis occurred in 2.8% of patients after aortic valve replacement and in 0.0% of patients after aortic valve replacement through a right anterior minithoracotomy surgery (P = .040). Intensive care unit stay (1.3 ± 1.2 days vs 2.6 ± 2.6 days) and hospital stay (5.7 ± 1.6 days vs 8.7 ± 4.4 days) were statistically significantly shorter in the aortic valve replacement through a right anterior minithoracotomy group. Aortic valve replacement through a right anterior minithoracotomy surgery resulted in reduced postoperative morbidity (odds ratio, 0.4; P replacement through a right anterior minithoracotomy surgery resulted in a reduced infection rate, diminished postoperative bleeding and blood

Abiotic Formation of Methyl Halides in the Terrestrial Environment

Science.gov (United States)

Keppler, F.

2011-12-01

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

Allele specific expression and methylation in the bumblebee, Bombus terrestris

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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.

Contrasting the surface ocean distribution of bromoform and methyl iodide; implications for boundary layer physics, chemistry and climate

Energy Technology Data Exchange (ETDEWEB)

Palmer, C J, E-mail: carl.j.palmer@gmail.co [Department of Oceanography, University of Cape Town, 7701 (South Africa)

2010-08-15

Bromoform and methyl iodide are both methane-like hydrocarbons with a halogen atom replacing one or more of the hydrogen atoms. Both of these compounds occur naturally in the environment as a result of their production from seaweed and kelp. They are of interest to climate science as a result of their catalytic destruction of boundary layer ozone (a potent greenhouse gas) and, specifically for methyl iodide, the proposed role in the formation of new cloud condensation nuclei with implications for climate. In this paper, the currently available data on the distribution of bromoform and methyl iodide are analysed and contrasted to show that the concentrations of bromoform and methyl iodide do not correlate, that, in contrast to bromoform, the parameterization of sea surface methyl iodide concentrations demands only the sea surface temperature, and that the pelagic distribution of methyl iodide appears to follow the solar zenith angle. These three observations together suggest that, while the pelagic source of bromoform is mostly biogenic, the source of methyl iodide is photochemical. This has implications for the understanding of planetary boundary layer chemistry and potential organohalogen mediated feedbacks to climate.

Contrasting the surface ocean distribution of bromoform and methyl iodide; implications for boundary layer physics, chemistry and climate

International Nuclear Information System (INIS)

Palmer, C J

2010-01-01

Bromoform and methyl iodide are both methane-like hydrocarbons with a halogen atom replacing one or more of the hydrogen atoms. Both of these compounds occur naturally in the environment as a result of their production from seaweed and kelp. They are of interest to climate science as a result of their catalytic destruction of boundary layer ozone (a potent greenhouse gas) and, specifically for methyl iodide, the proposed role in the formation of new cloud condensation nuclei with implications for climate. In this paper, the currently available data on the distribution of bromoform and methyl iodide are analysed and contrasted to show that the concentrations of bromoform and methyl iodide do not correlate, that, in contrast to bromoform, the parameterization of sea surface methyl iodide concentrations demands only the sea surface temperature, and that the pelagic distribution of methyl iodide appears to follow the solar zenith angle. These three observations together suggest that, while the pelagic source of bromoform is mostly biogenic, the source of methyl iodide is photochemical. This has implications for the understanding of planetary boundary layer chemistry and potential organohalogen mediated feedbacks to climate.

MethylMix 2.0: an R package for identifying DNA methylation genes.

Science.gov (United States)

Cedoz, Pierre-Louis; Prunello, Marcos; Brennan, Kevin; Gevaert, Olivier

2018-04-14

DNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is a major mechanism of gene expression deregulation in a wide range of diseases. At the same time, high-throughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements. We developed MethylMix, an algorithm implemented in R to identify disease specific hyper and hypomethylated genes. Here we present a new version of MethylMix that automates the construction of DNA-methylation and gene expression datasets from The Cancer Genome Atlas (TCGA). More precisely, MethylMix 2.0 incorporates two major updates: the automated downloading of DNA methylation and gene expression datasets from TCGA and the automated preprocessing of such datasets: value imputation, batch correction and CpG sites clustering within each gene. The resulting datasets can subsequently be analyzed with MethylMix to identify transcriptionally predictive methylation states. We show that the Differential Methylation Values created by MethylMix can be used for cancer subtyping. olivier.gevaert@stanford.edu. https://bioconductor.org/packages/release/bioc/manuals/MethylMix/man/MethylMix.pdf. MethylMix 2.0 was implemented as an R package and is available in bioconductor.

Global DNA methylation analysis using methyl-sensitive amplification polymorphism (MSAP).

Science.gov (United States)

Yaish, Mahmoud W; Peng, Mingsheng; Rothstein, Steven J

2014-01-01

DNA methylation is a crucial epigenetic process which helps control gene transcription activity in eukaryotes. Information regarding the methylation status of a regulatory sequence of a particular gene provides important knowledge of this transcriptional control. DNA methylation can be detected using several methods, including sodium bisulfite sequencing and restriction digestion using methylation-sensitive endonucleases. Methyl-Sensitive Amplification Polymorphism (MSAP) is a technique used to study the global DNA methylation status of an organism and hence to distinguish between two individuals based on the DNA methylation status determined by the differential digestion pattern. Therefore, this technique is a useful method for DNA methylation mapping and positional cloning of differentially methylated genes. In this technique, genomic DNA is first digested with a methylation-sensitive restriction enzyme such as HpaII, and then the DNA fragments are ligated to adaptors in order to facilitate their amplification. Digestion using a methylation-insensitive isoschizomer of HpaII, MspI is used in a parallel digestion reaction as a loading control in the experiment. Subsequently, these fragments are selectively amplified by fluorescently labeled primers. PCR products from different individuals are compared, and once an interesting polymorphic locus is recognized, the desired DNA fragment can be isolated from a denaturing polyacrylamide gel, sequenced and identified based on DNA sequence similarity to other sequences available in the database. We will use analysis of met1, ddm1, and atmbd9 mutants and wild-type plants treated with a cytidine analogue, 5-azaC, or zebularine to demonstrate how to assess the genetic modulation of DNA methylation in Arabidopsis. It should be noted that despite the fact that MSAP is a reliable technique used to fish for polymorphic methylated loci, its power is limited to the restriction recognition sites of the enzymes used in the genomic

New small molecule inhibitors of histone methyl transferase DOT1L with a nitrile as a non-traditional replacement for heavy halogen atoms.

Science.gov (United States)

Spurr, Sophie S; Bayle, Elliott D; Yu, Wenyu; Li, Fengling; Tempel, Wolfram; Vedadi, Masoud; Schapira, Matthieu; Fish, Paul V

2016-09-15

A number of new nucleoside derivatives are disclosed as inhibitors of DOT1L activity. SARs established that DOT1L inhibition could be achieved through incorporation of polar groups and small heterocycles at the 5-position (5, 6, 12) or by the application of alternative nitrogenous bases (18). Based on these results, CN-SAH (19) was identified as a potent and selective inhibitor of DOT1L activity where the polar 5-nitrile group was shown by crystallography to bind in the hydrophobic pocket of DOT1L. In addition, we show that a polar nitrile group can be used as a non-traditional replacement for heavy halogen atoms. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Ancestry dependent DNA methylation and influence of maternal nutrition.

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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.

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

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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.

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

Science.gov (United States)

Sommer, Roman; Hauck, Dirk; Varrot, Annabelle; Imberty, Anne; Künzler, Markus; Titz, Alexander

2016-01-01

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.

Methylation of MGMT Is Associated with Poor Prognosis in Patients with Stage III Duodenal Adenocarcinoma.

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Tao Fu

Full Text Available O6-methylguanine-DNA methyltransferase (MGMT methylation status has not been extensively investigated in duodenal adenocarcinoma (DA. The aim of this study was to evaluate the MGMT methylation status and examine its possible prognostic value in patients with stage III DA.Demographics, tumor characteristics and survival were available for 64 patients with stage III DA. MGMT methylation was detected by using MethyLight. A Cox proportional hazard model was built to predict survival, adjusted for clinicopathological characteristics and tumor molecular features, including the CpG island methylator phenotype (CIMP, microsatellite instability (MSI, and KRAS mutations.MGMT methylation was detected in 17 of 64 (26.6% patients, and was not correlated with sex, age, tumor differentiation, CIMP, MSI, or KRAS mutations. MGMT methylation was the only one factor associated with both overall survival (OS and disease-free survival (DFS on both univariate and multivariate analyses. In patients treated with surgery alone, MGMT-methylated group had worse OS and DFS when compared with MGMT-unmethylated group. However, in patients treated with chemotherapy/radiotherapy, outcomes became comparable between the two groups.Our results demonstrate MGMT methylation is a reliable and independent prognostic factor in DAs. Methylation of MGMT is associated with poor prognosis in patients with stage III DAs.

Replication of Vibrio cholerae chromosome I in Escherichia coli: dependence on dam methylation

DEFF Research Database (Denmark)

Koch, Birgit; Ma, Xiaofang; Løbner-Olesen, Anders

2010-01-01

. cholerae chromosome I replication, which similar to what is observed for E. coli. No hda homologue has been identified in V. cholerae yet. In V. cholerae, dam is essential for viability, whereas in E. coli, dam mutants are viable. Replacement of E. coli oriC with oriCIVc allowed us to specifically address...... the role of the Dam methyltransferase and SeqA in replication initiation from oriCIVc. We show that when E. coli's origin of replication is substituted by oriCIVc, dam, but not seqA, becomes important for growth, arguing that Dam methylation exerts a critical function at the origin of replication itself....... We propose that Dam methylation promotes DnaA-assisted successful duplex opening and replisome assembly at oriCIVc in E. coli. In this model, methylation at oriCIVc would ease DNA melting. This is supported by the fact that the requirement for dam can be alleviated by increasing negative supercoiling...

Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.).

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Keyte, Anna L; Percifield, Ryan; Liu, Bao; Wendel, Jonathan F

2006-01-01

Cytosine methylation is important in the epigenetic regulation of gene expression and development in plants and has been implicated in silencing duplicate genes after polyploid formation in several plant groups. Relatively little information exists, however, on levels and patterns of methylation polymorphism (MP) at homologous loci within species. Here we explored the levels and patterns of methylation-polymorphism diversity at CCGG sites within allotetraploid cotton, Gossypium hirsutum, using a methylation-sensitive amplified fragment length polymorphism screen and a selected set of 20 G. hirsutum accessions for which we have information on genetic polymorphism levels and relationships. Methylation and MP exist at high levels within G. hirsutum: of 150 HpaII/MspI sites surveyed, 48 were methylated at the inner cytosine (32%) and 32 of these were polymorphic (67%). Both these values are higher than comparable measures of genetic diversity using restriction fragment length polymorphisms. The high percentage of methylation-polymorphic sites and potential relationship to gene expression underscore the potential significance of MP within and among populations. We speculate that biased correlation of methylation-polymorphic sites and genes in cotton may be a consequence of polyploidy and the attendant doubling of all genes.

Preparation and Evaluation at the Delta Opioid Receptor of a Series of Linear Leu-Enkephalin Analogues Obtained by Systematic Replacement of the Amides

Science.gov (United States)

2013-01-01

Leu-enkephalin analogues, in which the amide bonds were sequentially and systematically replaced either by ester or N-methyl amide bonds, were prepared using classical organic chemistry as well as solid phase peptide synthesis (SPPS). The peptidomimetics were characterized using competition binding, ERK1/2 phosphorylation, receptor internalization, and contractility assays to evaluate their pharmacological profile over the delta opioid receptor (DOPr). The lipophilicity (LogD7.4) and plasma stability of the active analogues were also measured. Our results revealed that the last amide bond can be successfully replaced by either an ester or an N-methyl amide bond without significantly decreasing the biological activity of the corresponding analogues when compared to Leu-enkephalin. The peptidomimetics with an N-methyl amide function between residues Phe and Leu were found to be more lipophilic and more stable than Leu-enkephalin. Findings from the present study further revealed that the hydrogen-bond donor properties of the fourth amide of Leu-enkephalin are not important for its biological activity on DOPr. Our results show that the systematic replacement of amide bonds by isosteric functions represents an efficient way to design and synthesize novel peptide analogues with enhanced stability. Our findings further suggest that such a strategy can also be useful to study the biological roles of amide bonds. PMID:23650868

Application of multiplex nested methylated specific PCR in early diagnosis of epithelial ovarian cancer.

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Wang, Bi; Yu, Lei; Yang, Guo-Zhen; Luo, Xin; Huang, Lin

2015-01-01

To explore the application of multiplex nested methylated specific polymerase chain reaction (PCR) in the early diagnosis of epithelial ovarian carcinoma (EOC). Serum and fresh tissue samples were collected from 114 EOC patients. RUNX3, TFPI2 and OPCML served as target genes. Methylation levels of tissues were assessed by multiplex nested methylated specific PCR, the results being compared with those for carcinoma antigen 125 (CA125). The serum free deoxyribose nucleic acid (DNA) methylation spectrum of EOC patients was completely contained in the DNA spectrum of cancer tissues, providing an accurate reflection of tumor DNA methylation conditions. Serum levels of CA125 and free DNA methylation in the EOC group were evidently higher than those in benign lesion and control groups (p0.05). The sensitivity, specificity and positive predicative value (PPV) of multiplex nested methylated specific PCR were significantly higher for detection of all patients and those with early EOC than those for CA125 (pnested methylated specific PCR (p>0.05), but there was no significant difference in sensitivity (p>0.05). Serum free DNA methylation can be used as a biological marker for EOC and multiplex nested methylated specific PCR should be considered for early diagnosis since it can accurately determine tumor methylation conditions.

Mathematical aspects of molecular replacement. III. Properties of space groups preferred by proteins in the Protein Data Bank.

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Chirikjian, G; Sajjadi, S; Toptygin, D; Yan, Y

2015-03-01

The main goal of molecular replacement in macromolecular crystallography is to find the appropriate rigid-body transformations that situate identical copies of model proteins in the crystallographic unit cell. The search for such transformations can be thought of as taking place in the coset space Γ\\G where Γ is the Sohncke group of the macromolecular crystal and G is the continuous group of rigid-body motions in Euclidean space. This paper, the third in a series, is concerned with viewing nonsymmorphic Γ in a new way. These space groups, rather than symmorphic ones, are the most common ones for protein crystals. Moreover, their properties impact the structure of the space Γ\\G. In particular, nonsymmorphic space groups contain both Bieberbach subgroups and symmorphic subgroups. A number of new theorems focusing on these subgroups are proven, and it is shown that these concepts are related to the preferences that proteins have for crystallizing in different space groups, as observed in the Protein Data Bank.

Systemic effects of chronically administered methyl prednisolonate and methyl 17-deoxyprednisolonate.

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Olejniczak, E; Lee, H J

1984-06-01

The systemic activities of methyl prednisolonate and methyl 17-deoxyprednisolonate (1) were studied in rats. Methyl 17-deoxyprednisolonate produced significant changes in the amount of sodium ion (decreased) and potassium ion (increased) in urine; however, methyl prednisolonate had no effect on electrolyte balance. Both methyl prednisolonate and methyl 17-deoxyprednisolonate had no effect on liver glycogen content, plasma corticosterone level and relative adrenal weight. In contrast, the parent compound prednisolone caused a significant decrease in liver glycogen content, plasma corticosterone level and relative adrenal weight.

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

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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

Carcinogenicity of 1-methyl-3(p-chlorophenyl)-1-nitrosourea and its 1-methyl trideuterated derivative in rats.

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Schreiber, D; Martin, J; Mendel, J

1986-01-01

The carcinogenic activity of 1-methyl-3(p-chlorophenyl)-1-nitrosourea (Cl-MPNU) and its 1-methyl trideuterated analog (Cl-MPNU-d3) was compared by intragastric administration to hooded rats of equimolar doses of both compounds. A 100% frequency of forestomach tumors was observed in both groups. However, the mean latency period of the animals treated with Cl-MPNU-d3 was significantly longer (P less than 0.01). The results suggest the occurrence of a deuterium isotope effect in nitrosoureas but not as distinct as in nitrosamines.

Phonon interactions with methyl radicals in single crystals

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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.

Directed ortho-Lithiation: Observation of an Unexpected 1-Lithio to 3-Lithio Conversion of 1-Lithio-naphthyllithium Compounds with an ortho-Directing 2-(Dimethylamino)methyl Group

NARCIS (Netherlands)

Jastrzebski, J.T.B.H.; Arink, A.M.; Kleijn, H.; Braam, T.W.; Lutz, M.; Spek, A.L.; van Koten, G.

2013-01-01

Regioselectivity is an important aspect in the design of organic protocols involving Directed ortho-Lithiation (DoL) of arenes, in particular with those arenes containing heteroatom substituents as directing groups. The DoL of 2-[(dimethylamino)methyl]naphthalene (dman) that proceeds with low

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

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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.

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

BACKGROUND: Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. The relationship between DNA methylation, cytogenetic...... background, drug resistance and relapse in ALL is poorly understood. RESULTS: We surveyed the DNA methylation levels of 435,941 CpG sites in samples from 764 children at diagnosis of ALL and from 27 children at relapse. This survey uncovered four characteristic methylation signatures. First, compared...... 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...

Polymerization of Methyl Methacrylate Catalyzed by Co(II), Cu(II), and Zn(II) Complexes Bearing N-Methyl-N-((pyridin-2-yl)methyl) cyclohexanamine

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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.

Clinical Utility of promoter methylation of the tumor suppressor genes DKK3, and RASSF1A in breast cancer patients

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Marwa H. Saied

2018-04-01

Full Text Available Background: DNA methylation is the commonest known epigenetic change that results in silencing of tumor suppressor genes. Promoter methylation of tumor suppressor genes has the potential for early detection of breast cancer. Aim: Aim is to examine the potential usefulness of blood based methylation specific polymerase chain reaction (MSP of methylated DKK3 and RASSF1A genes in early detection of breast cancer. Method: Methylation status of DKK3 and RASSF1 was investigated in forty breast cancer patients, twenty fibroadenoma patients and twenty healthy ladies as control group using MSP. Results: Methylation of DKK3 promoter was found in 22.5% of breast cancer patients, while DKK3 methylation was absent in both fibroadenoma patients and control group. Similarly, methylation of RASSF1 promoter was found in 17.5% of breast cancer patients and in none of fibroadenoma and control group. Conclusion: Promoter methylation of DKK3 and RASSF1 was found in breast cancer patients while absent in control group suggesting that tumorspecific methylation of the two genes (DKK3 and RASSF1A might be a valuable biomarker for the early detection of breast cancer. Keywords: DNA methylation, Breast cancer, DKK3, RASSF1

Anaerobic C1 metabolism of the O-methyl-14C-labeled substituent of vanillate

International Nuclear Information System (INIS)

Frazer, A.C.; Young, L.Y.

1986-01-01

The O-methyl substituents of aromatic compounds constitute a C 1 growth substrate for a number of taxonomically diverse anaerobic acetogens. In this study, strain TH-001, an O-demethylating obligate anaerobe, was chosen to represent this physiological group, and the carbon flow when cells were grown on O-methyl substituents as a C 1 substrate was determined by 14 C radiotracer techniques. O-[methyl- 14 C]vanillate (4-hydroxy-3-methoxy-benzoate) was used as the labeled C 1 substrate. The data showed that for every O-methyl carbon converted to [ 14 C]acetate, two were oxidized to 14 CO 2 . Quantitation of the carbon recovered in the two products, acetate and CO 2 , indicated that acetate was formed in part by the fixation of unlabeled CO 2 . The specific activity of 14 C in acetate was 70% of that in the O-methyl substrate, suggesting that only one carbon of acetate was derived from the O-methyl group. Thus, it is postulated that the carboxyl carbon of the product acetate is derived from CO 2 and the methyl carbon is derived from the O-methyl substituent of vanillate

Subsets of microsatellite-unstable colorectal cancers exhibit discordance between the CpG island methylator phenotype and MLH1 methylation status.

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Kim, Jung H; Rhee, Ye-Y; Bae, Jeong-M; Kwon, Hyeong-J; Cho, Nam-Y; Kim, Mi J; Kang, Gyeong H

2013-07-01

Although the presence of MLH1 methylation in microsatellite-unstable colorectal cancer generally indicates involvement of the CpG island methylator phenotype (CIMP) in the development of the tumor, these two conditions do not always correlate. A minority of microsatellite-unstable colorectal cancers exhibit discordance between CIMP and MLH1 methylation statuses. However, the clinicopathological features of such microsatellite-unstable colorectal cancers with discrepant MLH1 methylation and CIMP statuses remain poorly studied. Microsatellite-unstable colorectal cancers (n=220) were analyzed for CIMP and MLH1 methylation statuses using the MethyLight assay. Based on the combinatorial CIMP and MLH1 methylation statuses, the microsatellite-unstable colorectal cancers were grouped into four subtypes (CIMP-high (CIMP-H) MLH1 methylation-positive (MLH1m+), CIMP-H MLH1 methylation-negative, CIMP-low/0 (CIMP-L/0) MLH1m+, and CIMP-L/0 MLH1 methylation-negative), which were compared in terms of their associations with clinicopathological and molecular features. The CIMP-L/0 MLH1 methylation-negative and CIMP-H MLH1m+ subtypes were predominant, comprising 63.6 and 24.1% of total microsatellite-unstable colorectal cancers, respectively. The discordant subtypes, CIMP-H MLH1 methylation-negative and CIMP-L/0 MLH1m+, were found in 5 and 7% of microsatellite-unstable colorectal cancers, respectively. The CIMP-H MLH1 methylation-negative subtype exhibited elevated incidence rates in male patients and was associated with larger tumor size, more frequent loss of MSH2 expression, increased frequency of KRAS mutation, and advanced cancer stage. The CIMP-L/0 MLH1m+ subtype was associated with onset at an earlier age, a predominance of MLH1 loss, and earlier cancer stage. None of the CIMP-L/0 MLH1m+ subtype patients succumbed to death during the follow-up. Our findings suggest that the discordant subtypes of colorectal cancers exhibit distinct clinicopathological and molecular features

Awareness, attitudes, need and demand on replacement of missing teeth among a group of partially dentate patients attending a University Dental Hospital.

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Jayasinghe, Rasika Manori; Perera, Janana; Jayasinghe, Vajira; Thilakumara, Indika P; Rasnayaka, Sumudu; Shiraz, Muhammad Hanafi Muhammad; Ranabahu, Indra; Kularatna, Sanjeewa

2017-07-27

Our objective was to assess awareness, attitudes, need and demand on replacement of missing teeth according to edentulous space, age, gender, ethnicity, educational level and socio-economical status of the patient. 76.2% of the study group was opined that the missing teeth should be replaced by prosthetic means. Majority were keen in getting them replaced mainly for the comfort in mastication. Although 77.9 and 32.9% were aware of the removable prostheses and implants respectively, only 25.2% knew about tooth supported bridges as an option of replacement of missing teeth. Participants' awareness on tooth and implant supported prostheses is at a higher level. Participants' opinion on need of regular dental visit was statistically significant when gender, ethnicity and education level were considered. The highest demand for replacement of missing teeth was observed in Kennedy class I and II situations in both upper and lower arches. Demand for fixed prostheses was significantly highest in Kennedy class II in upper and lower arches. In conclusion, although removable prosthodontic options are known to most of the patients, their awareness on tooth and implant supported prostheses is also at a higher level. The highest demand for replacement of missing teeth is by patients with Kennedy class I and II situations whereas Kennedy class II being the category with highest demand for fixed prostheses. We recommend that the location of missing teeth to be considered as a priority when educating patients on the most appropriate prosthetic treatment options. Dentists' involvement in educating patients on prosthetic options needs to be improved.

Quantitative Detection of ID4 Gene Aberrant Methylation in the Differentiation of Myelodysplastic Syndrome from Aplastic Anemia

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Mian-Yang Li

2015-01-01

Full Text Available Background: The diagnosis of myelodysplastic syndrome (MDS, especially hypoplastic MDS, and MDS with low blast counts or normal karyotype may be problematic. This study characterized ID4 gene methylation in patients with MDS and aplastic anemia (AA. Methods: The methylation status of ID4 was analyzed by bisulfite sequencing polymerase chain reaction (PCR and quantitative real-time methylation-specific PCR (MethyLight PCR in 100 patients with MDS and 31 patients with AA. Results: The MDS group had a higher ID4 gene methylation positivity rate (22.22% and higher methylation levels (0.21 [0-3.79] than the AA group (P < 0.05. Furthermore, there were significant differences between the hypoplastic MDS and AA groups, the MDS with low blast count and the AA groups, and the MDS with normal karyotype and the AA groups. The combination of genetic and epigenetic markers was used in much more patients with MDS (62.5% [35/56] than the use of genetic markers only (51.79% [29/56]. Conclusions: These results showed that the detection of ID4 methylation positivity rates and levels could be a useful biomarker for MDS diagnosis.

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

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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.

Genome-wide methylation analysis identifies genes silenced in non-seminoma cell lines.

Science.gov (United States)

Noor, Dzul Azri Mohamed; Jeyapalan, Jennie N; Alhazmi, Safiah; Carr, Matthew; Squibb, Benjamin; Wallace, Claire; Tan, Christopher; Cusack, Martin; Hughes, Jaime; Reader, Tom; Shipley, Janet; Sheer, Denise; Scotting, Paul J

2016-01-01

Silencing of genes by DNA methylation is a common phenomenon in many types of cancer. However, the genome-wide effect of DNA methylation on gene expression has been analysed in relatively few cancers. Germ cell tumours (GCTs) are a complex group of malignancies. They are unique in developing from a pluripotent progenitor cell. Previous analyses have suggested that non-seminomas exhibit much higher levels of DNA methylation than seminomas. The genomic targets that are methylated, the extent to which this results in gene silencing and the identity of the silenced genes most likely to play a role in the tumours' biology have not yet been established. In this study, genome-wide methylation and expression analysis of GCT cell lines was combined with gene expression data from primary tumours to address this question. Genome methylation was analysed using the Illumina infinium HumanMethylome450 bead chip system and gene expression was analysed using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Regulation by methylation was confirmed by demethylation using 5-aza-2-deoxycytidine and reverse transcription-quantitative PCR. Large differences in the level of methylation of the CpG islands of individual genes between tumour cell lines correlated well with differential gene expression. Treatment of non-seminoma cells with 5-aza-2-deoxycytidine verified that methylation of all genes tested played a role in their silencing in yolk sac tumour cells and many of these genes were also differentially expressed in primary tumours. Genes silenced by methylation in the various GCT cell lines were identified. Several pluripotency-associated genes were identified as a major functional group of silenced genes.

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

International Nuclear Information System (INIS)

Amatruda, James F; Frazier, A Lindsay; Poynter, Jenny N; Ross, Julie A; Christensen, Brock; Fustino, Nicholas J; Chen, Kenneth S; Hooten, Anthony J; Nelson, Heather; Kuriger, Jacquelyn K; Rakheja, Dinesh

2013-01-01

Aberrant DNA methylation is a prominent feature of many cancers, and may be especially relevant in germ cell tumors (GCTs) due to the extensive epigenetic reprogramming that occurs in the germ line during normal development. We used the Illumina GoldenGate Cancer Methylation Panel to compare DNA methylation in the three main histologic subtypes of pediatric GCTs (germinoma, teratoma and yolk sac tumor (YST); N = 51) and used recursively partitioned mixture models (RPMM) to test associations between methylation pattern and tumor and demographic characteristics. We identified genes and pathways that were differentially methylated using generalized linear models and Ingenuity Pathway Analysis. We also measured global DNA methylation at LINE1 elements and evaluated methylation at selected imprinted loci using pyrosequencing. Methylation patterns differed by tumor histology, with 18/19 YSTs forming a distinct methylation class. Four pathways showed significant enrichment for YSTs, including a human embryonic stem cell pluripotency pathway. We identified 190 CpG loci with significant methylation differences in mature and immature teratomas (q < 0.05), including a number of CpGs in stem cell and pluripotency-related pathways. Both YST and germinoma showed significantly lower methylation at LINE1 elements compared with normal adjacent tissue while there was no difference between teratoma (mature and immature) and normal tissue. DNA methylation at imprinted loci differed significantly by tumor histology and location. Understanding methylation patterns may identify the developmental stage at which the GCT arose and the at-risk period when environmental exposures could be most harmful. Further, identification of relevant genetic pathways could lead to the development of new targets for therapy

Fragrance material review on 2-methyl-5-phenylpentanol.

Science.gov (United States)

Scognamiglio, J; Jones, L; Letizia, C S; Api, A M

2012-09-01

A toxicologic and dermatologic review of 2-methyl-5-phenylpentanol when used as a fragrance ingredient is presented. 2-Methyl-5-phenylpentanol is a member of the fragrance structural group aryl alkyl alcohols and is a primary alcohol. The AAAs are a structurally diverse class of fragrance ingredients that includes primary, secondary, and tertiary alkyl alcohols covalently bonded to an aryl (Ar) group, which may be either a substituted or unsubstituted benzene ring. The common structural element for the AAA fragrance ingredients is an alcohol group -C-(R1)(R2)OH and generically the AAA fragrances can be represented as an Ar-C-(R1)(R2)OH or Ar-Alkyl-C-(R1)(R2)OH group. This review contains a detailed summary of all available toxicology and dermatology papers that are related to this individual fragrance ingredient and is not intended as a stand-alone document. Available data for 2-methyl-5-phenylpentanol were evaluated then summarized and includes physical properties, acute toxicity, skin irritation, mucous membrane (eye) irritation, skin sensitization, repeated dose, and genotoxicity data. A safety assessment of the entire aryl alkyl alcohols will be published simultaneously with this document; please refer to Belsito et al. (2012) for an overall assessment of the safe use of this material and all other branched chain saturated alcohols in fragrances. Copyright © 2011 Elsevier Ltd. All rights reserved.

(E-2-Methyl-6-{[(5-methylpyridin-2-ylimino]methyl}phenol

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Md. Azharul Arafath

2017-01-01

Full Text Available In the title compound, C14H14N2O, the dihedral angle between the aromatic rings is 5.54 (9°. The conformation is reinforced by an intramolecular O—H...N hydrogen bond, which closes an S(6 ring. The pyridine N atom and methyl group lie to opposite sides of the molecule. In the crystal, the molecules are linked into a zigzag chain propagating in [0-11] by weak C—H...O hydrogen bonds.

Replacing Lectures with Small Groups: The Impact of Flipping the Residency Conference Day

Science.gov (United States)

King, Andrew M.; Mayer, Chad; Barrie, Michael; Greenberger, Sarah; Way, David P.

2018-01-01

The flipped classroom, an educational alternative to the traditional lecture, has been widely adopted by educators at all levels of education and across many disciplines. In the flipped classroom, learners prepare in advance of the face-to-face meeting by learning content material on their own. Classroom time is reserved for application of the learned content to solving problems or discussing cases. Over the past year, we replaced most residency program lectures with small-group discussions using the flipped-classroom model, case-based learning, simulation and procedure labs. In the new model, residents prepared for conference by reviewing a patient case and studying suggested learning materials. Conference day was set aside for facilitated small-group discussions about the case. This is a cross-cohort study of emergency medicine residents who experienced the lecture-based curriculum to residents in the new flipped-classroom curriculum using paired comparisons (independent t-tests) on in-training exam scores while controlling for program year level. We also compared results of the evaluation of various program components. We observed no differences between cohorts on in-training examination scores. Small-group methods were rated the same across program years. Two program components in the new curriculum, an updated format of both adult and pediatric case conferences, were rated significantly higher on program quality. In preparation for didactics, residents in the new curriculum report spending more time on average with outside learning materials, including almost twice as much time reviewing textbooks. Residents found the new format of the case conferences to be of higher quality because of the inclusion of rapid-fire case discussions with targeted learning points. PMID:29383050

Replacement Value of fermented millet ( Pennisetum americanum ...

African Journals Online (AJOL)

The replacement value of fermented millet for maize in the diets of Clarias gariepinus fingerlings reared in a recirculation system was determined. Five isonitrogenous diets were formulated to contain graded levels of fermented millet meal replacing 0, 20, 40, 60 and 80% of maize and fed to triplicate groups of fingerlings ...

Methylation of the chicken vitellogenin gene: influence of estradiol administration.

Science.gov (United States)

Meijlink, F C; Philipsen, J N; Gruber, M; Ab, G

1983-01-01

The degree of methylation of the chicken vitellogenin gene has been investigated. Upon induction by administration of estradiol to a rooster, methyl groups at specific sites near the 5'-end of the gene are eliminated. The process of demethylation is slower than the activation of the gene. Demethylation is therefore probably not a prerequisite to gene transcription. At least two other sites in the coding region of the gene are methylated in the liver of estrogenized roosters, but not in the liver of a laying hen, where the gene is naturally active. Images PMID:6298743

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

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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.

Mitral-valve repair versus replacement for severe ischemic mitral regurgitation.

Science.gov (United States)

Acker, Michael A; Parides, Michael K; Perrault, Louis P; Moskowitz, Alan J; Gelijns, Annetine C; Voisine, Pierre; Smith, Peter K; Hung, Judy W; Blackstone, Eugene H; Puskas, John D; Argenziano, Michael; Gammie, James S; Mack, Michael; Ascheim, Deborah D; Bagiella, Emilia; Moquete, Ellen G; Ferguson, T Bruce; Horvath, Keith A; Geller, Nancy L; Miller, Marissa A; Woo, Y Joseph; D'Alessandro, David A; Ailawadi, Gorav; Dagenais, Francois; Gardner, Timothy J; O'Gara, Patrick T; Michler, Robert E; Kron, Irving L

2014-01-02

Ischemic mitral regurgitation is associated with a substantial risk of death. Practice guidelines recommend surgery for patients with a severe form of this condition but acknowledge that the supporting evidence for repair or replacement is limited. We randomly assigned 251 patients with severe ischemic mitral regurgitation to undergo either mitral-valve repair or chordal-sparing replacement in order to evaluate efficacy and safety. The primary end point was the left ventricular end-systolic volume index (LVESVI) at 12 months, as assessed with the use of a Wilcoxon rank-sum test in which deaths were categorized below the lowest LVESVI rank. At 12 months, the mean LVESVI among surviving patients was 54.6±25.0 ml per square meter of body-surface area in the repair group and 60.7±31.5 ml per square meter in the replacement group (mean change from baseline, -6.6 and -6.8 ml per square meter, respectively). The rate of death was 14.3% in the repair group and 17.6% in the replacement group (hazard ratio with repair, 0.79; 95% confidence interval, 0.42 to 1.47; P=0.45 by the log-rank test). There was no significant between-group difference in LVESVI after adjustment for death (z score, 1.33; P=0.18). The rate of moderate or severe recurrence of mitral regurgitation at 12 months was higher in the repair group than in the replacement group (32.6% vs. 2.3%, P<0.001). There were no significant between-group differences in the rate of a composite of major adverse cardiac or cerebrovascular events, in functional status, or in quality of life at 12 months. We observed no significant difference in left ventricular reverse remodeling or survival at 12 months between patients who underwent mitral-valve repair and those who underwent mitral-valve replacement. Replacement provided a more durable correction of mitral regurgitation, but there was no significant between-group difference in clinical outcomes. (Funded by the National Institutes of Health and the Canadian Institutes of

DNA methylation and temperature stress in an Antarctic polychaete, Spiophanes tcherniai.

Science.gov (United States)

Marsh, Adam G; Pasqualone, Annamarie A

2014-01-01

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 Spiophanes tcherniai from McMurdo Sound, Antarctica. We cultured adult worms at two temperatures, -1.5°C (ambient control) and +4°C (warm treatment), for 4 weeks. We observed a rapid capacity for S. tcherniai organismal respiration rates and underlying catalytic rates of citrate synthase at +4°C to return to control levels in less than 4 weeks. 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 3000 (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.

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.

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.

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...... in cytogenetically undefined ALL patient groups and could be implemented as a complementary method for diagnosis of ALL. The results of our study provide clues to the origin and development of leukemic transformation. The methylation status of the CpG sites constituting the classifiers also highlight relevant...

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

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Katarzyna Wińska

2016-10-01

Full Text Available 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.

Modulation of the degree and pattern of methyl-esterification of pectic homogalacturonan in plant cell walls. Implications for pectin methyl esterase action, matrix properties, and cell adhesion.

Science.gov (United States)

Willats, W G; Orfila, C; Limberg, G; Buchholt, H C; van Alebeek, G J; Voragen, A G; Marcus, S E; Christensen, T M; Mikkelsen, J D; Murray, B S; Knox, J P

2001-06-01

Homogalacturonan (HG) is a multifunctional pectic polysaccharide of the primary cell wall matrix of all land plants. HG is thought to be deposited in cell walls in a highly methyl-esterified form but can be subsequently de-esterified by wall-based pectin methyl esterases (PMEs) that have the capacity to remove methyl ester groups from HG. Plant PMEs typically occur in multigene families/isoforms, but the precise details of the functions of PMEs are far from clear. Most are thought to act in a processive or blockwise fashion resulting in domains of contiguous de-esterified galacturonic acid residues. Such de-esterified blocks of HG can be cross-linked by calcium resulting in gel formation and can contribute to intercellular adhesion. We demonstrate that, in addition to blockwise de-esterification, HG with a non-blockwise distribution of methyl esters is also an abundant feature of HG in primary plant cell walls. A partially methyl-esterified epitope of HG that is generated in greatest abundance by non-blockwise de-esterification is spatially regulated within the cell wall matrix and occurs at points of cell separation at intercellular spaces in parenchymatous tissues of pea and other angiosperms. Analysis of the properties of calcium-mediated gels formed from pectins containing HG domains with differing degrees and patterns of methyl-esterification indicated that HG with a non-blockwise pattern of methyl ester group distribution is likely to contribute distinct mechanical and porosity properties to the cell wall matrix. These findings have important implications for our understanding of both the action of pectin methyl esterases on matrix properties and mechanisms of intercellular adhesion and its loss in plants.

Accumulation of histone variant H3.3 with age is associated with profound changes in the histone methylation landscape

DEFF Research Database (Denmark)

Tvardovskiy, Andrey; Schwämmle, Veit; Kempf, Stefan J

2017-01-01

a causal relationship between H3 variant replacement and age-dependent changes in H3 methylation. Furthermore, the H3.3 level is drastically reduced in human hepatocarcinoma cells as compared to nontumoral hepatocytes, suggesting the potential utility of the H3.3 relative abundance as a biomarker...

Intra-mitochondrial Methylation Deficiency Due to Mutations in SLC25A26

NARCIS (Netherlands)

Kishita, Y.; Pajak, A.; Bolar, N.A.; Marobbio, C.M.; Maffezzini, C.; Miniero, D.V.; Monne, M.; Kohda, M.; Stranneheim, H.; Murayama, K.; Naess, K.; Lesko, N.; Bruhn, H.; Mourier, A.; Wibom, R.; Nennesmo, I.; Jespers, A.; Govaert, P.; Ohtake, A.; Laer, L. Van; Loeys, B.L.; Freyer, C.; Palmieri, F.; Wredenberg, A.; Okazaki, Y.; Wedell, A.

2015-01-01

S-adenosylmethionine (SAM) is the predominant methyl group donor and has a large spectrum of target substrates. As such, it is essential for nearly all biological methylation reactions. SAM is synthesized by methionine adenosyltransferase from methionine and ATP in the cytoplasm and subsequently

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.

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.

Calorimetric investigations of hydrogen bonding in binary mixtures containing pyridine and its methyl-substituted derivatives. II. The dilute solutions of methanol and 2-methyl-2-propanol

International Nuclear Information System (INIS)

Marczak, Wojciech; Heintz, Andreas; Bucek, Monika

2004-01-01

Enthalpies of solution of methanol and 2-methyl-2-propanol (tert-butanol) in pyridine and its methyl derivatives were investigated in the range of mole fractions of alcohol x≤0.02 at temperature 298.15 K by a titration calorimeter. Dissolution of methanol is an exothermic process, with heat effects very close to those for water reported in part I of this study. The negative enthalpy of solution increases in the following order: pyridine < 3-methylpyridine < 4-methylpyridine < 2-methylpyridine < 2,6-dimethylpyridine < 2,4,6-trimethylpyridine. Positive enthalpies of solution of 2-methyl-2-propanol increase as follows: 2-methylpyridine < 2,4,6-trimethylpyridine < 4-methylpyridine < 2,6-dimethylpyridine < 3-methylpyridine < pyridine. The propensity of pyridine derivatives to hydrogen bonding is enhanced by the ortho effect. Methyl groups are probably too small to prevent the nitrogen atom in the pyridine ring from hydrogen bonding. However, spacious hydrocarbon group in 2-methyl-2-propanol molecule makes the bonding difficult for 2,6-dimethylpyridine and 2,4,6-trimethylpyridine, thus the number of O-H···N bonds is smaller than that in the solutions of methanol or water. The two latter seem to be very close to each other

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.)

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

Science.gov (United States)

Latanowicz, L; Medycki, W; Jakubas, R

2009-11-01

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

An efficient protocol for the complete incorporation of methyl-protonated alanine in perdeuterated protein

International Nuclear Information System (INIS)

Ayala, Isabel; Sounier, Remy; Use, Nathalie; Gans, Pierre; Boisbouvier, Jerome

2009-01-01

A strategy for the introduction of ( 1 H, 13 C-methyl)-alanine into perdeuterated proteins is described. Specific protonation of alanine methyl groups to a level of 95% can be achieved by overexpressing proteins in M9/D 2 O based bacterial growth medium supplemented with 800 mg/l of 2-[ 2 H], 3-[ 13 C] l-alanine. However, though simple, this approach results in undesired, non-specific background labeling due to isotope scrambling via different amino acid metabolic pathways. Following a careful analysis of known metabolic pathways we found that co-addition of perdeuterated forms of α-ketoisovalerate-d 7 , succinate-d 4 and l-isoleucine-d 10 with labeled l-alanine, reduces undesired background labeling to <1%. When combined with recently developed methyl TROSY experiments, this methyl-specific labeling protocol permits the acquisition of excellent quality correlation spectra of alanine methyl groups in high molecular weight proteins. Our cost effective strategy offers a significant enhancement in the level of incorporation of methyl-labeled alanine in overexpressed proteins over previously reported methods

2-Acetyl-amino-1,3,4,6-tetra-O-(tri-methyl-silyl)-2-de-oxy-α-d-gluco-pyran-ose.

Science.gov (United States)

Cheng, Zhao-Dong; Cui, Yan-Li; Mao, Jian-Wei

2013-06-01

The title compound, C20H47NO6Si4, was synthesized by per-O-tri-methyl-silylation of N-acetyl-d-glucosa-mine using chloro-tri-methyl-silane in the presence of hexa-methyl-disiloxane. The tri-methyl-silyl group and acetamido group are located on the same side of the pyran ring, showing an α-configuration glycoside. One of the tri-methyl-silyl groups is disordered over two orientations, with site-occupancy factors of 0.625 (9) and 0.375 (9). In the crystal, N-H⋯O hydrogen bonds link the mol-ecules into supra-molecular chains along the a-axis direction.

Agonists and partial agonists of rhodopsin: retinal polyene methylation affects receptor activation.

Science.gov (United States)

Vogel, Reiner; Lüdeke, Steffen; Siebert, Friedrich; Sakmar, Thomas P; Hirshfeld, Amiram; Sheves, Mordechai

2006-02-14

Using Fourier transform infrared (FTIR) difference spectroscopy, we have studied the impact of sites and extent of methylation of the retinal polyene with respect to position and thermodynamic parameters of the conformational equilibrium between the Meta I and Meta II photoproducts of rhodopsin. Deletion of methyl groups to form 9-demethyl and 13-demethyl analogues, as well as addition of a methyl group at C10 or C12, shifted the Meta I/Meta II equilibrium toward Meta I, such that the retinal analogues behaved like partial agonists. This equilibrium shift resulted from an apparent reduction of the entropy gain of the transition of up to 65%, which was only partially offset by a concomitant reduction of the enthalpy increase. The analogues produced Meta II photoproducts with relatively small alterations, while their Meta I states were significantly altered, which accounted for the aberrant transitions to Meta II. Addition of a methyl group at C14 influenced the thermodynamic parameters but had little impact on the position of the Meta I/Meta II equilibrium. Neutralization of the residue 134 in the E134Q opsin mutant increased the Meta II content of the 13-demethyl analogue, but not of the 9-demethyl analogue, indicating a severe impairment of the allosteric coupling between the conserved cytoplasmic ERY motif involved in proton uptake and the Schiff base/Glu 113 microdomain in the 9-demethyl analogue. The 9-methyl group appears therefore essential for the correct positioning of retinal to link protonation of the cytoplasmic motif with protonation of Glu 113 during receptor activation.

Inhibitory effect of betel quid on the volatility of methyl mercaptan.

Science.gov (United States)

Wang, C K; Chen, S L; Wu, M G

2001-04-01

Betel quid, a popular natural masticatory in Taiwan, is mainly composed of fresh areca fruit, Piper betle (leaf or inflorescence), and slaked lime paste. People say that halitosis disappears during betel quid chewing. In this study, the removal of mouth odor during betel quid chewing was discussed by using a model system which measured its inhibition on the volatility of methyl mercaptan. Results showed that crude extracts of betel quid (the mixture of areca fruit, Piper betle, and slaked lime paste) and extracts of the mixture of areca fruit and slaked lime paste exhibited marked effects on the volatility of methyl mercaptan, and the inhibition function increased when increasing amounts of slaked lime paste were added. The same condition (increased inhibition) was also found by replacing the slaked lime paste with alkaline salts (calcium hydroxide, potassium hydroxide, or sodium hydroxide). Areca fruit, the major ingredient of betel quid, contained abundant phenolics. However, the crude phenolic extract of areca fruit did not show any inhibitory activity on the volatility of methyl mercaptan. Great inhibitory activity occurred only when the crude phenolic extract of areca fruit was treated with alkali. Further studies by using gel filtration determined that the effect probably came from the oxidative polymerization of phenolics of areca fruit after alkaline treatment.

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.

Reactions of guanine with methyl chloride and methyl bromide: O6-methylation versus charge transfer complex formation

Science.gov (United States)

Shukla, P. K.; Mishra, P. C.; Suhai, S.

Density functional theory (DFT) at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels was employed to study O6-methylation of guanine due to its reactions with methyl chloride and methyl bromide and to obtain explanation as to why the methyl halides cause genotoxicity and possess mutagenic and carcinogenic properties. Geometries of the various isolated species involved in the reactions, reactant complexes (RCs), and product complexes (PCs) were optimized in gas phase. Transition states connecting the reactant complexes with the product complexes were also optimized in gas phase at the same levels of theory. The reactant complexes, product complexes, and transition states were solvated in aqueous media using the polarizable continuum model (PCM) of the self-consistent reaction field theory. Zero-point energy (ZPE) correction to total energy and the corresponding thermal energy correction to enthalpy were made in each case. The reactant complexes of the keto form of guanine with methyl chloride and methyl bromide in water are appreciably more stable than the corresponding complexes involving the enol form of guanine. The nature of binding in the product complexes was found to be of the charge transfer type (O6mG+ · X-, X dbond Cl, Br). Binding of HCl, HBr, and H2O molecules to the PCs obtained with the keto form of guanine did not alter the positions of the halide anions in the PCs, and the charge transfer character of the PCs was also not modified due to this binding. Further, the complexes obtained due to the binding of HCl, HBr, and H2O molecules to the PCs had greater stability than the isolated PCs. The reaction barriers involved in the formation of PCs were found to be quite high (?50 kcal/mol). Mechanisms of genotoxicity, mutagenesis and carcinogenesis caused by the methyl halides appear to involve charge transfer-type complex formation. Thus the mechanisms of these processes involving the methyl halides appear to be quite different from those that involve the

Trans-methylation reactions in plants: focus on the activated methyl cycle.

Science.gov (United States)

Rahikainen, Moona; Alegre, Sara; Trotta, Andrea; Pascual, Jesús; Kangasjärvi, Saijaliisa

2018-02-01

Trans-methylation reactions are vital in basic metabolism, epigenetic regulation, RNA metabolism, and posttranslational control of protein function and therefore fundamental in determining the physiological processes in all living organisms. The plant kingdom is additionally characterized by the production of secondary metabolites that undergo specific hydroxylation, oxidation and methylation reactions to obtain a wide array of different chemical structures. Increasing research efforts have started to reveal the enzymatic pathways underlying the biosynthesis of complex metabolites in plants. Further engineering of these enzymatic machineries offers significant possibilities in the development of bio-based technologies, but necessitates deep understanding of their potential metabolic and regulatory interactions. Trans-methylation reactions are tightly coupled with the so-called activated methyl cycle (AMC), an essential metabolic circuit that maintains the trans-methylation capacity in all living cells. Tight regulation of the AMC is crucial in ensuring accurate trans-methylation reactions in different subcellular compartments, cell types, developmental stages and environmental conditions. This review addresses the organization and posttranslational regulation of the AMC and elaborates its critical role in determining metabolic regulation through modulation of methyl utilization in stress-exposed plants. © 2017 Scandinavian Plant Physiology Society.

Assignment of methyl NMR resonances of a 52 kDa protein with residue-specific 4D correlation maps

International Nuclear Information System (INIS)

Mishra, Subrata H.; Frueh, Dominique P.

2015-01-01

Methyl groups have become key probes for structural and functional studies by nuclear magnetic resonance. However, their NMR signals cluster in a small spectral region and assigning their resonances can be a tedious process. Here, we present a method that facilitates assignment of methyl resonances from assigned amide groups. Calculating the covariance between sensitive methyl and amide 3D spectra, each providing correlations to C α and C β separately, produces 4D correlation maps directly correlating methyl groups to amide groups. Optimal correlation maps are obtained by extracting residue-specific regions, applying derivative to the dimensions subject to covariance, and multiplying 4D maps stemming from different 3D spectra. The latter procedure rescues weak signals that may be missed in traditional assignment procedures. Using these covariance correlation maps, nearly all assigned isoleucine, leucine, and valine amide resonances of a 52 kDa nonribosomal peptide synthetase cyclization domain were paired with their corresponding methyl groups

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.

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...

Cytosine methylation is a conserved epigenetic feature found throughout the phylum Platyhelminthes

Science.gov (United States)

2013-01-01

Background The phylum Platyhelminthes (flatworms) contains an important group of bilaterian organisms responsible for many debilitating and chronic infectious diseases of human and animal populations inhabiting the planet today. In addition to their biomedical and veterinary relevance, some platyhelminths are also frequently used models for understanding tissue regeneration and stem cell biology. Therefore, the molecular (genetic and epigenetic) characteristics that underlie trophic specialism, pathogenicity or developmental maturation are likely to be pivotal in our continued studies of this important metazoan group. Indeed, in contrast to earlier studies that failed to detect evidence of cytosine or adenine methylation in parasitic flatworm taxa, our laboratory has recently defined a critical role for cytosine methylation in Schistosoma mansoni oviposition, egg maturation and ovarian development. Thus, in order to identify whether this epigenetic modification features in other platyhelminth species or is a novelty of S. mansoni, we conducted a study simultaneously surveying for DNA methylation machinery components and DNA methylation marks throughout the phylum using both parasitic and non-parasitic representatives. Results Firstly, using both S. mansoni DNA methyltransferase 2 (SmDNMT2) and methyl-CpG binding domain protein (SmMBD) as query sequences, we illustrate that essential DNA methylation machinery components are well conserved throughout the phylum. Secondly, using both molecular (methylation specific amplification polymorphism, MSAP) and immunological (enzyme-linked immunoabsorbent assay, ELISA) methodologies, we demonstrate that representative species (Echinococcus multilocularis, Protopolystoma xenopodis, Schistosoma haematobium, Schistosoma japonicum, Fasciola hepatica and Polycelis nigra) within all four platyhelminth classes (Cestoda, Monogenea, Trematoda and ‘Turbellaria’) contain methylated cytosines within their genome compartments

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

African Journals Online (AJOL)

etchie

2013-02-20

Feb 20, 2013 ... Key words: Methyl-DNA immunoprecipitation, next-generation sequencing, Hidden ... its response to environmental cues. .... have a great potential to become the most cost-effective ... hg18 reference genome (set to 0 if not present in retrieved reads). ..... DNA methylation patterns and epigenetic memory.

Enzymatic methylation of band 3 anion transporter in intact human erythrocytes

International Nuclear Information System (INIS)

Lou, L.L.; Clarke, S.

1987-01-01

Band 3, the anion transport protein of erythrocyte membranes, is a major methyl-accepting substrate of the intracellular erythrocyte protein carboxyl methyltransferase (S-adenosyl-L-methionine: protein-D-aspartate O-methyltransferase; EC 2.1.1.77). The localization of methylation sites in intact cells by analysis of proteolytic fragments indicated that sites were present in the cytoplasmic N-terminal domain as well as the membranous C-terminal portion of the polypeptide. The amino acid residues that serve as carboxyl methylation sites of the erythrocyte anion transporter were also investigated. 3 H-Methylated band 3 was purified from intact erythrocytes incubated with L-[methyl- 3 H]methionine and from trypsinized and lysed erythrocytes incubated with S-adenosyl-L-[methyl- 3 H]methionine. After proteolytic digestion with carboxypeptidase Y, D-aspartic acid beta-[ 3 H]methyl ester was isolated in low yields (9% and 1%, respectively) from each preparation. The bulk of the radioactivity was recovered as [ 3 H]methanol, and the amino acid residue(s) originally associated with these methyl groups could not be determined. No L-aspartic acid beta-[ 3 H]methyl ester or glutamyl gamma-[ 3 H]methyl ester was detected. The formation of D-aspartic acid beta-[ 3 H]methyl esters in this protein in intact cells resulted from protein carboxyl methyltransferase activity since it was inhibited by adenosine and homocysteine thiolactone, which increases the intracellular concentration of the potent product inhibitor S-adenosylhomocysteine, and cycloleucine, which prevents the formation of the substrate S-adenosyl-L-[methyl- 3 H]methionine

Micro-syntheses for the use of carbon 13 or carbon 14. Micro-preparations of methyl alcohol, methyl iodide, and sodium acetate labeled in the methyl group

International Nuclear Information System (INIS)

Baret, C.; Pichat, L.

1951-11-01

Apparatus and technique are described in detail for (1) reduction of CO 2 to CH 3 OH with LiAlH 4 , (2) conversion of the methanol to CH 3 I by HI, (3) formation of the Mg Grignard reagent, and (4) addition of inactive CO 2 to form CH 3 COOH. All these operations have been carried out on 0.005 moles. Methyl-labeled Na acetate has been prepared in 67% yield based on the Ba 14 CO 3 used as starting material. (author) [fr

Binding of indomethacin methyl ester to cyclooxygenase-2. A computational study.

Science.gov (United States)

Sárosi, Menyhárt-Botond

2018-06-05

Inhibitors selective towards the second isoform of prostaglandin synthase (cyclooxygenase, COX-2) are promising nonsteroidal anti-inflammatory drugs and antitumor medications. Methylation of the carboxylate group in the relatively nonselective COX inhibitor indomethacin confers significant COX-2 selectivity. Several other modifications converting indomethacin into a COX-2 selective inhibitor have been reported. Earlier experimental and computational studies on neutral indomethacin derivatives suggest that the methyl ester derivative likely binds to COX-2 with a similar binding mode as that observed for the parent indomethacin. However, docking studies followed by molecular dynamics simulations revealed two possible binding modes in COX-2 for indomethacin methyl ester, which differs from the experimental binding mode found for indomethacin. Both alternative binding modes might explain the observed COX-2 selectivity of indomethacin methyl ester. Graphical abstract Binding of indomethacin methyl ester to cyclooxygenase-2.

Synthesis and Characterization of Fatty Acid Methyl Ester by In-Situ Transesterification in Capparis Deciduas Seed

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Prasad E FUNDE

2008-12-01

Full Text Available (FAME Fatty acid methyl ester is made virgin or used vegetable oils (both edible and non-edible and animal fats. Fatty acid methyl ester operates in compression ignition engines like petro-diesel. Fatty acid methyl ester can be blended in any ratio with petroleum diesel fuels. It can be stored just like the petroleum diesel fuel. Petrodiesel can be replaced by biodiesel due to its superiority. It has various advantages. The seeds of Capparis deciduas are found to contain non-edible oil in the range of about 63.75 %. The percentage of biodiesel yield increases with concentration of KOH as a catalyst. The aim of this article is to demonstrate the cost effective new source of energy by single step reaction i.e. production of oil by combining extraction and reaction of extract with the mixture of alcohols. In this article the effect of catalyst concentration, time, water content and temperature on in-situ transesterification is studied to obtain optimum yield and Fatty acid methyl ester (Biodiesel Fuel characterization tests show the striking similarity of various physical & chemical properties and campers to ASTM standards.

DNA Methylation and Methylation Polymorphism in Genetically Stable In vitro Regenerates of Jatropha curcas L. Using Methylation-Sensitive AFLP Markers.

Science.gov (United States)

Rathore, Mangal S; Jha, Bhavanath

2016-03-01

The present investigation aimed to evaluate the degree and pattern of DNA methylation using methylation-sensitive AFLP (MS-AFLP) markers in genetically stable in vitro regenerates of Jatropha curcas L.. The genetically stable in vitro regenerates were raised through direct organogenesis via enhanced axillary shoot bud proliferation (Protocol-1) and in vitro-derived leaf regeneration (Protocol-2). Ten selective combinations of MS-AFLP primers produced 462 and 477 MS-AFLP bands in Protocol-1 (P-1) and Protocol-2 (P-2) regenerates, respectively. In P-1 regenerates, 15.8-31.17 % DNA was found methylated with an average of 25.24 %. In P-2 regenerates, 15.93-32.7 % DNA was found methylated with an average of 24.11 %. Using MS-AFLP in P-1 and P-2 regenerates, 11.52-25.53 % and 13.33-25.47 % polymorphism in methylated DNA was reported, respectively. Compared to the mother plant, P-1 regenerates showed hyper-methylation while P-2 showed hypo-methylation. The results clearly indicated alternation in degree and pattern of DNA methylation; hence, epigenetic instability in the genetically stable in vitro regenerates of J. curcas, developed so far using two different regeneration systems and explants of two different origins. The homologous nucleotide fragments in genomes of P-1 and P-2 regenerates showing methylation re-patterning might be involved in immediate adaptive responses and developmental processes through differential regulation of transcriptome under in vitro conditions.

Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers.

Science.gov (United States)

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

2002-12-01

AFLP analysis using restriction enzyme isoschizomers that differ in their sensitivity to methylation of their recognition sites has been used to analyse the methylation state of anonymous CCGG sequences in Arabidopsis thaliana. The technique was modified to improve the quality of fingerprints and to visualise larger numbers of scorable fragments. Sequencing of amplified fragments indicated that detection was generally associated with non-methylation of the cytosine to which the isoschizomer is sensitive. Comparison of EcoRI/ HpaII and EcoRI/ MspI patterns in different ecotypes revealed that 35-43% of CCGG sites were differentially digested by the isoschizomers. Interestingly, the pattern of digestion among different plants belonging to the same ecotype is highly conserved, with the rate of intra-ecotype methylation-sensitive polymorphisms being less than 1%. However, pairwise comparisons of methylation patterns between samples belonging to different ecotypes revealed differences in up to 34% of the methylation-sensitive polymorphisms. The lack of correlation between inter-ecotype similarity matrices based on methylation-insensitive or methylation-sensitive polymorphisms suggests that whatever the mechanisms regulating methylation may be, they are not related to nucleotide sequence variation.

Perioperative management of patient with Bombay blood group undergoing mitral valve replacement

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Shio Priye

2015-01-01

Full Text Available Bombay red blood cell phenotype is an extremely rare blood type for which patients can receive only autologous or Bombay phenotype red blood cells. We report a case of stenotic mitral valve with Bombay phenotype who underwent minimal invasive right lateral thoracotomy for the replacement of the mitral valve. A male patient from Bangladesh presented to the hospital with New York Heart Association III symptoms. His medical evaluation revealed severe mitral valve stenosis and mild aortic valve regurgitation. The patient received erythropoietin, intravenous iron succinate and folic acid tablets. Autologous blood transfusion was carried out. The mitral valve was replaced with a prosthetic valve successfully. After weaning off from cardiopulmonary bypass, heparinisation was corrected with protamine. Post-operatively, the patient received autologous red blood cells. The patient recovered after 1-day of inotropic support with adrenaline and milrinone, and diuretics and was discharged on the 5 th post-operative day.

Methylated nucleosides in tRNA and tRNA methyltransferases

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Hiroyuki eHori

2014-05-01

Full Text Available To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s. Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon–anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.

[Variation of long-chain 3-hydroxyacyl-CoA dehydrogenase DNA methylation in placenta of different preeclampsia-like mouse models].

Science.gov (United States)

Han, Yiwei; Yang, Zi; Ding, Xiaoyan; Yu, Huan; Yi, Yanhong

2015-10-01

By detecting the variation of long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) DNA methylation in preeclampsia-like mouse models generated by different ways, to explore the roles of multifactor and multiple pathways in preeclampsia pathogenesis on molecular basis. Established preeclampsia-like mouse models in different ways and divided into groups as follows: (1) Nw-nitro-L-arginine-methyl ester (L-NAME) group: wild-type pregnant mouse received subcutaneous injection of L-NAME; (2) lipopolysaccharide (LPS) group: wild-type pregnant mouse received intraperitoneal injection of LPS; (3) apolipoprotein C-III (ApoC3) group: ApoC3 transgenic pregnant mouse with dysregulated lipid metabolism received subcutaneous injection of L-NAME; (4) β2 glycoprotein I (β-2GPI) group: wild-type pregnant mouse received subcutaneous injection of β-2GPI. According to the first injection time (on day 3, 11, 16 respectively), the L-NAME, LPS and ApoC3 groups were further subdivided into: pre-implantation (PI) experimental stage, early gestation (EG) experimental stage, and late gestation (LG) experimental stage. β-2GPI group was only injected before implantation. LCHAD gene methylation levels in placental were detected in different experimental stage. Normal saline control groups were set within wild-type and ApoC3 transgenic pregnant mice simultaneously. (1) CG sites in LCHAD DNA: 45 CG sites were detected in the range of 728 bp before LCHAD gene transcription start site, the 5, 12, 13, 14, 15, 16, 19, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 43 CG sites were complex sites which contained two or more CG sequences, others were single site which contained one CG sequence. The 3, 5, 6, 11, 13, 14, 18, 28 sites in L-NAME, LPS, ApoC3 and β-2GPI groups showed different high levels of methylation; the 16, 25, 31, 42, 44 sites showed different low levels of methylation; other 32 sites were unmethylated. (2) Comparison of LCHAD gene methylation between different groups: the methylation levels

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 ...

Language Profile in Congenital Hypothyroid Children Receiving Replacement Therapy.

Science.gov (United States)

Soliman, Hend; Abdel Hady, Aisha Fawzy; Abdel Hamid, Asmaa; Mahmoud, Heba

2016-01-01

The aim of this work was to evaluate receptive and expressive language skills in children with congenital hypothyroidism receiving early hormonal replacement treatment before the age of 3 months and to identify any subtle areas of weaknesses in their language development to check the necessity for future language intervention. The study was conducted on 30 hypothyroid children receiving hormonal replacement. They were subdivided into group I (5-8 years 11 months; 12 cases) and group II (9-12 years 11 months; 18 cases). All patients were subjected to a protocol of assessment applied in the Diabetes, Endocrine and Metabolism Pediatric Unit (DEMPU) and evaluation of language skills by the REAL scale. The younger group reached average Arabic language scores, while the older group showed moderate language delay. Early replacement therapy supports language development in young children. However, longitudinal and follow-up studies are required to identify difficulties presenting at older ages that may affect children in the academic settings. © 2016 S. Karger AG, Basel.

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.

The global DNA methylation surrogate LINE-1 methylation is correlated with MGMT promoter methylation and is a better prognostic factor for glioma.

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Fumiharu Ohka

Full Text Available Gliomas are the most frequently occurring primary brain tumor in the central nervous system of adults. Glioblastoma multiformes (GBMs, WHO grade 4 have a dismal prognosis despite the use of the alkylating agent, temozolomide (TMZ, and even low grade gliomas (LGGs, WHO grade 2 eventually transform to malignant secondary GBMs. Although GBM patients benefit from promoter hypermethylation of the O(6-methylguanine-DNA methyltransferase (MGMT that is the main determinant of resistance to TMZ, recent studies suggested that MGMT promoter methylation is of prognostic as well as predictive significance for the efficacy of TMZ. Glioma-CpG island methylator phenotype (G-CIMP in the global genome was shown to be a significant predictor of improved survival in patients with GBM. Collectively, we hypothesized that MGMT promoter methylation might reflect global DNA methylation. Additionally in LGGs, the significance of MGMT promoter methylation is still undetermined. In the current study, we aimed to determine the correlation between clinical, genetic, and epigenetic profiles including LINE-1 and different cancer-related genes and the clinical outcome in newly diagnosed 57 LGG and 54 GBM patients. Here, we demonstrated that (1 IDH1/2 mutation is closely correlated with MGMT promoter methylation and 1p/19q codeletion in LGGs, (2 LINE-1 methylation levels in primary and secondary GBMs are lower than those in LGGs and normal brain tissues, (3 LINE-1 methylation is proportional to MGMT promoter methylation in gliomas, and (4 higher LINE-1 methylation is a favorable prognostic factor in primary GBMs, even compared to MGMT promoter methylation. As a global DNA methylation marker, LINE-1 may be a promising marker in gliomas.

[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.

Autologous blood transfusion in total knee replacement surgery.

Science.gov (United States)

Sarkanović, Mirka Lukić; Gvozdenović, Ljiljana; Savić, Dragan; Ilić, Miroslav P; Jovanović, Gordana

2013-03-01

Total knee replacement (TKR) surgery is one of the most frequent and the most extensive procedures in orthopedic surgery, accompanied with some serious complications. Perioperative blood loss is one of the most serious losses, so it is vital to recognize and treat such losses properly. Autologous blood transfusion is the only true alternative for the allogeneic blood. The aim of this study was to to examine if autologous blood transfusion reduces usage of allogenic blood in total knee replacement surgery, as well as to examine possible effect of autologous blood transfusion on postoperative complications, recovery and hospital stay of patients after total knee replacement surgery. During the controlled, prospective, randomised study we compared two groups of patients (n = 112) with total prosthesis implanted in their knee. The group I consisted of the patients who received the transfusion of other people's (allogeneic) blood (n = 57) and the group II of the patients whose blood was collected postoperatively and then given them [their own (autologous) blood] (n = 55). The transfusion trigger for both groups was hemoglobin level of 85 g/L. In the group of patients whose blood was collected perioperatively only 9 (0.9%) of the patients received transfusion of allogeneic blood, as opposed to the control group in which 98.24% of the patients received the transfusion of allogeneic blood (p blood was collected stayed in hospital for 6.18 days, while the patients of the control group stayed 7.67 days (p blood transfusion is a very effective method for reducing consumption of allogenic blood and thus, indirectly for reducing all complications related to allogenic blood transfusion. There is also a positive influence on postoperative recovery after total knee replacement surgery due to the reduction of hospital stay, and indirectly on the reduction of hospital costs.

Recognition of methylated DNA through methyl-CpG binding domain proteins

DEFF Research Database (Denmark)

Zou, Xueqing; Ma, Wen; Solov'yov, Ilia

2012-01-01

DNA methylation is a key regulatory control route in epigenetics, involving gene silencing and chromosome inactivation. It has been recognized that methyl-CpG binding domain (MBD) proteins play an important role in interpreting the genetic information encoded by methylated DNA (mDNA). Although...... the function of MBD proteins has attracted considerable attention and is well characterized, the mechanism underlying mDNA recognition by MBD proteins is still poorly understood. In this article, we demonstrate that the methyl-CpG dinucleotides are recognized at the MBD-mDNA interface by two MBD arginines...

Genome-wide DNA methylation profiling in cultured eutopic and ectopic endometrial stromal cells.

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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.

Genome-Wide DNA Methylation Patterns of Bovine Blastocysts Developed In Vivo from Embryos Completed Different Stages of Development In Vitro.

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Dessie Salilew-Wondim

Full Text Available Early embryonic loss and altered gene expression in in vitro produced blastocysts are believed to be partly caused by aberrant DNA methylation. However, specific embryonic stage which is sensitive to in vitro culture conditions to alter the DNA methylation profile of the resulting blastocysts remained unclear. Therefore, the aim of this study was to investigate the stage specific effect of in vitro culture environment on the DNA methylation response of the resulting blastocysts. For this, embryos cultured in vitro until zygote (ZY, 4-cell (4C or 16-cell (16C were transferred to recipients and the blastocysts were recovery at day 7 of the estrous cycle. Another embryo group was cultured in vitro until blastocyst stage (IVP. Genome-wide DNA methylation profiles of ZY, 4C, 16C and IVP blastocyst groups were then determined with reference to blastocysts developed completely under in vivo condition (VO using EmbryoGENE DNA Methylation Array. To assess the contribution of methylation changes on gene expression patterns, the DNA methylation data was superimposed to the transcriptome profile data. The degree of DNA methylation dysregulation in the promoter and/or gene body regions of the resulting blastocysts was correlated with successive stages of development the embryos advanced under in vitro culture before transfer to the in vivo condition. Genomic enrichment analysis revealed that in 4C and 16C blastocyst groups, hypermethylated loci were outpacing the hypomethylated ones in intronic, exonic, promoter and proximal promoter regions, whereas the reverse was observed in ZY blastocyst group. However, in the IVP group, as much hypermethylated as hypomethylated probes were detected in gene body and promoter regions. In addition, gene ontology analysis indicated that differentially methylated regions were found to affected several biological functions including ATP binding in the ZY group, programmed cell death in the 4C, glycolysis in 16C and genetic

Phosphatidylcholine synthesis in the rat: The substrate for methylation and regulation by choline

International Nuclear Information System (INIS)

Datko, A.H.; Aksamit, R.R.; Mudd, S.H.

1990-01-01

Two lines of evidence led us to reexamine the possibility that methylation of phosphoethanolamine and its partially methylated derivatives, in addition to methylation of the corresponding phosphatidyl derivatives, plays a role in mammalian phosphatidylcholine biosynthesis: (a) Results obtained by Salerno and Beeler with rat appear to strongly support such a role for methylation of phosphobases; (b) Such reactions have recently been shown to play major roles in phosphatidylcholine synthesis by higher plants. We found that, following continuous labeling of rat liver with L-[methyl-3H]methionine for 10.4 min (intraperitoneal administration) or for 0.75 min (intraportal administration), virtually no 3H was detected in methylated derivatives of phosphoethanolamine, but readily detectable amounts of 3H were present in the base moiety of each methylated derivative of phosphatidylethanolamine. Thus, there was no indication that phospho-base methylation makes a significant contribution. Studies of cultured rat hepatoma cells showed definitively for the first time in a mammalian system that choline deprivation up-regulates the rate of flow of methyl groups originating in methionine into phosphatidylethanolamine and derivatives. Even under these conditions, methylation of phosphoethanolamine bases appeared to play a negligible role

Bromide-free TEMPO-mediated oxidation of primary alcohol groups in starch and methyl alpha-D-glucopyranoside.

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Bragd, P L; Besemer, A C; van Bekkum, H

2000-09-22

TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl)-mediated oxidation of potato starch and methyl alpha-D-glucopyranoside (MGP) was performed in the absence of sodium bromide (NaBr) as co-catalyst, solely using sodium hypochlorite (NaOCl) as the primary oxidant. The low reaction rate associated with a bromide-free process was increased by performing the oxidation at increased temperatures. The reaction proceeded stoichiometrically and with high selectivity and with only minor depolymerisation, provided that temperature and pH were kept or = 25 degrees C) and under more alkaline conditions (pH > or = 9.0) degradation of the starch skeleton occurred. Simultaneously, side-reactions of the nitrosonium ion lowered the yield of the oxidation. Despite the absence of the NaBr catalyst, the reaction rate-controlling step was found to be the oxidation of the primary hydroxyl groups with the nitrosonium ion. The reaction was first-order in MGP and in TEMPO.

DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas

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Gavery Mackenzie R

2010-08-01

Full Text Available Abstract Background DNA methylation is an epigenetic mechanism with important regulatory functions in animals. While the mechanism itself is evolutionarily ancient, the distribution and function of DNA methylation is diverse both within and among phylogenetic groups. Although DNA methylation has been well studied in mammals, there are limited data on invertebrates, particularly molluscs. Here we characterize the distribution and investigate potential functions of DNA methylation in the Pacific oyster (Crassostrea gigas. Results Methylation sensitive PCR and bisulfite sequencing PCR approaches were used to identify CpG methylation in C. gigas genes and demonstrated that this species possesses intragenic methylation. In silico analysis of CpGo/e ratios in publicly available sequence data suggests that DNA methylation is a common feature of the C. gigas genome, and that specific functional categories of genes have significantly different levels of methylation. Conclusions The Pacific oyster genome displays intragenic DNA methylation and contains genes necessary for DNA methylation in animals. Results of this investigation suggest that DNA methylation has regulatory functions in Crassostrea gigas, particularly in gene families that have inducible expression, including those involved in stress and environmental responses.

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

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Houtepen, LC

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

Microarray-based DNA methylation study of Ewing's sarcoma of the bone.

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Park, Hye-Rim; Jung, Woon-Won; Kim, Hyun-Sook; Park, Yong-Koo

2014-10-01

Alterations in DNA methylation patterns are a hallmark of malignancy. However, the majority of epigenetic studies of Ewing's sarcoma have focused on the analysis of only a few candidate genes. Comprehensive studies are thus lacking and are required. The aim of the present study was to identify novel methylation markers in Ewing's sarcoma using microarray analysis. The current study reports the microarray-based DNA methylation study of 1,505 CpG sites of 807 cancer-related genes from 69 Ewing's sarcoma samples. The Illumina GoldenGate Methylation Cancer Panel I microarray was used, and with the appropriate controls (n=14), a total of 92 hypermethylated genes were identified in the Ewing's sarcoma samples. The majority of the hypermethylated genes were associated with cell adhesion, cell regulation, development and signal transduction. The overall methylation mean values were compared between patients who survived and those that did not. The overall methylation mean was significantly higher in the patients who did not survive (0.25±0.03) than in those who did (0.22±0.05) (P=0.0322). However, the overall methylation mean was not found to significantly correlate with age, gender or tumor location. GDF10 , OSM , APC and HOXA11 were the most significant differentially-methylated genes, however, their methylation levels were not found to significantly correlate with the survival rate. The DNA methylation profile of Ewing's sarcoma was characterized and 92 genes that were significantly hypermethylated were detected. A trend towards a more aggressive behavior was identified in the methylated group. The results of this study indicated that methylation may be significant in the development of Ewing's sarcoma.

A genome-wide methylation study on obesity Differential variability and differential methylation

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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

13C and 1H nuclear magnetic resonance of methyl-substituted acetophenones and methyl benzoates: steric hindrance and inhibited conjugation.

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Budesínský, Milos; Kulhánek, Jirí; Böhm, Stanislav; Cigler, Petr; Exner, Otto

2004-10-01

The 1H and 13C NMR spectra of 14 methyl-substituted acetophenones and 14 methyl-substituted methyl benzoates were assigned and interpreted with respect to the conformation of the C(ar)-C(O) bond. The substituent effects are proportional in the two series and can be divided into polar and steric: each has different effects on the 13C SCS of the individual atoms. In the case of C atoms C(O), C(1) and CH3(CO), the steric effects were quantitatively separated by comparing SCS in the ortho and para positions. The steric effects are proportional for the individual C atoms and also to steric effects estimated from other physical quantities. However, they do not depend simply on the angle of torsion phi of the functional group as anticipated hitherto. A better description distinguishes two classes of compounds: sterically not hindered or slightly hindered planar molecules and strongly sterically hindered, markedly non-planar. In order to confirm this reasoning without empirical correlations, the J(C,C) coupling constants were measured for three acetophenone derivatives labeled with 13C in the acetyl methyl group. The constants confirm unambiguously the conformation of 2-methylacetophenone; their zero values are in accord with the conformation of 2,6-dimethylacetophenone. The zero values in the unsubstituted acetophenone are at variance with previous erroneous report but all J(C,C) values are in accord with calculations at the B3LYP/6-311++G(2d,2p)//B3LYP/6-311+G(d,p) level. Copyright 2004 John Wiley & Sons, Ltd.

Deletion and aberrant CpG island methylation of Caspase 8 gene in medulloblastoma.

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Gonzalez-Gomez, Pilar; Bello, M Josefa; Inda, M Mar; Alonso, M Eva; Arjona, Dolores; Amiñoso, Cinthia; Lopez-Marin, Isabel; de Campos, Jose M; Sarasa, Jose L; Castresana, Javier S; Rey, Juan A

2004-09-01

Aberrant methylation of promoter CpG islands in human genes is an alternative genetic inactivation mechanism that contributes to the development of human tumors. Nevertheless, few studies have analyzed methylation in medulloblastomas. We determined the frequency of aberrant CpG island methylation for Caspase 8 (CASP8) in a group of 24 medulloblastomas arising in 8 adult and 16 pediatric patients. Complete methylation of CASP8 was found in 15 tumors (62%) and one case displayed hemimethylation. Three samples amplified neither of the two primer sets for methylated or unmethylated alleles, suggesting that genomic deletion occurred in the 5' flanking region of CASP8. Our findings suggest that methylation commonly contributes to CASP8 silencing in medulloblastomas and that homozygous deletion or severe sequence changes involving the promoter region may be another mechanism leading to CASP8 inactivation in this neoplasm.

Comprehensive analysis of genome-wide DNA methylation across human polycystic ovary syndrome ovary granulosa cell.

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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.

Different Levels of DNA Methylation Detected in Human Sperms after Morphological Selection Using High Magnification Microscopy

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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.

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

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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].

Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia

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Wan, Zi Yi; Xia, Jun Hong; Lin, Grace; Wang, Le; Lin, Valerie C. L.; Yue, Gen Hua

2016-01-01

Sexual dimorphism is an interesting biological phenomenon. Previous studies showed that DNA methylation might play a role in sexual dimorphism. However, the overall picture of the genome-wide methylation landscape in sexually dimorphic species remains unclear. We analyzed the DNA methylation landscape and transcriptome in hybrid tilapia (Oreochromis spp.) using whole genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq). We found 4,757 sexually dimorphic differentially methylated regions (DMRs), with significant clusters of DMRs located on chromosomal regions associated with sex determination. CpG methylation in promoter regions was negatively correlated with the gene expression level. MAPK/ERK pathway was upregulated in male tilapia. We also inferred active cis-regulatory regions (ACRs) in skeletal muscle tissues from WGBS datasets, revealing sexually dimorphic cis-regulatory regions. These results suggest that DNA methylation contribute to sex-specific phenotypes and serve as resources for further investigation to analyze the functions of these regions and their contributions towards sexual dimorphisms. PMID:27782217

DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes.

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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.

[Association of etheno-DNA adduct and DNA methylation level among workers exposed to diesel engine exhaust].

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Shen, M L; He, Z N; Zhang, X; Duan, H W; Niu, Y; Bin, P; Ye, M; Meng, T; Dai, Y F; Yu, S F; Chen, W; Zheng, Y X

2017-06-06

Objective: To investigate the association between etheno-DNA adduct and the promoter of DNA methylation levels of cyclin dependent kinase inhibitor 2A (P16), Ras association domain family 1 (RASSF1A) and O-6-methylguanine-DNA methyltransferase (MGMT) in workers with occupational exposure to diesel engine exhaust (DEE). Methods: We recruited 124 diesel engine testing workers as DEE exposure group and 112 water pump operator in the same area as control group in Henan province in 2012 using cluster sampling. The demographic data were obtained by questionnaire survey; urine after work and venous blood samples were collected from each subject. The urinary etheno-DNA adducts were detected using UPLC-MS/MS, including 1,N6-etheno-2'-deoxyadenosine (εdA) and 3,N4-etheno-2'-deoxycytidine(εdC). The DNA methylation levels of P16, RASSF1A, and MGMT were evaluated using bisulfite-pyrosequencing assay. The percentage of methylation was expressed as the 5-methylcytosine (5mC) over the sum of cytosines (%5mC). Spearman correlation and multiple linear regression were applied to analyze the association between etheno-DNA adducts and DNA methylation of P16, RASSF1A, and MGMT. Results: The median ( P (25)- P (75)) of urinary εdA level was 230.00 (98.04-470.91) pmol/g creatinine in DEE exposure group, and 102.10 (49.95-194.48) creatinine in control group. The level of εdA was higher in DEE exposure group than control group ( P 0.05) . Multiple linear regression confirmed the negative correlation between εdA and DNA methylation levels of P16, RASSF1A, and MGMT in non-smoking group (β (95 %CI ) was -0.068 (-0.132--0.003), -0.082 (-0.159--0.004) and -0.048 (-0.090--0.007), P values were 0.039, 0.039 and 0.024, respectively). Moreover, εdC was negative associated with DNA methylation level of MGMT in non-smoking group (β (95 %CI ) was -0.094 (-0.179--0.008), P= 0.032). Conclusion: DEE exposure could induce the increased of εdA and decreased of DNA methylation levels of P16, RASSF1A

Aberrant TET1 Methylation Closely Associated with CpG Island Methylator Phenotype in Colorectal Cancer.

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Ichimura, Norihisa; Shinjo, Keiko; An, Byonggu; Shimizu, Yasuhiro; Yamao, Kenji; Ohka, Fumiharu; Katsushima, Keisuke; Hatanaka, Akira; Tojo, Masayuki; Yamamoto, Eiichiro; Suzuki, Hiromu; Ueda, Minoru; Kondo, Yutaka

2015-08-01

Inactivation of methylcytosine dioxygenase, ten-eleven translocation (TET) is known to be associated with aberrant DNA methylation in cancers. Tumors with a CpG island methylator phenotype (CIMP), a distinct subgroup with extensive DNA methylation, show characteristic features in the case of colorectal cancer. The relationship between TET inactivation and CIMP in colorectal cancers is not well understood. The expression level of TET family genes was compared between CIMP-positive (CIMP-P) and CIMP-negative (CIMP-N) colorectal cancers. Furthermore, DNA methylation profiling, including assessment of the TET1 gene, was assessed in colorectal cancers, as well as colon polyps. The TET1 was silenced by DNA methylation in a subset of colorectal cancers as well as cell lines, expression of which was reactivated by demethylating agent. TET1 methylation was more frequent in CIMP-P (23/55, 42%) than CIMP-N (2/113, 2%, P CIMP-P, 16/40, 40%; CIMP-N, 2/24, 8%; P = 0.002), suggesting that TET1 methylation is an early event in CIMP tumorigenesis. TET1 methylation was significantly associated with BRAF mutation but not with hMLH1 methylation in the CIMP-P colorectal cancers. Colorectal cancers with TET1 methylation have a significantly greater number of DNA methylated genes and less pathological metastasis compared to those without TET1 methylation (P = 0.007 and 0.045, respectively). Our data suggest that TET1 methylation may contribute to the establishment of a unique pathway in respect to CIMP-mediated tumorigenesis, which may be incidental to hMLH1 methylation. In addition, our findings provide evidence that TET1 methylation may be a good biomarker for the prediction of metastasis in colorectal cancer. ©2015 American Association for Cancer Research.

Delay in onset of metabolic alkalosis during regional citrate anti-coagulation in continous renal replacement therapy with calcium-free replacement solution

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See Kay

2009-01-01

Full Text Available Regional citrate anti-coagulation for continuous renal replacement therapy chelates calcium to produce the anti- coagulation effect. We hypothesise that a calcium-free replacement solution will require less citrate and produce fewer metabolic side effects. Fifty patients, in a Medical Intensive Care Unit of a tertiary teaching hospital (25 in each group, received continuous venovenous hemofiltration using either calcium-containing or calcium-free replacement solutions. Both groups had no significant differences in filter life, metabolic alkalosis, hypernatremia, hypocalcemia, and hypercalcemia. However, patients using calcium-containing solution developed metabolic alkalosis earlier, compared to patients using calcium-free solution (mean 24.6 hours,CI 0.8-48.4 vs. 37.2 hours, CI 9.4-65, P = 0.020. When calcium-containing replacement solution was used, more citrate was required (mean 280ml/h, CI 227.2-332.8 vs. 265ml/h, CI 203.4-326.6, P = 0.069, but less calcium was infused (mean 21.2 ml/h, CI 1.2-21.2 vs 51.6ml/h, CI 26.8-76.4, P ≤ 0.0001.

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

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Maruoka Shuichiro

2008-12-01

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

Synthesis of methyl ester sulphonate by sulfonation of soybean oil methyl ester for chemical flooding application

International Nuclear Information System (INIS)

Richie Adi Putra; Renisa Ismayanti; Agam Duma Kalista W

2018-01-01

This research has accomplished the synthesis of Surfactant Methyl Ester Sulphonate from Methyl Soyate and Sodium Bisulfite as sulfonating agent. The Steps of the synthesis were reaction, purification, neutralization, and separation. The reaction done by several variated condition such as Reaction Temperature (100, 110, 120)°C, Reaction time (210, 270, 330)minute, and the mole ratio between Methyl Soyate and NaHSO 3 (1:1, 1:1.5, 1:2) with 1.5 % of Al 2 O 3 as catalyst of sulfonation reaction. The purification process was conducted at 55 °C and 60 minute by adding Methanol 35 % v/v. The neutralization done was conducted by 20 % of NaOH until pH 6-8. And the rest of the methanol are separated from MES using rotary evaporator. MES which is pass the compatibility Test is MES at the condition of reaction (100 °C, 210 minute and 1 : 2 mole ratio).This MES has tested by FT - IR to see the existence of the Sulphonate group.The FT-IR test result has shown the existence of the Sulphonate group at wave length between 1000 until 1300 cm -1 . Which is the highest peak at 1176 cm-1. From the qualitative test above, then the MES performed by IFT Test with light oil of X- field as comparison. The IFT results has shown a decrease of the interfacial tensions between 12,000 ppm of brine water and the light oil with addition of 0.3 % (v/v) MES, from 3.36 dyne/cm 2 to 1.54 dyne/cm 2 . (author)

An 11bp region with stem formation potential is essential for de novo DNA methylation of the RPS element.

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Matthew Gentry

Full Text Available The initiation of DNA methylation in Arabidopsis is controlled by the RNA-directed DNA methylation (RdDM pathway that uses 24nt siRNAs to recruit de novo methyltransferase DRM2 to the target site. We previously described the REPETITIVE PETUNIA SEQUENCE (RPS fragment that acts as a hot spot for de novo methylation, for which it requires the cooperative activity of all three methyltransferases MET1, CMT3 and DRM2, but not the RdDM pathway. RPS contains two identical 11nt elements in inverted orientation, interrupted by a 18nt spacer, which resembles the features of a stemloop structure. The analysis of deletion/substitution derivatives of this region showed that deletion of one 11nt element RPS is sufficient to eliminate de novo methylation of RPS. In addition, deletion of a 10nt region directly adjacent to one of the 11nt elements, significantly reduced de novo methylation. When both 11nt regions were replaced by two 11nt elements with altered DNA sequence but unchanged inverted repeat homology, DNA methylation was not affected, indicating that de novo methylation was not targeted to a specific DNA sequence element. These data suggest that de novo DNA methylation is attracted by a secondary structure to which the two 11nt elements contribute, and that the adjacent 10nt region influences the stability of this structure. This resembles the recognition of structural features by DNA methyltransferases in animals and suggests that similar mechanisms exist in plants.

Alpha male replacements and delayed dispersal in crested macaques (Macaca nigra).

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Marty, Pascal R; Hodges, Keith; Agil, Muhammad; Engelhardt, Antje

2017-07-01

In species with a high male reproductive skew, competition between males for the top dominant position is high and escalated fights are common between competitors. As a consequence, challenges incur potentially high costs. Selection should favor males who time an alpha male challenge to maximize chances of a successful outcome minimizing costs. Despite the importance of alpha male replacements for individual males, we know little about the timing of challenges and the condition of the challenger. We investigated the timing and process of alpha male replacements in a species living in multi-male groups with high male reproductive skew, the crested macaque. We studied four wild groups over 6 years in the Tangkoko Reserve, North Sulawesi, Indonesia, during which 16 alpha male replacements occurred. Although unusual for cercopithecines, male crested macaques delayed their natal dispersal until they attained maximum body mass and therefore fighting ability whereupon they emigrated and challenged the alpha male in another group. Accordingly, all observed alpha male replacements were from outside males. Ours is the first report of such a pattern in a primate species living in multi-male groups. Although the majority of alpha male replacements occurred through direct male-male challenges, many also took place opportunistically (i.e., after the alpha male had already been injured or had left the group). Furthermore, alpha male tenures were very short (averaging ca. 12 months). We hypothesize that this unusual pattern of alpha male replacements in crested macaques is related to the species-specific combination of high male reproductive skew with a large number of males per group. Am. J. Primatol. 79:e22448, 2017. © 2015 The Authors. American Journal of Primatology Published by Wiley Periodicals, Inc. © 2015 The Authors. American Journal of Primatology Published by Wiley Periodicals, Inc.

Patterns of DNMT1 Promoter Methylation in Patients with Acute Lymphoblastic Leukemia.

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Rahmani, Tirdad; Azad, Mehdi; Chahardouli, Bahram; Nasiri, Hajar; Vatanmakanian, Mousa; Kaviani, Saeid

2017-07-01

Background: Acute lymphoblastic leukemia (ALL) is a clonal malignant disorder characterized by an uncontrolled proliferation of immature T or B lymphocytes. Extensive studies have shown that the epigenetic changes, especially modified DNA methylation patterns in the regulatory regions through the DNA methyltransferase (DNMTs), play an important role in the development of genetic disorders and abnormal growth and maturation capacity of leukemic stem cells (LSCs).The aim of this study was to evaluate the changes in DNMT1 promoter methylation and its expression pattern in patients with ALL. Materials and Methods: In this experimental study, methylation specific PCR (MSP) was used to assess the methylation status of DNMT1 promoter regions in samples collected from ALL patients (n=45) and healthy control subjects. According to this method, un-methylated cytosine nucleotides are converted to uracil by sodium bisulfite and the proliferation of methylated and un-methylated regions are performed using specific primers for target sequences. Results: None of the patients with B and T-ALL showed methylated promoter regions of the DNMT1 gene, while the methylation pattern of both pre-B ALL patients and the control group showed a relative promoter methylation. Conclusion: Analysis of promoter methylation patterns in various subgroups of ALL has revealed the importance of DNMT1 in the regulation of gene expression. Likewise, extensive data have also highlighted the methylation-based mechanisms exerted by DNAM1 as one of the main participants regulating gene expression in B-ALL and T-ALL patients. Investigation of the overall DNA methylation pattern offers significant improvements in the prediction of disease prognosis and treatment response.

Biological methylation of inorganic mercury by Saccharomyces cerevisiae - a possible environmental process

International Nuclear Information System (INIS)

Reisinger, K.; Stoeppler, M.; Nuernberg, H.W.

1983-01-01

The biological methylation of inorganic mercury by S-adenosylmethione (SAM) was investigated by incubation experiments with Saccharomyces cerevisae (''bakers' yeast''). The methyl donor (methionine) and the acceptor (Hg 2+ as HgCl 2 ) were also applied in their labelled form (double labelling). Methylmercury as a result of a possibly biological methyl group transfer could not be detected. As reaction product only small amounts (0.01per mille yield) of elemental mercury (Hg 0 ) were found, while the overwhelming amount of HgCl 2 had not reacted. (orig.) [de

DNA Methylation in Peripheral Blood Cells of Pigs Cloned by Somatic Cell Nuclear Transfer

DEFF Research Database (Denmark)

Gao, Fei; Li, Shengting; Lin, Lin

2011-01-01

To date, the genome-wide DNA methylation status of cloned pigs has not been investigated. Due to the relatively low success rate of pig cloning by somatic cell nuclear transfer, a better understanding of the epigenetic reprogramming and the global methylation patterns associated with development...... in cloned pigs is required. In this study we applied methylation-specific digital karyotyping tag sequencing by Solexa technology and investigated the genome-wide DNA methylation profiles of peripheral blood cells in cloned pigs with normal phenotypes in comparison with their naturally bred controls....... In the result, we found that globally there was no significant difference of DNA methylation patterns between the two groups. Locus-specifically, some genes involved in embryonic development presented a generally increased level of methylation. Our findings suggest that in cloned pigs with normal phenotypes...

The altered promoter methylation of oxytocin receptor gene in autism.

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Elagoz Yuksel, Mine; Yuceturk, Betul; Karatas, Omer Faruk; Ozen, Mustafa; Dogangun, Burak

Autism spectrum disorder (ASD) is one of the lifelong existing disorders. Abnormal methylation status of gene promoters of oxytonergic system has been implicated as among the etiologic factors of ASDs. We, therefore, investigated the methylation frequency of oxytocin receptor gene (OXTR) promoter from peripheral blood samples of children with autistic features. Our sample includes 66 children in total (22-94 months); 27 children with ASDs according to the DSM-IV-TR and the Childhood Autism Rating Scale (CARS) and 39 children who do not have any autistic like symptoms as the healthy control group. We investigated the DNA methylation status of OXTR promoter by methylation specific enzymatic digestion of genomic DNA and polymerase chain reaction. A significant relationship has been found between ASDs and healthy controls for the reduction of methylation frequency of the regions MT1 and MT3 of OXTR. We could not find any association in the methylation frequency of MT2 and MT4 regions of OXTR. Although our findings indicate high frequency of OXTR promoter hypomethylation in ASDs, there is need for independent replication of the results for a bigger sample set. We expect that future studies with the inclusion of larger, more homogeneous samples will attempt to disentangle the causes of ASDs.

MethylMeter(®): bisulfite-free quantitative and sensitive DNA methylation profiling and mutation detection in FFPE samples.

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McCarthy, David; Pulverer, Walter; Weinhaeusel, Andreas; Diago, Oscar R; Hogan, Daniel J; Ostertag, Derek; Hanna, Michelle M

2016-06-01

Development of a sensitive method for DNA methylation profiling and associated mutation detection in clinical samples. Formalin-fixed and paraffin-embedded tumors received by clinical laboratories often contain insufficient DNA for analysis with bisulfite or methylation sensitive restriction enzymes-based methods. To increase sensitivity, methyl-CpG DNA capture and Coupled Abscription PCR Signaling detection were combined in a new assay, MethylMeter(®). Gliomas were analyzed for MGMT methylation, glioma CpG island methylator phenotype and IDH1 R132H. MethylMeter had 100% assay success rate measuring all five biomarkers in formalin-fixed and paraffin-embedded tissue. MGMT methylation results were supported by survival and mRNA expression data. MethylMeter is a sensitive and quantitative method for multitarget DNA methylation profiling and associated mutation detection. The MethylMeter-based GliomaSTRAT assay measures methylation of four targets and one mutation to simultaneously grade gliomas and predict their response to temozolomide. This information is clinically valuable in management of gliomas.

Ethamsylate and blood loss in total hip replacement.

Science.gov (United States)

Keith, I

1979-01-01

Nineteen consecutive patients undergoing total hip replacement under epidural anaesthesia were randomly divided into two groups. The treatment group received 1000 mg of ethamsylate intravenously before induction of anaesthesia. Blood lost during surgery was measured by a colorimetric technique. Closed suction drains were used and all blood lost after operation collected for measurement. Ethamsylate did not decrease the average volumes of blood lost during or after the operation. Neither did it reduce the requirements for blood transfusion. Although there were no side-effects attributable to ethamyslate, there seems to be no indication for its use in total hip replacement under epidural anaesthesia.

Direct observation of vibrational energy dispersal via methyl torsions.

Science.gov (United States)

Gardner, Adrian M; Tuttle, William D; Whalley, Laura E; Wright, Timothy G

2018-02-28

Explicit evidence for the role of methyl rotor levels in promoting energy dispersal is reported. A set of coupled zero-order vibration/vibration-torsion (vibtor) levels in the S 1 state of para -fluorotoluene ( p FT) are investigated. Two-dimensional laser-induced fluorescence (2D-LIF) and two-dimensional zero-kinetic-energy (2D-ZEKE) spectra are reported, and the assignment of the main features in both sets of spectra reveals that the methyl torsion is instrumental in providing a route for coupling between vibrational levels of different symmetry classes. We find that there is very localized, and selective, dissipation of energy via doorway states, and that, in addition to an increase in the density of states, a critical role of the methyl group is a relaxation of symmetry constraints compared to direct vibrational coupling.

Growth Performances of Female and Male Holstein Calves Fed Milk and Milk Replacers

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Tahir BAYRIL

2015-01-01

Full Text Available The objective of this study was to compare growth performances of male and female Holstein calves fed milk and milk replacers. A total of 60 Holstein calves were used in the study. Calves were divided into three equal groups. In each group, there were 10 female and 10 male calves. Calves were offered colostrum for 3 days after birth and were weighed at fourth day for the trial. Initial body weights of calves in dietary treatments were statistically similar. The first, second and third groups were fed milk, milk replacer-I (CP 21% and CF 16.5% and milk replacer-II (CP 24% and CF 18%, respectively. In addition to milk and milk replacers, calves were supplemented with ad libitum concentrate feed and alfalfa. Dietary treatment was significantly effective (P<0.05 on body weight of calves at 60 days of age. In conclusion, growth performances of calves increased with increasing protein content of milk replacer had better than those of calves fed milk replacer containing low-protein. Therefore, during the suckling period, in feeding of Holstein calves, milk or milk replacer containing high-protein should be preferred primarily.

Epigenetic subgroups of esophageal and gastric adenocarcinoma with differential GATA5 DNA methylation associated with clinical and lifestyle factors.

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Xinhui Wang

Full Text Available BACKGROUND: Adenocarcinomas located near the gastroesophageal junction have unclear etiology and are difficult to classify. We used DNA methylation analysis to identify subtype-specific markers and new subgroups of gastroesophageal adenocarcinomas, and studied their association with epidemiological risk factors and clinical outcomes. METHODOLOGY/PRINCIPAL FINDINGS: We used logistic regression models and unsupervised hierarchical cluster analysis of 74 DNA methylation markers on 45 tumor samples (44 patients of esophageal and gastric adenocarcinomas obtained from a population-based case-control study to uncover epigenetic markers and cluster groups of gastroesophageal adenocarcinomas. No distinct epigenetic differences were evident between subtypes of gastric and esophageal cancers. However, we identified two gastroesophageal adenocarcinoma subclusters based on DNA methylation profiles. Group membership was best predicted by GATA5 DNA methylation status. We analyzed the associations between these two epigenetic groups and exposure using logistic regression, and the associations with survival time using Cox regression in a larger set of 317 tumor samples (278 patients. There were more males with esophageal and gastric cardia cancers in Cluster Group 1 characterized by higher GATA5 DNA methylation values (all p<0.05. This group also showed associations of borderline statistical significance with having ever smoked (p-value = 0.07, high body mass index (p-value = 0.06, and symptoms of gastroesophageal reflux (p-value = 0.07. Subjects in cluster Group 1 showed better survival than those in Group 2 after adjusting for tumor differentiation grade, but this was not found to be independent of tumor stage. CONCLUSIONS/SIGNIFICANCE: DNA methylation profiling can be used in population-based studies to identify epigenetic subclasses of gastroesophageal adenocarcinomas and class-specific DNA methylation markers that can be linked to

Stereochemistry of nitrogenous heterocycles. 61. Synthesis and configuration of an eighth isomer of 2-methyl-4-hydroxydecahydroquinoline

International Nuclear Information System (INIS)

Litvinenko, G.S.; Voronenko, L.A.

1987-01-01

Reduction of 1-benzoyl-2α-methyl-4-oxo-cis-decahydroquinoline with dodium borohydride and sodium in alcohol has given 1-benzoyl-2α-methyl-4β-hydroxy-cis-decahydroquinoline, which exists in the steroidal conformation with diaxial α, α'-substituents in the piperidine ring and with an equatorial hydroxy-group. Debenzoylation of this has given the last of the eight theoretically possible isomers of 2-methyl-4-hydroxydecahydroquinoline, namely 2α-methyl-4β-hydroxy-cis-decahydroquinoline, which exists in the nonsteroidal conformation with an axial hydroxy-group. IR spectra were obtained on a UR-20 spectrometer in KBr disks, and PMR spectra on a BS487 instrument (80 MHz), internal standard HMDS

Resource base influences genome-wide DNA methylation levels in wild baboons (Papio cynocephalus)

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Lea, Amanda J.; Altmann, Jeanne; Alberts, Susan C.; Tung, Jenny

2015-01-01

Variation in resource availability commonly exerts strong effects on fitness-related traits in wild animals. However, we know little about the molecular mechanisms that mediate these effects, or about their persistence over time. To address these questions, we profiled genome-wide whole blood DNA methylation levels in two sets of wild baboons: (i) ‘wild-feeding’ baboons that foraged naturally in a savanna environment and (ii) ‘Lodge’ baboons that had ready access to spatially concentrated human food scraps, resulting in high feeding efficiency and low daily travel distances. We identified 1,014 sites (0.20% of sites tested) that were differentially methylated between wild-feeding and Lodge baboons, providing the first evidence that resource availability shapes the epigenome in a wild mammal. Differentially methylated sites tended to occur in contiguous stretches (i.e., in differentially methylated regions or DMRs), in promoters and enhancers, and near metabolism-related genes, supporting their functional importance in gene regulation. In agreement, reporter assay experiments confirmed that methylation at the largest identified DMR, located in the promoter of a key glycolysis-related gene, was sufficient to causally drive changes in gene expression. Intriguingly, all dispersing males carried a consistent epigenetic signature of their membership in a wild-feeding group, regardless of whether males dispersed into or out of this group as adults. Together, our findings support a role for DNA methylation in mediating ecological effects on phenotypic traits in the wild, and emphasize the dynamic environmental sensitivity of DNA methylation levels across the life course. PMID:26508127

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.

8-Methoxypsoralen-nucleic acid photoreaction. Effect of methyl substitution on pyrone vs. furan photoaddition

International Nuclear Information System (INIS)

Kanne, D.; Rapoport, H.; Hearst, J.E.

1984-01-01

We have synthesized a series of 8-[3H]methoxypsoralens in which methyl and hydrogen are systematically varied at the 4- and 5'-positions. Analysis of the products resulting from the photoaddition of these four psoralens with the nucleic acid poly(dA-dT) reveals that the product distribution depends on the presence or absence of a 4-methyl substituent. Compounds with the 4-methyl group show an overwhelming preference (approximately 98%) for addition to the furan double bond, while compounds without the 4-methyl show a substantial amount (approximately 18%) of addition to the pyrone double bond

CpG island methylator phenotype-low (CIMP-low) colorectal cancer shows not only few methylated CIMP-high-specific CpG islands, but also low-level methylation at individual loci.

Science.gov (United States)

Kawasaki, Takako; Ohnishi, Mutsuko; Nosho, Katsuhiko; Suemoto, Yuko; Kirkner, Gregory J; Meyerhardt, Jeffrey A; Fuchs, Charles S; Ogino, Shuji

2008-03-01

The CpG island methylator phenotype (CIMP or CIMP-high) with widespread promoter methylation is a distinct phenotype in colorectal cancer. However, the concept of CIMP-low with less extensive CpG island methylation is still evolving. Our aim is to examine whether density of methylation in individual CpG islands was different between CIMP-low and CIMP-high tumors. Utilizing MethyLight technology and 889 population-based colorectal cancers, we quantified DNA methylation (methylation index, percentage of methylated reference) at 14 CpG islands, including 8 CIMP-high-specific loci (CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1). Methylation positivity in each locus was defined as methylation index>4. Low-level methylation (methylation index>0, CIMP-high-specific locus was significantly more common in 340 CIMP-low tumors (1/8-5/8 methylation-positive loci) than 133 CIMP-high tumors (> or =6/8 methylation-positive loci) and 416 CIMP-0 tumors (0/8 methylation-positive loci) (PCIMP-high, low-level methylation, was not persistently more prevalent in CIMP-low tumors. In conclusion, compared to CIMP-high and CIMP-0 tumors, CIMP-low colorectal cancers show not only few methylated CIMP-high-specific CpG islands, but also more frequent low-level methylation at individual loci. Our data may provide supporting evidence for a difference in pathogenesis of DNA methylation between CIMP-low and CIMP-high tumors.

Inter- and intra-individual variation in allele-specific DNA methylation and gene expression in children conceived using assisted reproductive technology.

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Nahid Turan

2010-07-01

Full Text Available Epidemiological studies have reported a higher incidence of rare disorders involving imprinted genes among children conceived using assisted reproductive technology (ART, suggesting that ART procedures may be disruptive to imprinted gene methylation patterns. We examined intra- and inter-individual variation in DNA methylation at the differentially methylated regions (DMRs of the IGF2/H19 and IGF2R loci in a population of children conceived in vitro or in vivo. We found substantial variation in allele-specific methylation at both loci in both groups. Aberrant methylation of the maternal IGF2/H19 DMR was more common in the in vitro group, and the overall variance was also significantly greater in the in vitro group. We estimated the number of trophoblast stem cells in each group based on approximation of the variance of the binomial distribution of IGF2/H19 methylation ratios, as well as the distribution of X chromosome inactivation scores in placenta. Both of these independent measures indicated that placentas of the in vitro group were derived from fewer stem cells than the in vivo conceived group. Both IGF2 and H19 mRNAs were significantly lower in placenta from the in vitro group. Although average birth weight was lower in the in vitro group, we found no correlation between birth weight and IGF2 or IGF2R transcript levels or the ratio of IGF2/IGF2R transcript levels. Our results show that in vitro conception is associated with aberrant methylation patterns at the IGF2/H19 locus. However, very little of the inter- or intra-individual variation in H19 or IGF2 mRNA levels can be explained by differences in maternal DMR DNA methylation, in contrast to the expectations of current transcriptional imprinting models. Extraembryonic tissues of embryos cultured in vitro appear to be derived from fewer trophoblast stem cells. It is possible that this developmental difference has an effect on placental and fetal growth.

Variation of global DNA methylation levels with age and in autistic children.

Science.gov (United States)

Tsang, Shui-Ying; Ahmad, Tanveer; Mat, Flora W K; Zhao, Cunyou; Xiao, Shifu; Xia, Kun; Xue, Hong

2016-09-23

The change in epigenetic signatures, in particular DNA methylation, has been proposed as risk markers for various age-related diseases. However, the course of variation in methylation levels with age, the difference in methylation between genders, and methylation-disease association at the whole genome level is unclear. In the present study, genome-wide methylation levels in DNA extracted from peripheral blood for 2116 healthy Chinese in the 2-97 age range and 280 autistic trios were examined using the fluorescence polarization-based genome-wide DNA methylation quantification method developed by us. Genome-wide or global DNA methylation levels proceeded through multiple phases of variation with age, consisting of a steady increase from age 2 to 25 (r = 0.382) and another rise from age 41 to 55 to reach a peak level of ~80 % (r = 0.265), followed by a sharp decrease to ~40 % in the mid-1970s (age 56 to 75; r = -0.395) and leveling off thereafter. Significant gender effect in methylation levels was observed only for the 41-55 age group in which methylation in females was significantly higher than in males (p = 0.010). In addition, global methylation level was significantly higher in autistic children than in age-matched healthy children (p < 0.001). The multiphasic nature of changes in global methylation levels with age was delineated, and investigation into the factors underlying this profile will be essential to a proper understanding of the aging process. Furthermore, this first report of global hypermethylation in autistic children also illustrates the importance of age-matched controls in characterization of disease-associated variations in DNA methylation.

Chromatographic study of highly methoxylated lime pectins deesterified by different pectin methyl-esterases.

Science.gov (United States)

Ralet, M C; Bonnin, E; Thibault, J F

2001-03-25

The inter-molecular distribution of free carboxyl groups of two highly methoxylated pectins enzymatically deesterified by plant and fungus pectin methyl-esterases were investigated by size-exclusion (SEC) and ion-exchange chromatography (IEC). "Homogeneous" populations with respect to molar mass or charge density were thereby obtained and their chemical composition and physico-chemical properties (transport parameter for monovalent cations and calcium, calcium activity coefficient) were studied. Chemical analysis showed that the composition varies from one SEC fraction to another, the highest molar mass fraction being richer in rhamnose and galactose and exhibiting a slightly higher degree of methylation. Separation of pectins by IEC revealed a quite homogeneous charge density distribution for F58 contrary to P60 which exhibited a large distribution of methoxyl groups. The free carboxyl groups distributions and calcium binding behaviours of SEC and IEC fractions were shown to differ widely for highly methoxylated pectins deesterified by plant and fungus pectin methyl-esterases.

Inactivation of ultraviolet repair in normal and xeroderma pigmentosum cells by methyl methanesulfonate

International Nuclear Information System (INIS)

Cleaver, J.E.

1982-01-01

Excision repair of ultraviolet damage in the DNA of normal and xeroderma pigmentosum (Groups C, D, and variant) cells was inactivated by exposure of cells to methyl methanesulfonate immediately before irradiation independent of the presence of 0 to 10% fetal calf serum. The inactivation could be represented by a semilog relationship between the amount of repair and methyl methanesulfonate concentration up to approximately 5 mM. The inactivation can be considered to occur as the result of alkylation of a large (about 10(6) daltons) repair enzyme complex, and the dose required to reduce repair to 37% for most cells types was between 4 and 7 mM. No consistent, large difference in sensitivity to methyl methanesulfonate was found in any xeroderma pigmentosum complementation group compared to normal cells, implying that reduced repair in these groups may be caused by small inherited changes in the amino acid composition (i.e., point mutations or small deletions) rather than by losses of major components of the repair enzyme complex

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

Energy Technology Data Exchange (ETDEWEB)

Wolff, G.A.; Lamb, N.A.; Maxwell, J.R.

1986-03-01

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

Analysis of DNA Cytosine Methylation Patterns Using Methylation-Sensitive Amplification Polymorphism (MSAP).

Science.gov (United States)

Guevara, María Ángeles; de María, Nuria; Sáez-Laguna, Enrique; Vélez, María Dolores; Cervera, María Teresa; Cabezas, José Antonio

2017-01-01

Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is the methylation-sensitive amplified polymorphism technique (MSAP) which is a modification of amplified fragment length polymorphism (AFLP). It has been used to study methylation of anonymous CCGG sequences in different fungi, plants, and animal species. The main variation of this technique resides on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent-cutter restriction enzyme. For each sample, MSAP analysis is performed using both EcoRI/HpaII- and EcoRI/MspI-digested samples. A comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) methylation-insensitive polymorphisms that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples and (2) methylation-sensitive polymorphisms which are associated with the amplified fragments that differ in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses the modifications that can be applied to adjust the technology to different species of interest.

Cadmium plating replacements

Energy Technology Data Exchange (ETDEWEB)

Nelson, M.J.; Groshart, E.C.

1995-03-01

The Boeing Company has been searching for replacements to cadmium plate. Two alloy plating systems seem close to meeting the needs of a cadmium replacement. The two alloys, zinc-nickel and tin-zinc are from alloy plating baths; both baths are neutral pH. The alloys meet the requirements for salt fog corrosion resistance, and both alloys excel as a paint base. Currently, tests are being performed on standard fasteners to compare zinc-nickel and tin-zinc on threaded hardware where cadmium is heavily used. The Hydrogen embrittlement propensity of the zinc-nickel bath has been tested, and just beginning for the tin-zinc bath. Another area of interest is the electrical properties on aluminum for tin-zinc and will be discussed. The zinc-nickel alloy plating bath is in production in Boeing Commercial Airplane Group for non-critical low strength steels. The outlook is promising that these two coatings will help The Boeing Company significantly reduce its dependence on cadmium plating.

[Analysis of genomic DNA methylation level in radish under cadmium stress by methylation-sensitive amplified polymorphism technique].

Science.gov (United States)

Yang, Jin-Lan; Liu, Li-Wang; Gong, Yi-Qin; Huang, Dan-Qiong; Wang, Feng; He, Ling-Li

2007-06-01

The level of cytosine methylation induced by cadmium in radish (Raphanus sativus L.) genome was analysed using the technique of methylation-sensitive amplified polymorphism (MSAP). The MSAP ratios in radish seedling exposed to cadmium chloride at the concentration of 50, 250 and 500 mg/L were 37%, 43% and 51%, respectively, and the control was 34%; the full methylation levels (C(m)CGG in double strands) were at 23%, 25% and 27%, respectively, while the control was 22%. The level of increase in MSAP and full methylation indicated that de novo methylation occurred in some 5'-CCGG sites under Cd stress. There was significant positive correlation between increase of total DNA methylation level and CdCl(2) concentration. Four types of MSAP patterns: de novo methylation, de-methylation, atypical pattern and no changes of methylation pattern were identified among CdCl(2) treatments and the control. DNA methylation alteration in plants treated with CdCl(2) was mainly through de novo methylation.

[GSTP1, APC and RASSF1 gene methylation in prostate cancer samples: comparative analysis of MS-HRM method and Infinium HumanMethylation450 BeadChip beadchiparray diagnostic value].

Science.gov (United States)

Skorodumova, L O; Babalyan, K A; Sultanov, R; Vasiliev, A O; Govorov, A V; Pushkar, D Y; Prilepskaya, E A; Danilenko, S A; Generozov, E V; Larin, A K; Kostryukova, E S; Sharova, E I

2016-11-01

There is a clear need in molecular markers for prostate cancer (PC) risk stratification. Alteration of DNA methylation is one of processes that occur during ÐÑ progression. Methylation-sensitive PCR with high resolution melting curve analysis (MS-HRM) can be used for gene methylation analysis in routine laboratory practice. This method requires very small amounts of DNA for analysis. Numerous results have been accumulated on DNA methylation in PC samples analyzed by the Infinium HumanMethylation450 BeadChip (HM450). However, the consistency of MS-HRM results with chip hybridization results has not been examined yet. The aim of this study was to assess the consistency of results of GSTP1, APC and RASSF1 gene methylation analysis in ÐÑ biopsy samples obtained by MS-HRM and chip hybridization. The methylation levels of each gene determined by MS-HRM were statistically different in the group of PC tissue samples and the samples without signs of tumor growth. Chip hybridization data analysis confirmed the results obtained with the MS-HRM. Differences in methylation levels between tumor tissue and histologically intact tissue of each sample determined by MS-HRM and chip hybridization, were consistent with each other. Thus, we showed that the assessment of GSTP1, APC and RASSF1 gene methylation analysis using MS-HRM is suitable for the design of laboratory assays that will differentiate the PC tissue from the tissue without signs of tumor growth.

Reaction products from N-methyl-N-nitrosourea and deoxyribonucleic acid containing thymidine residues. Synthesis and identification of a new methylation product, O4-methyl-thymidine

Science.gov (United States)

Lawley, P. D.; Orr, D. J.; Shah, S. A.; Farmer, P. B.; Jarman, M.

1973-01-01

1. DNA was treated with N-methyl-N-nitrosourea at pH7–8, 37°C, degraded to yield 3- and 7-methylpurines and deoxyribonucleosides and the reaction products were separated by chromatography on ion-exchange resins. The following methods for identification and determination of products were used: with unlabelled N-methyl-N-nitrosourea, u.v. absorption; use of methyl-14C-labelled N-methyl-N-nitrosourea and use of [14C]thymine-labelled DNA. 2. The synthesis of O4-methylthymidine and its identification by u.v. and mass spectroscopy are reported. 3. 3-Methylthymidine and O4-methylthymidine were found as methylation products from N-methyl-N-nitrosourea with thymidine and with DNA, in relatively small yields. Unidentified products containing thymine were found in enzymic digests of N-methyl-N-nitrosourea-treated DNA, which may be phosphotriesters. 4. The possible role of formation of methylthymines in mutagenesis by N-methyl-N-nitrosourea is discussed. PMID:4798180

Changing trends in total knee replacement

OpenAIRE

Goudie, Ewan; Robinson, Cal; Walmsley, Phil; Brenkel, Ivan

2017-01-01

Introduction:  This study evaluates a possible change in the demographics and surgical practice observed in a large cohort of patients undergoing total knee replacement (TKR). Patients and methods:  We performed a retrospective analysis of a prospectively collected data on two groups of consecutive patients undergoing primary TKR. Group one consisted of patients who underwent surgery between 1994 and 1998. Group two consisted of patients who had surgery between 2009 and 2012. Results:  The me...

Screening for Methylated Poly(⌊-histidine with Various Dimethylimidazolium/Methylimidazole/Imidazole Contents as DNA Carrier

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Shoichiro Asayama

2015-08-01

Full Text Available Methylated poly(l-histidine (PLH-Me, our original polypeptide, has controlled the contents of dimethylimidazolium, τ/π-methylimidazole and imidazole groups for efficient gene delivery. The screening for the PLH-Me as DNA carrier has been carried out by use of the PLH with 25 mol% (τ-methyl, 16 mol%; π-methyl, 17 mol%; deprotonated imidazole, 41 mol%, 68 mol% (τ-methyl, 16 mol%; π-methyl, 8 mol%; deprotonated imidazole, 8 mol% and 87 mol% (τ-methyl, 7 mol%; π-methyl, 4 mol%; deprotonated imidazole, 2 mol% dimethylimidazolium groups, that is, PLH-Me(25, PLH-Me(68 and PLH-Me(87, respectively. The screening of the chemical structure of PLH-Me has been carried out for DNA carrier properties, which are the stability of its DNA polyion complexes and gene expression. The DNA complexes with the 25 mol% and 68 mol% dimethylated PLH-Me possessed almost same ability to retain DNA, as compared with the 87 mol% dimethylated PLH-Me, which was examined by competitive exchange with dextran sulfate. From the gene transfection experiment against HepG2 cells, human hepatoma cell line, the PLH-Me(25/DNA complex was revealed to mediate highest gene expression. These results suggest that the dimethyl-imidazolium/methylimidazole/imidazole balance of the PLH-Me is important for DNA carrier design.

Synthesis of [methyl-14C]crotonobetaine from DL-[methyl-14C]carnitine

International Nuclear Information System (INIS)

Loester, H.; Seim, H.

1996-01-01

The causes of carnitine deficiency syndromes are not completely understood, but decomposition of L-carnitine in vivo is likely to be involved. Carnitine is metabolized to γ-butyrobetaine, and crotonobetaine is probably an intermediate in this pathway. To validate experimentally the precursor-product relationship between the three physiologically occuring γ-betaines - L-carnitine, crotonobetaine, γ-butyrobetaine - labelling with stable or radioactive isotopes became necessary. Methyl-labelled carnitine isomers (L(-)-, D(+)- or DL-) or γ-butyrobetaine can be easily synthesized by methylation of 4-amino-3-hydroxybutyric acid isomers or 4-aminobutyric acid, respectively. Because of problems with the 4-aminocrotonic acid, we synthesized labelled crotonbetaine from labelled carnitine. Thus, DL-[methyl- 14 C]carnitine was dehydrated by reaction with concentrated sulfuric acid. After removal of the latter the products were separated and purified by ion exchange chromatography on DOWEX 50 WX8 (200 - 400 mesh) and gradient elution with hydrochloric acid. In addition to the labelled main product [methyl- 14 C]crotonobetaine (yield about 50 %), [methyl- 14 C]glycine betaine and [methyl- 14 C]acetonyl-trimethylammonium (ATMA) were formed. The end products were identified by combined thin layer chromatography/autoradiography and quantified by liquid scintillation counting. (Author)

Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation.

Science.gov (United States)

Dou, John; Schmidt, Rebecca J; Benke, Kelly S; Newschaffer, Craig; Hertz-Picciotto, Irva; Croen, Lisa A; Iosif, Ana-Maria; LaSalle, Janine M; Fallin, M Daniele; Bakulski, Kelly M

2018-01-01

Cord blood DNA methylation is associated with numerous health outcomes and environmental exposures. Whole cord blood DNA reflects all nucleated blood cell types, while centrifuging whole blood separates red blood cells, generating a white blood cell buffy coat. Both sample types are used in DNA methylation studies. Cell types have unique methylation patterns and processing can impact cell distributions, which may influence comparability. We evaluated differences in cell composition and DNA methylation between cord blood buffy coat and whole cord blood samples. Cord blood DNA methylation was measured with the Infinium EPIC BeadChip (Illumina) in eight individuals, each contributing buffy coat and whole blood samples. We analyzed principal components (PC) of methylation, performed hierarchical clustering, and computed correlations of mean-centered methylation between pairs. We conducted moderated t-tests on single sites and estimated cell composition. DNA methylation PCs were associated with individual (P PC1 = 1.4 × 10 -9 ; P PC2 = 2.9 × 10 -5 ; P PC3 = 3.8 × 10 -5 ; P PC4 = 4.2 × 10 -6 ; P PC5 = 9.9 × 10 -13 , P PC6 = 1.3 × 10 -11 ) and not with sample type (P PC1-6 >0.7). Samples hierarchically clustered by individual. Pearson correlations of mean-centered methylation between paired samples ranged from r = 0.66 to r = 0.87. No individual site significantly differed between buffy coat and whole cord blood when adjusting for multiple comparisons (five sites had unadjusted Pcoat and whole cord blood are much lower than inter-individual variation, demonstrating that both sample preparation types can be analytically combined and compared.

DNA methylation and histone deacetylation regulating insulin sensitivity due to chronic cold exposure.

Science.gov (United States)

Wang, Xiaoqing; Wang, Lai; Sun, Yizheng; Li, Ruiping; Deng, Jinbo; Deng, Jiexin

2017-02-01

In this study, we investigated the causal relationship between chronic cold exposure and insulin resistance and the mechanisms of how DNA methylation and histone deacetylation regulate cold-reduced insulin resistance. 46 adult male mice from postnatal day 90-180 were randomly assigned to control group and cold-exposure group. Mice in cold-exposure group were placed at temperature from -1 to 4 °C for 30 days to mimic chronic cold environment. Then, fasting blood glucose, blood insulin level and insulin resistance index were measured with enzymatic methods. Immunofluorescent labeling was carried out to visualize the insulin receptor substrate 2 (IRS2), Obese receptor (Ob-R, a leptin receptor), voltage-dependent anion channel protein 1 (VDAC1), cytochrome C (cytC), 5-methylcytosine (5-mC) positive cells in hippocampal CA1 area. Furthermore, the expressions of some proteins mentioned above were detected with Western blot. The results showed: ① Chronic cold exposure could reduce the insulin resistance index (P cold-exposure group than in control group with both immunohistochemical staining and Western blot (P cold exposure increased DNA methylation and histone deacetylation in the pyramidal cells of CA1 area and led to an increase in the expression of histone deacetylase 1 (HDAC1) and DNA methylation relative enzymes (P cold exposure can improve insulin sensitivity, with the involvement of DNA methylation, histone deacetylation and the regulation of mitochondrial energy metabolism. These epigenetic modifications probably form the basic mechanism of cold-reduced insulin resistance. Copyright © 2016 Elsevier Inc. All rights reserved.

Methyl methacrylate oligomerically-modified clay and its poly(methyl methacrylate) nanocomposites

International Nuclear Information System (INIS)

Zheng Xiaoxia; Jiang, David D.; Wilkie, Charles A.

2005-01-01

A methyl methacrylate oligomerically-modified clay was used to prepare poly(methyl methacrylate) clay nanocomposites by melt blending and the effect of the clay loading level on the modified clay and corresponding nanocomposite was studied. These nanocomposites were characterized by X-ray diffraction, transmission electron microscopy, thermogravimetric analysis and cone calorimetry. The results show a mixed intercalated/delaminated morphology with good nanodispersion. The compatibility between the methylacrylate-subsituted clay and poly(methyl methacrylate) (PMMA) are greatly improved compared to other oligomerically-modified clays

Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies.

Science.gov (United States)

Needhamsen, Maria; Ewing, Ewoud; Lund, Harald; Gomez-Cabrero, David; Harris, Robert Adam; Kular, Lara; Jagodic, Maja

2017-11-15

The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Methylation BeadChips has shown great utility in clinical studies, no equivalent tool is available for rodent animal samples. We examined the feasibility of using the new Infinium MethylationEPIC BeadChip for studying DNA methylation in mouse. In silico, we identified 19,420 EPIC probes (referred as mEPIC probes), which align with a unique best alignment score to the bisulfite converted reference mouse genome mm10. Further annotation revealed that 85% of mEPIC probes overlapped with mm10.refSeq genes at different genomic features including promoters (TSS1500 and TSS200), 1st exons, 5'UTRs, 3'UTRs, CpG islands, shores, shelves, open seas and FANTOM5 enhancers. Hybridization of mouse samples to Infinium Human MethylationEPIC BeadChips showed successful measurement of mEPIC probes and reproducibility between inter-array biological replicates. Finally, we demonstrated the utility of mEPIC probes for data exploration such as hierarchical clustering. Given the absence of cost and labor convenient genome-wide technologies in the murine system, our findings show that the Infinium MethylationEPIC BeadChip platform is suitable for investigation of the mouse methylome. Furthermore, we provide the "mEPICmanifest" with genomic features, available to users of Infinium Human MethylationEPIC arrays for mouse samples.

Acceleration of age-associated methylation patterns in HIV-1-infected adults.

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Tammy M Rickabaugh

Full Text Available Patients with treated HIV-1-infection experience earlier occurrence of aging-associated diseases, raising speculation that HIV-1-infection, or antiretroviral treatment, may accelerate aging. We recently described an age-related co-methylation module comprised of hundreds of CpGs; however, it is unknown whether aging and HIV-1-infection exert negative health effects through similar, or disparate, mechanisms. We investigated whether HIV-1-infection would induce age-associated methylation changes. We evaluated DNA methylation levels at >450,000 CpG sites in peripheral blood mononuclear cells (PBMC of young (20-35 and older (36-56 adults in two separate groups of participants. Each age group for each data set consisted of 12 HIV-1-infected and 12 age-matched HIV-1-uninfected samples for a total of 96 samples. The effects of age and HIV-1 infection on methylation at each CpG revealed a strong correlation of 0.49, p<1 x 10(-200 and 0.47, p<1 x 10(-200. Weighted gene correlation network analysis (WGCNA identified 17 co-methylation modules; module 3 (ME3 was significantly correlated with age (cor=0.70 and HIV-1 status (cor=0.31. Older HIV-1+ individuals had a greater number of hypermethylated CpGs across ME3 (p=0.015. In a multivariate model, ME3 was significantly associated with age and HIV status (Data set 1: βage=0.007088, p=2.08 x 10(-9; βHIV=0.099574, p=0.0011; Data set 2: βage=0.008762, p=1.27 x 10(-5; βHIV=0.128649, p=0.0001. Using this model, we estimate that HIV-1 infection accelerates age-related methylation by approximately 13.7 years in data set 1 and 14.7 years in data set 2. The genes related to CpGs in ME3 are enriched for polycomb group target genes known to be involved in cell renewal and aging. The overlap between ME3 and an aging methylation module found in solid tissues is also highly significant (Fisher-exact p=5.6 x 10(-6, odds ratio=1.91. These data demonstrate that HIV-1 infection is associated with methylation patterns that

Methanogenesis from acetate by Methanosarcina barkeri: Catalysis of acetate formation from methyl iodide, CO/sub 2/, and H/sub 2/ by the enzyme system involved

Energy Technology Data Exchange (ETDEWEB)

Laufer, K; Eikmanns, B; Frimmer, U; Thauer, R K

1987-04-01

Cell suspensions of Methanosarcina barkeri grown on acetate catalyze the formation of methane and CO/sub 2/ from acetate as well as an isotopic exchange between the carboxyl group of acetate and CO/sub 2/. Here we report that these cells also mediate the synthesis of acetate from methyl iodide, CO/sub 2/, and reducing equivalents (H/sub 2/ or CO), the methyl group of acetate being derived from methyl iodide and the carboxyl group from CO/sub 2/. Methyl chloride and methyltosylate but not methanol can substitute for methyl iodide in this reaction. Acetate formation from methyl iodide, CO/sub 2/, and reducing equivalents is coupled with the phosphorylation of ADP. Evidence is presented that methyl iodide is incorporated into the methyl group of acetate via a methyl corrinoid intermediate (deduced from inhibition experiments with propyl iodide) and that CO/sub 2/ is assimilated into the carboxyl group via a C/sub 1/ intermediate which does not exchange with free formate or free CO. The effects of protonophores, of the proton-translocating ATPase inhibitor N,N'-dicyclohexylcarbodiimide, and of arsenate on acetate formation are interpreted to indicate that the reduction of CO/sub 2/ to the oxidation level of the carboxyl group of acetate requires the presence of an electrochemical proton potential and that acetyl-CoA or acetyl-phosphate rather than free acetate is the immediate product of the condensation reaction. These results are dicsussed with respect to the mechanism of methanogenesis from acetate.

Alpha male replacements in nonhuman primates: Variability in processes, outcomes, and terminology.

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Teichroeb, Julie A; Jack, Katharine M

2017-07-01

Alpha male replacements occur in all primates displaying a dominance hierarchy but the process can be extremely variable. Here, we review the primate literature to document differences in patterns of alpha male replacements, showing that group composition and dispersal patterns account for a large proportion of this variability. We also examine the consequences of alpha male replacements in terms of sexual selection theory, infanticide, and group compositions. Though alpha male replacements are often called takeovers in the literature, this term masks much of the variation that is present in these processes. We argue for more concise terminology and provide a list of terms that we suggest more accurately define these events. Finally, we introduce the papers in this special issue on alpha male replacements in the American Journal of Primatology and discuss areas where data are still lacking. © 2017 Wiley Periodicals, Inc.

A novel method to quantify local CpG methylation density by regional methylation elongation assay on microarray

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Qiao Yingjuan

2008-01-01

Full Text Available Abstract Background DNA methylation based techniques are important tools in both clinical diagnostics and therapeutics. But most of these methods only analyze a few CpG sites in a target region. Indeed, difference of site-specific methylation may also lead to a change of methylation density in many cases, and it has been found that the density of methylation is more important than methylation of single CpG site for gene silencing. Results We have developed a novel approach for quantitative analysis of CpG methylation density on the basis of microarray-based hybridization and incorporation of Cy5-dCTP into the Cy3 labeled target DNA by using Taq DNA Polymerase on microarray. The quantification is achieved by measuring Cy5/Cy3 signal ratio which is proportional to methylation density. This methylation-sensitive technique, termed RMEAM (regional methylation elongation assay on microarray, provides several advantages over existing methods used for methylation analysis. It can determine an exact methylation density of the given region, and has potential of high throughput. We demonstrate a use of this method in determining the methylation density of the promoter region of the tumor-related gene MLH1, TERT and MGMT in colorectal carcinoma patients. Conclusion This technique allows for quantitative analysis of regional methylation density, which is the representative of all allelic methylation patterns in the sample. The results show that this technique has the characteristics of simplicity, rapidness, specificity and high-throughput.

Hip joint replacement

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Hip arthroplasty; Total hip replacement; Hip hemiarthroplasty; Arthritis - hip replacement; Osteoarthritis - hip replacement ... Your hip joint is made up of 2 major parts. One or both parts may be replaced during surgery: ...

Effects of Qi-Fang-Xi-Bi-Granules on Cartilage Morphology and C/ebpα Promoter Methylation in Rats with Knee Osteoarthritis

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Xinxin Wang

2018-01-01

Full Text Available Objective. To investigate the effects of Qi-Fang-Xi-Bi-Granules (QFXBGs on cartilage morphology and methylation of C/ebpα (CCAAT/enhancer binding proteinα at the promoter region. Methods. Knee osteoarthritis (KOA modeling was performed in rats in accordance with Hulth’s method, and control group received sham operation. Eight weeks after KOA modeling, the rats in the KOA modeling group were further divided into 6 groups. Each group was given the appropriate drug. After 8 weeks, half of the rats were used for Micro-CT scan, HE staining, ABH/OG staining, immunohistochemistry, and TUNNEL staining of the knee joint tissue, and the other half were used to examine C/ebpα promoter methylation. Results. The three dose groups of QFXBGs all showed lower degrees of surface fissures and flaking, thicker cartilage layer, and restored chondrocyte and subchondral bone morphology, compared with the KOA model group. C/ebpα-22 promoter methylation levels in the high- and low-dose groups were significantly higher than that in the KOA modeling group (p<0.05, while C/ebpα-2 promoter methylation level in the medium-dose group was significantly higher than that in the KOA modeling group (p<0.05. Conclusions. QFXBGs may alleviate articular cartilage degeneration through promoting C/ebpα-2 or C/ebpα-22 methylation at specific promoter sites.

2-Bromo-2-methyl-N-p-tolylpropanamide

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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.

Fatalities due to methyl alcohol intoxication in Turkey: an 8-year study.

Science.gov (United States)

Yayci, Nesime; Ağritmiş, Hasan; Turla, Ahmet; Koç, Sermet

2003-01-09

The aim of this study is to examine methyl alcohol poisoning cases from the medico-legal point of view. The records of the Morgue Department of Council of the Forensic Medicine were reviewed retrospectively for all methyl alcohol poisonings for the period of 27.10.1992 and 30.05.2001. The victim's age, sex, death year, death place, methyl alcohol blood levels, the source of methyl alcohol, accompanying laboratory results and histopathologic tissue changes were recorded. The number of deaths due to the methyl alcohol poisoning was 271 during that period of time. Two hundred and forty-two of the (89.3%) total 271 methyl alcohol fatalities were men and 29 (10.7%) of were women. The largest age group was 36-40 years old, followed by 41-45. The methyl alcohol blood concentrations ranged widely from 50 to 755 mg for per 100 ml. There were 222 cases (81.9%) with the methyl alcohol blood concentrations over 100 mg/dl. Twenty-nine (10.7%) victims were poisoned through the consumption of cologne and three of them with alcoholic beverage named "Raki". Consumed products were not known in all other cases because of insufficient patient history and data. As a conclusion, regarding the distribution according to years, mortality due to methyl alcohol intoxication in our country have been proceeding on a certain level. In order to decrease the mortality due to methyl alcohol intoxication, some precautions should be developed that could prevent the production and consumption of alcoholic beverages illegally produced.

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

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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

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

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

2012-08-23

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

Fragrance material review on 2-methyl-4-phenyl-2-butanol.

Science.gov (United States)

Scognamiglio, J; Jones, L; Letizia, C S; Api, A M

2012-09-01

A toxicologic and dermatologic review of 2-methyl-4-phenyl-2-butanol when used as a fragrance ingredient is presented. 2-methyl-4-phenyl-2-butanol is a member of the fragrance structural group Aryl Alkyl Alcohols and is a tertiary alcohol. The AAAs are a structurally diverse class of fragrance ingredients that includes primary, secondary, and tertiary alkyl alcohols covalently bonded to an aryl (Ar) group, which may be either a substituted or unsubstituted benzene ring. The common structural element for the AAA fragrance ingredients is an alcohol group -C-(R1)(R2)OH and generically the AAA fragrances can be represented as an Ar-C-(R1)(R2)OH or Ar-Alkyl-C-(R1)(R2)OH group. This review contains a detailed summary of all available toxicology and dermatology papers that are related to this individual fragrance ingredient and is not intended as a stand-alone document. Available data for 2-methyl-4-phenyl-2-butanol were evaluated then summarized and includes physical properties, acute toxicity, skin irritation, and skin sensitization data. A safety assessment of the entire Aryl Alkyl Alcohols will be published simultaneously with this document; please refer to Belsito et al. (2012) for an overall assessment of the safe use of this material and all Aryl Alkyl Alcohols in fragrances. assessment of aryl alkyl alcohols when used as fragrance ingredients. Copyright © 2011 Elsevier Ltd. All rights reserved.

Concordance analysis of methylation biomarkers detection in self-collected and physician-collected samples in cervical neoplasm

International Nuclear Information System (INIS)

Chang, Cheng-Chang; Huang, Rui-Lan; Liao, Yu-Ping; Su, Po-Hsuan; Hsu, Yaw-Wen; Wang, Hui-Chen; Tien, Chau-Yang; Yu, Mu-Hsien; Lin, Ya-Wen; Lai, Hung-Cheng

2015-01-01

Non-attendance at gynecological clinics is a major limitation of cervical cancer screening and self-collection of samples may improve this situation. Although HPV testing of self-collected vaginal samples is acceptable, the specificity is inadequate. The current focus is increasing self-collection of vaginal samples to minimize clinic visits. In this study, we analyzed the concordance and clinical performance of DNA methylation biomarker (PAX1, SOX1, and ZNF582) detection in self-collected vaginal samples and physician-collected cervical samples for the identification of cervical neoplasm. We enrolled 136 cases with paired methylation data identified from abnormal Pap smears (n = 126) and normal controls (n = 10) regardless of HPV status at gynecological clinics. The study group comprised 37 cervical intraepithelial neoplasm I (CIN1), 23 cervical intraepithelial neoplasm II (CIN2), 16 cervical intraepithelial neoplasm III (CIN3), 30 carcinoma in situ (CIS), 13 squamous cell carcinomas (SCCs) and seven adenocarcinomas (ACs)/adenosquamous carcinomas (ASCs). PAX1, SOX1 and ZNF582 methylation in study samples was assessed by real-time quantitative methylation-specific polymerase chain reaction analysis. We generated methylation index cutoff values for the detection of CIN3+ in physician-collected cervical samples for analysis of the self-collected group. Concordance between the physician-collected and self-collected groups was evaluated by Cohen’s Kappa. Sensitivity, specificity and area under curve (AUC) were calculated for detection of CIN3+ lesions. Finally, we produced an optimal cutoff value with the best sensitivity from the self-collected groups. We generated a methylation index cutoff value from physician-collected samples for detection of CIN3+. There were no significant differences in sensitivity, specificity of PAX1, SOX1 and ZNF582 between the self-collected and physician-collected groups. The methylation status of all three genes in the normal control

Acceleration of Age-Associated Methylation Patterns in HIV-1-Infected Adults

Science.gov (United States)

Sehl, Mary; Sinsheimer, Janet S.; Hultin, Patricia M.; Hultin, Lance E.; Quach, Austin; Martínez-Maza, Otoniel; Horvath, Steve; Vilain, Eric; Jamieson, Beth D.

2015-01-01

Patients with treated HIV-1-infection experience earlier occurrence of aging-associated diseases, raising speculation that HIV-1-infection, or antiretroviral treatment, may accelerate aging. We recently described an age-related co-methylation module comprised of hundreds of CpGs; however, it is unknown whether aging and HIV-1-infection exert negative health effects through similar, or disparate, mechanisms. We investigated whether HIV-1-infection would induce age-associated methylation changes. We evaluated DNA methylation levels at >450,000 CpG sites in peripheral blood mononuclear cells (PBMC) of young (20-35) and older (36-56) adults in two separate groups of participants. Each age group for each data set consisted of 12 HIV-1-infected and 12 age-matched HIV-1-uninfected samples for a total of 96 samples. The effects of age and HIV-1 infection on methylation at each CpG revealed a strong correlation of 0.49, pmodules; module 3 (ME3) was significantly correlated with age (cor=0.70) and HIV-1 status (cor=0.31). Older HIV-1+ individuals had a greater number of hypermethylated CpGs across ME3 (p=0.015). In a multivariate model, ME3 was significantly associated with age and HIV status (Data set 1: βage= 0.007088, p=2.08 x 10-9; βHIV= 0.099574, p=0.0011; Data set 2: βage= 0.008762, p=1.27x 10-5; βHIV= 0.128649, p= 0.0001). Using this model, we estimate that HIV-1 infection accelerates age-related methylation by approximately 13.7 years in data set 1 and 14.7 years in data set 2. The genes related to CpGs in ME3 are enriched for polycomb group target genes known to be involved in cell renewal and aging. The overlap between ME3 and an aging methylation module found in solid tissues is also highly significant (Fisher-exact p=5.6 x 10-6, odds ratio=1.91). These data demonstrate that HIV-1 infection is associated with methylation patterns that are similar to age-associated patterns and suggest that general aging and HIV-1 related aging work through some common cellular

Alteration in Methylation Pattern of Retinoblastoma 1 Gene Promotor Region in Intestinal Metaplasia with or without Helicobacter pylori and Gastric Cancer Patients.

Science.gov (United States)

Boyacioglu, Seda Orenay; Kasap, Elmas; Yuceyar, Hakan; Korkmaz, Mehmet

2016-01-01

Helicobacter pylori, intestinal metaplasia (IM), and gene methylation play important roles in gastric carcinogenesis. However, the association among H. pylori infection, IM, gastric cancer (GC), and gene methylation is not fully understood. Cell cycle control involving retinoblastoma 1 (RB1) gene is one of the main regulatory pathways reported to be altered in gastric carcinogenesis. The purpose of this research is to assess the methylation status of RB1 gene in GC and IM with or without H. pylori infection, and to discuss the possible role of H. pylori-induced RB1 gene methylation in the mechanism of gastric carcinogenesis. The methylation profile of RB1 gene was analyzed by sodium bisulfite modification and methylation-specific PCR in GC (n = 24), IM patients with H. pylori positive (n = 20) and negative (n = 20), and control subjects (n = 20). According to methylation levels in RB1 gene; the high correlation values were detected between H. pylori positive-IM group and GC group, and between H. pylori positive-IM and H. pylori negative-IM groups (p gene. High methylation levels in RB1 gene in H. pylori positive individuals may suggest an elevated risk of gastric cancer occurrence.

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

Science.gov (United States)

Peraza-Echeverria, S; Herrera-Valencia, V A.; Kay, A -J.

2001-07-01

The extent of DNA methylation polymorphisms was evaluated in micropropagated banana (Musa AAA cv. 'Grand Naine') derived from either the vegetative apex of the sucker or the floral apex of the male inflorescence using the methylation-sensitive amplification polymorphism (MSAP) technique. In all, 465 fragments, each representing a recognition site cleaved by either or both of the isoschizomers were amplified using eight combinations of primers. A total of 107 sites (23%) were found to be methylated at cytosine in the genome of micropropagated banana plants. In plants micropropagated from the male inflorescence explant 14 (3%) DNA methylation events were polymorphic, while plants micropropagated from the sucker explant produced 8 (1.7%) polymorphisms. No DNA methylation polymorphisms were detected in conventionally propagated banana plants. These results demonstrated the usefulness of MSAP to detect DNA methylation events in micropropagated banana plants and indicate that DNA methylation polymorphisms are associated with micropropagation.

ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices.

Science.gov (United States)

Dang, Cuong Cao; Lefort, Vincent; Le, Vinh Sy; Le, Quang Si; Gascuel, Olivier

2011-10-01

Amino acid replacement rate matrices are an essential basis of protein studies (e.g. in phylogenetics and alignment). A number of general purpose matrices have been proposed (e.g. JTT, WAG, LG) since the seminal work of Margaret Dayhoff and co-workers. However, it has been shown that matrices specific to certain protein groups (e.g. mitochondrial) or life domains (e.g. viruses) differ significantly from general average matrices, and thus perform better when applied to the data to which they are dedicated. This Web server implements the maximum-likelihood estimation procedure that was used to estimate LG, and provides a number of tools and facilities. Users upload a set of multiple protein alignments from their domain of interest and receive the resulting matrix by email, along with statistics and comparisons with other matrices. A non-parametric bootstrap is performed optionally to assess the variability of replacement rate estimates. Maximum-likelihood trees, inferred using the estimated rate matrix, are also computed optionally for each input alignment. Finely tuned procedures and up-to-date ML software (PhyML 3.0, XRATE) are combined to perform all these heavy calculations on our clusters. http://www.atgc-montpellier.fr/ReplacementMatrix/ olivier.gascuel@lirmm.fr Supplementary data are available at http://www.atgc-montpellier.fr/ReplacementMatrix/

Micro-syntheses for the use of carbon 13 or carbon 14. Micro-preparations of methyl alcohol, methyl iodide, and sodium acetate labeled in the methyl group; Microsyntheses pour l'emploi de carbone 13 ou de carbone 14. Micropreparations d'alcool methylique, d'iodure de methyle et d'acetate de sodium marque sur le groupement methyle

Energy Technology Data Exchange (ETDEWEB)

Baret, C; Pichat, L

1951-11-01

Apparatus and technique are described in detail for (1) reduction of CO{sub 2} to CH{sub 3}OH with LiAlH{sub 4}, (2) conversion of the methanol to CH{sub 3}I by HI, (3) formation of the Mg Grignard reagent, and (4) addition of inactive CO{sub 2} to form CH{sub 3}COOH. All these operations have been carried out on 0.005 moles. Methyl-labeled Na acetate has been prepared in 67% yield based on the Ba{sup 14}CO{sub 3} used as starting material. (author) [French] Description detaillee d'une technique deja connue pour la reduction du gaz carbonique en alcool methylique par LiAlH{sub 4}. Conversion du methanol en iodure de methyle. Ce dernier transforme en reactif de Grigard, et carbonate, fournit de l'acide acetique. Toutes ces operations on ete effectuees sur 5 x 10{sup -3} moles. La methode a ete appliquee a la synthese d'acetate de sodium marque par le groupement methyle par {sup 14}C avec un rendement global de 67% base sur le carbonate de baryum radioactif mis en oeuvre. (auteurs)

The MTHFR 677TT genotype and folate intake interact to lower global leukocyte DNA methylation in young Mexican American women.

OpenAIRE

Axume, Juan; Smith, Steven S; Pogribny, Igor P; Moriarty, David J.; Caudill., Marie A.

2007-01-01

DNA methylation is an epigenetic feature that is associated with X chromosome inactivation, genomic imprinting, transcriptional silencing of genes and genomic stability. Folate provides a labile source of methyl groups which may be used for cellular methylation reactions including DNA methylation. The methylenetetrahydrofolate reductase (MTHFR) 677C→T variant is an important determinant of folate nutriture and may influence DNA methylation. This study sought to assess the influence of the MTH...

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...

Myopodin methylation is a prognostic biomarker and predicts antiangiogenic response in advanced kidney cancer.

Science.gov (United States)

Pompas-Veganzones, N; Sandonis, V; Perez-Lanzac, Alberto; Beltran, M; Beardo, P; Juárez, A; Vazquez, F; Cozar, J M; Alvarez-Ossorio, J L; Sanchez-Carbayo, Marta

2016-10-01

Myopodin is a cytoskeleton protein that shuttles to the nucleus depending on the cellular differentiation and stress. It has shown tumor suppressor functions. Myopodin methylation status was useful for staging bladder and colon tumors and predicting clinical outcome. To our knowledge, myopodin has not been tested in kidney cancer to date. The purpose of this study was to evaluate whether myopodin methylation status could be clinically useful in renal cancer (1) as a prognostic biomarker and 2) as a predictive factor of response to antiangiogenic therapy in patients with metastatic disease. Methylation-specific polymerase chain reactions (MS-PCR) were used to evaluate myopodin methylation in 88 kidney tumors. These belonged to patients with localized disease and no evidence of disease during follow-up (n = 25) (group 1), and 63 patients under antiangiogenic therapy (sunitinib, sorafenib, pazopanib, and temsirolimus), from which group 2 had non-metastatic disease at diagnosis (n = 32), and group 3 showed metastatic disease at diagnosis (n = 31). Univariate and multivariate Cox analyses were utilized to assess outcome and response to antiangiogenic agents taking progression, disease-specific survival, and overall survival as clinical endpoints. Myopodin was methylated in 50 out of the 88 kidney tumors (56.8 %). Among the 88 cases analyzed, 10 of them recurred (11.4 %), 51 progressed (57.9 %), and 40 died of disease (45.4 %). Myopodin methylation status correlated to MSKCC Risk score (p = 0.050) and the presence of distant metastasis (p = 0.039). Taking all patients, an unmethylated myopodin identified patients with shorter progression-free survival, disease-specific survival, and overall survival. Using also in univariate and multivariate models, an unmethylated myopodin predicted response to antiangiogenic therapy (groups 2 and 3) using progression-free survival, disease-specific, and overall survival as clinical endpoints. Myopodin was revealed

Genetic diversity analysis of Jatropha curcas L. (Euphorbiaceae) based on methylation-sensitive amplification polymorphism.

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Kanchanaketu, T; Sangduen, N; Toojinda, T; Hongtrakul, V

2012-04-13

Genetic analysis of 56 samples of Jatropha curcas L. collected from Thailand and other countries was performed using the methylation-sensitive amplification polymorphism (MSAP) technique. Nine primer combinations were used to generate MSAP fingerprints. When the data were interpreted as amplified fragment length polymorphism (AFLP) markers, 471 markers were scored. All 56 samples were classified into three major groups: γ-irradiated, non-toxic and toxic accessions. Genetic similarity among the samples was extremely high, ranging from 0.95 to 1.00, which indicated very low genetic diversity in this species. The MSAP fingerprint was further analyzed for DNA methylation polymorphisms. The results revealed differences in the DNA methylation level among the samples. However, the samples collected from saline areas and some species hybrids showed specific DNA methylation patterns. AFLP data were used, together with methylation-sensitive AFLP (MS-AFLP) data, to construct a phylogenetic tree, resulting in higher efficiency to distinguish the samples. This combined analysis separated samples previously grouped in the AFLP analysis. This analysis also distinguished some hybrids. Principal component analysis was also performed; the results confirmed the separation in the phylogenetic tree. Some polymorphic bands, involving both nucleotide and DNA methylation polymorphism, that differed between toxic and non-toxic samples were identified, cloned and sequenced. BLAST analysis of these fragments revealed differences in DNA methylation in some known genes and nucleotide polymorphism in chloroplast DNA. We conclude that MSAP is a powerful technique for the study of genetic diversity for organisms that have a narrow genetic base.

Distinct DNA Methylation Profiles in Ovarian Tumors: Opportunities for Novel Biomarkers

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Lorena Losi

2018-05-01

Full Text Available Aberrant methylation of multiple promoter CpG islands could be related to the biology of ovarian tumors and its determination could help to improve treatment strategies. DNA methylation profiling was performed using the Methylation Ligation-dependent Macroarray (MLM, an array-based analysis. Promoter regions of 41 genes were analyzed in 102 ovarian tumors and 17 normal ovarian samples. An average of 29% of hypermethylated promoter genes was observed in normal ovarian tissues. This percentage increased slightly in serous, endometrioid, and mucinous carcinomas (32%, 34%, and 45%, respectively, but decreased in germ cell tumors (20%. Ovarian tumors had methylation profiles that were more heterogeneous than other epithelial cancers. Unsupervised hierarchical clustering identified four groups that are very close to the histological subtypes of ovarian tumors. Aberrant methylation of three genes (BRCA1, MGMT, and MLH1, playing important roles in the different DNA repair mechanisms, were dependent on the tumor subtype and represent powerful biomarkers for precision therapy. Furthermore, a promising relationship between hypermethylation of MGMT, OSMR, ESR1, and FOXL2 and overall survival was observed. Our study of DNA methylation profiling indicates that the different histotypes of ovarian cancer should be treated as separate diseases both clinically and in research for the development of targeted therapies.

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

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

1986-03-01

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

Synthesis of methyl-2 O-tolyl-3 quinazolone-4 {sup 14}C-2; Synthese de la methyl-2 O-tolyl-3 quinazolone-4 {sup 14}C-2

Energy Technology Data Exchange (ETDEWEB)

Herbert, M; Pichat, L [Commissariat a l' Energie Atomique, Saclay (France).Centre d' Etudes Nucleaires

1959-07-01

Description of the preparation of methyl-2 O-tolyl-3 quinazolone-4 {sup 14}C-2 (abbreviated to M.T.Q.), using N-acetyl {sup 14}C-1 anthranilic acid. The overall yield reaches 72 per cent with respect to acetyl chloride {sup 14}C-1. By applying the same method to acetyl chloride {sup 14}C-2, M.T.Q. labelled on the methyl group could be obtained. (author) [French] Description de la preparation de la methyl-2 O-tolyl-3 quinazolone-4 {sup 14}C-2 (abregee en M.T.Q.) par l'intermediaire de l'acide N-acetyl {sup 14}C-1 anthranilique. Le rendement global atteint 72 pour cent par rapport au chlorure d'acetyle {sup 14}C-1. La meme methode appliquee au chlorure d'acetyle {sup 14}C-2 permettrait d'obtenir la M.T.Q. marquee sur le groupement methyle. (auteur)

A genome-wide methylation study on obesity: differential variability and differential methylation.

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Xu, Xiaojing; Su, Shaoyong; Barnes, Vernon A; De Miguel, Carmen; Pollock, Jennifer; Ownby, Dennis; Shi, Hidong; Zhu, Haidong; Snieder, Harold; Wang, Xiaoling

2013-05-01

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 complex disease. We analyzed genome-wide methylation profiles of over 470,000 CpGs in peripheral blood samples from 48 obese and 48 lean African-American youth aged 14-20 y old. A substantial number of differentially variable CpG sites (DVCs), using statistics based on variances, as well as a substantial number of differentially methylated CpG sites (DMCs), using statistics based on means, were identified. Similar to the findings in cancers, DVCs generally exhibited an outlier structure and were more variable in cases than in controls. By randomly splitting the current sample into a discovery and validation set, we observed that both the DVCs and DMCs identified from the first set could independently predict obesity status in the second set. Furthermore, both the genes harboring DMCs and the genes harboring DVCs showed significant enrichment of genes identified by genome-wide association studies on obesity and related diseases, such as hypertension, dyslipidemia, type 2 diabetes and certain types of cancers, supporting their roles in the etiology and pathogenesis of obesity. We generalized the recent finding on methylation variability in cancer research to obesity and demonstrated that differential variability is also an important feature of obesity-related methylation changes. Future studies on the epigenetics of obesity will benefit from both statistics based on means and statistics based on variances.

Detection and discrimination of maintenance and de novo CpG methylation events using MethylBreak.

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Hsu, William; Mercado, Augustus T; Hsiao, George; Yeh, Jui-Ming; Chen, Chung-Yung

2017-05-15

Understanding the principles governing the establishment and maintenance activities of DNA methyltransferases (DNMTs) can help in the development of predictive biomarkers associated with genetic disorders and diseases. A detection system was developed that distinguishes and quantifies methylation events using methylation-sensitive endonucleases and molecular beacon technology. MethylBreak (MB) is a 22-mer oligonucleotide with one hemimethylated and two unmethylated CpG sites, which are also recognition sites for Sau96I and SacII, and is attached to a fluorophore and a quencher. Maintenance methylation was quantified by fluorescence emission due to the digestion of SacII when the hemimethylated CpG site is methylated, which inhibits Sau96I cleavage. The signal difference between SacII digestion of both MB substrate and maintenance methylated MB corresponds to de novo methylation event. Our technology successfully discriminated and measured both methylation activities at different concentrations of MB and achieved a high correlation coefficient of R 2 =0.997. Additionally, MB was effectively applied to normal and cancer cell lines and in the analysis of enzymatic kinetics and RNA inhibition of recombinant human DNMT1. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

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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

Single-tooth replacement: factors affecting different prosthetic treatment modalities

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Al-Quran Firas A

2011-12-01

Full Text Available Abstract Background The choice between several treatment options for replacing a single missing tooth is influenced by clinical, dentist- and patient-immanent factors. This study aimed to determine the patient factors that would affect the treatment decision to replace a single missing tooth and to assess the satisfaction with several options. Method 200 volunteers involved (121 females and 79 males divided into four groups, Group A: consisted of patients with conventional fixed partial dentures or patients with resin bonded fixed partial dentures. Group B: consisted of patients who received removable partial dentures while Group C: consisted of patients who received a single implant supported crown, and a control group D: consisted of patients who received no treatment. Data were collected using a questionnaire. Results The highest percentage of males within groups (58% was within the removable prostheses category. The majority of the subjects in the study reported that the main reason for replacing a missing tooth was for esthetic and function. Most important factor affecting the choice between treatment modalities was damaging the neighboring teeth. Pain, post operative sensitivity and dental phobia were important factors in choosing the prosthesis type and affected the control group patients not to have any treatment. The highest satisfaction percentage among groups studied was recorded for dental implants then FPD groups, while the least percentage were in both the control and RPD groups, for all aspects of function, esthetic and speech efficiency. Conclusions The final choice between FPD, RPD and implant depended on several factors which affected the decision making; among these is cost and patients' awareness of the different treatment options.

DNA methylation polymorphism in flue-cured tobacco and candidate markers for tobacco mosaic virus resistance*

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Zhao, Jie-hong; Zhang, Ji-shun; Wang, Yi; Wang, Ren-gang; Wu, Chun; Fan, Long-jiang; Ren, Xue-liang

2011-01-01

DNA methylation plays an important role in the epigenetic regulation of gene expression during plant growth, development, and polyploidization. However, there is still no distinct evidence in tobacco regarding the distribution of the methylation pattern and whether it contributes to qualitative characteristics. We studied the levels and patterns of methylation polymorphism at CCGG sites in 48 accessions of allotetraploid flue-cured tobacco, Nicotiana tabacum, using a methylation-sensitive amplified polymorphism (MSAP) technique. The results showed that methylation existed at a high level among tobacco accessions, among which 49.3% sites were methylated and 69.9% allelic sites were polymorphic. A cluster analysis revealed distinct patterns of geography-specific groups. In addition, three polymorphic sites significantly related to tobacco mosaic virus (TMV) resistance were explored. This suggests that tobacco breeders should pay more attention to epigenetic traits. PMID:22042659

DNA methylation polymorphism in flue-cured tobacco and candidate markers for tobacco mosaic virus resistance.

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Zhao, Jie-hong; Zhang, Ji-shun; Wang, Yi; Wang, Ren-gang; Wu, Chun; Fan, Long-jiang; Ren, Xue-liang

2011-11-01

DNA methylation plays an important role in the epigenetic regulation of gene expression during plant growth, development, and polyploidization. However, there is still no distinct evidence in tobacco regarding the distribution of the methylation pattern and whether it contributes to qualitative characteristics. We studied the levels and patterns of methylation polymorphism at CCGG sites in 48 accessions of allotetraploid flue-cured tobacco, Nicotiana tabacum, using a methylation-sensitive amplified polymorphism (MSAP) technique. The results showed that methylation existed at a high level among tobacco accessions, among which 49.3% sites were methylated and 69.9% allelic sites were polymorphic. A cluster analysis revealed distinct patterns of geography-specific groups. In addition, three polymorphic sites significantly related to tobacco mosaic virus (TMV) resistance were explored. This suggests that tobacco breeders should pay more attention to epigenetic traits.

Promoter DNA methylation pattern identifies prognostic subgroups in childhood T-cell acute lymphoblastic leukemia.

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Magnus Borssén

Full Text Available BACKGROUND: Treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL has improved, but there is a considerable fraction of patients experiencing a poor outcome. There is a need for better prognostic markers and aberrant DNA methylation is a candidate in other malignancies, but its potential prognostic significance in T-ALL is hitherto undecided. DESIGN AND METHODS: Genome wide promoter DNA methylation analysis was performed in pediatric T-ALL samples (n = 43 using arrays covering >27000 CpG sites. Clinical outcome was evaluated in relation to methylation status and compared with a contemporary T-ALL group not tested for methylation (n = 32. RESULTS: Based on CpG island methylator phenotype (CIMP, T-ALL samples were subgrouped as CIMP+ (high methylation and CIMP- (low methylation. CIMP- T-ALL patients had significantly worse overall and event free survival (p = 0.02 and p = 0.001, respectively compared to CIMP+ cases. CIMP status was an independent factor for survival in multivariate analysis including age, gender and white blood cell count. Analysis of differently methylated genes in the CIMP subgroups showed an overrepresentation of transcription factors, ligands and polycomb target genes. CONCLUSIONS: We identified global promoter methylation profiling as being of relevance for subgrouping and prognostication of pediatric T-ALL.

Mobility and molecular ions of dimethyl methyl phosphonate, methyl salicylate and acetone

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Nowak, D. M.

1983-06-01

The mobilities of positive and negative reactant ions are reported for (H2O)nH(+); (H2O)2O2 and (H2O)2CO3(-) ion clusters. The formation of positive DMMP monomer and dimer is reported, and equilbria molecular reactions are reported. Acetone is reported as forming a dimer at 81 ppb with a reduced mobility (K sub o) of 1.82, Methyl salicylate is shown to form a protonated and hydrated positive monomer. Mixtures of DMMP and methyl salicylate with acetone showed a substantial change in DMMP ion clustering and little or no change in the methyl salicylate mobility spectra. Negative ions were not observed for DMMP, methyl salicylate, acetone and the mixtures under the conditions reported.

The correlation between pulmonary fibrosis and methylation of peripheral Smad3 in cases of pigeon breeder's lung in a Chinese Uygur population.

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Wu, Chao; Ding, Wei; Li, Qifeng; Wang, Wenyi; Deng, Mingqin; Jin, Rong; Pang, Baosen; Yang, Xiaohong

2017-06-27

Smad3 is a key protein in the transforming growth factor-beta (TGF-β)/Smad signaling pathway, which is involved in fibrosis in many organs. We investigated the relationship between Smad3 gene methylation and pulmonary fibrosis in pigeon breeder's lung (PBL). Twenty Uygur PBL patients with pulmonary fibrosis in Kashi between October 2015 and March 2016 were enrolled. Twenty PBL-free pigeon breeders and 20 healthy non-pigeon breeders enrolled during the same period constituted the negative and normal control groups, respectively. Participants' data and peripheral blood samples were collected, and three Smad3 CpG loci were examined. Distributions of CpG_2 and CpG_4 methylation rates did not differ across groups, whereas distributions of CpG_3 methylation rates were significantly different among the three groups. The CpG_3 methylation rate was significantly lower in the patient group than in the negative control group. Smad3 mRNA expression was significantly higher in the patient group than in the negative control group but did not differ between the two control groups. TGF-βlevels were significantly higher in the patient group than in either control group (both Ppulmonary fibrosis in Uygur PBL patients via increased Smad3 mRNA expression. Smad3 methylation, Smad3 mRNA expression and TGF-β level were correlated with the number of pigeons bred by patients.

DNA methylation dynamics in the rat EGF gene promoter after partial hepatectomy

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Deming Li

2014-06-01

Full Text Available Epidermal growth factor (EGF, a multifunctional growth factor, is a regulator in a wide variety of physiological processes. EGF plays an important role in the regulation of liver regeneration. This study was aimed at investigating the methylation level of EGF gene throughout liver regeneration. DNA of liver tissue from control rats and partial hepatectomy (PH rats at 10 time points was extracted and a 354 bp fragment including 10 CpG sites from the transcription start was amplified after DNA was modified by sodium bisulfate. The result of sequencing suggested that methylation ratio of four CpG sites was found to be significantly changed when PH group was compared to control group, in particular two of them were extremely striking. mRNA expression of EGF was down-regulated in total during liver regeneration. We think that the rat EGF promoter region is regulated by variation in DNA methylation during liver regeneration.

Evolution of DNA Methylation across Insects.

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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.

DNA methylation in a Scottish family multiply affected by bipolar disorder and major depressive disorder.

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Walker, Rosie May; Christoforou, Andrea Nikie; McCartney, Daniel L; Morris, Stewart W; Kennedy, Nicholas A; Morten, Peter; Anderson, Susan Maguire; Torrance, Helen Scott; Macdonald, Alix; Sussmann, Jessika Elizabeth; Whalley, Heather Clare; Blackwood, Douglas H R; McIntosh, Andrew Mark; Porteous, David John; Evans, Kathryn Louise

2016-01-01

Bipolar disorder (BD) is a severe, familial psychiatric condition. Progress in understanding the aetiology of BD has been hampered by substantial phenotypic and genetic heterogeneity. We sought to mitigate these confounders by studying a multi-generational family multiply affected by BD and major depressive disorder (MDD), who carry an illness-linked haplotype on chromosome 4p. Within a family, aetiological heterogeneity is likely to be reduced, thus conferring greater power to detect illness-related changes. As accumulating evidence suggests that altered DNA methylation confers risk for BD and MDD, we compared genome-wide methylation between (i) affected carriers of the linked haplotype (ALH) and married-in controls (MIs), (ii) well unaffected haplotype carriers (ULH) and MI, (iii) ALH and ULH and (iv) all haplotype carriers (LH) and MI. Nominally significant differences in DNA methylation were observed in all comparisons, with differences withstanding correction for multiple testing when the ALH or LH group was compared to the MIs. In both comparisons, we observed increased methylation at a locus in FANCI, which was accompanied by increased FANCI expression in the ALH group. FANCI is part of the Fanconi anaemia complementation (FANC) gene family, which are mutated in Fanconi anaemia and participate in DNA repair. Interestingly, several FANC genes have been implicated in psychiatric disorders. Regional analyses of methylation differences identified loci implicated in psychiatric illness by genome-wide association studies, including CACNB2 and the major histocompatibility complex. Gene ontology analysis revealed enrichment for methylation differences in neurologically relevant genes. Our results highlight altered DNA methylation as a potential mechanism by which the linked haplotype might confer risk for mood disorders. Differences in the phenotypic outcome of haplotype carriers might, in part, arise from additional changes in DNA methylation that converge on

Replacing American Breakfast Foods with Ready-To-Eat (RTE) Cereals Increases Consumption of Key Food Groups and Nutrients among US Children and Adults: Results of an NHANES Modeling Study.

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Rehm, Colin D; Drewnowski, Adam

2017-09-13

Replacing the typical American breakfast with ready-to-eat cereals (RTECs) may improve diet quality. Our goal was to assess the impact of RTECs on diet quality measures for different age groups, using substitution modeling. Dietary intakes came from the 2007-2010 National Health and Examination Surveys (NHANES; n = 18,112). All breakfast foods, excluding beverages, were replaced on a per calorie basis, with frequency-weighted and age/race specific RTECs. Model 1 replaced foods with RTECs alone; Model 2 replaced foods with RTECs and milk. Diet quality measures were based on desirable food groups and nutrients, Healthy Eating Index (HEI)-2010 scores, and estimated diet costs. Model 1 diets were significantly higher in whole grains (+84.6%), fiber (+14.3%), vitamin D (+14.0%), iron (+54.5%) and folic acid (+104.6%), as compared to observed diets. Model 2 diets were additionally higher in dairy (+15.8%), calcium (+11.3%) and potassium (+3.95%). In Model 1, added sugar increased (+5.0%), but solid fats declined (-10.9%). Energy from solid fats and added sugars declined (-3.2%) in both models. Model 2 offered higher diet quality (57.1 vs. 54.6, p -value < 0.01) at a lower cost ($6.70 vs. $6.92; p < 0.01), compared to observed diets. Substitution modeling of NHANES data can assess the nutritional and economic impact of dietary guidance.

msap: a tool for the statistical analysis of methylation-sensitive amplified polymorphism data.

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Pérez-Figueroa, A

2013-05-01

In this study msap, an R package which analyses methylation-sensitive amplified polymorphism (MSAP or MS-AFLP) data is presented. The program provides a deep analysis of epigenetic variation starting from a binary data matrix indicating the banding pattern between the isoesquizomeric endonucleases HpaII and MspI, with differential sensitivity to cytosine methylation. After comparing the restriction fragments, the program determines if each fragment is susceptible to methylation (representative of epigenetic variation) or if there is no evidence of methylation (representative of genetic variation). The package provides, in a user-friendly command line interface, a pipeline of different analyses of the variation (genetic and epigenetic) among user-defined groups of samples, as well as the classification of the methylation occurrences in those groups. Statistical testing provides support to the analyses. A comprehensive report of the analyses and several useful plots could help researchers to assess the epigenetic and genetic variation in their MSAP experiments. msap is downloadable from CRAN (http://cran.r-project.org/) and its own webpage (http://msap.r-forge.R-project.org/). The package is intended to be easy to use even for those people unfamiliar with the R command line environment. Advanced users may take advantage of the available source code to adapt msap to more complex analyses. © 2013 Blackwell Publishing Ltd.

Correlation of SHOX2 Gene Amplification and DNA Methylation in Lung Cancer Tumors

International Nuclear Information System (INIS)

Schneider, Katja U; Liebenberg, Volker; Kneip, Christoph; Seegebarth, Anke; Erdogan, Fikret; Rappold, Gudrun; Schmidt, Bernd; Dietrich, Dimo; Fleischhacker, Michael; Leschber, Gunda; Merk, Johannes; Schäper, Frank; Stapert, Henk R; Vossenaar, Erik R; Weickmann, Sabine

2011-01-01

DNA methylation in the SHOX2 locus was previously used to reliably detect lung cancer in a group of critical controls, including 'cytologically negative' samples with no visible tumor cell content, at a high specificity based on the analysis of bronchial lavage samples. This study aimed to investigate, if the methylation correlates with SHOX2 gene expression and/or copy number alterations. An amplification of the SHOX2 gene locus together with the observed tumor-specific hypermethylation might explain the good performance of this marker in bronchial lavage samples. SHOX2 expression, gene copy number and DNA methylation were determined in lung tumor tissues and matched morphologically normal adjacent tissues (NAT) from 55 lung cancer patients. Quantitative HeavyMethyl (HM) real-time PCR was used to detect SHOX2 DNA methylation levels. SHOX2 expression was assayed with quantitative real-time PCR, and copy numbers alterations were measured with conventional real-time PCR and array CGH. A hypermethylation of the SHOX2 locus in tumor tissue as compared to the matched NAT from the same patient was detected in 96% of tumors from a group of 55 lung cancer patients. This correlated highly significantly with the frequent occurrence of copy number amplification (p < 0.0001), while the expression of the SHOX2 gene showed no difference. Frequent gene amplification correlated with hypermethylation of the SHOX2 gene locus. This concerted effect qualifies SHOX2 DNA methylation as a biomarker for lung cancer diagnosis, especially when sensitive detection is needed, i.e. in bronchial lavage or blood samples

Central alarm system replacement in NPP Krsko

International Nuclear Information System (INIS)

Cicvaric, D.; Susnic, M.; Djetelic, N.

2004-01-01

Current NPP Krsko central alarm system consists of three main segments. Main Control Board alarm system (BETA 1000), Ventilation Control Board alarm system (BETA 1000) and Electrical Control Board alarm system (BETA 1100). All sections are equipped with specific BetaTone audible alarms and silence, acknowledge as well as test push buttons. The main reason for central alarm system replacement is system obsolescence and problems with maintenance, due to lack of spare parts. Other issue is lack of system redundancy, which could lead to loss of several Alarm Light Boxes in the event of particular power supply failure. Current central alarm system does not provide means of alarm optimization, grouping or prioritization. There are three main options for central alarm system replacement: Conventional annunciator system, hybrid annunciator system and advanced alarm system. Advanced alarm system implementation requires Main Control Board upgrade, integration of process instrumentation and plant process computer as well as long time for replacement. NPP Krsko has decided to implement hybrid alarm system with patchwork approach. The new central alarm system will be stand alone, digital, with advanced filtering and alarm grouping options. Sequence of event recorder will be linked with plant process computer and time synchronized with redundant GPS signal. Advanced functions such as link to plant procedures will be implemented with plant process computer upgrade in outage 2006. Central alarm system replacement is due in outage 2004.(author)

Shoulder replacement - discharge

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Total shoulder arthroplasty - discharge; Endoprosthetic shoulder replacement - discharge; Partial shoulder replacement - discharge; Partial shoulder arthroplasty - discharge; Replacement - shoulder - discharge; Arthroplasty - shoulder - discharge

Replacing penalties

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Vitaly Stepashin

2017-01-01

Full Text Available УДК 343.24The subject. The article deals with the problem of the use of "substitute" penalties.The purpose of the article is to identify criminal and legal criteria for: selecting the replacement punishment; proportionality replacement leave punishment to others (the formalization of replacement; actually increasing the punishment (worsening of legal situation of the convicted.Methodology.The author uses the method of analysis and synthesis, formal legal method.Results. Replacing the punishment more severe as a result of malicious evasion from serving accused designated penalty requires the optimization of the following areas: 1 the selection of a substitute punishment; 2 replacement of proportionality is serving a sentence other (formalization of replacement; 3 ensuring the actual toughening penalties (deterioration of the legal status of the convict. It is important that the first two requirements pro-vide savings of repression in the implementation of the replacement of one form of punishment to others.Replacement of punishment on their own do not have any specifics. However, it is necessary to compare them with the contents of the punishment, which the convict from serving maliciously evaded. First, substitute the punishment should assume a more significant range of restrictions and deprivation of certain rights of the convict. Second, the perfor-mance characteristics of order substitute the punishment should assume guarantee imple-mentation of the new measures.With regard to replacing all forms of punishment are set significant limitations in the application that, in some cases, eliminates the possibility of replacement of the sentence, from serving where there has been willful evasion, a stricter measure of state coercion. It is important in the context of the topic and the possibility of a sentence of imprisonment as a substitute punishment in cases where the original purpose of the strict measures excluded. It is noteworthy that the

Complex formation of technetium with the methyl esters of MAG2 and MAG1

International Nuclear Information System (INIS)

Noll, B.; Noll, S.; Grosse, B.; Johannsen, B.; Spies, H.

1993-01-01

Mercaptoacetylglycine methyl ester (MAG 2 ester) and mercaptoacetyldiglycine methyl ester (MAG 1 ester) were included to investigate complex formation of SH/amide ligands with technetium. The studies are aimed at finding out how blocking the carboxylic groups influences the complexation reaction, with a view to finding an approach to new lipophilic species. (orig./BBR)

Outcome of double vs. single valve replacement for rheumatic heart disease

International Nuclear Information System (INIS)

Akhtar, R.P.; Abid, A.R.

2010-01-01

To compare the follow-up results of double valve replacement (DVR) i.e. mitral valve replacement (MVR) and aortic valve replacement (AVR) vs. isolated MVR or AVR for rheumatic heart disease. Study Design: An interventional qausi-experimental study. Prospective follow-up of 493 patients with mechanical heart valves was carried out using clinical assessment, international normalized ratio and echocardiography. Patients were divided into three groups: group I having MVR, group II having AVR and group III having DVR. Survival, time and causes of mortality, and frequency of valve thrombosis, haemorrhage and cerebrovascular haemorrhage was noted in the three groups and described as proportions. Actuarial survival was analyzed by Kaplan-Meier method. There were 493 with 287 (58.3%) in group I, 87 (17.6%) in group II and 119 (24.1%) in group III. Total follow-up was 2429.2 patient (pt)-years. Of 77 (15.6%) deaths, 19 (3.8%) were in-hospital and 58 (11.8%) were late. In-hospital mortality was highest 4 (4.6%) in group II followed by 5 (4.2%) group III and 10 (3.5%) group I. Late deaths were 39 (13.4%) in group I, 9 (10.2%) in group II and 10 (8.3%) in group III. The total actuarial survival was 84.4% with survival of 83%, 85.1%, 87.4% in groups I, II and III respectively. On follow-up valve thrombosis occurred in 12 (0.49%/pt-years) patients; 9 (0.67%/pt-years) group I, 1 (0.22%/pt-years) in group II and 2 (0.31%/pt-years) in group III. Severe haemorrhage occurred in 19 (0.78%/pt-years); 14 in (1.04%/pt-years) in group I, 3 (0.66%/pt-years) group II and 2 (0.31%/pt-years) in group III. Cerebrovascular accidents occurred in 34 (1.3%/pt-years); 26 (1.95%/pt-years) in group I and 4 in groups II (0.89%/pt-years) and III (0.62%/pt-years) each. In patients with rheumatic heart disease having combined mitral and aortic valve disease DVR should be performed whenever indicated as it has similar in-hospital mortality and better late survival as compared to isolated aortic or mitral

Methylation screening of the TGFBI promoter in human lung and prostate cancer by methylation-specific PCR

International Nuclear Information System (INIS)

Shah, Jinesh N; Shao, Genze; Hei, Tom K; Zhao, Yongliang

2008-01-01

Hypermethylation of the TGFBI promoter has been shown to correlate with decreased expression of this gene in human tumor cell lines. In this study, we optimized a methylation-specific polymerase chain reaction (MSP) method and investigated the methylation status of the TGFBI promoter in human lung and prostate cancer specimens. Methylation-specific primers were designed based on the methylation profiles of the TGFBI promoter in human tumor cell lines, and MSP conditions were optimized for accurate and efficient amplification. Genomic DNA was isolated from lung tumors and prostatectomy tissues of prostate cancer patients, bisulfite-converted, and analyzed by MSP. Among 50 lung cancer samples, 44.0% (22/50) harbored methylated CpG sites in the TGFBI promoter. An analysis correlating gene methylation status with clinicopathological cancer features revealed that dense methylation of the TGFBI promoter was associated with a metastatic phenotype, with 42.9% (6/14) of metastatic lung cancer samples demonstrating dense methylation vs. only 5.6% (2/36) of primary lung cancer samples (p < 0.05). Similar to these lung cancer results, 82.0% (41/50) of prostate cancer samples harbored methylated CpG sites in the TGFBI promoter, and dense methylation of the promoter was present in 38.9% (7/18) of prostate cancer samples with the feature of locoregional invasiveness vs. only 19.4% (6/31) of prostate cancer samples without locoregional invasiveness (p < 0.05). Furthermore, promoter hypermethylation correlated with highly reduced expression of the TGFBI gene in human lung and prostate tumor cell lines. We successfully optimized a MSP method for the precise and efficient screening of TGFBI promoter methylation status. Dense methylation of the TGFBI promoter correlated with the extent of TGFBI gene silencing in tumor cell lines and was related to invasiveness of prostate tumors and metastatic status of lung cancer tumors. Thus, TGFBI promoter methylation can be used as a potential

Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA.

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Guang Liu

2010-12-01

Full Text Available Many taxonomically diverse prokaryotes enzymatically modify their DNA by replacing a non-bridging oxygen with a sulfur atom at specific sequences. The biological implications of this DNA S-modification (phosphorothioation were unknown. We observed that simultaneous expression of the dndA-E gene cluster from Streptomyces lividans 66, which is responsible for the DNA S-modification, and the putative Streptomyces coelicolor A(32 Type IV methyl-dependent restriction endonuclease ScoA3McrA (Sco4631 leads to cell death in the same host. A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites. Double-strand cleavage occurred 16-28 nucleotides away from the phosphorothioate links. DNase I footprinting demonstrated binding of ScoA3McrA to the Dcm methylation site, but no clear binding could be detected at the S-modified site under cleavage conditions. This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA.

Clinical Significance of Retinoic Acid Receptor Beta Promoter Methylation in Prostate Cancer: A Meta-Analysis.

Science.gov (United States)

Dou, MengMeng; Zhou, XueLiang; Fan, ZhiRui; Ding, XianFei; Li, LiFeng; Wang, ShuLing; Xue, Wenhua; Wang, Hui; Suo, Zhenhe; Deng, XiaoMing

2018-01-01

Retinoic acid receptor beta (RAR beta) is a retinoic acid receptor gene that has been shown to play key roles during multiple cancer processes, including cell proliferation, apoptosis, migration and invasion. Numerous studies have found that methylation of the RAR beta promoter contributed to the occurrence and development of malignant tumors. However, the connection between RAR beta promoter methylation and prostate cancer (PCa) remains unknown. This meta-analysis evaluated the clinical significance of RAR beta promoter methylation in PCa. We searched all published records relevant to RAR beta and PCa in a series of databases, including PubMed, Embase, Cochrane Library, ISI Web of Science and CNKI. The rates of RAR beta promoter methylation in the PCa and control groups (including benign prostatic hyperplasia and normal prostate tissues) were summarized. In addition, we evaluated the source region of available samples and the methods used to detect methylation. To compare the incidence and variation in RAR beta promoter methylation in PCa and non-PCa tissues, the odds ratio (OR) and 95% confidence interval (CI) were calculated accordingly. All the data were analyzed with the statistical software STATA 12.0. Based on the inclusion and exclusion criteria, 15 articles assessing 1,339 samples were further analyzed. These data showed that the RAR beta promoter methylation rates in PCa tissues were significantly higher than the rates in the non-PCa group (OR=21.65, 95% CI: 9.27-50.57). Subgroup analysis according to the source region of samples showed that heterogeneity in Asia was small (I2=0.0%, P=0.430). Additional subgroup analysis based on the method used to detect RAR beta promoter methylation showed that the heterogeneity detected by MSP (methylation-specific PCR) was relatively small (I2=11.3%, P=0.343). Although studies reported different rates for RAR beta promoter methylation in PCa tissues, the total analysis demonstrated that RAR beta promoter methylation

Clinical Significance of Retinoic Acid Receptor Beta Promoter Methylation in Prostate Cancer: A Meta-Analysis

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MengMeng Dou

2018-03-01

Full Text Available Background/Aims: Retinoic acid receptor beta (RAR beta is a retinoic acid receptor gene that has been shown to play key roles during multiple cancer processes, including cell proliferation, apoptosis, migration and invasion. Numerous studies have found that methylation of the RAR beta promoter contributed to the occurrence and development of malignant tumors. However, the connection between RAR beta promoter methylation and prostate cancer (PCa remains unknown. This meta-analysis evaluated the clinical significance of RAR beta promoter methylation in PCa. Materials and Methods: We searched all published records relevant to RAR beta and PCa in a series of databases, including PubMed, Embase, Cochrane Library, ISI Web of Science and CNKI. The rates of RAR beta promoter methylation in the PCa and control groups (including benign prostatic hyperplasia and normal prostate tissues were summarized. In addition, we evaluated the source region of available samples and the methods used to detect methylation. To compare the incidence and variation in RAR beta promoter methylation in PCa and non-PCa tissues, the odds ratio (OR and 95% confidence interval (CI were calculated accordingly. All the data were analyzed with the statistical software STATA 12.0. Results: Based on the inclusion and exclusion criteria, 15 articles assessing 1,339 samples were further analyzed. These data showed that the RAR beta promoter methylation rates in PCa tissues were significantly higher than the rates in the non-PCa group (OR=21.65, 95% CI: 9.27-50.57. Subgroup analysis according to the source region of samples showed that heterogeneity in Asia was small (I2=0.0%, P=0.430. Additional subgroup analysis based on the method used to detect RAR beta promoter methylation showed that the heterogeneity detected by MSP (methylation-specific PCR was relatively small (I2=11.3%, P=0.343. Conclusion: Although studies reported different rates for RAR beta promoter methylation in PCa

DNA methylation and memory formation.

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Day, Jeremy J; Sweatt, J David

2010-11-01

Memory formation and storage require long-lasting changes in memory-related neuronal circuits. Recent evidence indicates that DNA methylation may serve as a contributing mechanism in memory formation and storage. These emerging findings suggest a role for an epigenetic mechanism in learning and long-term memory maintenance and raise apparent conundrums and questions. For example, it is unclear how DNA methylation might be reversed during the formation of a memory, how changes in DNA methylation alter neuronal function to promote memory formation, and how DNA methylation patterns differ between neuronal structures to enable both consolidation and storage of memories. Here we evaluate the existing evidence supporting a role for DNA methylation in memory, discuss how DNA methylation may affect genetic and neuronal function to contribute to behavior, propose several future directions for the emerging subfield of neuroepigenetics, and begin to address some of the broader implications of this work.

Enzyme replacement therapy for infantile-onset Pompe disease.

Science.gov (United States)

Chen, Min; Zhang, Lingli; Quan, Shuyan

2017-11-20

Infantile-onset Pompe disease is a rare and progressive autosomal-recessive disorder caused by a deficiency of the lysosomal enzyme acid alpha-glucosidase (GAA). Current treatment involves enzyme replacement therapy (with recombinant human alglucosidase alfa) and symptomatic therapies (e.g. to control secretions). Children who are cross-reactive immunological material (CRIM)-negative require immunomodulation prior to commencing enzyme replacement therapy.Enzyme replacement therapy was developed as the most promising therapeutic approach for Pompe disease; however, the evidence is lacking, especially regarding the optimal dose and dose frequency. To assess the effectiveness, safety and appropriate dose regimen of enzyme replacement therapy for treating infantile-onset Pompe disease. We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group's Inborn Errors of Metabolism Trials Register, which is compiled from electronic database searches and handsearching of journals and conference abstract books. We also searched the Cochrane Central Register of Controlled Trials (CENTRAL), Embase (Ovid), PubMed and LILACS, and CBM, CNKI, VIP, and WANFANG for literature published in Chinese. In addition, we searched three online registers: WHO International Clinical Trials Registry Platform ClinicalTrials.gov, and www.genzymeclinicalresearch.com. We also searched the reference lists of relevant articles and reviews.Date of last search of the Group's Inborn Errors of Metabolism Trials Register: 24 November 2016. Randomized and quasi-randomized controlled trials of enzyme replacement therapy in children with infantile-onset Pompe disease. Two authors independently selected relevant trials, assessed the risk of bias and extracted data. We contacted investigators to obtain important missing information. We found no trials comparing the effectiveness and safety of enzyme replacement therapy to another intervention, no intervention or placebo.We found one trial (18 participants

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....

Histone Lysine Methylation and Neurodevelopmental Disorders

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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.

Avocado and olive oil methyl esters

International Nuclear Information System (INIS)

Knothe, Gerhard

2013-01-01

Biodiesel, the mono-alkyl esters of vegetable oils, animal fats or other triacylglycerol-containing materials and an alternative to conventional petroleum-based diesel fuel, has been derived from a variety of feedstocks. Numerous feedstocks have been investigated as potential biodiesel sources, including commodity oils, however, the methyl esters of avocado and olive oil would likely be suitable as biodiesel fuel. In order to expand the database and comprehensive evaluation of the properties of vegetable oil esters, in this work the fuel-related properties of avocado and olive oil methyl esters, which exhibit similar fatty acid profiles including high oleic acid content, are determined. The cetane numbers of avocado oil methyl esters and olive oil methyl esters are relatively high, determined as 59.2 and 62.5, respectively, due to their elevated content of methyl oleate. Other properties are well within the ranges specified in biodiesel standards. The cloud points of both esters are slightly above 0 °C due to their content of saturated esters, especially methyl palmitate. Overall, avocado and olive oil yield methyl esters with fuel properties comparable to methyl esters from other commodity vegetable oils. The 1 H and 13 C NMR spectra of avocado and olive oil methyl esters are reported. -- Highlights: • Methyl esters of avocado and olive oil meet biodiesel fuel standards. • Provides comparison for methyl esters of other vegetable oils with high oleic content. • Discusses and compares present results with prior literature

Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

Science.gov (United States)

Pritišanac, Iva; Degiacomi, Matteo T; Alderson, T Reid; Carneiro, Marta G; Ab, Eiso; Siegal, Gregg; Baldwin, Andrew J

2017-07-19

Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.

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.

Short communication: Absorption of protein and immunoglobulin g in calves fed a colostrum replacer.

Science.gov (United States)

Smith, G W; Foster, D M

2007-06-01

A well-managed colostrum program on farms is the most important step in reducing disease in neonatal calves. In the last few years, colostrum replacers have increased in popularity and are designed to be an alternative to colostrum on farms that have poor colostrum quality, limited colostrum reserves, or to break the cycle of transmission for certain infectious diseases. However, it is important to make sure these products are effective and are capable of providing adequate serum immunoglobulin concentrations. The objective of this study was to evaluate the efficacy of a commercially available colostrum replacer product in dairy calves. Holstein calves from a single dairy were randomly assigned to 1 of 3 groups at birth. Group 1 (n = 21) calves were given 4 quarts of colostrum via esophageal feeder within 3 h of birth and served as the control group for this study. Group 2 (n = 21) received 2 packages of a colostrum replacer product, and group 3 (n = 21) received 3 packages of the colostrum replacer product within 3 h of birth. Blood samples from all calves were collected 24 h after colostrum administration and analyzed for serum total protein and IgG concentrations. Calves fed fresh colostrum had significantly higher serum total protein levels and IgG concentrations compared with calves fed the colostrum replacer product. Calves fed the colostrum replacer also had a significantly higher percentage of calves with failure of passive transfer (serum IgG <1,000 mg/dL). The colostrum replacer product evaluated in this study failed to routinely provide adequate IgG concentrations when fed according to label directions.

Access to and coverage of renal replacement therapy in minorities and ethnic groups in Venezuela.

Science.gov (United States)

Bellorin-Font, Ezequiel; Pernalete, Nidia; Meza, Josefina; Milanes, Carmen Luisa; Carlini, Raul G

2005-08-01

Access to and coverage of renal replacement therapy in minorities and ethnic groups in Venezuela. Numerous studies have documented the presence of racial and minority disparities regarding the impact of renal disease and access to renal replacement therapy (RRT). This problem is less well documented in Latin America. Venezuela, like most countries in the region, is subject to severe constraints in the allocation of resources for high-cost chronic diseases, which limits the access of patients with chronic kidney disease to RRT. Although access to health care is universal, there is both a deficit in coverage and disparity in the access to RRT, largely as a result of socioeconomic limitations and budget constrains. With current rising trends of the incidence of end-stage renal disease (ESRD) and costs of medical technology, the long-term goal of complete RRT coverage will become increasingly out of reach. Current evidence suggests that prevention of progression of renal disease is possible at relatively low cost and broad coverage. Based on this evidence, the Ministry of Health has redesigned its policy with respect to renal disease based on 4 elements: 1. Prevention by means of early detection and referral to multidisciplinary health teams, as well as promotion of health habits in the community. 2. Prevention of progression of renal disease by pharmacologic and nonpharmacologic means. 3. An increase in the rate of coverage and reduction of disparities in the access to dialysis. 4. An increase in the rates of renal transplantation through better organ procurement programs and reinforcement of transplant centers. However, the projected increase in the number of patients with ESKD receiving RRT will represent a serious burden to the health care system. Therefore, implementation of these policies will require the involvement of international agencies as well as an adequate partnership between nephrologists and health care planners, so that meeting the increasing demands

Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis

Science.gov (United States)

Sorokin, Dimitry Y.; Makarova, Kira S.; Abbas, Ben; Ferrer, Manuel; Golyshin, Peter N.; Galinski, Erwin A.; Ciordia, Sergio; Mena, María Carmen; Merkel, Alexander Y.; Wolf, Yuri I.; van Loosdrecht, Mark C.M.; Koonin, Eugene V.

2017-01-01

Methanogenic archaea are major players in the global carbon cycle and in the biotechnology of anaerobic digestion. The phylum Euryarchaeota includes diverse groups of methanogens that are interspersed with non-methanogenic lineages. So far methanogens inhabiting hypersaline environments have been identified only within the order Methanosarcinales. We report the discovery of a deep phylogenetic lineage of extremophilic methanogens in hypersaline lakes, and present analysis of two nearly complete genomes from this group. Within the phylum Euryarchaeota, these isolates form a separate, class-level lineage “Methanonatronarchaeia” that is most closely related to the class Halobacteria. Similar to the Halobacteria, “Methanonatronarchaeia” are extremely halophilic and do not accumulate organic osmoprotectants. The high intracellular concentration of potassium implies that “Methanonatronarchaeia” employ the “salt-in” osmoprotection strategy. These methanogens are heterotrophic methyl-reducers that utilize C1-methylated compounds as electron acceptors and formate or hydrogen as electron donors. The genomes contain an incomplete and apparently inactivated set of genes encoding the upper branch of methyl group oxidation to CO2 as well as membrane-bound heterosulfide reductase and cytochromes. These features differentiates “Methanonatronarchaeia” from all known methyl-reducing methanogens. The discovery of extremely halophilic, methyl-reducing methanogens related to haloarchaea provides insights into the origin of methanogenesis and shows that the strategies employed by methanogens to thrive in salt-saturating conditions are not limited to the classical methylotrophic pathway. PMID:28555626

[Study of relationship between arsenic methylation and skin lesion in a population with long-term high arsenic exposure].

Science.gov (United States)

Su, Liqin; Cheng, Yibin; Lin, Shaobin; Wu, Chuanye

2007-05-01

To investigate the difference of arsenic metabolism in populations with long-term high arsenic exposure and explore the relationship between arsenic metabolism diversity and skin lesion. 327 residents in an arsenic polluted village were voluntarily enrolled in this study. Questionnaire survey and medical examination were carried out to learn basic information and detect skin lesions. Urinary inorganic and methylated arsenic were speciated by high performance liquid chromatography combined with hydride-generation atomic fluorescence spectrometry. Total arsenic concentration in hair was determined with DDC-Ag method. Hair arsenic content of studied polutions was generally high, but no significant difference were found among the studied four groups. MMA and DMA concentration in urine increased with studied polution age, and were positively related with skin lesion grade. The relative proportion of MMA in serious skin lesion group was significantly higher than in other 3 groups, while DMA/MMA ratio was significantly lower than control and mild group. The relative proportion of MMA was positively related with skin lesion grade, DMA/ MMA ratio was negatively related with skin lesion grade. Males could have higher arsenic cumulation and lower methylation capacity than those of females. The population of above 40 years old may have higher methylation capacity than those of adults below 40yeas old. Smokers and drinkers seemed lower methylation capacity than those of non-smokers and non-drinkers respectively. The methylation of arsenic could affect by several factors, including age gender, smoking and drinking. Arsenic methylation copacity mey be associated with skin lesion induced by arsenic exposure.

Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles.

Science.gov (United States)

Aiba, Toshiki; Saito, Toshiyuki; Hayashi, Akiko; Sato, Shinji; Yunokawa, Harunobu; Maruyama, Toru; Fujibuchi, Wataru; Kurita, Hisaka; Tohyama, Chiharu; Ohsako, Seiichiroh

2017-03-09

It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. By combining it with amplified fragment length polymorphism (AFLP) analysis, we developed a new method, MSD-AFLP. Methylated site display libraries consist of only DNAs derived from DNA fragments that are CpG methylated at the 5' end in the original genomic DNA sample. To test the effectiveness of this method, CpG methylation levels in liver, kidney, and hippocampal tissues of mice were compared to examine if MSD-AFLP can detect subtle differences in the levels of tissue-specific differentially methylated CpGs. As a result, many CpG sites suspected to be tissue-specific differentially methylated were detected. Nucleotide sequences adjacent to these methyl-CpG sites were identified and we determined the methylation level by methylation-sensitive restriction endonuclease (MSRE)-PCR analysis to confirm the accuracy of AFLP analysis. The differences of the methylation level among tissues were almost identical among these methods. By MSD-AFLP analysis, we detected many CpGs showing less than 5% statistically significant tissue-specific difference and less than 10% degree of variability. Additionally, MSD-AFLP analysis could be used to identify CpG methylation sites in other organisms including humans. MSD-AFLP analysis can potentially be used to measure slight changes in CpG methylation level. Regarding the remarkable precision, sensitivity, and throughput of MSD-AFLP analysis studies, this method will be advantageous in a variety of epigenetics-based research.

Genome-wide DNA methylation analysis of pseudohypoparathyroidism patients with GNAS imprinting defects.

Science.gov (United States)

Rochtus, Anne; Martin-Trujillo, Alejandro; Izzi, Benedetta; Elli, Francesca; Garin, Intza; Linglart, Agnes; Mantovani, Giovanna; Perez de Nanclares, Guiomar; Thiele, Suzanne; Decallonne, Brigitte; Van Geet, Chris; Monk, David; Freson, Kathleen

2016-01-01

Pseudohypoparathyroidism (PHP) is caused by (epi)genetic defects in the imprinted GNAS cluster. Current classification of PHP patients is hampered by clinical and molecular diagnostic overlaps. The European Consortium for the study of PHP designed a genome-wide methylation study to improve molecular diagnosis. The HumanMethylation 450K BeadChip was used to analyze genome-wide methylation in 24 PHP patients with parathyroid hormone resistance and 20 age- and gender-matched controls. Patients were previously diagnosed with GNAS-specific differentially methylated regions (DMRs) and include 6 patients with known STX16 deletion (PHP(Δstx16)) and 18 without deletion (PHP(neg)). The array demonstrated that PHP patients do not show DNA methylation differences at the whole-genome level. Unsupervised clustering of GNAS-specific DMRs divides PHP(Δstx16) versus PHP(neg) patients. Interestingly, in contrast to the notion that all PHP patients share methylation defects in the A/B DMR while only PHP(Δstx16) patients have normal NESP, GNAS-AS1 and XL methylation, we found a novel DMR (named GNAS-AS2) in the GNAS-AS1 region that is significantly different in both PHP(Δstx16) and PHP(neg), as validated by Sequenom EpiTYPER in a larger PHP cohort. The analysis of 58 DMRs revealed that 8/18 PHP(neg) and 1/6 PHP(Δstx16) patients have multi-locus methylation defects. Validation was performed for FANCC and SVOPL DMRs. This is the first genome-wide methylation study for PHP patients that confirmed that GNAS is the most significant DMR, and the presence of STX16 deletion divides PHP patients in two groups. Moreover, a novel GNAS-AS2 DMR affects all PHP patients, and PHP patients seem sensitive to multi-locus methylation defects.

DNA methylation in sugarcane somaclonal variants assessed through methylation-sensitive amplified polymorphism.

Science.gov (United States)

Francischini, J H M B; Kemper, E L; Costa, J B; Manechini, J R V; Pinto, L R

2017-05-04

Micropropagation is an important tool for large-scale multiplication of plant superior genotypes. However, somaclonal variation is one of the drawbacks of this process. Changes in DNA methylation have been widely reported as one of the main causes of somaclonal variations in plants. In order to investigate the occurrence of changes in the methylation pattern of sugarcane somaclonal variants, the MSAP (methylation-sensitive amplified polymorphism) technique was applied to micro-propagated plantlets sampled at the third subculture phase. The mother plant, in vitro normal plantlets, and in vitro abnormal plantlets (somaclonal variants) of four sugarcane clones were screened against 16 MSAP selective primers for EcoRI/MspI and EcoRI/HpaII restriction enzymes. A total of 1005 and 1200 MSAP-derived markers with polymorphism percentages of 28.36 and 40.67 were obtained for EcoRI/HpaII and EcoRI/MspI restriction enzyme combinations, respectively. The genetic similarity between the mother plant and the somaclonal variants ranged from 0.877 to 0.911 (EcoRI/MspI) and from 0.928 to 0.955 (EcoRI/HpaII). Most of the MASPs among mother plant and micro-propagated plantlets were derived from EcoRI/MspI restriction enzymes suggesting alteration due to gain or loss of internal cytosine methylation. A higher rate of loss of methylation (hypomethylation) than gain of methylation (hypermethylation) was observed in the abnormal in vitro sugarcane plantlets. Although changes in the methylation pattern were also observed in the in vitro normal plantlets, they were lower than those observed for the in vitro abnormal plantlets. The MASP technique proved to be a promising tool to early assessment of genetic fidelity of micro-propagated sugarcane plants.

Matched cohort study of topical tranexamic acid in cementless primary total hip replacement.

Science.gov (United States)

Sanz-Reig, Javier; Mas Martinez, Jesus; Verdu Román, Carmen; Morales Santias, Manuel; Martínez Gimenez, Enrique; Bustamante Suarez de Puga, David

2018-03-29

Tranexamic acid has been shown to be effective in reducing blood loss after total hip replacement. The purpose of this study was to prospectively assess the effectiveness of topical TXA use to reduce blood loss after primary total hip replacement and to compare these outcomes with those of a matched control group from a similar cohort that did not have received tranexamic acid. This is a prospective matched control study to assess the effect of a 2 g topical tranexamic acid in 50 mL physiological saline solution in total hip replacement. Primary outcomes were hemoglobin and hematocrit drop, and total blood loss. Secondary outcomes were transfusion rates, length of hospital stay, deep vein thrombosis, and pulmonary embolism events. We could match 100 patients to a control group. There were no statistical significantly differences between the two groups. The hemoglobin and hematocrit postoperative values were significantly higher in topical tranexamic acid group than in control group (P tranexamic acid group and 1163 in control group with significant differences (P = 0.001), which meant 34% reduction in total blood loss. Length of stay was lower in topical tranexamic acid group. The risk of deep vein thrombosis and pulmonary events did not increase. A single dose of 2 g tranexamic acid in 50 mL physiological saline solution topical administration was effective and safe in reducing bleeding in patients undergoing unilateral primary non-cemented total hip replacement compared to a matched control group.

Malfunctioning and infected tunneled infusion catheters: over-the-wire catheter exchange versus catheter removal and replacement.

Science.gov (United States)

Guttmann, David M; Trerotola, Scott O; Clark, Timothy W; Dagli, Mandeep; Shlansky-Goldberg, Richard D; Itkin, Maxim; Soulen, Michael C; Mondschein, Jeffrey I; Stavropoulos, S William

2011-05-01

To compare the safety and effectiveness of over-the-wire catheter exchange (catheter-exchange) with catheter removal and replacement (removal-replacement) at a new site for infected or malfunctioning tunneled infusion catheters. Using a quality assurance database, 61 patients with tunneled infusion catheters placed during the period July 2001 to June 2009 were included in this study. Patients receiving hemodialysis catheters were excluded. Catheter-exchange was performed in 25 patients, and same-day removal-replacement was performed in 36 patients. Data collected included demographic information, indication for initial catheter placement and replacement, dwell time for the new catheter, and ultimate fate of the new device. Statistical comparisons between the two cohorts were analyzed using the Kaplan-Meier technique and Fisher exact test. Catheters exchanged over the wire remained functional without infection for a median of 102 days (range, 2-570 days), whereas catheters removed and replaced were functional for a median 238 days (range, 1-292 days, P = .12). After catheter replacement, there were 11 instances of subsequent infection in the catheter-exchange group and 7 instances in the removal-replacement cohort, accounting for infection rates of 4.4 and 2.3 per 1,000 catheter days (P = .049). Patients in the catheter-exchange group had 3.2 greater odds of infection compared with patients in the removal-replacement group. Five malfunction events occurred in each group, accounting for 2.0 and 1.7 malfunctions per 1,000 catheter days in the catheter-exchange and removal-replacement groups (P = .73). Catheter-exchange of tunneled infusion catheters results in a higher infection rate compared with removal-replacement at a new site. The rate of catheter malfunction is not significantly different between the two groups. Catheter-exchange is an alternative for patients with tunneled infusion catheters who have limited venous access, but this technique should not be

Low Barrier Methyl Rotation in 3-PENTYN-1-OL as Observed by Microwave Spectroscopy

Science.gov (United States)

Eibl, Konrad; Kannengießer, Raphaela; Stahl, Wolfgang; Nguyen, Ha Vinh Lam; Kleiner, Isabelle

2016-06-01

It is known that the barrier to internal rotation of the methyl groups in ethane (1) is about 1000 wn. If a C-C-triple bond is inserted between the methyl groups as a spacer (2), the torsional barrier is assumed to be dramatically lower, which is a common feature of ethinyl groups in general. To study this effect of almost free internal rotation, we measured the rotational spectrum of 3-pentyn-1-ol (3) by pulsed jet Fourier transform microwave spectroscopy in the frequency range from 2 to 26.5 GHz. Quantum chemical calculations at the MP2/6-311++G(d,p) level of theory yielded five stable conformers on the potential energy surface. The most stable conformer, which possesses C1 symmetry, was assigned and fitted using two theoretical approaches treating internal rotations, the rho axis method (BELGI-C1) and the combined axis method (XIAM). The molecular parameters as well as the internal rotation parameters were determined. A very low barrier to internal rotation of the methyl group of only 9.4545(95) wn was observed. R. M. Pitzer, Acc. Chem. Res., 1983, 16, 207-210

Functional characterization of O-methyltransferases used to catalyse site-specific methylation in the post-tailoring steps of pradimicin biosynthesis.

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Han, J W; Ng, B G; Sohng, J K; Yoon, Y J; Choi, G J; Kim, B S

2018-01-01

To identify the roles of the two O-methyltransferase homologous genes pdmF and pdmT in the pradimicin biosynthetic gene cluster of Actinomadura hibisca P157-2. Pradimicins are pentangular polyphenol antibiotics synthesized by bacterial type II polyketide synthases (PKSs) and tailoring enzymes. Pradimicins are naturally derivatized by combinatorial O-methylation at two positions (i.e., 7-OH and 11-OH) of the benzo[α]naphthacenequinone structure. PdmF and PdmT null mutants (PFKO and PTKO) were generated. PFKO produced the 11-O-demethyl shunt metabolites 11-O-demethylpradimicinone II (1), 11-O-demethyl-7-methoxypradimicinone II (2), 11-O-demethylpradimicinone I (3) and 11-O-demethylpradimicin A (4), while PTKO generated the 7-O-demethyl derivatives pradimicinone II (5) and 7-hydroxypradimicin A (6). Pradimicinones 1, 2, 3, and 5 were fed to a heterologous host Escherichia coli harbouring expression plasmid pET-22b::pdmF or pET-28a::pdmT. PdmF catalysed 11-O-methylation of pradimicinones 1, 2, and 3 regardless of O-methylation at the C-7 position, while PdmT was unable to catalyse 7-O-methylation when the C-11 hydroxyl group was methylated (5). PdmF and PdmT were involved in 11-O- and 7-O-methylations of the benzo[α]naphthacenequinone moiety of pradimicin, respectively. Methylation of the C-7 hydroxyl group precedes methylation of the C-11 hydroxyl group in pradimicin biosynthesis. This is the first reported demonstration of the functions of PdmF and PdmT for regiospecific O-methylation, which contributes to better understanding of the post-PKS modifications in pradimicin biosynthesis as well as to rational engineering of the pradimicin biosynthetic machinery. © 2017 The Society for Applied Microbiology.

Ankle replacement

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Ankle arthroplasty - total; Total ankle arthroplasty; Endoprosthetic ankle replacement; Ankle surgery ... Ankle replacement surgery is most often done while you are under general anesthesia. This means you will ...

A novel method for identification and quantification of consistently differentially methylated regions.

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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.

Methylation associated transcriptional repression of ELOVL5 in novel colorectal cancer cell lines.

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Arnoud Boot

Full Text Available Genetic and epigenetic alterations mark colorectal cancer (CRC. Global hypomethylation is observed in nearly all CRC, but a distinct subset of CRC show the CpG Island Methylator Phenotype (CIMP. These tumors show DNA hypermethylation of a specific subset of CpG islands, resulting in transcriptional downregulation of nearby genes. Recently we reported the establishment of novel CRC cell lines derived from primary and metastatic CRC tissues. In this study we describe the DNA methylation profiling of these low passage CRC cell lines. We generated global DNA methylation profiles with Infinium HumanMethylation450 BeadChips and analysed them in conjunction with matching gene expression profiles. Multidimensional scaling of the DNA methylation and gene expression datasets showed that BRAF mutated cell lines form a distinct group. In this group we investigated the 706 loci which we have previously identified to be hypermethylated in BRAF mutant CRC. We validated the significant findings in the The Cancer Genome Atlas colon adenocarcinoma dataset. Our analysis identified ELOVL5, FAM127B, MTERF1, ZNF606 to be subject to transcriptional downregulation through DNA hypermethylation in CRC. We further investigated ELOVL5 with qPCR and immunohistochemical staining, validating our results, but did not find a clear relation between ELOVL5 expression and tumor stage or relapse free survival. ELOVL5, FAM127B, MTERF1, ZNF606 are involved in important cellular processes such as apoptosis, lipogenesis and the downstream transcriptional effect of the MAPK-pathway. We have identified a DNA methylation profile regulating key cellular processes in CRC, resulting in a growth advantage to the tumor cells.

Accessing ns-μs side chain dynamics in ubiquitin with methyl RDCs

International Nuclear Information System (INIS)

Fares, Christophe; Lakomek, Nils-Alexander; Walter, Korvin F. A.; Frank, Benedikt T. C.; Meiler, Jens; Becker, Stefan; Griesinger, Christian

2009-01-01

This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098-6107, 2001; Lakomek in J Biomol NMR 34:101-115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-τ c dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time τ c . In fact, the average amplitude of motion expressed in terms of order parameters S 2 associated with the supra-τ c window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959-8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471-1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains

Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep

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Yang Cao

2017-11-01

Full Text Available Objective The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. Methods Six samples (three in each group were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs between the two groups. Results 23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions. Compared with Small Tailed Han sheep, we observed a tendency toward a global loss of DNA methylation in these DMRs in the crossbred group. Gene ontology enrichment analysis found several gene sets which were hypo-methylated in gene-body region, including nucleoside binding, motor activity, phospholipid binding and cell junction. Numerous genes were found to be differentially methylated between the two groups with several genes significantly differentially methylated, including transforming growth factor beta 3 (TGFB3, acyl-CoA synthetase long chain family member 1 (ACSL1, ryanodine receptor 1 (RYR1, acyl-CoA oxidase 2 (ACOX2, peroxisome proliferator activated receptor-gamma2 (PPARG2, netrin 1 (NTN1, ras and rab interactor 2 (RIN2, microtubule associated protein RP/EB family member 1 (MAPRE1, ADAM metallopeptidase with thrombospondin type 1 motif 2 (ADAMTS2, myomesin 1 (MYOM1, zinc finger, DHHC type containing 13 (ZDHHC13, and SH3 and PX domains 2B (SH3PXD2B. The real-time quantitative polymerase chain reaction validation showed that the 12 genes are differentially expressed between the two groups. Conclusion In the current study, a tendency to a global loss of DNA methylation in these DMRs in the crossbred group was found. Twelve genes, TGFB3, ACSL1, RYR1, ACOX2, PPARG2, NTN1, RIN2, MAPRE1, ADAMTS2, MYOM1, ZDHHC13, and SH3

Analysis of RET promoter CpG island methylation using methylation-specific PCR (MSP), pyrosequencing, and methylation-sensitive high-resolution melting (MS-HRM): impact on stage II colon cancer patient outcome.

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Draht, Muriel X G; Smits, Kim M; Jooste, Valérie; Tournier, Benjamin; Vervoort, Martijn; Ramaekers, Chantal; Chapusot, Caroline; Weijenberg, Matty P; van Engeland, Manon; Melotte, Veerle

2016-01-01

Already since the 1990s, promoter CpG island methylation markers have been considered promising diagnostic, prognostic, and predictive cancer biomarkers. However, so far, only a limited number of DNA methylation markers have been introduced into clinical practice. One reason why the vast majority of methylation markers do not translate into clinical applications is lack of independent validation of methylation markers, often caused by differences in methylation analysis techniques. We recently described RET promoter CpG island methylation as a potential prognostic marker in stage II colorectal cancer (CRC) patients of two independent series. In the current study, we analyzed the RET promoter CpG island methylation of 241 stage II colon cancer patients by direct methylation-specific PCR (MSP), nested-MSP, pyrosequencing, and methylation-sensitive high-resolution melting (MS-HRM). All primers were designed as close as possible to the same genomic region. In order to investigate the effect of different DNA methylation assays on patient outcome, we assessed the clinical sensitivity and specificity as well as the association of RET methylation with overall survival for three and five years of follow-up. Using direct-MSP and nested-MSP, 12.0 % (25/209) and 29.6 % (71/240) of the patients showed RET promoter CpG island methylation. Methylation frequencies detected by pyrosequencing were related to the threshold for positivity that defined RET methylation. Methylation frequencies obtained by pyrosequencing (threshold for positivity at 20 %) and MS-HRM were 13.3 % (32/240) and 13.8 % (33/239), respectively. The pyrosequencing threshold for positivity of 20 % showed the best correlation with MS-HRM and direct-MSP results. Nested-MSP detected RET promoter CpG island methylation in deceased patients with a higher sensitivity (33.1 %) compared to direct-MSP (10.7 %), pyrosequencing (14.4 %), and MS-HRM (15.4 %). While RET methylation frequencies detected by nested

Replacing American Breakfast Foods with Ready-To-Eat (RTE) Cereals Increases Consumption of Key Food Groups and Nutrients among US Children and Adults: Results of an NHANES Modeling Study

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Rehm, Colin D.; Drewnowski, Adam

2017-01-01

Replacing the typical American breakfast with ready-to-eat cereals (RTECs) may improve diet quality. Our goal was to assess the impact of RTECs on diet quality measures for different age groups, using substitution modeling. Dietary intakes came from the 2007–2010 National Health and Examination Surveys (NHANES; n = 18,112). All breakfast foods, excluding beverages, were replaced on a per calorie basis, with frequency-weighted and age/race specific RTECs. Model 1 replaced foods with RTECs alone; Model 2 replaced foods with RTECs and milk. Diet quality measures were based on desirable food groups and nutrients, Healthy Eating Index (HEI)-2010 scores, and estimated diet costs. Model 1 diets were significantly higher in whole grains (+84.6%), fiber (+14.3%), vitamin D (+14.0%), iron (+54.5%) and folic acid (+104.6%), as compared to observed diets. Model 2 diets were additionally higher in dairy (+15.8%), calcium (+11.3%) and potassium (+3.95%). In Model 1, added sugar increased (+5.0%), but solid fats declined (−10.9%). Energy from solid fats and added sugars declined (−3.2%) in both models. Model 2 offered higher diet quality (57.1 vs. 54.6, p-value < 0.01) at a lower cost ($6.70 vs. $6.92; p < 0.01), compared to observed diets. Substitution modeling of NHANES data can assess the nutritional and economic impact of dietary guidance. PMID:28902145

Nicotine replacement therapy

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Smoking cessation - nicotine replacement; Tobacco - nicotine replacement therapy ... Before you start using a nicotine replacement product, here are some things to know: The more cigarettes you smoke, the higher the dose you may need to ...

of surfactant replacement therapy at Johannesburg Hospital ...

African Journals Online (AJOL)

To assess the impact of surfactant replacement therapy (SRl) on the outcome of ... oxygen requirements) was compared with that of a historical control group of ... The use of SRT added to the total cost of treating a patient ventilated for HMD.

Heart valve replacement with the Sorin tilting-disc prosthesis. A 10-year experience.

Science.gov (United States)

Milano, A; Bortolotti, U; Mazzucco, A; Mossuto, E; Testolin, L; Thiene, G; Gallucci, V

1992-02-01

From 1978 to 1988, 697 patients with a mean age of 48 +/- 11 years (range 5 to 75 years) received a Sorin tilting-disc prosthesis; 358 had had aortic valve replacement, 247 mitral valve replacement, and 92 mitral and aortic valve replacement. Operative mortality rates were 7.8%, 11.3%, and 10.8%, respectively, in the three groups. Cumulative duration of follow-up is 1650 patient-years for aortic valve replacement (maximum follow-up 11.4 years), 963 patient-years for mitral valve replacement (maximum follow-up 9.9 years) and 328 patient-years for mitral and aortic valve replacement (maximum follow-up 9.4 years). Actuarial survival at 9 years is 72% +/- 4% after mitral valve replacement, 70% +/- 3% after aortic valve replacement, and 50% +/- 12% after mitral and aortic valve replacement, and actuarial freedom from valve-related deaths is 97% +/- 2% after mitral valve replacement, 92% +/- 2% after aortic valve replacement, and 62% +/- 15% after mitral and aortic valve replacement. Thromboembolic events occurred in 21 patients with aortic valve replacement (1.3% +/- 0.2%/pt-yr), in 12 with mitral valve replacement (1.2% +/- 0.3% pt-yr), and in seven with mitral and aortic valve replacement (2.1% +/- 0.8%), with one case of prosthetic thrombosis in each group; actuarial freedom from thromboembolism at 9 years is 92% +/- 3% after mitral valve replacement, 91% +/- 3% after aortic valve replacement, and 74% +/- 16% after mitral and aortic valve replacement. Anticoagulant-related hemorrhage was observed in 15 patients after aortic valve replacement (0.9% +/- 0.2%/pt-yr), in 9 after mitral valve replacement (0.9% +/- 0.3%/pt-yr), and in 6 with mitral and aortic valve replacement (0.9% +/- 0.5%/pt-yr); actuarial freedom from this complication at 9 years is 94% +/- 2% after aortic valve replacement, 91% +/- 4% after mitral valve replacement, and 68% +/- 16% after mitral and aortic valve replacement. Actuarial freedom from reoperation at 9 years is 97% +/- 2% after mitral and

Hip Replacement Surgery

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... Outreach Initiative Breadcrumb Home Health Topics English Español Hip Replacement Surgery Basics In-Depth Download Download EPUB ... PDF What is it? Points To Remember About Hip Replacement Surgery Hip replacement surgery removes damaged or ...

Protection against de novo methylation is instrumental in maintaining parent-of-origin methylation inherited from the gametes.

Science.gov (United States)

Proudhon, Charlotte; Duffié, Rachel; Ajjan, Sophie; Cowley, Michael; Iranzo, Julian; Carbajosa, Guillermo; Saadeh, Heba; Holland, Michelle L; Oakey, Rebecca J; Rakyan, Vardhman K; Schulz, Reiner; Bourc'his, Déborah

2012-09-28

Identifying loci with parental differences in DNA methylation is key to unraveling parent-of-origin phenotypes. By conducting a MeDIP-Seq screen in maternal-methylation free postimplantation mouse embryos (Dnmt3L-/+), we demonstrate that maternal-specific methylation exists very scarcely at midgestation. We reveal two forms of oocyte-specific methylation inheritance: limited to preimplantation, or with longer duration, i.e. maternally imprinted loci. Transient and imprinted maternal germline DMRs (gDMRs) are indistinguishable in gametes and preimplantation embryos, however, de novo methylation of paternal alleles at implantation delineates their fates and acts as a major leveling factor of parent-inherited differences. We characterize two new imprinted gDMRs, at the Cdh15 and AK008011 loci, with tissue-specific imprinting loss, again by paternal methylation gain. Protection against demethylation after fertilization has been emphasized as instrumental in maintaining parent-of-origin methylation inherited from the gametes. Here we provide evidence that protection against de novo methylation acts as an equal major pivot, at implantation and throughout life. Copyright © 2012 Elsevier Inc. All rights reserved.

Differential DNA methylation patterns define status epilepticus and epileptic tolerance.

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Miller-Delaney, Suzanne F C; Das, Sudipto; Sano, Takanori; Jimenez-Mateos, Eva M; Bryan, Kenneth; Buckley, Patrick G; Stallings, Raymond L; Henshall, David C

2012-02-01

Prolonged seizures (status epilepticus) produce pathophysiological changes in the hippocampus that are associated with large-scale, wide-ranging changes in gene expression. Epileptic tolerance is an endogenous program of cell protection that can be activated in the brain by previous exposure to a non-harmful seizure episode before status epilepticus. A major transcriptional feature of tolerance is gene downregulation. Here, through methylation analysis of 34,143 discrete loci representing all annotated CpG islands and promoter regions in the mouse genome, we report the genome-wide DNA methylation changes in the hippocampus after status epilepticus and epileptic tolerance in adult mice. A total of 321 genes showed altered DNA methylation after status epilepticus alone or status epilepticus that followed seizure preconditioning, with >90% of the promoters of these genes undergoing hypomethylation. These profiles included genes not previously associated with epilepsy, such as the polycomb gene Phc2. Differential methylation events generally occurred throughout the genome without bias for a particular chromosomal region, with the exception of a small region of chromosome 4, which was significantly overrepresented with genes hypomethylated after status epilepticus. Surprisingly, only few genes displayed differential hypermethylation in epileptic tolerance. Nevertheless, gene ontology analysis emphasized the majority of differential methylation events between the groups occurred in genes associated with nuclear functions, such as DNA binding and transcriptional regulation. The present study reports select, genome-wide DNA methylation changes after status epilepticus and in epileptic tolerance, which may contribute to regulating the gene expression environment of the seizure-damaged hippocampus.

UV action spectroscopy of protonated PAH derivatives. Methyl substituted quinolines

DEFF Research Database (Denmark)

Klærke, Benedikte; Holm, Anne; Andersen, Lars Henrik

2011-01-01

using the electrostatic storage ring ELISA, an electrospray ion source and 3 ns UV laser pulses. Results. It is shown that the absorption profile is both redshifted and broadened when moving the methyl group from the heterocycle containing nitrogen to the homoatomic ring. The absorption profiles......Aims. We investigate the production of molecular photofragments upon UV excitation of PAH derivatives, relevant for the interstellar medium. Methods. The action absorption spectra of protonated gas-phase methyl-substituted quinolines (CH3−C9H7NH+) have been recorded in the 215–338 nm spectral range...

Prospective study of ascending venogram following total hip replacement or total knee replacement

Energy Technology Data Exchange (ETDEWEB)

Youm, Chang Seon; Suh, Jin Seok; Lee, Jong Doo; Park, Chang Yun; Kim, Young Hoo [College of Medicine, Yonsei University, Seoul (Korea, Republic of)

1987-04-15

The ascending leg venogram was performed in one hundred forty six lower extremities on the 7th day following total hip replacement (THR) or total knee replacement (TKR). The results were as follows; 1.Overall incidence of deep vein thrombosis (DVT) in 146 limbs who underwent THR or TKR was 10%: DVT was detected in 8 limbs among 110 limbs following THR (7%) and 6 limbs among 36 limbs following TKR (17%). 2.The anatomic distribution of DVT was as follows: In THR, 12.5% in FV, 25% in FV and PV, 25% in FV and PV and CV, 12.5% in FV and CV, and 25% in CV. In TKR, 100% in CV. 3.There were many anatomic variations in deep veins of lower extremities: Accessory SFV (41 limbs), double PV(24), accessory SFV and double PV(7), duplication of SFV and PV(3), accessory SFV and multiple PV(2), and accessory SFV and double PV(1). 4.There were multiple SFV in 37%, and 19% of these limbs had DVT. It represented statistically higher than 4% in limbs with a single SFV (P-value < 0.05). 5.The incidence of DVT was 8% in cases of multiple PV, and there was no statistically significant difference between these groups and single PV groups. 6.We could assess number of values from popliteal vein to common femoral vein in 72 limbs. Mean number of value was 5.45 and there was no statistically significant difference between groups having valve over 5 and under 5.

Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl-Cytosine

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Mahdi Bagherpoor Helabad

2014-07-01

Full Text Available Distortions in the DNA sequence, such as damage or mispairs, are specifically recognized and processed by DNA repair enzymes. Many repair proteins and, in particular, glycosylases flip the target base out of the DNA helix into the enzyme’s active site. Our molecular dynamics simulations of DNA with intact and damaged (oxidized methyl-cytosine show that the probability of being flipped is similar for damaged and intact methyl-cytosine. However, the accessibility of the different 5-methyl groups allows direct discrimination of the oxidized forms. Hydrogen-bonded patterns that vary between methyl-cytosine forms carrying a carbonyl oxygen atom are likely to be detected by the repair enzymes and may thus help target site recognition.

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

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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.

Epigenetic mechanism of maternal post-traumatic stress disorder in delayed rat offspring development: dysregulation of methylation and gene expression.

Science.gov (United States)

Zhang, X G; Zhang, H; Liang, X L; Liu, Q; Wang, H Y; Cao, B; Cao, J; Liu, S; Long, Y J; Xie, W Y; Peng, D Z

2016-08-19

Maternal post-traumatic stress disorder (PTSD) increases the risk of adverse neurodevelopmental outcomes in the child. Epigenetic alternations may play an essential role in the negative effects of PTSD. This study was aimed to investigate the possible epigenetic alterations of maternal PTSD, which underpins the developmental and behavioral impact. 24 pregnant Sprague-Dawley (SD) rats were randomly grouped into PTSD and control groups. Open-field tests (OFTs), elevated pull maze (EPM) assays, gene expression profile chip tests, and methylated DNA immunoprecipitation sequencing (MeDIP-Seq) were performed on the offsprings 30 days after birth. The results showed that PTSD offsprings had lower body weights and OFT scores than control offsprings. Enzyme-linked immunosorbent assays showed that serotonin receptor (5-HT) and dopamine levels were significantly lower in PTSD offsprings than in control offsprings. In contrast, corticosterone levels were higher in the PTSD group than in the control group. In a comparison of the PTSD group versus the control group, 4,160 significantly differentially methylated loci containing 30,657 CpGs were identified; 2,487 genes, including 13 dysmethylated genes, were validated by gene expression profiling, showing a negative correlation between methylation and gene expression (R = -0.617, P = 0.043). In conclusion, maternal PTSD could delay the physical and behavioral development of offsprings, and the underlying mechanism could contribute to changes in neurotransmitters and gene expression, owing to dysregulation of whole-genome methylation. These findings could support further clinical research on appropriate interventions for maternal PTSD to prevent methylation dysregulation and developmental retardation.

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.

Are clinicopathological features of colorectal cancers with methylation in half of CpG island methylator phenotype panel markers different from those of CpG island methylator phenotype-high colorectal cancers?

Science.gov (United States)

Bae, Jeong Mo; Rhee, Ye-Young; Kim, Kyung Ju; Wen, Xianyu; Song, Young Seok; Cho, Nam-Yun; Kim, Jung Ho; Kang, Gyeong Hoon

2016-01-01

CpG island methylator phenotype (CIMP)-high (CIMP-H) colorectal cancer (CRC) is defined when a tumor shows methylation at greater than or equal to 60% of CIMP panel markers. Although CRCs with methylation at 50% of panel markers are classified as CIMP-low/CIMP-0 tumors, little is known regarding the clinicopathological and molecular features of CRCs with methylation at 4/8 panel markers (4/8 methylated markers) and whether they are akin to CIMP-H or CIMP-low/CIMP-0 CRCs in terms of their clinicopathological or molecular features. A total of 1164 cases of surgically resected CRC were analyzed for their methylation status in 8 CIMP panel markers, and the frequencies of various clinicopathological and molecular features were compared between CRCs with 0/8, 1/8 to 3/8, 4/8, and 5/8 to 8/8 methylated markers. CRCs with 4/8 methylated markers were closer to CRCs with 5/8 to 8/8 methylated markers in terms of sex distribution, mucin production, serration, nodal metastasis, CK7 expression, CK20 loss, and CDX2 loss frequencies and overall survival rate. CRCs with methylation at 4/8 markers were closer to CRCs with 1/8 to 3/8 methylated markers in terms of less frequent right colon location and poor differentiation. CRCs with 4/8 methylated markers showed the shortest overall survival time compared with CRCs with 0/8, 1/8 to 3/8, 4/8, or 5/8 to 8/8 methylated markers. In terms of clinicopathological and molecular features, CRCs with 4/8 methylated markers appeared to be closer to CIMP-H than to CIMP-low/CIMP-0 and would thus be better classified as CIMP-H if the CRCs require classification into either CIMP-H or CIMP-low/CIMP-0. Copyright © 2015 Elsevier Inc. All rights reserved.

DNA methylation of IGF2DMR and H19 is associated with fetal and infant growth: the generation R study.

Directory of Open Access Journals (Sweden)

Marieke I Bouwland-Both

Full Text Available Changes in epigenetic programming of embryonic growth genes during pregnancy seem to affect fetal growth. Therefore, in a population-based prospective birth cohort in the Netherlands, we examined associations between fetal and infant growth and DNA methylation of IGF2DMR, H19 and MTHFR. For this study, we selected 69 case children born small-for-gestational age (SGA, birth weight <-2SDS and 471 control children. Fetal growth was assessed with serial ultrasound measurements. Information on birth outcomes was retrieved from medical records. Infant weight was assessed at three and six months. Methylation was assessed in DNA extracted from umbilical cord white blood cells. Analyses were performed using linear mixed models with DNA methylation as dependent variable. The DNA methylation levels of IGF2DMR and H19 in the control group were, median (90% range, 53.6% (44.5-61.6 and 30.0% (25.6-34.2 and in the SGA group 52.0% (43.9-60.9 and 30.5% (23.9-32.9, respectively. The MTHFR region was found to be hypomethylated with limited variability in the control and SGA group, 2.5% (1.4-4.0 and 2.4% (1.5-3.8, respectively. SGA was associated with lower IGF2DMR DNA methylation (β = -1.07, 95% CI -1.93; -0.21, P-value = 0.015, but not with H19 methylation. A weight gain in the first three months after birth was associated with lower IGF2DMR DNA methylation (β = -0.53, 95% CI -0.91; -0.16, P-value = 0.005. Genetic variants in the IGF2/H19 locus were associated with IGF2DMR DNA methylation (P-value<0.05, but not with H19 methylation. Furthermore, our results suggest a possibility of mediation of DNA methylation in the association between the genetic variants and SGA. To conclude, IGF2DMR and H19 DNA methylation is associated with fetal and infant growth.

Methylation of BDNF in women with bulimic eating syndromes: associations with childhood abuse and borderline personality disorder.

Science.gov (United States)

Thaler, Lea; Gauvin, Lise; Joober, Ridha; Groleau, Patricia; de Guzman, Rosherrie; Ambalavanan, Amirthagowri; Israel, Mimi; Wilson, Samantha; Steiger, Howard

2014-10-03

DNA methylation allows for the environmental regulation of gene expression and is believed to link environmental stressors to such mental-illness phenotypes as eating disorders. Numerous studies have shown an association between bulimia nervosa (BN) and variations in brain-derived neurotrophic factor (BDNF). BDNF has also been linked to borderline personality disorder (BPD) and to such traits as reward dependence. We examined the extent to which BDNF methylation corresponded to bulimic or normal-eater status, and also to the presence of comorbid borderline personality disorder (BPD) and childhood abuse. Our sample consisted of 64 women with BN and 32 normal-eater (NE) control women. Participants were assessed for eating-disorder symptoms, comorbid psychopathology, and childhood trauma, and then they were required to provide blood samples for methylation analyses. We observed a significant site×group (BN vs. NE) interaction indicating that women with BN showed increases in methylation at specific regions of the BDNF promoter. Furthermore, examining effects of childhood abuse and BPD, we observed significant site×group interactions such that groups composed of individuals with childhood abuse or BPD had particularly high levels of methylation at selected CpG sites. Our findings suggest that BN, especially when co-occurring with childhood abuse or BPD, is associated with a propensity towards elevated methylation at specific BDNF promoter region sites. These findings imply that hypermethylation of the BDNF gene may be related to eating disorder status, developmental stress exposure, and comorbid psychopathology. Copyright © 2014 Elsevier Inc. All rights reserved.

DNA methylation patterns of genes related to immune response in the different clinical forms of oral lichen planus.

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Cruz, Aline Fernanda; de Resende, Renata Gonçalves; de Lacerda, Júlio César Tanos; Pereira, Núbia Braga; Melo, Leonardo Augusto; Diniz, Marina Gonçalves; Gomes, Carolina Cavalieri; Gomez, Ricardo Santiago

2018-01-01

The oral lichen planus is a chronic inflammatory disease. Although its aetiology is not well understood, the role of T lymphocytes in its inflammatory events is recognised. Identifying the epigenetic mechanisms involved in the pathogenesis of this immune-mediated condition is fundamental for understanding the inflammatory reaction that occurs in the disease. The purpose of this work was to evaluate the methylation pattern of 21 immune response-related genes in the different clinical forms of oral lichen planus. A cross-sectional study was performed to analyse the DNA methylation patterns in three distinct groups of oral lichen planus: (i) reticular/plaque lesions; (ii) erosive lesions; (iii) normal oral mucosa (control group). After DNA extraction from biopsies, the samples were submitted to digestions by methylation-sensitive and methylation-dependent enzymes and double digestion. The relative percentage of methylated DNA for each gene was provided using real-time polymerase chain reaction arrays. Hypermethylation of the STAT5A gene was observed only in the control group (59.0%). A higher hypermethylation of the ELANE gene was found in reticular/plaque lesions (72.1%) compared to the erosive lesions (50.0%). Our results show variations in the methylation profile of immune response-related genes, according to the clinical type of oral lichen planus after comparing with the normal oral mucosa. Further studies are necessary to validate these findings using gene expression analysis. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The interplay between transient a-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts

DEFF Research Database (Denmark)

Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M

2011-01-01

and retinoid receptors (ACTR). We find that small differences in the methyl carbon chemical shifts due to the ¿-gauche effect may provide information about the side chain rotamer distributions. However, the effects of neighboring residues on the methyl group chemical shifts obscure the direct observation...... of ¿-gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The (13)C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow...

How does methylation suppress the electron-induced decomposition of 1-methyl-nitroimidazoles?

Science.gov (United States)

Kossoski, F.; Varella, M. T. do N.

2017-10-01

The efficient decomposition of nitroimidazoles (NIs) by low energy electrons is believed to underlie their radiosensitizing properties. Recent dissociative electron attachment (DEA) measurements showed that methylation at the N1 site unexpectedly suppresses the electron-induced reactions in 4(5)-NI. We report theoretical results that provide a clear interpretation of that astounding finding. Around 1.5 eV, DEA reactions into several fragments are initiated by a π* resonance, not considered in previous studies. The autoionization lifetime of this anion state, which limits the predissociation dynamics, is considerably shorter in the methylated species, thereby suppressing the DEA signals. On the other hand, the lifetime of the π* resonance located around 3 eV is less affected by methylation, which explains why DEA is still observed at these energies. Our results demonstrate how even a simple methylation can significantly modify the probabilities for DEA reactions, which may be significant for NI-based cancer therapy.

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.

2-Acetyl­amino-1,3,4,6-tetra-O-(tri­methyl­silyl)-2-de­oxy-α-d-gluco­pyran­ose

Science.gov (United States)

Cheng, Zhao-Dong; Cui, Yan-Li; Mao, Jian-Wei

2013-01-01

The title compound, C20H47NO6Si4, was synthesized by per-O-tri­methyl­silylation of N-acetyl-d-glucosa­mine using chloro­tri­methyl­silane in the presence of hexa­methyl­disiloxane. The tri­methyl­silyl group and acetamido group are located on the same side of the pyran ring, showing an α-configuration glycoside. One of the tri­methyl­silyl groups is disordered over two orientations, with site-occupancy factors of 0.625 (9) and 0.375 (9). In the crystal, N—H⋯O hydrogen bonds link the mol­ecules into supra­molecular chains along the a-axis direction. PMID:23795087

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.

DNA methylation changes detected by methylation-sensitive amplified polymorphism in two contrasting rice genotypes under salt stress.

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Wang, Wensheng; Zhao, Xiuqin; Pan, Yajiao; Zhu, Linghua; Fu, Binying; Li, Zhikang

2011-09-20

DNA methylation, one of the most important epigenetic phenomena, plays a vital role in tuning gene expression during plant development as well as in response to environmental stimuli. In the present study, a methylation-sensitive amplified polymorphism (MSAP) analysis was performed to profile DNA methylation changes in two contrasting rice genotypes under salt stress. Consistent with visibly different phenotypes in response to salt stress, epigenetic markers classified as stable inter-cultivar DNA methylation differences were determined between salt-tolerant FL478 and salt-sensitive IR29. In addition, most tissue-specific DNA methylation loci were conserved, while many of the growth stage-dependent DNA methylation loci were dynamic between the two genotypes. Strikingly, salt stress induced a decrease in DNA methylation specifically in roots at the seedling stage that was more profound in IR29 than in the FL478. This result may indicate that demethylation of genes is an active epigenetic response to salt stress in roots at the seedling stage, and helps to further elucidate the implications of DNA methylation in crop growth and development. Copyright © 2011. Published by Elsevier Ltd.

Knee Replacement

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Knee replacement is surgery for people with severe knee damage. Knee replacement can relieve pain and allow you to ... Your doctor may recommend it if you have knee pain and medicine and other treatments are not ...

Choline and methionine differentially alter methyl carbon metabolism in bovine neonatal hepatocytes.

Science.gov (United States)

Chandler, Tawny L; White, Heather M

2017-01-01

Intersections in hepatic methyl group metabolism pathways highlights potential competition or compensation of methyl donors. The objective of this experiment was to examine the expression of genes related to methyl group transfer and lipid metabolism in response to increasing concentrations of choline chloride (CC) and DL-methionine (DLM) in primary neonatal hepatocytes that were or were not exposed to fatty acids (FA). Primary hepatocytes isolated from 4 neonatal Holstein calves were maintained as monolayer cultures for 24 h before treatment with CC (61, 128, 2028, and 4528 μmol/L) and DLM (16, 30, 100, 300 μmol/L), with or without a 1 mmol/L FA cocktail in a factorial arrangement. After 24 h of treatment, media was collected for quantification of reactive oxygen species (ROS) and very low-density lipoprotein (VLDL), and cell lysates were collected for quantification of gene expression. No interactions were detected between CC, DLM, or FA. Both CC and DLM decreased the expression of methionine adenosyltransferase 1A (MAT1A). Increasing CC did not alter betaine-homocysteine S-methyltranferase (BHMT) but did increase 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR) and methylenetetrahydrofolate reductase (MTHFR) expression. Increasing DLM decreased expression of BHMT and MTR, but did not affect MTHFR. Expression of both phosphatidylethanolamine N-methyltransferase (PEMT) and microsomal triglyceride transfer protein (MTTP) were decreased by increasing CC and DLM, while carnitine palmitoyltransferase 1A (CPT1A) was unaffected by either. Treatment with FA decreased the expression of MAT1A, MTR, MTHFR and tended to decrease PEMT but did not affect BHMT and MTTP. Treatment with FA increased CPT1A expression. Increasing CC increased secretion of VLDL and decreased the accumulation of ROS in media. Within neonatal bovine hepatocytes, choline and methionine differentially regulate methyl carbon pathways and suggest that choline may play a critical role in

Synthesis of [methyl-{sup 14}C]crotonobetaine from DL-[methyl-{sup 14}C]carnitine

Energy Technology Data Exchange (ETDEWEB)

Loester, H.; Seim, H. [Leipzig Univ. (Germany). Inst. of Clinical Chemistry and Pathobiochemistry

1996-02-01

The causes of carnitine deficiency syndromes are not completely understood, but decomposition of L-carnitine in vivo is likely to be involved. Carnitine is metabolized to {gamma}-butyrobetaine, and crotonobetaine is probably an intermediate in this pathway. To validate experimentally the precursor-product relationship between the three physiologically occuring {gamma}-betaines - L-carnitine, crotonobetaine, {gamma}-butyrobetaine - labelling with stable or radioactive isotopes became necessary. Methyl-labelled carnitine isomers (L(-)-, D(+)- or DL-) or {gamma}-butyrobetaine can be easily synthesized by methylation of 4-amino-3-hydroxybutyric acid isomers or 4-aminobutyric acid, respectively. Because of problems with the 4-aminocrotonic acid, we synthesized labelled crotonbetaine from labelled carnitine. Thus, DL-[methyl-{sup 14}C]carnitine was dehydrated by reaction with concentrated sulfuric acid. After removal of the latter the products were separated and purified by ion exchange chromatography on DOWEX 50 WX8 (200 - 400 mesh) and gradient elution with hydrochloric acid. In addition to the labelled main product [methyl-{sup 14}C]crotonobetaine (yield about 50 %), [methyl-{sup 14}C]glycine betaine and [methyl-{sup 14}C]acetonyl-trimethylammonium (ATMA) were formed. The end products were identified by combined thin layer chromatography/autoradiography and quantified by liquid scintillation counting. (Author).

Hardware replacements and software tools for digital control computers

International Nuclear Information System (INIS)

Walker, R.A.P.; Wang, B-C.; Fung, J.

1996-01-01

Technological obsolescence is an on-going challenge for all computer use. By design, and to some extent good fortune, AECL has had a good track record with respect to the march of obsolescence in CANDU digital control computer technology. Recognizing obsolescence as a fact of life, AECL has undertaken a program of supporting the digital control technology of existing CANDU plants. Other AECL groups are developing complete replacement systems for the digital control computers, and more advanced systems for the digital control computers of the future CANDU reactors. This paper presents the results of the efforts of AECL's DCC service support group to replace obsolete digital control computer and related components and to provide friendlier software technology related to the maintenance and use of digital control computers in CANDU. These efforts are expected to extend the current lifespan of existing digital control computers through their mandated life. This group applied two simple rules; the product, whether new or replacement should have a generic basis, and the products should be applicable to both existing CANDU plants and to 'repeat' plant designs built using current design guidelines. While some exceptions do apply, the rules have been met. The generic requirement dictates that the product should not be dependent on any brand technology, and should back-fit to and interface with any such technology which remains in the control design. The application requirement dictates that the product should have universal use and be user friendly to the greatest extent possible. Furthermore, both requirements were designed to anticipate user involvement, modifications and alternate user defined applications. The replacements for hardware components such as paper tape reader/punch, moving arm disk, contact scanner and Ramtek are discussed. The development of these hardware replacements coincide with the development of a gateway system for selected CANDU digital control

THE EFFECTS OF N-2-HYDROXYETHYL-N-METHYL-P-TOLUIDINE ON METHYL METHACRYLATE RADICAL POLYMERIZATION AND ACRYLONITRILE PHOTOINDUCED POLYMERIZATION

Institute of Scientific and Technical Information of China (English)

QIU Kunyuan; ZHANG Zhanghua; FENG Xinde

1992-01-01

The effects of N-2-hydroxyethyl-N-methyl-p-toluidine (HMT) on MMA polymerization using organic peroxide as an initiator and on AN photoinduced polymerization have been investigated respectively. The kinetics of polymerization and the overall activation energy of polymerization were determined. Based on kinetics study and the end group analysis of the polymer obtained by UV spectrum method, the initiation mechanism is proposed.

Primary Total Knee Replacement: Is Suction a Portal of Infection?

Science.gov (United States)

Budnar, Vijaya M; Amirfeyz, Rouin; Ng, Michael; Bannister, Gordon C; Blom, Ashley W

2009-01-01

INTRODUCTION Pulsed lavage during a total knee replacement usually leaves a pool of fluid on the surgical drapes. It is common practice to suck away this fluid using the same suction device used intra-operatively. This could be a cause of direct wound contamination. We hypothesised that bacteria contaminate fluid that collects around the foot in total knee replacement surgery and that suction equipment could be a portal of contamination. We also hypothesised that bacterial count in the fluid is lower if chlorhexidine, rather than saline, is used in the pulsed lavage. PATIENTS AND METHODS Forty patients undergoing primary total knee replacement were divided into two groups. The first group had pulsed lavage with normal saline and the second with 0.05% chlorhexidine. RESULTS At the end of the operation, 20 ml of fluid, pooled on the surgical drapes was aspirated and cultured for bacterial growth. None of the fluid samples showed bacterial growth. CONCLUSIONS Suction device used peri-operatively during knee replacement is unlikely to be a cause of wound contamination. Pulsed lavage with normal saline is as effective as lavage with chlorhexidine. PMID:19335972

Process for the production of methyl methacrylate

NARCIS (Netherlands)

Eastham, G.R.; Johnson, D.W.; Straathof, A.J.J.; Fraaije, Marco; Winter, Remko

2015-01-01

A process of producing methyl methacrylate or derivatives thereof is described. The process includes the steps of; (i) converting 2-butanone to methyl propionate using a Baeyer-Villiger monooxygenase, and (ii) treating the methyl propionate produced to obtain methyl methacrylate or derivatives

Methylation patterns in marginal zone lymphoma.

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Arribas, Alberto J; Bertoni, Francesco

Promoter DNA methylation is a major regulator of gene expression and transcription. The identification of methylation changes is important for understanding disease pathogenesis, for identifying prognostic markers and can drive novel therapeutic approaches. In this review we summarize the current knowledge regarding DNA methylation in MALT lymphoma, splenic marginal zone lymphoma, nodal marginal zone lymphoma. Despite important differences in the study design for different publications and the existence of a sole large and genome-wide methylation study for splenic marginal zone lymphoma, it is clear that DNA methylation plays an important role in marginal zone lymphomas, in which it contributes to the inactivation of tumor suppressors but also to the expression of genes sustaining tumor cell survival and proliferation. Existing preclinical data provide the rationale to target the methylation machinery in these disorders. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterization of Metal-Doped Methylated Microporous Silica for Molecular Separations

DEFF Research Database (Denmark)

El-Feky, Hany Hassan; Briceno, Kelly; Szalata, Kamila

2015-01-01

Novel silica xerogels are prepared and developed by sol-gel method in the present study. The preparation involves cobalt-doping within the organic templated silica matrices, where methyltriethoxysilane (MTES), which contains methyl groups as a covalently bonded organic template is used. The synth...

Synthesis of methyl (13(2)R/S)-alkyl-pyropheophorbide a and a non-epimerized chlorophyll a mimic.

Science.gov (United States)

Ogasawara, Shin; Tamiaki, Hitoshi

2015-10-15

The (13(2)R/S)-methoxycarbonyl group of methyl pheophorbides a/a' (chlorophyll a/a' derivatives) was converted to methyl, ethyl, propyl, and isopropyl groups through the C13(2)-alkylation under basic conditions followed by pyrolysis in 2,4,6-collidine with lithium iodide. All the resulting products, methyl 13(2)-alkyl-pyropheophorbides a, predominantly gave the (13(2)R)-stereoisomers with about one tenth of the (13(2)S)-epimers. Their stereochemistry was determined by 1D/2D NMR and their optical properties were characterized by visible absorption and circular dichroism spectroscopy. Methyl (13(2)R)-propyl-pyropheophorbide a was converted to (13(2)R)-propyl-pyrochlorophyll a by ester exchanging and magnesium chelating reactions. The synthetic chlorophyll a analogue showed non-epimerization at the 13(2)-position in pyridine-d5 at 40°C, while naturally occurring chlorophyll a was easily epimerized under the same conditions to give its epimeric mixture. Copyright © 2015 Elsevier Ltd. All rights reserved.

No effect of folic acid supplementation on global DNA methylation in men and women with moderately elevated homocysteine.

Directory of Open Access Journals (Sweden)

Audrey Y Jung

Full Text Available A global loss of cytosine methylation in DNA has been implicated in a wide range of diseases. There is growing evidence that modifications in DNA methylation can be brought about by altering the intake of methyl donors such as folate. We examined whether long-term daily supplementation with 0.8 mg of folic acid would increase global DNA methylation compared with placebo in individuals with elevated plasma homocysteine. We also investigated if these effects were modified by MTHFR C677T genotype. Two hundred sixteen participants out of 818 subjects who had participated in a randomized double-blind placebo-controlled trial were selected, pre-stratified on MTHFR C677T genotype and matched on age and smoking status. They were allocated to receive either folic acid (0.8 mg/d; n = 105 or placebo treatment (n = 111 for three years. Peripheral blood leukocyte DNA methylation and serum and erythrocyte folate were assessed. Global DNA methylation was measured using liquid chromatography-tandem mass spectrometry and expressed as a percentage of 5-methylcytosines versus the total number of cytosine. There was no difference in global DNA methylation between those randomized to folic acid and those in the placebo group (difference = 0.008, 95%CI = -0.05,0.07, P = 0.79. There was also no difference between treatment groups when we stratified for MTHFR C677T genotype (CC, n = 76; CT, n = 70; TT, n = 70, baseline erythrocyte folate status or baseline DNA methylation levels. In moderately hyperhomocysteinemic men and women, long-term folic acid supplementation does not increase global DNA methylation in peripheral blood leukocytes.ClinicalTrials.gov NCT00110604.

No effect of folic acid supplementation on global DNA methylation in men and women with moderately elevated homocysteine.

Science.gov (United States)

Jung, Audrey Y; Smulders, Yvo; Verhoef, Petra; Kok, Frans J; Blom, Henk; Kok, Robert M; Kampman, Ellen; Durga, Jane

2011-01-01

A global loss of cytosine methylation in DNA has been implicated in a wide range of diseases. There is growing evidence that modifications in DNA methylation can be brought about by altering the intake of methyl donors such as folate. We examined whether long-term daily supplementation with 0.8 mg of folic acid would increase global DNA methylation compared with placebo in individuals with elevated plasma homocysteine. We also investigated if these effects were modified by MTHFR C677T genotype. Two hundred sixteen participants out of 818 subjects who had participated in a randomized double-blind placebo-controlled trial were selected, pre-stratified on MTHFR C677T genotype and matched on age and smoking status. They were allocated to receive either folic acid (0.8 mg/d; n = 105) or placebo treatment (n = 111) for three years. Peripheral blood leukocyte DNA methylation and serum and erythrocyte folate were assessed. Global DNA methylation was measured using liquid chromatography-tandem mass spectrometry and expressed as a percentage of 5-methylcytosines versus the total number of cytosine. There was no difference in global DNA methylation between those randomized to folic acid and those in the placebo group (difference = 0.008, 95%CI = -0.05,0.07, P = 0.79). There was also no difference between treatment groups when we stratified for MTHFR C677T genotype (CC, n = 76; CT, n = 70; TT, n = 70), baseline erythrocyte folate status or baseline DNA methylation levels. In moderately hyperhomocysteinemic men and women, long-term folic acid supplementation does not increase global DNA methylation in peripheral blood leukocytes.ClinicalTrials.gov NCT00110604.

Differential pulse voltammetric determination of methyl parathion based on multiwalled carbon nanotubes–poly(acrylamide) nanocomposite film modified electrode

International Nuclear Information System (INIS)

Zeng, Yanbo; Yu, Dajun; Yu, Yanyan; Zhou, Tianshu; Shi, Guoyue

2012-01-01

Highlights: ► A sensitive electrochemical sensor for detecting methyl parathion in environmental samples. ► The preparation, characterization and application of this novel MWCNTs–PAAM nanocomposite. ► The MWCNTs–PAAM/GCE exhibited a high adsorption and strong affinity toward methyl parathion. ► Wide linear range and low detection limit of the proposed method for detecting methyl parathion. - Abstract: A sensitive electrochemical differential pulse voltammetry method was developed for detecting methyl parathion based on multiwalled carbon nanotubes–poly(acrylamide) (MWCNTs–PAAM) nanocomposite film modified glassy carbon electrode. The novel MWCNTs–PAAM nanocomposite, containing high content of amide groups, was synthesized by PAAM polymerizing at the vinyl group functionalized MWCNTs surface using free radical polymerization. The MWCNTs–PAAM nanocomposite was characterized by Fourier transform infrared spectroscopy, thermal gravimetric analysis and scanning electron microscopy. Electrochemical behavior and interference studies of MWCNTs–PAAM/GCE for methyl parathion were investigated. The experimental results demonstrated that the MWCNTs–PAAM/GCE exhibited a high adsorption and strong affinity toward methyl parathion compared with some metal ions and nitroaromatic compounds, which exist in environmental samples. The adsorbed amount of methyl parathion on the MWCNTs–PAAM/GCE approached the equilibrium value upon 5 min adsorption time. A linear calibration curve for methyl parathion was obtained in the concentration range from 5.0 × 10 −9 to 1.0 × 10 −5 mol L −1 , with a detection limit of 2.0 × 10 −9 mol L −1 . The MWCNTs–PAAM/GCE was proved to be a suitable sensing tool for the fast, sensitive and selective determination of methyl parathion in environmental water samples.

Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene

DEFF Research Database (Denmark)

Candiloro, Ida Lm; Mikeska, Thomas; Hokland, Peter

2008-01-01

ABSTRACT: BACKGROUND: Methylation-sensitive high resolution melting (MS-HRM) methodology is able to recognise heterogeneously methylated sequences by their characteristic melting profiles. To further analyse heterogeneously methylated sequences, we adopted a digital approach to MS-HRM (dMS-HRM) t......ABSTRACT: BACKGROUND: Methylation-sensitive high resolution melting (MS-HRM) methodology is able to recognise heterogeneously methylated sequences by their characteristic melting profiles. To further analyse heterogeneously methylated sequences, we adopted a digital approach to MS-HRM (d......MS-HRM) that involves the amplification of single templates after limiting dilution to quantify and to determine the degree of methylation. We used this approach to study methylation of the CDKN2B (p15) cell cycle progression inhibitor gene which is inactivated by DNA methylation in haematological malignancies...... the methylated alleles and assess the degree of methylation. Direct sequencing of selected dMS-HRM products was used to determine the exact DNA methylation pattern and confirmed the degree of methylation estimated by dMS-HRM. CONCLUSION: dMS-HRM is a powerful technique for the analysis of methylation in CDKN2B...

DGKI methylation status modulates the prognostic value of MGMT in glioblastoma patients treated with combined radio-chemotherapy with temozolomide.

Directory of Open Access Journals (Sweden)

Amandine Etcheverry

Full Text Available Consistently reported prognostic factors for glioblastoma (GBM are age, extent of surgery, performance status, IDH1 mutational status, and MGMT promoter methylation status. We aimed to integrate biological and clinical prognostic factors into a nomogram intended to predict the survival time of an individual GBM patient treated with a standard regimen. In a previous study we showed that the methylation status of the DGKI promoter identified patients with MGMT-methylated tumors that responded poorly to the standard regimen. We further evaluated the potential prognostic value of DGKI methylation status.399 patients with newly diagnosed GBM and treated with a standard regimen were retrospectively included in this study. Survival modelling was performed on two patient populations: intention-to-treat population of all included patients (population 1 and MGMT-methylated patients (population 2. Cox proportional hazard models were fitted to identify the main prognostic factors. A nomogram was developed for population 1. The prognostic value of DGKI promoter methylation status was evaluated on population 1 and population 2.The nomogram-based stratification of the cohort identified two risk groups (high/low with significantly different median survival. We validated the prognostic value of DGKI methylation status for MGMT-methylated patients. We also demonstrated that the DGKI methylation status identified 22% of poorly responding patients in the low-risk group defined by the nomogram.Our results improve the conventional MGMT stratification of GBM patients receiving standard treatment. These results could help the interpretation of published or ongoing clinical trial outcomes and refine patient recruitment in the future.

DGKI methylation status modulates the prognostic value of MGMT in glioblastoma patients treated with combined radio-chemotherapy with temozolomide.

Science.gov (United States)

Etcheverry, Amandine; Aubry, Marc; Idbaih, Ahmed; Vauleon, Elodie; Marie, Yannick; Menei, Philippe; Boniface, Rachel; Figarella-Branger, Dominique; Karayan-Tapon, Lucie; Quillien, Veronique; Sanson, Marc; de Tayrac, Marie; Delattre, Jean-Yves; Mosser, Jean

2014-01-01

Consistently reported prognostic factors for glioblastoma (GBM) are age, extent of surgery, performance status, IDH1 mutational status, and MGMT promoter methylation status. We aimed to integrate biological and clinical prognostic factors into a nomogram intended to predict the survival time of an individual GBM patient treated with a standard regimen. In a previous study we showed that the methylation status of the DGKI promoter identified patients with MGMT-methylated tumors that responded poorly to the standard regimen. We further evaluated the potential prognostic value of DGKI methylation status. 399 patients with newly diagnosed GBM and treated with a standard regimen were retrospectively included in this study. Survival modelling was performed on two patient populations: intention-to-treat population of all included patients (population 1) and MGMT-methylated patients (population 2). Cox proportional hazard models were fitted to identify the main prognostic factors. A nomogram was developed for population 1. The prognostic value of DGKI promoter methylation status was evaluated on population 1 and population 2. The nomogram-based stratification of the cohort identified two risk groups (high/low) with significantly different median survival. We validated the prognostic value of DGKI methylation status for MGMT-methylated patients. We also demonstrated that the DGKI methylation status identified 22% of poorly responding patients in the low-risk group defined by the nomogram. Our results improve the conventional MGMT stratification of GBM patients receiving standard treatment. These results could help the interpretation of published or ongoing clinical trial outcomes and refine patient recruitment in the future.

Effect of leptin gene methylation on glucose metabolism in pregnant rats

Directory of Open Access Journals (Sweden)

Zhen LI

2011-11-01

Full Text Available Objective To examine the dynamic level of progesterone,insulin,and leptin,as well as the change in the features of leptin gene methylation in the promoter region of pregnant rats during different gestation stages and to analyze the correlation and effect of these conditions on glucose metabolism during gestation.Methods C57BL/6J pregnant rats are divided to four different groups,namely,early,mid-,and late gestation,as well as seven days postpartum(five rats for each group.Five C57BL/6J non-pregnant rats are taken as the control group.The change in glucose metabolism during gestation was determined by measuring the glucose tolerance of rats in different groups and by testing the level of progesterone,insulin,and leptin in the sera and the level of the methylation of leptin gene promoters during different stages of gestation.Results The levels of insulin [(13.70±0.70,14.78±0.91,and 16.07±0.55mU/L],progesterone [(10.10±0.37,11.41±0.50,and 15.34±0.65μg/L],and leptin [(1356.73±100.41,1628.02±53.03,and 1954.12±39.71ng/L] in pregnant rats in the three groups(early,mid-,and late gestation are apparently higher than that of the non-pregnant rats [(12.25±1.62mU/L,(7.14±0.38μg/L,and(934.38±62.29ng/L] and the postpartum group [(12.46±0.93mU/L,(9.74±0.82μg/L,and(1259.19±105.74ng/L].The difference among the different stages of gestation has statistical significance(P < 0.01,but the difference between the non-pregnant and postpartum groups is statistically insignificant.Fasting blood glucose during gestation is low.The level of blood glucose in mid-gestation and late-gestation rats after being injected with glucose is apparently higher than that of the non-pregnant group(P < 0.01.The level of methylation in the leptin gene promoter zone of the placenta drops along with gestation.Conclusions High levels of progesterone,insulin,and leptin contribute to physiological insulin resistance during gestation,resulting in reduced fasting blood glucose

Evaluation of the dental structure loss produced during maintenance and replacement of occlusal amalgam restorations

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Fernanda Sardenberg

2008-09-01

Full Text Available The aim of this in vitro study was to evaluate four different approaches to the decision of changing or not defective amalgam restorations in first primary molar teeth concerning the loss of dental structure. Ditched amalgam restorations (n = 11 were submitted to four different treatments, as follows: Control group - polishing and finishing of the restorations were carried out; Amalgam group - the ditched amalgam restorations were replaced by new amalgam restorations; Composite resin group - the initial amalgam restorations were replaced by composite resin restorations; Flowable resin group - the ditching around the amalgam restorations was filled with flowable resin. Images of the sectioned teeth were made and the area of the cavities before and after the procedures was determined by image analysis software to assess structural loss. The data were submitted to ANOVA complemented by the Student Newman Keuls test (p < 0.05. The cavities in all the groups presented significantly greater areas after the procedures. However, the amalgam group showed more substantial dental loss. The other three groups presented no statistically significant difference in dental structure loss after the re-treatments. Thus, replacing ditched amalgam restorations by other similar restorations resulted in a significant dental structure loss while maintaining them or replacing them by resin restorations did not result in significant loss.

[Survival in acute renal failure with conventional therapy or continuous replacement therapy].

Science.gov (United States)

Santibáñez-Velázquez, Martín; Sánchez-Montoya, Felipe; Alvirde-Gutiérrez, Luis

2014-01-01

To know the survival rate in patients with RIFLE I and II stages on acute renal failure, treated with supportive care or continuous renal replacement therapy with PRISMA machine, at an intensive care unit. There were included patients of both sexes, aged 16 to 69 years, with acute renal failure in RIFLE I and II stages and score of scale APACHE II lower than 36 points. The sample studied was divided in two groups: a group was treated with supportive care, and the other group received continuous renal replacement therapy via PRISMA machine. We compared mortality between both groups and the association with the RIFLE stages with Pearson's chi-squared test. The average score of the scale APACHE I was 14 points, and the probability of death was 15 %. The patients with acute renal failure RIFLE I were 54.5 % and RIFLE II 45.5 %, with mortality of 30.4 % and 38.8 %, respectively. Patients in RIFLE I stage who received supportive care and continuous replacement therapy had non-statistical differences in mortality (p = 0.356). The mortality in patients with acute renal failure in RIFLE II stage treated with continuous replacement therapy was higher (p = 0.000). Because of its accessibility and lower mortality, supportive care should be the initial procedure in patients with acute renal failure in RIFLE I and II stages.

Peripheral SLC6A4 DNA methylation is associated with in vivo measures of human brain serotonin synthesis and childhood physical aggression.

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Dongsha Wang

Full Text Available The main challenge in addressing the role of DNA methylation in human behaviour is the fact that the brain is inaccessible to epigenetic analysis in living humans. Using positron emission tomography (PET measures of brain serotonin (5-HT synthesis, we found in a longitudinal sample that adult males with high childhood-limited aggression (C-LHPA had lower in vivo 5-HT synthesis in the orbitofrontal cortex (OBFC. Here we hypothesized that 5-HT alterations associated with childhood aggression were linked to differential DNA methylation of critical genes in the 5-HT pathway and these changes were also detectable in peripheral white blood cells. Using pyrosequencing, we determined the state of DNA methylation of SLC6A4 promoter in T cells and monocytes isolated from blood of cohort members (N = 25 who underwent a PET scan, and we examined whether methylation status in the blood is associated with in vivo brain 5-HT synthesis. Higher levels of methylation were observed in both T cells and monocytes at specific CpG sites in the C-LHPA group. DNA methylation of SLC6A4 in monocytes appears to be associated more reliably with group membership than T cells. In both cell types the methylation state of these CpGs was associated with lower in vivo measures of brain 5-HT synthesis in the left and right lateral OBFC (N = 20 where lower 5-HT synthesis in C-LHPA group was observed. Furthermore, in vitro methylation of the SLC6A4 promoter in a luciferase reporter construct suppresses its transcriptional activity supporting a functional role of DNA methylation in SLC6A4 promoter regulation. These findings indicate that state of SLC6A4 promoter methylation is altered in peripheral white blood cells of individuals with physical aggression during childhood. This supports the relevance of peripheral DNA methylation for brain function and suggests that peripheral SLC6A4 DNA methylation could be a marker of central 5-HT function.

Synthesis of 14C-labelled α-methyl tyrosine

International Nuclear Information System (INIS)

Rajagopal, S.; Venkatachalam, T.K.; Conway, T.; Diksic, M.

1992-01-01

A new route for the preparation of radioactively labelled α-methyl L-tyrosine is described. The labelling at the α position has been successfully achieved with 14 C-, 11 C- (very preliminary, unpublished), and 3 H-labelled methyl iodide. A detailed report on 14 C-labelling at the α position and the hydrolysis of 4-methoxy α-methyl phenylalanine is presented. The alkylation proceeds via the methylation of the carbanion of N-benzylidene 4-methoxy phenylalanine methyl ester 2. Hydrolysis of 4-O methyl tyrosine to tyrosine by HBr and HI were analysed and used in the optimization of the hydrolysis conditions of 4. Enantiomeric purity of the isolated L-isomer has been found to be 99% as judged by HPLC. Pseudo first-order rate constant for the hydrolysis of 14 C-labelled α-methyl 4-methoxy phenyl alanine methyl ester was determined. Preliminary findings of the 3 H- and 11 C-radiolabelled α-methyl tyrosine (methyl labelled) are also mentioned. For the first time it was shown that α-methyl D,L-tyrosine can be separated into enantiomerically pure α-methyl D- and L-tyrosine using a CHIRALPAK WH column. (author)

Influence of intramolecular hydrogen bonds on the binding potential of methylated β-cyclodextrin derivatives

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Gerhard Wenz

2012-11-01

Full Text Available Various heptasubstituted derivatives of β-cyclodextrin (β-CD bearing 1, 2 and 3 methyl substituents per glucose unit were synthesized by regioselective methods. Binding free energies and binding enthalpies of these hosts towards 4-tert-butylbenzoate and adamantane-1-carboxylate were determined by isothermal titration microcalorimetry (ITC. It was found that methyl substituents at the secondary positions of β-CD lead to a tremendous reduction of the binding potential, while methylation at the primary positions significantly improved binding. Stabilizing intramolecular hydrogen bonds between the glucose units were made responsible for the high binding potentials of those β-CD derivatives that possess secondary hydroxy groups.

DNA methylation of miRNA coding sequences putatively associated with childhood obesity.

Science.gov (United States)

Mansego, M L; Garcia-Lacarte, M; Milagro, F I; Marti, A; Martinez, J A

2017-02-01

Epigenetic mechanisms may be involved in obesity onset and its consequences. The aim of the present study was to evaluate whether DNA methylation status in microRNA (miRNA) coding regions is associated with childhood obesity. DNA isolated from white blood cells of 24 children (identification sample: 12 obese and 12 non-obese) from the Grupo Navarro de Obesidad Infantil study was hybridized in a 450 K methylation microarray. Several CpGs whose DNA methylation levels were statistically different between obese and non-obese were validated by MassArray® in 95 children (validation sample) from the same study. Microarray analysis identified 16 differentially methylated CpGs between both groups (6 hypermethylated and 10 hypomethylated). DNA methylation levels in miR-1203, miR-412 and miR-216A coding regions significantly correlated with body mass index standard deviation score (BMI-SDS) and explained up to 40% of the variation of BMI-SDS. The network analysis identified 19 well-defined obesity-relevant biological pathways from the KEGG database. MassArray® validation identified three regions located in or near miR-1203, miR-412 and miR-216A coding regions differentially methylated between obese and non-obese children. The current work identified three CpG sites located in coding regions of three miRNAs (miR-1203, miR-412 and miR-216A) that were differentially methylated between obese and non-obese children, suggesting a role of miRNA epigenetic regulation in childhood obesity. © 2016 World Obesity Federation.

Measurement of Antioxidant Effects on the Auto-oxidation Kinetics of Methyl Oleate – Methyl Laurate Blend as a Surrogate Biodiesel System

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Tjokorde Walmiki Samadhi

2017-05-01

Full Text Available This research investigates the feasibility of methyl oleate-methyl laurate blend as a surrogate biodiesel system which represents jatropha-coconut oil biodiesel, a potentially suitable formulation for tropical climate, to quantify the efficacy of antioxidant additives in terms of their kinetic parameters. This blend was tested by the Rancimat EN14112 standard method. The Rancimat tests results were used to determine the primary oxidation induction period (OIP and first-order rate constants and activation energies. Addition of BHT and EcotiveTM antioxidants reduces the rate constants (k, h-1 between 15 to 90% in the 50-200 ppm dose range, with EcotiveTM producing significantly lower k values. Higher dose reduces the rate constant, while oleate/laurate ratio produces no significant impact. Antioxidants increase the oxidation activation energy (Ea, kJ/mol by 180 to almost 400% relative to the non-antioxidant value of 27.0 kJ/mol. EcotiveTM exhibits lower Ea, implying that its higher efficacy stems from a better steric hindrance as apparent from its higher pre-exponential factors. The ability to quantify oxidation kinetic parameters is indicative of the usefulness of methyl oleate-laurate pure FAME blend as a biodiesel surrogate offering better measurement accuracy due to the absence of pre-existing antioxidants in the test samples. Copyright © 2017 BCREC GROUP. All rights reserved Received: 6th July 2016; Revised: 7th December 2016; Accepted: 30th January 2017 How to Cite: Samadhi, T.W., Hirotsu, T., Goto, S. (2017. Measurement of Antioxidant Effects on the Auto-oxidation Kinetics of Methyl Oleate-Methyl Laurate Blend as a Surrogate Biodiesel System. Bulletin of Chemical Reaction Engineering & Catalysis, 12 (2: 157-166 (doi:10.9767/bcrec.12.2.861.157-166 Permalink/DOI: http://dx.doi.org/10.9767/bcrec.12.2.861.157-166

Liberation of methyl acrylate from metallalactone complexes via M-O ring opening (M = Ni, Pd) with methylation agents

KAUST Repository

Lee, S. Y Tina; Ghani, Amylia Abdul; D'Elia, Valerio; Cokoja, Mirza; Herrmann, Wolfgang A.; Basset, Jean-Marie; Kü hn, Fritz

2013-01-01

Ring opening of various nickela- and palladalactones induced by the cleavage of the M-O bond by methyl trifluoromethanesulfonate (MeOTf) and methyl iodide (MeI) is examined. Experimental evidence supports the mechanism of ring opening by the alkylating agent followed by β-H elimination leading to methyl acrylate and a metal-hydride species. MeOTf shows by far higher efficiency in the lactone ring opening than any other methylating agent including the previously reported methyl iodide. © 2013 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.

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