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Sample records for chloroethyinitrosourea-derived ethano cytosine

  1. Modification of Cilembu sweet potato starch with ethanoic acid

    Science.gov (United States)

    Mahmudatussa'adah, A.; Rahmawati, Y.; Sudewi

    2016-04-01

    Cilembu sweet potato harvest was abundant, its use was still limited. Starch was required by various industries. Starch is generally beige, and requires a long time for the drying process. The purpose of this research was to produce a modified starch with ethanoic acid. The method used in this study was the experimental method. The results showed acid modified starch yield was 18%, with the color characteristics of L*: 96.38 ± 0.82; a*: -0.70±0.02 b*: 2.70±0.03 C: 2.79±0.02. Native starch yield was 16%, with the color characteristics of L*: 93.55 ± 0.91; a*: -0.86±0.06 b*: 2.93±0.04 C: 3.05±0.03. The conclusion of this study was modified starch of Cilembu sweet potato using ethanoic acid have higher yield and more white bright than native starch.

  2. The Cytosine Water Complex

    Science.gov (United States)

    Daly, A. M.; Mata, S.; Bermudez, C.; Berdakin, M.; Pena, I.; Cabezas, C.; Alonso, J. L.

    2013-06-01

    A multi FID system has been adapted into the operation sequence of the LA-MB-FTMW spectrometer. Thanks to the reached sensitivity, one monohydrate of cytosine (A= 3725.61 (26) MHz, B=980.385 (76) MHz, C=777.231 (46) MHz) has been detected in the supersonic expansion. J. --U. Grabow, W. Stahl, H. Dreizler, Rev. Sci. Instrum. 1996, 67, 4072 -- 4084. J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López, S. Blanco, Phys. Chem. Chem. Phys. 2009, 11, 617 -- 627.

  3. Raman Spectroscopic Study of the Vapour Phase of 1-Methylimidazolium Ethanoate, a Protic Ionic Liquid

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Canongia Lopes, Jose N.; Ferreira, Rui;

    2010-01-01

    The gas phase over the ionic liquid 1-methylimidazolium ethanoate, [Hmim][O2CCH3], was studied by means of Raman spectroscopy. Raman spectra are presented, the species in the gas phase are identified, and their bands are assigned. The results are interpreted using ab initio quantum mechanical cal...... calculations that also predict vibrational spectra. The obtained data reinforce a previous interpretation, based on FT-ICR mass spectrometric data, that the vapor phase over [Hmim][O2CCH3] consists predominantly of two neutral molecules, monomeric ethanoic acid and 1-methylimidazole....

  4. Synthesis and characterization of acetic acid and ethanoic acid (based)-maleimide

    Science.gov (United States)

    Poad, Siti Nashwa Mohd; Hassan, Nurul Izzaty; Hassan, Nur Hasyareeda

    2016-11-01

    A new route to the synthesis of maleimide is described. 2-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)acetic acid maleimide (1) and 2-(4-(2,5-Dioxo-2,5-dihydro- 1H-pyrrol-1-yl)phenyl)ethanoic acid maleimide (2) have been synthesized by the reaction of maleic anhydride with glycine and 4-aminophenyl acetic aicd. Maleimide (1) was synthesized by conventional technique while maleimide (2) was synthesized by microwave method. The compounds were characterized using FT-Infrared (FT-IR), 1H and 13C Nuclear Magnetic Resonance (NMR) spectroscopies and Mass Spectrometry.

  5. Analysis of DNA Cytosine Methylation on Cotton under Salt Stress

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    DNA methylation,especially methylation of cytosine in eukaryotic organisms,has been implicated in gene regulation,genomic imprinting,the timing of DNA replication,and determination of chromatin structure.It was reported that 6.5% of the whole cytosine residues in the nuclear DNA in higher

  6. Information Thermodynamics of Cytosine DNA Methylation.

    Science.gov (United States)

    Sanchez, Robersy; Mackenzie, Sally A

    2016-01-01

    Cytosine DNA methylation (CDM) is a stable epigenetic modification to the genome and a widespread regulatory process in living organisms that involves multicomponent molecular machines. Genome-wide cytosine methylation patterning participates in the epigenetic reprogramming of a cell, suggesting that the biological information contained within methylation positions may be amenable to decoding. Adaptation to a new cellular or organismal environment also implies the potential for genome-wide redistribution of CDM changes that will ensure the stability of DNA molecules. This raises the question of whether or not we would be able to sort out the regulatory methylation signals from the CDM background ("noise") induced by thermal fluctuations. Here, we propose a novel statistical and information thermodynamic description of the CDM changes to address the last question. The physical basis of our statistical mechanical model was evaluated in two respects: 1) the adherence to Landauer's principle, according to which molecular machines must dissipate a minimum energy ε = kBT ln2 at each logic operation, where kB is the Boltzmann constant, and T is the absolute temperature and 2) whether or not the binary stretch of methylation marks on the DNA molecule comprise a language of sorts, properly constrained by thermodynamic principles. The study was performed for genome-wide methylation data from 152 ecotypes and 40 trans-generational variations of Arabidopsis thaliana and 93 human tissues. The DNA persistence length, a basic mechanical property altered by CDM, was estimated with values from 39 to 66.9 nm. Classical methylome analysis can be retrieved by applying information thermodynamic modelling, which is able to discriminate signal from noise. Our finding suggests that the CDM signal comprises a language scheme properly constrained by molecular thermodynamic principles, which is part of an epigenomic communication system that obeys the same thermodynamic rules as do current

  7. Information Thermodynamics of Cytosine DNA Methylation.

    Directory of Open Access Journals (Sweden)

    Robersy Sanchez

    Full Text Available Cytosine DNA methylation (CDM is a stable epigenetic modification to the genome and a widespread regulatory process in living organisms that involves multicomponent molecular machines. Genome-wide cytosine methylation patterning participates in the epigenetic reprogramming of a cell, suggesting that the biological information contained within methylation positions may be amenable to decoding. Adaptation to a new cellular or organismal environment also implies the potential for genome-wide redistribution of CDM changes that will ensure the stability of DNA molecules. This raises the question of whether or not we would be able to sort out the regulatory methylation signals from the CDM background ("noise" induced by thermal fluctuations. Here, we propose a novel statistical and information thermodynamic description of the CDM changes to address the last question. The physical basis of our statistical mechanical model was evaluated in two respects: 1 the adherence to Landauer's principle, according to which molecular machines must dissipate a minimum energy ε = kBT ln2 at each logic operation, where kB is the Boltzmann constant, and T is the absolute temperature and 2 whether or not the binary stretch of methylation marks on the DNA molecule comprise a language of sorts, properly constrained by thermodynamic principles. The study was performed for genome-wide methylation data from 152 ecotypes and 40 trans-generational variations of Arabidopsis thaliana and 93 human tissues. The DNA persistence length, a basic mechanical property altered by CDM, was estimated with values from 39 to 66.9 nm. Classical methylome analysis can be retrieved by applying information thermodynamic modelling, which is able to discriminate signal from noise. Our finding suggests that the CDM signal comprises a language scheme properly constrained by molecular thermodynamic principles, which is part of an epigenomic communication system that obeys the same thermodynamic

  8. Analysis of DNA Cytosine Methylation on Cotton under Salt Stress

    Institute of Scientific and Technical Information of China (English)

    ZHAO Yun-le; YE Wu-wei; WANG Jun-juan; FAN Bao-xiang

    2008-01-01

    @@ DNA methylation,especially methylation of cytosine in eukaryotic organisms,has been implicated in gene regulation,genomic imprinting,the timing of DNA replication,and determination of chromatin structure.It was reported that 6.5% of the whole cytosine residues in the nuclear DNA in higher plants were methylated.The methylation of cytosine in plant nuclear DNA occurs usually in both CpG and CpNG sequences,and the methylation state can be maintained through the cycles of DNA replication and is likely to play an integral role in regulating gene expression.

  9. Profiling cytosine oxidation in DNA by LC-MS/MS.

    Science.gov (United States)

    Samson-Thibault, Francois; Madugundu, Guru S; Gao, Shanshan; Cadet, Jean; Wagner, J Richard

    2012-09-17

    Spontaneous and oxidant-induced damage to cytosine is probably the main cause of CG to TA transition mutations in mammalian genomes. The reaction of hydroxyl radical (·OH) and one-electron oxidants with cytosine derivatives produces numerous oxidation products, which have been identified in large part by model studies with monomers and short oligonucleotides. Here, we developed an analytical method based on LC-MS/MS to detect 10 oxidized bases in DNA, including 5 oxidation products of cytosine. The utility of this method is demonstrated by the measurement of base damage in isolated calf thymus DNA exposed to ionizing radiation in aerated aqueous solutions (0-200 Gy) and to well-known Fenton-like reactions (Fe(2+) or Cu(+) with H(2)O(2) and ascorbate). The following cytosine modifications were quantified as modified 2'-deoxyribonucleosides upon exposure of DNA to ionizing radiation in aqueous aerated solution: 5-hydroxyhydantoin (Hyd-Ura) > 5-hydroxyuracil (5-OHUra) > 5-hydroxycytosine (5-OHCyt) > 5,6-dihydroxy-5,6-dihydrouracil (Ura-Gly) > 1-carbamoyl-4,5-dihydroxy-2-oxoimidazolidine (Imid-Cyt). The total yield of cytosine oxidation products was comparable to that of thymine oxidation products (5,6-dihydroxy-5,6-dihydrothymine (Thy-Gly), 5-hydroxy-5-methylhydantotin (Hyd-Thy), 5-(hydroxymethyl)uracil (5-HmUra), and 5-formyluracil (5-ForUra)) as well as the yield of 8-oxo-7,8-dihydroguanine (8-oxoGua). The major oxidation product of cytosine in DNA was Hyd-Ura. In contrast, the formation of Imid-Cyt was a minor pathway of DNA damage, although it is the major product arising from irradiation of the monomers, cytosine, and 2'-deoxycytidine. The reaction of Fenton-like reagents with DNA gave a different distribution of cytosine derived products compared to ionizing radiation, which likely reflects the reaction of metal ions with intermediate peroxyl radicals or hydroperoxides. The analysis of the main cytosine oxidation products will help elucidate the complex

  10. Synthesis of magnetic cytosine-imprinted chitosan nanoparticles

    Science.gov (United States)

    Lee, Mei-Hwa; Ahluwalia, Arti; Chen, Jian-Zhou; Shih, Neng-Lang; Lin, Hung-Yin

    2017-02-01

    Molecularly imprinted polymer nanoparticles incorporating magnetic nanoparticles (MNPs) have been investigated for their selective adsorption properties. Here we describe the synthesis and characterization of magnetic cytosine-imprinted chitosan nanoparticles (CIPs) for gene delivery. In particular, CIPs carrying the mammalian expression plasmid of enhanced green fluorescent protein were prepared by the co-precipitation of MNPs, chitosan and a template nucleobase (cytosine). The results show that the selective reabsorption of cytosine to magnetic CIPs was at least double that of non-imprinted polymers and other nucleobases (such as adenine and thymine). The gene carrier CIPs were used for the transfection of human embryonic kidney 293 cells showing dramatic increase their efficiency with that of conventional chitosan nanoparticles. Furthermore, the gene carrier magnetic CIPs also exhibit low toxicity compared to that of commercially available cationic lipids.

  11. Conformational switching of ethano-bridged Cu,H2-bis-porphyrin induced by aromatic amines

    Directory of Open Access Journals (Sweden)

    Simona Bettini

    2015-11-01

    Full Text Available Cu,H2-bis-porphyrin (Cu,H2-Por2, in which copper porphyrin and free-base porphyrin are linked together by an ethano-bridge, was dissolved in chloroform and spread at the air/liquid subphase interface of a Langmuir trough. The bis-porphyrin derivative, floating film was characterized by reflection spectroscopy and the surface pressure of the floating film was studied as a function of the mean area per molecule. When aromatic amines are dissolved in the subphase, an evident interaction between the bis-porphyrin host and the aromatic amine guest is observed. A clear-cut variation of the profile of surface pressure vs area per molecule curve is observed. Reflection spectroscopy highlights that the aromatic amines dissolved in the subphase are able to induce the syn-to-anti conformational switching in the bis-porphyrin derivative. The Langmuir–Schaefer technique has been used to transfer the floating bis-porphyrin film (when using pure water as a subphase to a surface plasmon resonance (SPR substrate and the resulting device was able to detect the presence of aniline at concentrations as low as 1 nM in aqueous solution. The high selectivity of the SPR sensing device has been verified by checking the spectral response of the active layer towards other analytes dissolved in the aqueous solutions.

  12. Volumetric Properties of the Mixture Trichloromethane CHCl3 + C4H8O2 Ethyl ethanoate (VMSD1212, LB4146_V)

    Science.gov (United States)

    Cibulka, I.; Fontaine, J.-C.; Sosnkowska-Kehiaian, K.; Kehiaian, H. V.

    This document is part of Subvolume C 'Binary Liquid Systems of Nonelectrolytes III' of Volume 26 'Heats of Mixing, Vapor-Liquid Equilibrium, and Volumetric Properties of Mixtures and Solutions' of Landolt-Börnstein Group IV 'Physical Chemistry'. It contains the Chapter 'Volumetric Properties of the Mixture Trichloromethane CHCl3 + C4H8O2 Ethyl ethanoate (VMSD1212, LB4146_V)' providing data by calculation of molar excess volume from low-pressure density measurements at variable mole fraction and constant temperature.

  13. Volumetric Properties of the Mixture Trichloromethane CHCl3 + C4H8O2 Ethyl ethanoate (VMSD1111, LB4144_V)

    Science.gov (United States)

    Cibulka, I.; Fontaine, J.-C.; Sosnkowska-Kehiaian, K.; Kehiaian, H. V.

    This document is part of Subvolume C 'Binary Liquid Systems of Nonelectrolytes III' of Volume 26 'Heats of Mixing, Vapor-Liquid Equilibrium, and Volumetric Properties of Mixtures and Solutions' of Landolt-Börnstein Group IV 'Physical Chemistry'. It contains the Chapter 'Volumetric Properties of the Mixture Trichloromethane CHCl3 + C4H8O2 Ethyl ethanoate (VMSD1111, LB4144_V)' providing data from direct low-pressure measurement of mass density at variable mole fraction and constant temperature, in the single-phase region(s).

  14. Communication: UV photoionization of cytosine catalyzed by Ag+

    Science.gov (United States)

    Taccone, Martín I.; Féraud, Geraldine; Berdakin, Matías; Dedonder-Lardeux, Claude; Jouvet, Christophe; Pino, Gustavo A.

    2015-07-01

    The photo-induced damages of DNA in interaction with metal cations, which are found in various environments, still remain to be characterized. In this paper, we show how the complexation of a DNA base (cytosine (Cyt)) with a metal cation (Ag+) changes its electronic properties. By means of UV photofragment spectroscopy of cold ions, it was found that the photoexcitation of the CytAg+ complex at low energy (315-282) nm efficiently leads to ionized cytosine (Cyt+) as the single product. This occurs through a charge transfer state in which an electron from the p orbital of Cyt is promoted to Ag+, as confirmed by ab initio calculations at the TD-DFT/B3LYP and RI-ADC(2) theory level using the SV(P) basis set. The low ionization energy of Cyt in the presence of Ag+ could have important implications as point mutation of DNA upon sunlight exposition.

  15. Communication: UV photoionization of cytosine catalyzed by Ag(+).

    Science.gov (United States)

    Taccone, Martín I; Féraud, Geraldine; Berdakin, Matías; Dedonder-Lardeux, Claude; Jouvet, Christophe; Pino, Gustavo A

    2015-07-28

    The photo-induced damages of DNA in interaction with metal cations, which are found in various environments, still remain to be characterized. In this paper, we show how the complexation of a DNA base (cytosine (Cyt)) with a metal cation (Ag(+)) changes its electronic properties. By means of UV photofragment spectroscopy of cold ions, it was found that the photoexcitation of the CytAg(+) complex at low energy (315-282) nm efficiently leads to ionized cytosine (Cyt(+)) as the single product. This occurs through a charge transfer state in which an electron from the p orbital of Cyt is promoted to Ag(+), as confirmed by ab initio calculations at the TD-DFT/B3LYP and RI-ADC(2) theory level using the SV(P) basis set. The low ionization energy of Cyt in the presence of Ag(+) could have important implications as point mutation of DNA upon sunlight exposition.

  16. Effects of cytosine methylation on transcription factor binding sites

    KAUST Repository

    Medvedeva, Yulia A

    2014-03-26

    Background: DNA methylation in promoters is closely linked to downstream gene repression. However, whether DNA methylation is a cause or a consequence of gene repression remains an open question. If it is a cause, then DNA methylation may affect the affinity of transcription factors (TFs) for their binding sites (TFBSs). If it is a consequence, then gene repression caused by chromatin modification may be stabilized by DNA methylation. Until now, these two possibilities have been supported only by non-systematic evidence and they have not been tested on a wide range of TFs. An average promoter methylation is usually used in studies, whereas recent results suggested that methylation of individual cytosines can also be important.Results: We found that the methylation profiles of 16.6% of cytosines and the expression profiles of neighboring transcriptional start sites (TSSs) were significantly negatively correlated. We called the CpGs corresponding to such cytosines " traffic lights" We observed a strong selection against CpG " traffic lights" within TFBSs. The negative selection was stronger for transcriptional repressors as compared with transcriptional activators or multifunctional TFs as well as for core TFBS positions as compared with flanking TFBS positions.Conclusions: Our results indicate that direct and selective methylation of certain TFBS that prevents TF binding is restricted to special cases and cannot be considered as a general regulatory mechanism of transcription. 2013 Medvedeva et al.; licensee BioMed Central Ltd.

  17. Three-Dimensional Structure and Catalytic Mechanism of Cytosine Deaminase

    Energy Technology Data Exchange (ETDEWEB)

    R Hall; A Fedorov; C Xu; E Fedorov; S Almo; F Raushel

    2011-12-31

    Cytosine deaminase (CDA) from E. coli is a member of the amidohydrolase superfamily. The structure of the zinc-activated enzyme was determined in the presence of phosphonocytosine, a mimic of the tetrahedral reaction intermediate. This compound inhibits the deamination of cytosine with a K{sub i} of 52 nM. The zinc- and iron-containing enzymes were characterized to determine the effect of the divalent cations on activation of the hydrolytic water. Fe-CDA loses activity at low pH with a kinetic pKa of 6.0, and Zn-CDA has a kinetic pKa of 7.3. Mutation of Gln-156 decreased the catalytic activity by more than 5 orders of magnitude, supporting its role in substrate binding. Mutation of Glu-217, Asp-313, and His-246 significantly decreased catalytic activity supporting the role of these three residues in activation of the hydrolytic water molecule and facilitation of proton transfer reactions. A library of potential substrates was used to probe the structural determinants responsible for catalytic activity. CDA was able to catalyze the deamination of isocytosine and the hydrolysis of 3-oxauracil. Large inverse solvent isotope effects were obtained on k{sub cat} and k{sub cat}/K{sub m}, consistent with the formation of a low-barrier hydrogen bond during the conversion of cytosine to uracil. A chemical mechanism for substrate deamination by CDA was proposed.

  18. Cytosine modifications in the honey bee (Apis mellifera worker genome

    Directory of Open Access Journals (Sweden)

    Erik Magne Koscielniak Rasmussen

    2015-02-01

    Full Text Available Epigenetic changes enable genomes to respond to changes in the environment, such as altered nutrition, activity, or social setting. Epigenetic modifications, thereby, provides a source of phenotypic plasticity in many species. The honey bee (Apis mellifera uses nutritionally sensitive epigenetic control mechanisms in the development of the royal caste (queens and the workers. The workers are functionally sterile females that can take on a range of distinct physiological and/or behavioral phenotypes in response to environmental changes. Honey bees have a wide repertoire of epigenetic mechanisms which, as in mammals, includes cytosine methylation, hydroxymethylated cytosines, together with the enzymatic machinery responsible for these cytosine modifications. Current data suggests that honey bees provide an excellent system for studying the social repertoire of the epigenome. In this review, we elucidate what is known so far about the honey bee epigenome and its mechanisms. Our discussion includes what may distinguish honey bees from other model animals, how the epigenome can influence worker behavioral task separation, and how future studies can answer central questions about the role of the epigenome in social behavior.

  19. Arabidopsis PAI gene arrangements, cytosine methylation and expression.

    OpenAIRE

    Melquist, S.; Luff, B; Bender, J.

    1999-01-01

    Previous analysis of the PAI tryptophan biosynthetic gene family in Arabidopsis thaliana revealed that the Wassilewskija (WS) ecotype has four PAI genes at three unlinked sites: a tail-to-tail inverted repeat at one locus (PAI1-PAI4) plus singlet genes at two other loci (PAI2 and PAI3). The four WS PAI genes are densely cytosine methylated over their regions of DNA identity. In contrast, the Columbia (Col) ecotype has three singlet PAI genes at the analogous loci (PAI1, PAI2, and PAI3) and no...

  20. Communication: UV photoionization of cytosine catalyzed by Ag{sup +}

    Energy Technology Data Exchange (ETDEWEB)

    Taccone, Martín I.; Berdakin, Matías; Pino, Gustavo A., E-mail: gpino@fcq.unc.edu.ar [INFIQC (CONICET – Universidad Nacional de Córdoba), Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba (Argentina); Féraud, Geraldine; Dedonder-Lardeux, Claude; Jouvet, Christophe [Physique des Interactions Ioniques et Moléculaires (PIIM): UMR- 7345, CNRS, Aix Marseille Université, 13397 Marseille (France)

    2015-07-28

    The photo-induced damages of DNA in interaction with metal cations, which are found in various environments, still remain to be characterized. In this paper, we show how the complexation of a DNA base (cytosine (Cyt)) with a metal cation (Ag{sup +}) changes its electronic properties. By means of UV photofragment spectroscopy of cold ions, it was found that the photoexcitation of the CytAg{sup +} complex at low energy (315-282) nm efficiently leads to ionized cytosine (Cyt{sup +}) as the single product. This occurs through a charge transfer state in which an electron from the p orbital of Cyt is promoted to Ag{sup +}, as confirmed by ab initio calculations at the TD-DFT/B3LYP and RI-ADC(2) theory level using the SV(P) basis set. The low ionization energy of Cyt in the presence of Ag{sup +} could have important implications as point mutation of DNA upon sunlight exposition.

  1. Low temperature FTIR spectroscopy and hydrogen bonding in cytosine polycrystals

    Science.gov (United States)

    Rozenberg, M.; Shoham, G.; Reva, I.; Fausto, R.

    2004-01-01

    The FTIR spectra of both the pure NH and isotopically substituted ND (90% D) polycrystalline cytosine were recorded in the range 400-4000 cm -1 as a function of temperature (10-300 K). For the first time, uncoupled NH(D) stretching mode bands of amine and imine groups were observed in the spectra of isotopically diluted cytosine at low temperatures. These bands correspond to the three distinct H-bonds that are present in the crystal, in agreement with the available data obtained by structural methods. At least nine bands were observed below 1000 cm -1 and, in consonance with their temperature and isotopic exchange behavior, were assigned to the NH proton out-of-the-plane bending modes. Six of these bands were found to correspond to additional "disordered" H-bonds, which could not be observed by structural methods. Empirical correlations of spectral and thermodynamic parameters enabled to estimate the contribution of the H-bonds to the sublimation enthalpy of the crystal, in agreement with independent experimental data.

  2. Epigenetic regulation of HIV-1 latency by cytosine methylation.

    Directory of Open Access Journals (Sweden)

    Steven E Kauder

    2009-06-01

    Full Text Available Human immunodeficiency virus type 1 (HIV-1 persists in a latent state within resting CD4+ T cells of infected persons treated with highly active antiretroviral therapy (HAART. This reservoir must be eliminated for the clearance of infection. Using a cDNA library screen, we have identified methyl-CpG binding domain protein 2 (MBD2 as a regulator of HIV-1 latency. Two CpG islands flank the HIV-1 transcription start site and are methylated in latently infected Jurkat cells and primary CD4+ T cells. MBD2 and histone deacetylase 2 (HDAC2 are found at one of these CpG islands during latency. Inhibition of cytosine methylation with 5-aza-2'deoxycytidine (aza-CdR abrogates recruitment of MBD2 and HDAC2. Furthermore, aza-CdR potently synergizes with the NF-kappaB activators prostratin or TNF-alpha to reactivate latent HIV-1. These observations confirm that cytosine methylation and MBD2 are epigenetic regulators of HIV-1 latency. Clearance of HIV-1 from infected persons may be enhanced by inclusion of DNA methylation inhibitors, such as aza-CdR, and NF-kappaB activators into current antiviral therapies.

  3. Cyclophosphamide Perturbs Cytosine Methylation in Jurkat-T Cells through LSD1-mediated Stabilization of DNMT1 Protein

    OpenAIRE

    ZHANG Jing; Yuan, Bifeng; Zhang, Fan; Xiong, Lei; Wu, Jiang; Pradhan, Sriharsa; Wang, Yinsheng

    2011-01-01

    Aberrant cytosine methylation is known to be associated with cancer development. Here we assessed how common cancer chemotherapeutic agents perturb cytosine methylation in Jurkat-T acute lymphoblastic leukemia cells. We tested six anti-tumor agents and found that cyclophosphamide induced the most pronounced increase in global DNA cytosine methylation after a 24-hr treatment. Long-term treatment with cyclophosphamide led to a time-dependent increase in cytosine methylation level with up to 4 d...

  4. Prebiotic cytosine synthesis: a critical analysis and implications for the origin of life.

    Science.gov (United States)

    Shapiro, R

    1999-04-13

    A number of theories propose that RNA, or an RNA-like substance, played a role in the origin of life. Usually, such hypotheses presume that the Watson-Crick bases were readily available on prebiotic Earth, for spontaneous incorporation into a replicator. Cytosine, however, has not been reported in analyses of meteorites nor is it among the products of electric spark discharge experiments. The reported prebiotic syntheses of cytosine involve the reaction of cyanoacetylene (or its hydrolysis product, cyanoacetaldehyde), with cyanate, cyanogen, or urea. These substances undergo side reactions with common nucleophiles that appear to proceed more rapidly than cytosine formation. To favor cytosine formation, reactant concentrations are required that are implausible in a natural setting. Furthermore, cytosine is consumed by deamination (the half-life for deamination at 25 degrees C is approximately 340 yr) and other reactions. No reactions have been described thus far that would produce cytosine, even in a specialized local setting, at a rate sufficient to compensate for its decomposition. On the basis of this evidence, it appears quite unlikely that cytosine played a role in the origin of life. Theories that involve replicators that function without the Watson-Crick pairs, or no replicator at all, remain as viable alternatives.

  5. The ground and excited state electron affinities of cytosine and trans-azobenzene

    Science.gov (United States)

    Chen, Edward C. M.; Herder, Charles; Chen, Edward S.

    2007-06-01

    The electron capture detector, reduction potential, electron transfer and photon methods of determining electron affinities are compared. The adiabatic electron affinities are (in eV): t-azobenzene(O 2), 1.578(5); t-azobenzene, 1.378(5); cytosine, 1.043(5) from anion photoelectron spectra. The largest or ground state value for trans-azobenzene and an excited state electron affinity for cytosine, 0.70 eV are also determined by reduction potentials. Other excited state energies are (in eV): t-azobenzene, 0.328(5), 0.589(5), 0.690(5), 0.768(5), 0.954(5), 1.038(5), 1.150(5), 1.275(5) and cytosine, 0.089(5), 0.098(5), 0.198(5), 0.235(5). The cytosine values are consistent with electron transport and radiation damage and repair in DNA.

  6. DNA duplex stability of the thio-iso-guanine•methyl-iso-Cytosine base pair.

    Science.gov (United States)

    Lee, Dongkye; Switzer, Christopher

    2015-01-01

    We report the synthesis, incorporation into oligonucleotides, and base-pairing properties of the 2-thio-variant of iso-guanine. Iso-guanine is the purine component of a nonstandard base pair with 5-methyl-iso-cytosine. The 2-thio-iso-guanine • 5-methyl-iso-cytosine base pair is found to have similar stability to an adenine • thymine pair.

  7. Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants

    Indian Academy of Sciences (India)

    Sushil Kumar; Renu Kumari; Vishakha Sharma; Vinay Sharma

    2013-12-01

    Heritable information in plants consists of genomic information in DNA sequence and epigenetic information superimposed on DNA sequence. The latter is in the form of cytosine methylation at CG, CHG and CHH elements (where H = A, T or C) and a variety of histone modifications in nucleosomes. The epialleles arising from cytosine methylation marks on the nuclear genomic loci have better heritability than the epiallelic variation due to chromatin marks. Phenotypic variation is increased manifold by epiallele comprised methylomes. Plants (angiosperms) have highly conserved genetic mechanisms to establish, maintain or erase cytosine methylation from epialleles. The methylation marks in plants fluctuate according to the cell/tissue/organ in the vegetative and reproductive phases of plant life cycle. They also change according to environment. Epialleles arise by gain or loss of cytosine methylation marks on genes. The changes occur due to the imperfection of the processes that establish and maintain the marks and on account of spontaneous and stress imposed removal of marks. Cytosine methylation pattern acquired in response to abiotic or biotic stress is often inherited over one to several subsequent generations. Cytosine methylation marks affect physiological functions of plants via their effect(s) on gene expression levels. They also repress transposable elements that are abundantly present in plant genomes. The density of their distribution along chromosome lengths affects meiotic recombination rate, while their removal increases mutation rate. Transposon activation due to loss of methylation causes rearrangements such that new gene regulatory networks arise and genes for microRNAs may originate. Cytosine methylation dynamics contribute to evolutionary changes. This review presents and discusses the available evidence on origin, removal and roles of cytosine methylation and on related processes, such as RNA directed DNA methylation, imprinting, paramutation and

  8. Benchmark Thermochemistry for Biologically Relevant Adenine and Cytosine. A Combined Experimental and Theoretical Study.

    Science.gov (United States)

    Emel'yanenko, Vladimir N; Zaitsau, Dzmitry H; Shoifet, Evgeni; Meurer, Florian; Verevkin, Sergey P; Schick, Christoph; Held, Christoph

    2015-09-17

    The thermochemical properties available in the literature for adenine and cytosine are in disarray. A new condensed phase standard (p° = 0.1 MPa) molar enthalpy of formation at T = 298.15 K was measured by using combustion calorimetry. New molar enthalpies of sublimation were derived from the temperature dependence of vapor pressure measured by transpiration and by the quarz-crystal microbalance technique. The heat capacities of crystalline adenine and cytosine were measured by temperature-modulated DSC. Thermodynamic data on adenine and cytosine available in the literature were collected, evaluated, and combined with our experimental results. Thus, the evaluated collection of data together with the new experimental results reported here has helped to resolve contradictions in the available enthalpies of formation. A set of reliable thermochemical data is recommended for adenine and cytosine for further thermochemical calculations. Quantum-chemical calculations of the gas phase molar enthalpies of formation of adenine and cytosine have been performed by using the G4 method and results were in excellent agreement with the recommended experimental data. The standard molar entropies of formation and the standard molar Gibbs functions of formation in crystal and gas state have been calculated. Experimental vapor-pressure data measured in this work were used to estimate pure-component PC-SAFT parameters. This allowed modeling solubility of adenine and cytosine in water over the temperature interval 278-310 K.

  9. Cytosine methylation dysregulation in neonates following intrauterine growth restriction.

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    Francine Einstein

    Full Text Available BACKGROUND: Perturbations of the intrauterine environment can affect fetal development during critical periods of plasticity, and can increase susceptibility to a number of age-related diseases (e.g., type 2 diabetes mellitus; T2DM, manifesting as late as decades later. We hypothesized that this biological memory is mediated by permanent alterations of the epigenome in stem cell populations, and focused our studies specifically on DNA methylation in CD34+ hematopoietic stem and progenitor cells from cord blood from neonates with intrauterine growth restriction (IUGR and control subjects. METHODS AND FINDINGS: Our epigenomic assays utilized a two-stage design involving genome-wide discovery followed by quantitative, single-locus validation. We found that changes in cytosine methylation occur in response to IUGR of moderate degree and involving a restricted number of loci. We also identify specific loci that are targeted for dysregulation of DNA methylation, in particular the hepatocyte nuclear factor 4alpha (HNF4A gene, a well-known diabetes candidate gene not previously associated with growth restriction in utero, and other loci encoding HNF4A-interacting proteins. CONCLUSIONS: Our results give insights into the potential contribution of epigenomic dysregulation in mediating the long-term consequences of IUGR, and demonstrate the value of this approach to studies of the fetal origin of adult disease.

  10. Infrared spectra of protonated uracil, thymine and cytosine.

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    Salpin, Jean-Yves; Guillaumont, Sébastien; Tortajada, Jeanine; MacAleese, Luke; Lemaire, Joël; Maitre, Philippe

    2007-10-22

    The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d'Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm(-1) in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap.

  11. Spectral characterization, optical band gap calculations and DNA binding of some binuclear Schiff-base metal complexes derived from 2-amino-ethanoic acid and acetylacetone

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    Hussien, Mostafa A.; Nawar, Nagwa; Radwan, Fatima M.; Hosny, Nasser Mohammed

    2015-01-01

    Bi-nuclear metal complexes derived from the reaction of Cu(II), Co(II), Ni(II) and Zn(II) acetates with the Schiff-base ligand (H2L) resulted from the condensation of 2-amino-ethanoic acid (glycine) and acetylacetone have been synthesized and characterized by elemental analyses, Raman spectra, FT-IR, ES-MS, UV-Vis., 1H NMR, ESR, thermal analyses (TG, DTG and DTA) and magnetic measurements. The results showed that, the Schiff base ligand can bind two metal ions in the same time. It coordinates to the first metal ion as mono-negative bi-dentate through azomethine nitrogen and enolic carbonyl after deprotonation. At the same time, it binds to the second metal ion via carboxylate oxygen after deprotonation. The thermodynamic parameters E∗, ΔH∗, ΔG∗ and ΔS∗ have been calculated by Coats-Redfern (CR) and Horowitz-Metzger (HM) methods. The optical band gaps of the isolated complexes have been calculated from absorption spectra and the results indicated semi-conducting nature of the investigated complexes. The interactions between the copper (II) complex and calf thymus DNA (CT-DNA) have been studied by UV spectra. The results confirm that the Cu(II) complex binds to CT-DNA.

  12. Computation of Isobaric Vapor-Liquid Equilibrium Data for Binary and Ternary Mixtures of Methanol, Water, and Ethanoic Acid from T, p, x, and HmE Measurements

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    Daming Gao

    2012-01-01

    Full Text Available Vapor-liquid equilibrium (VLE data for the strongly associated ternary system methanol + water + ethanoic acid and the three constituent binary systems have been determined by the total pressure-temperature-liquid-phase composition-molar excess enthalpy of mixing of the liquid phase (p, T, x, HmE for the binary systems using a novel pump ebulliometer at 101.325 kPa. The vapor-phase compositions of these binary systems had been calculated from Tpx and HmE based on the Q function of molar excess Gibbs energy through an indirect method. Moreover, the experimental T, x data are used to estimate nonrandom two-liquid (NRTL, Wilson, Margules, and van Laar model parameters, and these parameters in turn are used to calculate vapor-phase compositions. The activity coefficients of the solution were correlated with NRTL, Wilson, Margules, and van Laar models through fitting by least-squares method. The VLE data of the ternary system were well predicted from these binary interaction parameters of NRTL, Wilson, Margules, and van Laar model parameters without any additional adjustment to build the thermodynamic model of VLE for the ternary system and obtain the vapor-phase compositions and the calculated bubble points.

  13. Real-time study of interactions between cytosine-cytosine pairs in DNA oligonucleotides and silver ions using dual polarization interferometry.

    Science.gov (United States)

    Zheng, Yu; Yang, Cheng; Yang, Fan; Yang, Xiurong

    2014-04-15

    The real-time conformational changes of cytosine (C)-rich ssDNA oligonucleotides upon binding with silver ions (Ag(+)) were studied using dual polarization interferometry (DPI). Upon the addition of Ag(+), Ag(+) selectively bound to cytosine-cytosine mismatches and formed C-Ag(+)-C complexes, inducing change of the structure of the C-rich ssDNA from random coil conformation to duplex conformation, whereas the control ssDNA without cytosine-cytosine mismatches had no such signal, which was consistent with circular dichroism (CD) characterization. The conformational change of DNA was reflected on the changes of the mass, thickness, and density values resolved by DPI. The calibration curves showed that as the concentration of Ag(+) increased from 10 nM to 8 μM, the thickness and mass values increased linearly while the density values decreased linearly. Other metal ions such as K(+), Ca(2+), Na(+), Mg(2+), Zn(2+), Mn(2+), Ni(2+), and Pb(2+) did not interfere with the interaction between Ag(+) and C-rich ssDNA, indicating that this method had a good selectivity. The practical application of this biosensor was also investigated in real samples such as drinking water. Besides, cysteine could specifically capture Ag(+) from C-Ag(+)-C complexes and transformed the structure of the C-rich DNA back from rigid double-stranded conformation to random coil conformation, which allowed cysteine to be detected selectively as well. It is expected that this biosensing strategy may be utilized to study the interaction of DNA with other molecules.

  14. Inheritance and variation of Cytosine methylation in three populus allotriploid populations with different heterozygosity.

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    Yujing Suo

    Full Text Available DNA methylation is an epigenetic mechanism with the potential to regulate gene expression and affect plant phenotypes. Both hybridization and genome doubling may affect the DNA methylation status of newly formed allopolyploid plants. Previous studies demonstrated that changes in cytosine methylation levels and patterns were different among individual hybrid plant, therefore, studies investigating the characteristics of variation in cytosine methylation status must be conducted at the population level to avoid sampling error. In the present study, an F1 hybrid diploid population and three allotriploid populations with different heterozygosity [originating from first-division restitution (FDR, second-division restitution (SDR, and post-meiotic restitution (PMR 2n eggs of the same female parent] were used to investigate cytosine methylation inheritance and variation relative to their common parents using methylation-sensitive amplification polymorphism (MSAP. The variation in cytosine methylation in individuals in each population exhibited substantial differences, confirming the necessity of population epigenetics. The total methylation levels of the diploid population were significantly higher than in the parents, but those of the three allotriploid populations were significantly lower than in the parents, indicating that both hybridization and polyploidization contributed to cytosine methylation variation. The vast majority of methylated status could be inherited from the parents, and the average percentages of non-additive variation were 6.29, 3.27, 5.49 and 5.07% in the diploid, FDR, SDR and PMR progeny populations, respectively. This study lays a foundation for further research on population epigenetics in allopolyploids.

  15. Single-Cell Quantification of Cytosine Modifications by Hyperspectral Dark-Field Imaging.

    Science.gov (United States)

    Wang, Xiaolei; Cui, Yi; Irudayaraj, Joseph

    2015-12-22

    Epigenetic modifications on DNA, especially on cytosine, play a critical role in regulating gene expression and genome stability. It is known that the levels of different cytosine derivatives are highly dynamic and are regulated by a variety of factors that act on the chromatin. Here we report an optical methodology based on hyperspectral dark-field imaging (HSDFI) using plasmonic nanoprobes to quantify the recently identified cytosine modifications on DNA in single cells. Gold (Au) and silver (Ag) nanoparticles (NPs) functionalized with specific antibodies were used as contrast-generating agents due to their strong local surface plasmon resonance (LSPR) properties. With this powerful platform we have revealed the spatial distribution and quantity of 5-carboxylcytosine (5caC) at the different stages in cell cycle and demonstrated that 5caC was a stably inherited epigenetic mark. We have also shown that the regional density of 5caC on a single chromosome can be mapped due to the spectral sensitivity of the nanoprobes in relation to the interparticle distance. Notably, HSDFI enables an efficient removal of the scattering noises from nonspecifically aggregated nanoprobes, to improve accuracy in the quantification of different cytosine modifications in single cells. Further, by separating the LSPR fingerprints of AuNPs and AgNPs, multiplex detection of two cytosine modifications was also performed. Our results demonstrate HSDFI as a versatile platform for spatial and spectroscopic characterization of plasmonic nanoprobe-labeled nuclear targets at the single-cell level for quantitative epigenetic screening.

  16. HPLC-UV, MALDI-TOF-MS and ESI-MS/MS analysis of the mechlorethamine DNA crosslink at a cytosine-cytosine mismatch pair.

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    Pornchai Rojsitthisak

    Full Text Available BACKGROUND: Mechlorethamine [ClCH(2CH(2N(CH(3CH(2CH(2Cl], a nitrogen mustard alkylating agent, has been proven to form a DNA interstrand crosslink at a cytosine-cytosine (C-C mismatch pair using gel electrophoresis. However, the atomic connectivity of this unusual crosslink is unknown. METHODOLOGY/PRINCIPAL FINDINGS: HPLC-UV, MALDI-TOF-MS, and ESI-MS/MS were used to determine the atomic connectivity of the DNA C-C crosslink formed by mechlorethamine, MALDI-TOF-MS of the HPLC-purified reaction product of mechlorethamine with the DNA duplex d[CTCACACCGTGGTTC]•d[GAACCACCGTGTGAG] (underlined bases are a C-C mismatch pair indicated formation of an interstrand crosslink at m/z 9222.088 [M-2H+Na](+. Following enzymatic digestion of the crosslinked duplex by snake venom phosphodiesterase and calf intestinal phosphatase, ESI-MS/MS indicated the presence of dC-mech-dC [mech = CH(2CH(2N(CH(3CH(2CH(2] at m/z 269.2 [M](2+ (expected m/z 269.6, exact mass 539.27 and its hydrolytic product dC-mech-OH at m/z 329.6 [M](+ (expected m/z 329.2. Fragmentation of dC-mech-dC gave product ions at m/z 294.3 and 236.9 [M](+, which are both due to loss of the 4-amino group of cytosine (as ammonia, in addition to dC and dC+HN(CH(3CH = CH(2, respectively. The presence of m/z 269.2 [M](2+ and loss of ammonia exclude crosslink formation at cytosine N(4 or O(2 and indicate crosslinking through cytosine N(3 with formation of two quaternary ammonium ions. CONCLUSIONS: Our results provide an important addition to the literature, as the first example of the use of HPLC and MS for analysis of a DNA adduct at the N(3 position of cytosine.

  17. Cytosine deamination and the precipitous decline of spontaneous mutation during Earth's history.

    Science.gov (United States)

    Lewis, Charles A; Crayle, Jesse; Zhou, Shuntai; Swanstrom, Ronald; Wolfenden, Richard

    2016-07-19

    The hydrolytic deamination of cytosine and 5-methylcytosine residues in DNA appears to contribute significantly to the appearance of spontaneous mutations in microorganisms and in human disease. In the present work, we examined the mechanism of cytosine deamination and the response of the uncatalyzed reaction to changing temperature. The positively charged 1,3-dimethylcytosinium ion was hydrolyzed at a rate similar to the rate of acid-catalyzed hydrolysis of 1-methylcytosine, for which it furnishes a satisfactory kinetic model and a probable mechanism. In agreement with earlier reports, uncatalyzed deamination was found to proceed at very similar rates for cytosine, 1-methylcytosine, cytidine, and cytidine 5'-phosphate, and also for cytosine residues in single-stranded DNA generated from a phagemid, in which we sequenced an insert representing the gene of the HIV-1 protease. Arrhenius plots for the uncatalyzed deamination of cytosine were linear over the temperature range from 90 °C to 200 °C and indicated a heat of activation (ΔH(‡)) of 23.4 ± 0.5 kcal/mol at pH 7. Recent evidence indicates that the surface of the earth has been cool enough to support life for more than 4 billion years and that life has been present for almost as long. If the temperature at Earth's surface is assumed to have followed Newton's law of cooling, declining exponentially from 100 °C to 25 °C during that period, then half of the cytosine-deaminating events per unit biomass would have taken place during the first 0.2 billion years, and <99.4% would have occurred during the first 2 billion years.

  18. Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Kostko, Oleg; Bravaya, Ksenia; Krylov, Anna; Ahmed, Musahid

    2009-12-14

    We report a combined theoretical and experimental study of ionization of cytosine monomers and dimers. Gas-phase molecules are generated by thermal vaporization of cytosine followed by expansion of the vapor in a continuous supersonic jet seeded in Ar. The resulting species are investigated by single photon ionization with tunable vacuum-ultraviolet (VUV) synchrotron radiation and mass analyzed using reflectron mass spectrometry. Energy onsets for the measured photoionization efficiency (PIE) spectra are 8.60+-0.05 eV and 7.6+-0.1 eV for the monomer and the dimer, respectively, and provide an estimate for the adiabatic ionization energies (AIE). The first AIE and the ten lowest vertical ionization energies (VIEs) for selected isomers of cytosine dimer computed using equation-of-motion coupled-cluster (EOM-IP-CCSD) method are reported. The comparison of the computed VIEs with the derivative of the PIE spectra, suggests that multiple isomers of the cytosine dimer are present in the molecular beam. The calculations reveal that the large red shift (0.7 eV) of the first IE of the lowest-energy cytosine dimer is due to strong inter-fragment electrostatic interactions, i.e., the hole localized on one of the fragments is stabilized by the dipole moment of the other. A sharp rise in the CH+ signal at 9.20+-0.05 eV is ascribed to the formation of protonated cytosine by dissociation of the ionized dimers. The dominant role of this channel is supported by the computed energy thresholds for the CH+ appearance and the barrierless or nearly barrierless ionization-induced proton transfer observed for five isomers of the dimer.

  19. Ultrafast internal conversion of excited cytosine via the lowest pipi electronic singlet state.

    Science.gov (United States)

    Merchán, Manuela; Serrano-Andrés, Luis

    2003-07-09

    Computational evidence at the CASPT2 level supports that the lowest excited state pipi* contributes to the S1/S0 crossing responsible for the ultrafast decay of singlet excited cytosine. The computed radiative lifetime, 33 ns, is consistent with the experimentally derived value, 40 ns. The nOpi* state does not play a direct role in the rapid repopulation of the ground state; it is involved in a S2/S1 crossing. Alternative mechanisms through excited states pisigma* or nNpi* are not competitive in cytosine.

  20. IRMPD Action Spectroscopy of Alkali Metal Cation-Cytosine Complexes: Effects of Alkali Metal Cation Size on Gas Phase Conformation

    NARCIS (Netherlands)

    Yang, B.; Wu, R.R.; Polfer, N.C.; Berden, G.; Oomens, J.; Rodgers, M.T.

    2013-01-01

    The gas-phase structures of alkali metal cation-cytosine complexes generated by electrospray ionization are probed via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra of five alkali metal cation-cytosine complexes exhibit both simi

  1. Global DNA cytosine methylation as an evolving trait: phylogenetic signal and correlated evolution with genome size in Angiosperms

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    Conchita eAlonso

    2015-01-01

    Full Text Available DNA cytosine methylation is a widespread epigenetic mechanism in eukaryotes, and plant genomes commonly are densely methylated. Genomic methylation can be associated with functional consequences such as mutational events, genomic instability or altered gene expression, but little is known on interspecific variation in global cytosine methylation in plants. In this paper, we compare global cytosine methylation estimates obtained by HPLC and use a phylogenetically-informed analytical approach to test for significance of evolutionary signatures of this trait across 54 angiosperm species in 25 families. We evaluate whether interspecific variation in global cytosine methylation is statistically related to phylogenetic distance and also whether it is evolutionarily correlated with genome size (C-value. Global cytosine methylation varied widely between species, ranging between 5.3% (Arabidopsis and 39.2% (Narcissus. Differences between species were related to their evolutionary trajectories, as denoted by the strong phylogenetic signal underlying interspecific variation. Global cytosine methylation and genome size were evolutionarily correlated, as revealed by the significant relationship between the corresponding phylogenetically independent contrasts. On average, a ten-fold increase in genome size entailed an increase of about 10% in global cytosine methylation. Results show that global cytosine methylation is an evolving trait in angiosperms whose evolutionary trajectory is significantly linked to changes in genome size, and suggest that the evolutionary implications of epigenetic mechanisms are likely to vary between plant lineages.

  2. IRMPD action spectroscopy of alkali metal cation-cytosine complexes: effects of alkali metal cation size on gas phase conformation.

    Science.gov (United States)

    Yang, Bo; Wu, R R; Polfer, N C; Berden, G; Oomens, J; Rodgers, M T

    2013-10-01

    The gas-phase structures of alkali metal cation-cytosine complexes generated by electrospray ionization are probed via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra of five alkali metal cation-cytosine complexes exhibit both similar and distinctive spectral features over the range of ~1000-1900 cm(-1). The IRMPD spectra of the Li(+)(cytosine), Na(+)(cytosine), and K(+)(cytosine) complexes are relatively simple but exhibit changes in the shape and shifts in the positions of several bands that correlate with the size of the alkali metal cation. The IRMPD spectra of the Rb(+)(cytosine) and Cs(+)(cytosine) complexes are much richer as distinctive new IR bands are observed, and the positions of several bands continue to shift in relation to the size of the metal cation. The measured IRMPD spectra are compared to linear IR spectra of stable low-energy tautomeric conformations calculated at the B3LYP/def2-TZVPPD level of theory to identify the conformations accessed in the experiments. These comparisons suggest that the evolution in the features in the IRMPD action spectra with the size of the metal cation, and the appearance of new bands for the larger metal cations, are the result of the variations in the intensities at which these complexes can be generated and the strength of the alkali metal cation-cytosine binding interaction, not the presence of multiple tautomeric conformations. Only a single tautomeric conformation is accessed for all five alkali metal cation-cytosine complexes, where the alkali metal cation binds to the O2 and N3 atoms of the canonical amino-oxo tautomer of cytosine, M(+)(C1).

  3. Improved cytotoxic effects of Salmonella-producing cytosine deaminase in tumour cells

    Science.gov (United States)

    Mesa-Pereira, Beatriz; Medina, Carlos; Camacho, Eva María; Flores, Amando; Santero, Eduardo

    2015-01-01

    In order to increase the cytotoxic activity of a Salmonella strain carrying a salicylate-inducible expression system that controls cytosine deaminase production, we have modified both, the vector and the producer bacterium. First, the translation rates of the expression module containing the Escherichia coli codA gene cloned under the control of the Pm promoter have been improved by using the T7 phage gene 10 ribosome binding site sequence and replacing the original GUG start codon by AUG. Second, to increase the time span in which cytosine deaminase may be produced by the bacteria in the presence of 5-fluorocytosine, a 5-fluorouracyl resistant Salmonella strain has been constructed by deleting its upp gene sequence. This new Salmonella strain shows increased cytosine deaminase activity and, after infecting tumour cell cultures, increased cytotoxic and bystander effects under standard induction conditions. In addition, we have generated a purD mutation in the producer strain to control its intracellular proliferation by the presence of adenine and avoid the intrinsic Salmonella cell death induction. This strategy allows the analysis and comparison of the cytotoxic effects of cytosine deaminase produced by different Salmonella strains in tumour cell cultures. PMID:25227763

  4. Expression systems for industrial Gram-positive bacteria with low guanine and cytosine content

    NARCIS (Netherlands)

    Vos, Willem M. de; Kleerebezem, Michiel; Kuipers, Oscar P.

    1997-01-01

    Recent years have seen an increase in the development of gene expression systems for industrial Gram-positive bacteria with low guanine and cytosine content that belong to the genera Bacillus, Clostridium, Lactococcus, Lactobacillus, Staphylococcus and Streptococcus. In particular, considerable adva

  5. Formulation, quality control and shelf life of the experimental cytostatic drug cyclopentenyl cytosine

    NARCIS (Netherlands)

    K. Schimmel; H.J. Guchelaar; E. van Kan

    2006-01-01

    This paper describes the formulation and quality control of an aqueous sterilized formulation of the experimental cytostatic drug cyclopentenyl cytosine (CPEC) to be used in Phase I/II clinical trials. The raw drug substance was extensively tested. A High Pressure Liquid Chromotography (HPLC) method

  6. Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines.

    Science.gov (United States)

    Zhang, Zhou; Zheng, Yinan; Zhang, Xu; Liu, Cong; Joyce, Brian Thomas; Kibbe, Warren A; Hou, Lifang; Zhang, Wei

    2016-02-01

    Inter-individual variation in cytosine modifications has been linked to complex traits in humans. Cytosine modification variation is partially controlled by single nucleotide polymorphisms (SNPs), known as modified cytosine quantitative trait loci (mQTL). However, little is known about the role of short tandem repeat polymorphisms (STRPs), a class of structural genetic variants, in regulating cytosine modifications. Utilizing the published data on the International HapMap Project lymphoblastoid cell lines (LCLs), we assessed the relationships between 721 STRPs and the modification levels of 283,540 autosomal CpG sites. Our findings suggest that, in contrast to the predominant cis-acting mode for SNP-based mQTL, STRPs are associated with cytosine modification levels in both cis-acting (local) and trans-acting (distant) modes. In local scans within the ±1 Mb windows of target CpGs, 21, 9, and 21 cis-acting STRP-based mQTL were detected in CEU (Caucasian residents from Utah, USA), YRI (Yoruba people from Ibadan, Nigeria), and the combined samples, respectively. In contrast, 139,420, 76,817, and 121,866 trans-acting STRP-based mQTL were identified in CEU, YRI, and the combined samples, respectively. A substantial proportion of CpG sites detected with local STRP-based mQTL were not associated with SNP-based mQTL, suggesting that STRPs represent an independent class of mQTL. Functionally, genetic variants neighboring CpG-associated STRPs are enriched with genome-wide association study (GWAS) loci for a variety of complex traits and diseases, including cancers, based on the National Human Genome Research Institute (NHGRI) GWAS Catalog. Therefore, elucidating these STRP-based mQTL in addition to SNP-based mQTL can provide novel insights into the genetic architectures of complex traits.

  7. In planta assays involving epigenetically silenced genes reveal inhibition of cytosine methylation by genistein

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    Arase Sachiko

    2012-03-01

    Full Text Available Abstract Background Cytosine methylation is involved in epigenetic control of gene expression in a wide range of organisms. An increasing number of examples indicate that changing the frequency of cytosine methylation in the genome is a feasible tool to engineer novel traits in plants. Although demethylating effects of compounds have been analyzed in human cultured cells in terms of suppressing cancer, their effect in plant cells has not been analyzed extensively. Here, we developed in planta assay systems to detect inhibition of cytosine methylation using plants that contain a transgene transcriptionally silenced by an epigenetic mechanism. Results Seeds of two transgenic plants were used: a petunia line that has been identified as a revertant of the co-suppression of the chalcone synthase-A (CHS-A gene and contains CHS-A transgenes whose transcription is repressed; Nicotiana benthamiana plants that contain the green fluorescent protein (GFP reporter gene whose transcription is repressed through virus-induced transcriptional gene silencing. Seeds of these plants were sown on a medium that contained a demethylating agent, either 5-azacytidine or trichostatin A, and the restoration of the transcriptionally active state of the transgene was detected in seedlings. Using these systems, we found that genistein, a major isoflavonoid compound, inhibits cytosine methylation, thus restoring transgene transcription. Genistein also restored the transcription of an epigenetically silenced endogenous gene in Arabidopsis plants. Conclusions Our assay systems allowed us to assess the inhibition of cytosine methylation, in particular of maintenance of methylation, by compounds in plant cells. These results suggest a novel role of flavonoids in plant cells and that genistein is useful for modifying the epigenetic state of plant genomes.

  8. Cytosine methylation alteration in natural populations of Leymus chinensis induced by multiple abiotic stresses.

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    Yingjie Yu

    Full Text Available BACKGROUND: Human activity has a profound effect on the global environment and caused frequent occurrence of climatic fluctuations. To survive, plants need to adapt to the changing environmental conditions through altering their morphological and physiological traits. One known mechanism for phenotypic innovation to be achieved is environment-induced rapid yet inheritable epigenetic changes. Therefore, the use of molecular techniques to address the epigenetic mechanisms underpinning stress adaptation in plants is an important and challenging topic in biological research. In this study, we investigated the impact of warming, nitrogen (N addition, and warming+nitrogen (N addition stresses on the cytosine methylation status of Leymus chinensis Tzvel. at the population level by using the amplified fragment length polymorphism (AFLP, methylation-sensitive amplified polymorphism (MSAP and retrotransposon based sequence-specific amplification polymorphism (SSAP techniques. METHODOLOGY/PRINCIPAL FINDINGS: Our results showed that, although the percentages of cytosine methylation changes in SSAP are significantly higher than those in MSAP, all the treatment groups showed similar alteration patterns of hypermethylation and hypomethylation. It meant that the abiotic stresses have induced the alterations in cytosine methylation patterns, and the levels of cytosine methylation changes around the transposable element are higher than the other genomic regions. In addition, the identification and analysis of differentially methylated loci (DML indicated that the abiotic stresses have also caused targeted methylation changes at specific loci and these DML might have contributed to the capability of plants in adaptation to the abiotic stresses. CONCLUSIONS/SIGNIFICANCE: Our results demonstrated that abiotic stresses related to global warming and nitrogen deposition readily evoke alterations of cytosine methylation, and which may provide a molecular basis for rapid

  9. Clinical implications of cytosine deletion of exon 5 of P53 gene in non small cell lung cancer patients

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    Rashid Mir

    2016-01-01

    Full Text Available Aim: Lung cancer is considered to be the most common cancer in the world. In humans, about 50% or more cancers have a mutated tumor suppressor p53 gene thereby resulting in accumulation of p53 protein and losing its function to activate the target genes that regulate the cell cycle and apoptosis. Extensive research conducted in murine cancer models with activated p53, loss of p53, or p53 missense mutations have facilitated researchers to understand the role of this key protein. Our study was aimed to evaluate the frequency of cytosine deletion in nonsmall cell lung cancer (NSCLC patients. Methods: One hundred NSCLC patients were genotyped for P53 (exon5, codon168 cytosine deletion leading to loss of its function and activate the target genes by allele-specific polymerase chain reaction. The P53 cytosine deletion was correlated with all the clinicopathological parameters of the patients. Results and Analysis: 59% cases were carrying P53 cytosine deletion. Similarly, the significantly higher incidence of cytosine deletion was reported in current smokers (75% in comparison to exsmoker and nonsmoker. Significantly higher frequency of cytosine deletion was reported in adenocarcinoma (68.08% than squamous cell carcinoma (52.83%. Also, a significant difference was reported between p53 cytosine deletion and metastasis (64.28%. Further, the majority of the cases assessed for response carrying P53 cytosine deletion were found to show faster disease progression. Conclusion: The data suggests that there is a significant association of the P53 exon 5 deletion of cytosine in codon 168 with metastasis and staging of the disease.

  10. Chloridotris[μ2-2-(dimethyl­amino)­ethano­lato]-μ3-hydroxido-tri-μ2-trifluoro­acetato-tetra­copper(II) tetra­hydro­furan solvate

    OpenAIRE

    Hussain, S. Tajammul; Bakar, Shahzad Abu; Mazhar, Mohammad; Zeller, Matthias

    2010-01-01

    The title compound, [Cu4(C2F3O2)3(C4H10NO)3Cl(OH)]·C4H8O or [Cu4(TFA)3(dmae)3Cl(OH)]·THF (dmae is dimeth­yl­amino­ethano­late, TFA is trifluoro­acetate and THF is tetra­hydro­furan), has an approximate mol­ecular threefold symmetry with three equivalent {Cu(dmae)(TFA)} units bridging between a Cu—Cl and a hydroxide unit, with the latter two lying on the mol­ecular threefold axis. However, in the solid state, the tetranuclear complex has Ci symmetry. The Cu atom bonded to the Cl atom has a dis...

  11. A computational study of adenine, uracil, and cytosine adsorption upon AlN and BN nano-cages

    Energy Technology Data Exchange (ETDEWEB)

    Baei, Mohammad T. [Department of Chemistry, Islamic Azad University, Azadshahr Branch, Azadshahr, Golestan (Iran, Islamic Republic of); Taghartapeh, Mohammad Ramezani [Young Researchers and Elite Club, Islamic Azad University, Gorgan Branch, Gorgan (Iran, Islamic Republic of); Lemeski, E. Tazikeh [Department of Chemistry, Islamic Azad University, Gorgan Branch, Gorgan (Iran, Islamic Republic of); Soltani, Alireza, E-mail: alireza.soltani46@yahoo.com [Young Researchers and Elite Club, Islamic Azad University, Gorgan Branch, Gorgan (Iran, Islamic Republic of)

    2014-07-01

    Density-functional theory calculations are used to investigate the interaction of Al{sub 12}N{sub 12} and B{sub 12}N{sub 12} clusters with the adenine (A), uracil (U), and cytosine (C) molecules. The current calculations demonstrate that these hybrid adsorbent materials are able to adsorb the adenine, uracil, and cytosine molecules through exothermic processes. Our theoretical results reveal improvement in the adsorption of adenine, uracil, and cytosine on Al{sub 12}N{sub 12} and B{sub 12}N{sub 12}. It is observed that B{sub 12}N{sub 12} is highly sensitive to adenine, uracil, and cytosine compared with Al{sub 12}N{sub 12} to serve as a biochemical sensor.

  12. Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere

    Science.gov (United States)

    Kang, C.; Berger, I.; Lockshin, C.; Ratliff, R.; Moyzis, R.; Rich, A.

    1995-01-01

    In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.

  13. Cytosine methylation in insects: new routes for the comprehension of insect complexity

    Directory of Open Access Journals (Sweden)

    Mauro Mandrioli

    2015-09-01

    Full Text Available Cytosine methylation is one of the most studied epigenetic modifications and its occurrence has been deeply studied in mammals and plants. DNA methylation (together with other epigenetic modifications of DNA and histones plays an important role in different processes. Indeed, several morphological and/or behavioural traits may origin as a consequence of the epigenetic modulation of genes so that identical genes can results in different “morphs”. Despite considerable progress during recent years, many questions remain since it is largely unknown how the environment triggers alterations in the epigenome. In the present review we discuss the use of aphids and honey bees as epigenetic experimental model to understand how cytosine methylation is directly or indirectly linked to environmental factors. Indeed, the epigenetic changes of DNA could be at the basis of unexpected morphological differences explaining also complex traits.

  14. Intramolecular tautomerisation and the conformational variability of some classical mutagens – cytosine derivatives: quantum chemical study

    OpenAIRE

    Hovorun D. M.; Brovarets’ O. O.

    2011-01-01

    Aim. To determine the lifetime of the mutagenic cytosine derivatives through the investigation of the physicochemical mechanisms of their intramolecular proton transfer. Methods. Non-empirical quantum chemistry, the analysis of the electron density by means of Bader’s atoms in molecules (AIM) theory and physicochemical kinetics were used. Results. It is shown that the modification of all investigated compounds, except DCyt, prevents their pairing in both mutagenic and canonical tautomeric for...

  15. Hydrogen-bonded proton transfer in the protonated guanine-cytosine (GC+H)+ base pair.

    Science.gov (United States)

    Lin, Yuexia; Wang, Hongyan; Gao, Simin; Schaefer, Henry F

    2011-10-13

    The single proton transfer at the different sites of the Watson-Crick (WC) guanine-cytosine (GC) DNA base pair are studied here using density functional methods. The conventional protonated structures, transition state (TS) and proton-transferred product (PT) structures of every relevant species are optimized. Each transition state and proton-transferred product structure has been compared with the corresponding conventional protonated structure to demonstrate the process of proton transfer and the change of geometrical structures. The relative energies of the protonated tautomers and the proton-transfer energy profiles in gas and solvent are analyzed. The proton-transferred product structure G(+H(+))-H(+)C(N3)(-H(+))(PT) has the lowest relative energy for which only two hydrogen bonds exist. Almost all 14 isomers of the protonated GC base pair involve hydrogen-bonded proton transfer following the three pathways, with the exception of structure G-H(+)C(O2). When the positive charge is primarily "located" on the guanine moiety (H(+)G-C, G-H(+)C(C4), and G-H(+)C(C6)), the H(1) proton transfers from the N(1) site of guanine to the N(3) site of cytosine. The structures G-H(+)C(C5) and G-H(+)C(C4) involve H(4a) proton transfer from the N(4) of cytosine to the O(6) site of guanine. H(2a) proton transfer from the N(2) site of guanine to the O(2) site of cytosine is found only for the structure G-H(+)C(C4). The structures to which a proton is added on the six-centered sites adjoining the hydrogen bonds are more prone to proton transfer in the gas phase, whereas a proton added on the minor groove and the sites adjoining the hydrogen bonds is favorable to the proton transfer in energy in the aqueous phase.

  16. Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

    Science.gov (United States)

    Ngo, Thuy T. M.; Yoo, Jejoong; Dai, Qing; Zhang, Qiucen; He, Chuan; Aksimentiev, Aleksei; Ha, Taekjip

    2016-02-01

    Cytosine can undergo modifications, forming 5-methylcytosine (5-mC) and its oxidized products 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). Despite their importance as epigenetic markers and as central players in cellular processes, it is not well understood how these modifications influence physical properties of DNA and chromatin. Here we report a comprehensive survey of the effect of cytosine modifications on DNA flexibility. We find that even a single copy of 5-fC increases DNA flexibility markedly. 5-mC reduces and 5-hmC enhances flexibility, and 5-caC does not have a measurable effect. Molecular dynamics simulations show that these modifications promote or dampen structural fluctuations, likely through competing effects of base polarity and steric hindrance, without changing the average structure. The increase in DNA flexibility increases the mechanical stability of the nucleosome and vice versa, suggesting a gene regulation mechanism where cytosine modifications change the accessibility of nucleosomal DNA through their effects on DNA flexibility.

  17. The Eukaryotic DNMT2 Genes Encode a New Class of Cytosine-5 DNA Methyltransferases

    Institute of Scientific and Technical Information of China (English)

    Lin-YaTang; M.NarsaReddy; VanyaRasheva; Tai-LinLee; Meng-JauLin; Ming-ShiuHung; C.-K.JamesShen

    2005-01-01

    DNMT2 is a subgroup of the eukaryotic cytosine-5 DNA methyltransferase gene family. Unlike the other family members, proteins encoded by DNMT2 genes were not known before to possess DNA methyltransferase activities. Most recently, we have showm that thegenome of Drosophila S2 cells stably expressing an exogenous Drosophila dDNMT2 cDNA became anoma-lously methylated at the 5'-positions of cytosines(Reddy, M. N., Tang, L. Y., Lee, T. L., and Shen, C.-K. J.(2003) Oncogene, in press). We present evidence here that the genomes of transgenic flies overexpressing the dDnmt2 protein also became hypermethylated at specific regions. Furthermore, transient transfection studies in combination with sodium bisulfite sequencing demonstrated that dDnmt2 as well as its mousc ortholog, mDnmt2, are capable of methylating a cotrans-fected plasmid DNA. These data provide solid evidence that the fly and mouse DNMT2 gene products are genuine cytosine-5 DNA methyltransferases.

  18. The Three-Dimensional Structure and Catalytic Mechanism of Cytosine Deaminase†

    Science.gov (United States)

    Hall, Richard S.; Fedorov, Alexander A.; Xu, Chengfu; Fedorov, Elena V.; Almo, Steven C.; Raushel, Frank M.

    2011-01-01

    Cytosine deaminase (CDA) from E. coli is a member of the amidohydrolase superfamily. The structure of the zinc-activated enzyme was determined in the presence of phosphonocytosine, a mimic of the tetrahedral reaction intermediate. This compound inhibits the deamination of cytosine with a Ki of 52 nM. The zinc and iron containing enzymes were characterized to determine the effect of the divalent cations on activation of the hydrolytic water. Fe-CDA loses activity at low pH with a kinetic pKa of 6.0 and Zn-CDA has a kinetic pKa of 7.3. Mutation of Gln-156 decreased the catalytic activity by more than 5 orders of magnitude, supporting its role in substrate binding. Mutation of Glu-217, Asp-313, and His-246 significantly decreased catalytic activity supporting the role of these three residues in activation of the hydrolytic water molecule and facilitation of proton transfer reactions. A library of potential substrates was used to probe the structural determinants responsible for catalytic activity. CDA was able to catalyze the deamination of isocytosine and the hydrolysis of 3-oxauracil. Large inverse solvent isotope effects were obtained on kcat and kcat/Km, consistent with the formation of a low-barrier hydrogen bond during the conversion of cytosine to uracil. A chemical mechanism for substrate deamination by CDA was proposed. PMID:21545144

  19. Cytosine hypomethylation at CHG and CHH sites in the pleiotropic mutants of Mendelian inheritance in Catharanthus roseus

    Indian Academy of Sciences (India)

    Renu Kumari; Gitanjali Yadav; Vishakha Sharma; Vinay Sharma; Sushil Kumar

    2013-12-01

    The 5S and 18S rDNA sequences of Catharanthus roseus cv ‘Nirmal’ (wild type) and its leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill) single mutants and lli egd, lli ill and egd ill double mutants were characterized. The lli, egd and ill mutants of Mendelian inheritance bore the names after their most conspicuous morphological feature(s). They had been chemically induced and isolated for their salt tolerance. The double mutants were isolated as morphological segregants from crosses between single mutants. The morphological features of the two parents accompanied salt tolerance in the double mutants. All the six mutants were hypomethylated at repeat sequences, upregulated and downregulated for many genes and carried pleiotropic alterations for several traits. Here the 5S and 18S rDNAs of C. roseus were found to be relatively low in cytosine content. Cytosines were preponderantly in CG context (53%) and almost all of them were methylated (97%). The cytosines in CHH and CHG (where H = A, T or C) contexts were largely demethylated (92%) in mutants. The demethylation was attributable to reduced expression of RDR2 and DRM2 led RNA dependant DNA methylation and CMT3 led maintenance methylation pathways. Mutants had gained some cytosines by substitution of C at T sites. These perhaps arose on account of errors in DNA replication, mediated by widespread cytosine demethylation at CHG and CHH sites. It was concluded that the regulation of cytosine methylation mechanisms was disturbed in the mutants. ILL, EGD and LLI genes were identified as the positive regulators of other genes mediating the RdDM and CMT3 pathways, for establishment and maintenance of cytosine methylation in C. roseus.

  20. Specific and Modular Binding Code for Cytosine Recognition in Pumilio/FBF (PUF) RNA-binding Domains

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Shuyun; Wang, Yang; Cassidy-Amstutz, Caleb; Lu, Gang; Bigler, Rebecca; Jezyk, Mark R.; Li, Chunhua; Tanaka Hall, Traci M.; Wang, Zefeng (NIH); (Beijing U); (UNC)

    2011-10-28

    Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and the cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence.

  1. Specific and modular binding code for cytosine recognition in Pumilio/FBF (PUF) RNA-binding domains.

    Science.gov (United States)

    Dong, Shuyun; Wang, Yang; Cassidy-Amstutz, Caleb; Lu, Gang; Bigler, Rebecca; Jezyk, Mark R; Li, Chunhua; Hall, Traci M Tanaka; Wang, Zefeng

    2011-07-29

    Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and the cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence.

  2. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed Missael Vargas;

    2014-01-01

    data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery...... of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues...

  3. Modified-cytosine restriction-system-induced recombinant cloning artefacts in Escherichia coli

    DEFF Research Database (Denmark)

    Williamson, M R; Doherty, J P; Woodcock, D M

    1993-01-01

    We have tested whether, and to what extent, recombinant clones from DNA segments with 5-methylation of cytosines recovered in methylation-restrictive (mcr+) hosts contain mutations. We constructed a model system in which the tetracycline-resistance-encoding gene (tet) from pBR322 was cloned.......HpaII plus M.HhaI) or (2) methylated with M.SssI which methylates at all CpG dinucleotides. These two protocols generated theoretical levels of DNA methylation in the central fragment of 10.5% and 33%, respectively. The construct was transformed into a series of isogenic (recA+) bacterial strains that were...

  4. Determination of the Methanoic Acid, Ethanoic Acid and Propanoic Acid in Bio-diesels via Ion Chromatography%离子色谱法测定生物柴油中甲酸、乙酸、丙酸

    Institute of Scientific and Technical Information of China (English)

    胡琳琳; 容晓文

    2009-01-01

    The paper introduced the method of determining the methanoic acid, ethanoic acid and propanoic acid in bio-diesels via ion chromatography. Under the conditions in which metrosep organic acids 250 was used with 0.5 mmol/L of H2SO4 in mobile phase, volume of 20 μL, speed of 0.5 mL/min and 25 mmol/L LiClinhibitor, the calibration curves of both methanoic acid and ethanoic acid were 1.0~ 10.0 mg/L while the calibration curve of propanoic acid was 0.05~0.50 mg/L.The correlation coefficients were 1.00000, 0.99999 and 0.99981, respectively. The recovery rates were 98.5 %, 99.4 % and 99.0 %, respectively. The method was easy to operate, with high accuracy, high sensitivity and fine recovery rate.%文章建立了用离子色谱法测定生物柴油中的甲酸、乙酸、丙酸的方法.在Metrosep Organic Acids 250有机酸柱;0.5mmol/LH2SO4流动相;20 μL进样体积;0.5 mL/min流速和25 mmol/L LiCl抑制液的实验条件下,甲酸和乙酸的工作曲线范围均为1.0~10.0 mg/L、丙酸的工作曲线范围为0.05~0.50 mg/L,其相关系数分别为1.00000、0.99999、0.99981,回收率分别为98.5%、99.4%、99.0%.该方法简单易行,结果准确;精度高、灵敏度高、回收率好.

  5. Base flip in DNA studied by molecular dynamics simulationsof differently-oxidized forms of methyl-Cytosine.

    Science.gov (United States)

    Helabad, Mahdi Bagherpoor; Kanaan, Natalia; Imhof, Petra

    2014-07-03

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  7. H{sup .} atom and OH{sup .} radical reactions with 5-methyl-cytosine

    Energy Technology Data Exchange (ETDEWEB)

    Grand, A.; Morell, C.; Labet, V.; Cadet, J. [CEA Grenoble, Lab Les Acides Nucl, DRFMC/SCIB, UMR-E 3, CEA-UJF, F-38054 Grenoble, (France); Eriksson, L.A. [Univ Orebro, Dept Nat Sci and Orebro Life Sci Ctr, S-70182 Orebro, (Sweden)

    2007-07-01

    The reactions between either a hydrogen atom or a hydroxyl radical and 5-methyl-cytosine (5-MeCyt) are studied by using the hybrid kinetic energy meta-GGA functional MPW1B95. H{sup .} atom and OH{sup .} radical addition to positions C5 and C6 of 5-MeCyt, or OH{sup .} radical induced H-abstraction from the C5 methyl group, are explored. All systems are optimized in bulk solvent. The data presented show that the barriers to reaction are very low: ca. 7 kCal/mol for the H{sup .} atom additions and 1 kCal/mol for the reactions involving the OH{sup .} radical. Thermodynamically, the two C6 radical adducts and the H{sup .}- abstraction product are the most stable ones. The proton hyperfine coupling constants (HFCC), computed at the IEFPCM/MPW1B95/6-311++G(2d,2p) level, agree well with B3LYP results and available experimental and theoretical data on related thymine and cytosine radicals. (authors)

  8. Intramolecular tautomerisation and the conformational variability of some classical mutagens – cytosine derivatives: quantum chemical study

    Directory of Open Access Journals (Sweden)

    Hovorun D. M.

    2011-04-01

    Full Text Available Aim. To determine the lifetime of the mutagenic cytosine derivatives through the investigation of the physicochemical mechanisms of their intramolecular proton transfer. Methods. Non-empirical quantum chemistry, the analysis of the electron density by means of Bader’s atoms in molecules (AIM theory and physicochemical kinetics were used. Results. It is shown that the modification of all investigated compounds, except DCyt, prevents their pairing in both mutagenic and canonical tautomeric forms with a base which is an interacting partner. This effect can inhibit their mutagenic potential. It is also established that Watson-Crick tautomeric hypothesis can be formally expanded for the investigated molecules so far as a lifetime of the mutagenic tautomers much more exceeds characteristic time for the incorporation of one nucleotides pair by DNA biosynthesis machinery. It seems that just within the frame of this hypothesis it will be possible to give an adequate explanation of the mechanisms of mutagenic action of N4-aminocytosine, N4-methoxycytosine, N4-hydroxycytosine and N4dehydrocytosine, which have much more energy advantageous imino form in comparison with amino form. Conclusions. For the first time the comprehensive conformational analysis of a number of classical mutagens, namely cytosine derivatives, has been performed using the methods of non-empirical quantum chemistry at the MP2/6-311++G (2df,pd//B3LYP/6-311++G(d,p level of theory

  9. The experimental and theoretical gas phase acidities of adenine, guanine, cytosine, uracil, thymine and halouracils

    Science.gov (United States)

    Chen, Edward C. M.; Herder, Charles; Chen, Edward S.

    2006-10-01

    The gas phase acidities GPA (Δ H (298) for deprotonation) of the most stable tautomers of adenine, guanine, cytosine, uracil and thymine are evaluated. New GPA are obtained from electron impact spectra and acid dissociation constants measured in dimethylsulfoxide for A, U and 5-FU. The average experimental GPA are: [N1 sbnd H] C 340(2); T 333(2); U 333(2); 5-FU 329(4); [N9 sbnd H] A 333(1); G 332(4); all in kcal/mol. Only cytosine is a weaker acid than HCl in the gas phase. The most acidic hydrogens in the nucleotides are replaced by the sugar in DNA and RNA. The experimental N3 sbnd H GPA are G 334(4); U 347(2), T 347(4), while the predicted N3 sbnd H 5-FU GPA is 343 kcal/mol. The NH sbnd H GPA are: C 346(4); A 352(2); G 336(4) (all in kcal/mol). These are supported by semi-empirical multiconfiguration configuration interaction calculations. The predicted C8 sbnd H acidities of G and A and the C6 sbnd H of T are about the same, 360(2) kcal/mol. The remaining CH acidities are 370-380 kcal/mol. The 5-halouracils are predicted to be more acidic than HCl.

  10. Reprint of: Enantiomeric separation of functionalized ethano-bridged Tröger bases using macrocyclic cyclofructan and cyclodextrin chiral selectors in high-performance liquid chromatography and capillary electrophoresis with application of principal component analysis.

    Science.gov (United States)

    Weatherly, Choyce A; Na, Yun-Cheol; Nanayakkara, Yasith S; Woods, Ross M; Sharma, Ankit; Lacour, Jérôme; Armstrong, Daniel W

    2014-10-01

    The enantiomeric separation of a series of racemic functionalized ethano-bridged Tröger base compounds was examined by high performance liquid chromatography (HPLC) and capillary electrophoresis (CE). Using HPLC and CE the entire set of 14 derivatives was separated by chiral stationary phases (CSPs) and chiral additives composed of cyclodextrin (native and derivatized) and cyclofructan (derivatized). Baseline separations (Rs ≥ 1.5) in HPLC were achieved for 13 of the 14 compounds with resolution values as high as 5.0. CE produced 2 baseline separations. The separations on the cyclodextrin CSPs showed optimum results in the reversed phase mode, and the LARIHC cyclofructan CSPs separations showed optimum results in the normal phase mode. HPLC separation data of the compounds was analyzed using principal component analysis (PCA). The PCA biplot analysis showed that retention is governed by the size of the R1 substituent in the case of derivatized cyclofructan and cyclodextrin CSPs, and enantiomeric resolution closely correlated with the size of the R2 group in the case of non-derivatized γ-cyclodextrin CSP. It is clearly shown that chromatographic retention is necessary but not sufficient for the enantiomeric separations of these compounds.

  11. Enantiomeric separation of functionalized ethano-bridged Tröger bases using macrocyclic cyclofructan and cyclodextrin chiral selectors in high-performance liquid chromatography and capillary electrophoresis with application of principal component analysis.

    Science.gov (United States)

    Weatherly, Choyce A; Na, Yun-Cheol; Nanayakkara, Yasith S; Woods, Ross M; Sharma, Ankit; Lacour, Jérôme; Armstrong, Daniel W

    2014-04-01

    The enantiomeric separation of a series of racemic functionalized ethano-bridged Tröger base compounds was examined by high performance liquid chromatography (HPLC) and capillary electrophoresis (CE). Using HPLC and CE the entire set of 14 derivatives was separated by chiral stationary phases (CSPs) and chiral additives composed of cyclodextrin (native and derivatized) and cyclofructan (derivatized). Baseline separations (Rs≥1.5) in HPLC were achieved for 13 of the 14 compounds with resolution values as high as 5.0. CE produced 2 baseline separations. The separations on the cyclodextrin CSPs showed optimum results in the reversed phase mode, and the LARIHC™ cyclofructan CSPs separations showed optimum results in the normal phase mode. HPLC separation data of the compounds was analyzed using principal component analysis (PCA). The PCA biplot analysis showed that retention is governed by the size of the R1 substituent in the case of derivatized cyclofructan and cyclodextrin CSPs, and enantiomeric resolution closely correlated with the size of the R2 group in the case of non-derivatized γ-cyclodextrin CSP. It is clearly shown that chromatographic retention is necessary but not sufficient for the enantiomeric separations of these compounds.

  12. Solid-phase molecular recognition of cytosine based on proton-transfer reaction. Part II. supramolecular architecture in the cocrystals of cytosine and its 5-Fluoroderivative with 5-Nitrouracil

    Directory of Open Access Journals (Sweden)

    Portalone Gustavo

    2011-09-01

    Full Text Available Abstract Background Cytosine is a biologically important compound owing to its natural occurrence as a component of nucleic acids. Cytosine plays a crucial role in DNA/RNA base pairing, through several hydrogen-bonding patterns, and controls the essential features of life as it is involved in genetic codon of 17 amino acids. The molecular recognition among cytosines, and the molecular heterosynthons of molecular salts fabricated through proton-transfer reactions, might be used to investigate the theoretical sites of cytosine-specific DNA-binding proteins and the design for molecular imprint. Results Reaction of cytosine (Cyt and 5-fluorocytosine (5Fcyt with 5-nitrouracil (Nit in aqueous solution yielded two new products, which have been characterized by single-crystal X-ray diffraction. The products include a dihydrated molecular salt (CytNit having both ionic and neutral hydrogen-bonded species, and a dihydrated cocrystal of neutral species (5FcytNit. In CytNit a protonated and an unprotonated cytosine form a triply hydrogen-bonded aggregate in a self-recognition ion-pair complex, and this dimer is then hydrogen bonded to one neutral and one anionic 5-nitrouracil molecule. In 5FcytNit the two neutral nucleobase derivatives are hydrogen bonded in pairs. In both structures conventional N-H...O, O-H...O, N-H+...N and N-H...N- intermolecular interactions are most significant in the structural assembly. Conclusion The supramolecular structure of the molecular adducts formed by cytosine and 5-fluorocytosine with 5-nitrouracil, CytNit and 5FcytNit, respectively, have been investigated in detail. CytNit and 5FcytNit exhibit widely differing hydrogen-bonding patterns, though both possess layered structures. The crystal structures of CytNit (Dpka = -0.7, molecular salt and 5FcytNit (Dpka = -2.0, cocrystal confirm that, at the present level of knowledge about the nature of proton-transfer process, there is not a strict correlation between the Dpka values

  13. Chemotherapy with cyclophosphamide, vincristine, cytosine arabinoside, and prednisone (COAP) in childhood acute lymphoblastic leukemia (ALL).

    Science.gov (United States)

    Sallan, S E; Camitta, B M; Chan, D M; Traggis, D; Jaffe, N

    1977-01-01

    Three groups of children with acute lymphoblastic leukemia (ALL) were treated with intermittent cyclophosphamide, vincristine, cytosine arabinoside, and prednisone (COAP). Group A (no prior relapse) and Group B (prior single-agent relapse) received COAP after 12 months on another chemotherapy regimen. Children in Group C (prior relapse on multiagent regimens) received COAP following A-COAP (asparaginase plus COAP) reinduction. Median disease-free survival after beginning COAP was not reached for Group A, but was only 7 months for Groups B and C. As of November 1976, there were 8 of 15 Group A patients, 1 of 12 Group B patients, and 1 of 28 Group C patients who had remained disease-free from 38 to 60 (median 54.5) months and were off chemotherapy. COAP has activity in childhood ALL. However, effectiveness is markedly diminished in patients with prior bone marrow relapse.

  14. Hypomethylation of cytosine residues in cold-sensitive regions of Cestrum strigilatum (Solanaceae).

    Science.gov (United States)

    Guarido, Paula Carolina Paes; de Paula, Adriano Alves; da Silva, Carlos Roberto Maximiano; Rodriguez, Carmen; Vanzela, André Luís Laforga

    2012-04-01

    Heterochromatin comprises a fraction of the genome usually with highly repeated DNA sequences and lacks of functional genes. This region can be revealed by using Giemsa C-banding, fluorochrome staining and cytomolecular tools. Some plant species are of particular interest through having a special type of heterochromatin denominated the cold-sensitive region (CSR). Independent of other chromosomal regions, when biological materials are subjected to low temperatures (about 0 °C), CSRs appear slightly stained and decondensed. In this study, we used Cestrum strigilatum (Solanaceae) to understand some aspects of CSR condensation associated with cytosine methylation levels, and to compare the behavior of different heterochromatin types of this species, when subjected to low temperatures.

  15. Hypomethylation of cytosine residues in cold-sensitive regions of Cestrum strigilatum (Solanaceae

    Directory of Open Access Journals (Sweden)

    Paula Carolina Paes Guarido

    2012-01-01

    Full Text Available Heterochromatin comprises a fraction of the genome usually with highly repeated DNA sequences and lacks of functional genes. This region can be revealed by using Giemsa C-banding, fluorochrome staining and cytomolecular tools. Some plant species are of particular interest through having a special type of heterochromatin denominated the cold-sensitive region (CSR. Independent of other chromosomal regions, when biological materials are subjected to low temperatures (about 0 °C, CSRs appear slightly stained and decondensed. In this study, we used Cestrum strigilatum (Solanaceae to understand some aspects of CSR condensation associated with cytosine methylation levels, and to compare the behavior of different heterochromatin types of this species, when subjected to low temperatures.

  16. Protection of leukemic cells by deoxycytidine: in vitro measures of protection against cytosine arabinoside.

    Science.gov (United States)

    Cohen, J D; Strock, D J; LaGuardia, E A; Mao, Z; Teik, J E

    1998-05-01

    Plasma deoxycytidine levels can be very high in leukemia patients. Such levels strongly protected leukemia cell lines against cytosine arabinoside (araC), fludarabine and 2-chlorodeoxyadenosine when using clonogenic survival as the endpoint. This endpoint is not easily used when studying protection in clinical leukemia cell samples. Therefore, we tested other ways to quantify protection based on biochemical measures of viability or drug metabolism. The estimates of the strength of protection based on rates of DNA synthesis, cellular araC uptake and incorporation of araC into DNA were much lower than the estimates using clonogenic survival. The MTT viability assay gave excellent estimates and appears promising for studying protection in primary leukemia cell samples.

  17. Mutation Processes in 293-Based Clones Overexpressing the DNA Cytosine Deaminase APOBEC3B.

    Directory of Open Access Journals (Sweden)

    Monica K Akre

    Full Text Available Molecular, cellular, and clinical studies have combined to demonstrate a contribution from the DNA cytosine deaminase APOBEC3B (A3B to the overall mutation load in breast, head/neck, lung, bladder, cervical, ovarian, and other cancer types. However, the complete landscape of mutations attributable to this enzyme has yet to be determined in a controlled human cell system. We report a conditional and isogenic system for A3B induction, genomic DNA deamination, and mutagenesis. Human 293-derived cells were engineered to express doxycycline-inducible A3B-eGFP or eGFP constructs. Cells were subjected to 10 rounds of A3B-eGFP exposure that each caused 80-90% cell death. Control pools were subjected to parallel rounds of non-toxic eGFP exposure, and dilutions were done each round to mimic A3B-eGFP induced population fluctuations. Targeted sequencing of portions of TP53 and MYC demonstrated greater mutation accumulation in the A3B-eGFP exposed pools. Clones were generated and microarray analyses were used to identify those with the greatest number of SNP alterations for whole genome sequencing. A3B-eGFP exposed clones showed global increases in C-to-T transition mutations, enrichments for cytosine mutations within A3B-preferred trinucleotide motifs, and more copy number aberrations. Surprisingly, both control and A3B-eGFP clones also elicited strong mutator phenotypes characteristic of defective mismatch repair. Despite this additional mutational process, the 293-based system characterized here still yielded a genome-wide view of A3B-catalyzed mutagenesis in human cells and a system for additional studies on the compounded effects of simultaneous mutation mechanisms in cancer cells.

  18. Mutation of Escherichia coli cytosine deaminase significantly enhances molecular chemotherapy of human glioma.

    Science.gov (United States)

    Kaliberov, S A; Market, J M; Gillespie, G Y; Krendelchtchikova, V; Della Manna, D; Sellers, J C; Kaliberova, L N; Black, M E; Buchsbaum, D J

    2007-07-01

    Combined treatment using adenoviral (Ad)-directed enzyme/prodrug therapy and radiation therapy has the potential to become a powerful method of cancer therapy. We have developed an Ad vector encoding a mutant bacterial cytosine deaminase (bCD) gene (AdbCD-D314A), which has a higher affinity for cytosine than wild-type bCD (bCDwt). The purpose of this study was to evaluate cytotoxicity in vitro and therapeutic efficacy in vivo of the combination of AdbCD-D314A with the prodrug 5-fluorocytosine (5-FC) and ionizing radiation against human glioma. The present study demonstrates that AdbCD-D314A infection resulted in increased 5-FC-mediated cell killing, compared with AdbCDwt. Furthermore, a significant increase in cytotoxicity following AdbCD-D314A and radiation treatment of glioma cells in vitro was demonstrated as compared to AdbCDwt. Animal studies showed significant inhibition of subcutaneous or intracranial tumor growth of D54MG glioma xenografts by the combination of AdbCD-D314A/5-FC with ionizing radiation as compared with either agent alone, and with AdbCDwt/5-FC plus radiation. The results suggest that the combination of AdbCD-D314A/5-FC with radiation produces markedly increased cytotoxic effects in cancer cells in vitro and in vivo. These data indicate that combined treatment with this novel mutant enzyme/prodrug therapy and radiotherapy provides a promising approach for cancer therapy.

  19. Additional cytosine inside mitochondrial C-tract D-loop as a progression risk factor in oral precancer cases

    Science.gov (United States)

    Pandey, Rahul; Mehrotra, Divya; Mahdi, Abbas Ali; Sarin, Rajiv; Kowtal, Pradnya

    2014-01-01

    Introduction Alterations inside Polycytosine tract (C-tract) of mitochondrial DNA (mtDNA) have been described in many different tumor types. The Poly-Cytosine region is located within the mtDNA D-loop region which acts as point of mitochondrial replication origin. A suggested pathogenesis is that it interferes with the replication process of mtDNA which in turn affects the mitochondrial functioning and generates disease. Methodology 100 premalignant cases (50 leukoplakia & 50 oral submucous fibrosis) were selected and the mitochondrial DNA were isolated from the lesion tissues and from the blood samples. Polycytosine tract in mtDNA was sequenced by direct capillary sequencing. Results 40 (25 leukoplakia & 15 oral submucous fibrosis) patients harbored lesions that displayed one additional cytosine after nucleotide thymidine (7CT6C) at nt position 316 in C-tract of mtDNA which were absent in corresponding mtDNA derived from blood samples. Conclusion Our results show an additional cytosine in the mtDNA at polycytosine site in oral precancer cases. It is postulated that any increase/decrease in the number of cytosine residues in the Poly-Cytosine region may affect the rate of mtDNA replication by impairing the binding of polymerase and other transacting factors. By promoting mitochondrial genomic instability, it may have a central role in the dysregulation of mtDNA functioning, for example alterations in energy metabolism that may promote tumor development. We, therefore, report and propose that this alteration may represent the early development of oral cancer. Further studies with large number of samples are needed in to confirm the role of such mutation in carcinogenesis. PMID:25737911

  20. Chloridotris[μ2-2-(dimethyl­amino)­ethano­lato]-μ3-hydroxido-tri-μ2-trifluoro­acetato-tetra­copper(II) tetra­hydro­furan solvate

    Science.gov (United States)

    Hussain, S. Tajammul; Bakar, Shahzad Abu; Mazhar, Mohammad; Zeller, Matthias

    2010-01-01

    The title compound, [Cu4(C2F3O2)3(C4H10NO)3Cl(OH)]·C4H8O or [Cu4(TFA)3(dmae)3Cl(OH)]·THF (dmae is dimeth­yl­amino­ethano­late, TFA is trifluoro­acetate and THF is tetra­hydro­furan), has an approximate mol­ecular threefold symmetry with three equivalent {Cu(dmae)(TFA)} units bridging between a Cu—Cl and a hydroxide unit, with the latter two lying on the mol­ecular threefold axis. However, in the solid state, the tetranuclear complex has Ci symmetry. The Cu atom bonded to the Cl atom has a distorted tetra­hedral geometry. The other three Cu atoms have distorted square-pyramidal geometries with an NO4 coordination environment. The bonds within the CuNO3 base of the pyramid range from 1.953 (2) to 2.033 (3) Å, while the apical Cu—O bonds are significantly longer, ranging from 2.286 (2) to 2.377 (2) Å. The square-pyramidal geometries are augmented by weak inter­actions towards a sixth O atom, forming a highly distorted octa­hedral coordination environment [long Cu—O distances = 2.712 (2)–2.824 (2) Å]. The hydroxide group is hydrogen bonded to the tetra­hydro­furan solvent mol­ecule. One of the –CF3 groups shows minor disorder over two positions, with a refined occupancy ratio of 0.894 (4):0.106 (5). PMID:21587732

  1. Synthesis of adenine, guanine, cytosine, and other nitrogen organic compounds by a Fischer-Tropsch-like process.

    Science.gov (United States)

    Yang, C. C.; Oro, J.

    1971-01-01

    Study of the formation of purines, pyrimidines, and other bases from CO, H2, and NH3 under conditions similar to those used in the Fischer-Tropsch process. It is found that industrial nickel/iron alloy catalyzes the synthesis of adenine, guanine, cytosine, and other nitrogenous compounds from mixtures of CO, H2, and NH3 at temperatures of about 600 C. Sufficient sample was accumulated to isolate as solid products adenine, guanine, and cytosine, which were identified by infrared spectrophotometry. In the absence of nickel/iron catalyst, at 650 C, or in the presence of this catalyst, at 450 C, no purines or pyrimidines were synthesized. These results confirm and extend some of the work reported by Kayatsu et al. (1968).

  2. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine.

    Science.gov (United States)

    Grimme, Stefan; Bauer, Christopher Alexander

    2015-01-01

    The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.

  3. Biophysical and molecular docking insight into the interaction of cytosine β-D arabinofuranoside with human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Alam, Parvez; Chaturvedi, Sumit Kumar [Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP (India); Anwar, Tamanna [Center of Bioinformatics Research and Technology, Aligarh 202002 (India); Siddiqi, Mohammad Khursheed; Ajmal, Mohd Rehan [Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP (India); Badr, Gamal [Laboratory of Immunology & Molecular Physiology, Zoology Department, Faculty of Science, Assiut University, 71516 Assiut (Egypt); Mahmoud, Mohamed H. [Food Science and Nutrition Department, National Research Center, Dokki, Cairo (Egypt); Deanship of Scientific Research, King Saud University, Riyadh (Saudi Arabia); Hasan Khan, Rizwan, E-mail: rizwanhkhan@hotmail.com [Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP (India)

    2015-08-15

    Interaction of pharmacologically important anticancer drug cytosine β-D arabinofuranoside with human serum albumin (HSA) at physiological pH 7.4 has been studied by utilizing various spectroscopic and molecular docking strategies. Fluorescence results revealed that cytosine β-D arabinofuranoside interacts with HSA through static quenching mechanism with binding affinity of 2.4×10{sup 3} M{sup −1}. The average binding distance between drug and Trp{sup 214} of HSA was found to be 2.23 nm on the basis of the theory of Förster's energy transfer. Synchronous fluorescence data indicated that interaction of drug with HSA changed the microenvironment around the tryptophan residue. UV–visible spectroscopy and circular dichroism results deciphered the complex formation and conformational alterations in the HSA respectively. Dynamic light scattering was utilized to understand the topology of protein in absence and presence of drug. Thermodynamic parameters obtained from isothermal titration calorimetry (ΔH=−26.01 kJ mol{sup −1} and TΔS=6.5 kJ mol{sup −1}) suggested the involvement of van der Waal interaction and hydrogen bonding. Molecular docking and displacement study with site specific markers suggested that cytosine β-D arabinofuranoside binds to subdomain IB of HSA which is also known as the hemin binding site. This study will be helpful to understand the binding mechanism of cytosine β-D arabinofuranoside with HSA and associated alterations. - Highlights: • Comprehensive insight into the interaction of CBDA with HSA. • The interaction process is spontaneous and exothermic. • The main governing forces for stabilizing HSA–CBDA complex are van der Waal interaction and hydrogen bonding. • CBDA binds at subdomain IB on HSA.

  4. Synthesis and cytotoxic activity of two novel 1-dodecylthio-2-decyloxypropyl-3-phosphatidic acid conjugates with gemcitabine and cytosine arabinoside.

    Science.gov (United States)

    Alexander, Richard L; Morris-Natschke, Susan L; Ishaq, Khalid S; Fleming, Ronald A; Kucera, Gregory L

    2003-09-11

    Cytosine arabinoside (ara-C) and gemcitabine (dFdC) are two standard chemotherapy drugs used in the treatment of patients with various cancers. To alter the pharmacokinetic and pharmacodynamic properties of these molecules, we conjugated a synthetic phospholipid to both ara-C and dFdC and investigated their chemotherapeutic potential. The dFdC conjugate had greater cytotoxic activity compared with the ara-C conjugate and demonstrated notable cytotoxicity against all human cell lines tested.

  5. Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair.

    Science.gov (United States)

    Dumat, Blaise; Larsen, Anders Foller; Wilhelmsson, L Marcus

    2016-06-20

    Herein, we report on the use of a tricyclic cytosine FRET pair, incorporated into DNA with different base pair separations, to study Z-DNA and B-Z DNA junctions. With its position inside the DNA structure, the FRET pair responds to a B- to Z-DNA transition with a distinct change in FRET efficiency for each donor/acceptor configuration allowing reliable structural probing. Moreover, we show how fluorescence spectroscopy and our cytosine analogues can be used to determine rate constants for the B- to Z-DNA transition mechanism. The modified cytosines have little influence on the transition and the FRET pair is thus an easily implemented and virtually non-perturbing fluorescence tool to study Z-DNA. This nucleobase analogue FRET pair represents a valuable addition to the limited number of fluorescence methods available to study Z-DNA and we suggest it will facilitate, for example, deciphering the B- to Z-DNA transition mechanism and investigating the interaction of DNA with Z-DNA binding proteins.

  6. Methyl-Cytosine-Driven Structural Changes Enhance Adduction Kinetics of an Exon 7 fragment of the p53 Gene

    Science.gov (United States)

    Malla, Spundana; Kadimisetty, Karteek; Fu, You-Jun; Choudhary, Dharamainder; Schenkman, John B.; Rusling, James F.

    2017-01-01

    Methylation of cytosine (C) at C-phosphate-guanine (CpG) sites enhances reactivity of DNA towards electrophiles. Mutations at CpG sites on the p53 tumor suppressor gene that can result from these adductions are in turn correlated with specific cancers. Here we describe the first restriction-enzyme-assisted LC-MS/MS sequencing study of the influence of methyl cytosines (MeC) on kinetics of p53 gene adduction by model metabolite benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE), using methodology applicable to correlate gene damage sites for drug and pollutant metabolites with mutation sites. This method allows direct kinetic measurements by LC-MS/MS sequencing for oligonucleotides longer than 20 base pairs (bp). We used MeC and non-MeC (C) versions of a 32 bp exon 7 fragment of the p53 gene. Methylation of 19 cytosines increased the rate constant 3-fold for adduction on G at the major reactive CpG in codon 248 vs. the non-MeC fragment. Rate constants for non-CpG codons 244 and 243 were not influenced significantly by MeC. Conformational and hydrophobicity changes in the MeC-p53 exon 7 fragment revealed by CD spectra and molecular modeling increase the BPDE binding constant to G in codon 248 consistent with a pathway in which preceding reactant binding greatly facilitates the rate of covalent SN2 coupling.

  7. Methyl-Cytosine-Driven Structural Changes Enhance Adduction Kinetics of an Exon 7 fragment of the p53 Gene

    Science.gov (United States)

    Malla, Spundana; Kadimisetty, Karteek; Fu, You-Jun; Choudhary, Dharamainder; Schenkman, John B.; Rusling, James F.

    2017-01-01

    Methylation of cytosine (C) at C-phosphate-guanine (CpG) sites enhances reactivity of DNA towards electrophiles. Mutations at CpG sites on the p53 tumor suppressor gene that can result from these adductions are in turn correlated with specific cancers. Here we describe the first restriction-enzyme-assisted LC-MS/MS sequencing study of the influence of methyl cytosines (MeC) on kinetics of p53 gene adduction by model metabolite benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE), using methodology applicable to correlate gene damage sites for drug and pollutant metabolites with mutation sites. This method allows direct kinetic measurements by LC-MS/MS sequencing for oligonucleotides longer than 20 base pairs (bp). We used MeC and non-MeC (C) versions of a 32 bp exon 7 fragment of the p53 gene. Methylation of 19 cytosines increased the rate constant 3-fold for adduction on G at the major reactive CpG in codon 248 vs. the non-MeC fragment. Rate constants for non-CpG codons 244 and 243 were not influenced significantly by MeC. Conformational and hydrophobicity changes in the MeC-p53 exon 7 fragment revealed by CD spectra and molecular modeling increase the BPDE binding constant to G in codon 248 consistent with a pathway in which preceding reactant binding greatly facilitates the rate of covalent SN2 coupling. PMID:28102315

  8. Sequence-selective binding of phenazinium dyes phenosafranin and safranin O to guanine-cytosine deoxyribopolynucleotides: spectroscopic and thermodynamic studies.

    Science.gov (United States)

    Saha, Ishita; Hossain, Maidul; Suresh Kumar, Gopinatha

    2010-11-25

    The sequence selectivity of the DNA binding of the phenazinium dyes phenosafranin and safranin O have been investigated with four sequence-specific deoxyribopolynucleotides from spectroscopic and calorimetric studies. The alternating guanine-cytosine sequence selectivity of the dyes has been revealed from binding affinity values, circular dichroism, thermal melting, competition dialysis, and calorimetric results. The binding affinities of both the dyes to the polynucleotides were of the order of 10(5) M(-1), but the values were higher for the guanine-cytosine polynucleotides over adenine-thymine ones. Phenosafranin had a higher binding affinity compared to safranin O. Isothermal titration calorimetric studies revealed that the binding reactions were exothermic and favored by negative enthalpy and predominantly large positive entropy contributions in all cases except poly(dA)·poly(dT) where the profile was anomalous. Although charged, nonpolyelectrolytic contribution was revealed to be dominant to the free energy of binding. The negative heat capacity values obtained from the temperature dependence of enthalpy changes, which were higher for phenosafranin compared to safranin O, suggested significant hydrophobic contribution to the binding process. In aggregate, the data presents evidence for the alternating guanine-cytosine base pair selectivity of these phenazinium dyes and a stronger binding of phenosafranin over safranin O.

  9. Novel photodynamic effect of a psoralen-conjugated oligonucleotide for the discrimination of the methylation of cytosine in DNA.

    Science.gov (United States)

    Yamayoshi, Asako; Matsuyama, Yohei; Kushida, Mikihiko; Kobori, Akio; Murakami, Akira

    2014-01-01

    DNA methylation and demethylation significantly affect the deactivation and activation processes of gene expression significantly. In particular, C-5-methylation of cytosine in the CpG islands is important for the epigenetic modification in genes, which plays a key role in regulating gene expression. The determination of the location and frequency of DNA methylation is important for the elucidation of the mechanisms of cell differentiation and carcinogenesis. Here we designed a psoralen-conjugated oligonucleotide (PS-oligo) for the discrimination of 5-methylcytosine (5-mC) in DNA. The cross-linking behavior of psoralen derivatives with pyrimidine bases, such as thymine, uracil and cytosine has been well discussed, but there are no reports which have examined whether cross-linking efficiency of psoralen with cytosine would be changed with or without C-5 methylation. We found that the cross-linking efficiency of PS-oligo with target-DNA containing 5-mC was greatly increased compared to the case of target-DNA without 5-mC, approximately seven-fold higher. Here we report a new aspect of the photocross-linking behavior of psoralen with 5-mC that is applicable to a simple, sequence-specific and quantitative analysis for the discrimination of 5-mC in DNA, which can be applicable to study the epigenetic behavior of gene expressions.

  10. Patterns of Cytosine Methylation in Parental Lines and Their Hybrids of Large White and Meishan Reciprocal Crosses

    Institute of Scientific and Technical Information of China (English)

    JIANG Cao-de; DENG Chang-yan; XIONG Yuan-zhu

    2004-01-01

    The extent and patterns of cytosine methylation in blood DNA were assessed, using the technique of methylation-sensitive amplified polymorphism(MSAP),in Meishan, Large White pigs and hybrids of their reciprocal crosses. In all, 1 508 fragments, each representing a recognition site cleaved by either or both of the isoschizomers, MspI and HpaII, were amplified using 20 pairs of selective primers. 10.3% of CCGG sites were methylated in Meishan pigs, 10.5% in Large White pigs, and 10.2% in the hybrids. Cytosine methylation was not significantly different among parental lines and hybrids of reciprocal crosses. Four classes of patterns were identified in a comparative assay of cytosine methylation in the parents and hybrids: (1) the same level of methylation in both parental lines and the hybrids; (2) the same level of methylation in either parent or hybrid; (3) an increased level of methylation in the hybrids compared to the parents, and (4) a decreased level of methylation in the hybrids. 11 crossspecific methylation sites were detected in F1 hybrids of Large White×Meishan, and 10 crossspecific methylation sites in the hybrid of Meishan×LargeWhite. In conclusion, (1) the whole methylation status between parental lines and hybrids was not different, but specific sites were differentially methylated; (2) specific sites were differentially methylated between reciprocal crosses; (3) demethylation and hypermethylation of many sites accounted for mostly (more than 50%) methylated sites in the hybrids compared to parental lines.

  11. RNA-mediated epigenetic heredity requires the cytosine methyltransferase Dnmt2.

    Directory of Open Access Journals (Sweden)

    Jafar Kiani

    2013-05-01

    Full Text Available RNA-mediated transmission of phenotypes is an important way to explain non-Mendelian heredity. We have previously shown that small non-coding RNAs can induce hereditary epigenetic variations in mice and act as the transgenerational signalling molecules. Two prominent examples for these paramutations include the epigenetic modulation of the Kit gene, resulting in altered fur coloration, and the modulation of the Sox9 gene, resulting in an overgrowth phenotype. We now report that expression of the Dnmt2 RNA methyltransferase is required for the establishment and hereditary maintenance of both paramutations. Our data show that the Kit paramutant phenotype was not transmitted to the progeny of Dnmt2(-/- mice and that the Sox9 paramutation was also not established in Dnmt2(-/- embryos. Similarly, RNA from Dnmt2-negative Kit heterozygotes did not induce the paramutant phenotype when microinjected into Dnmt2-deficient fertilized eggs and microinjection of the miR-124 microRNA failed to induce the characteristic giant phenotype. In agreement with an RNA-mediated mechanism of inheritance, no change was observed in the DNA methylation profiles of the Kit locus between the wild-type and paramutant mice. RNA bisulfite sequencing confirmed Dnmt2-dependent tRNA methylation in mouse sperm and also indicated Dnmt2-dependent cytosine methylation in Kit RNA in paramutant embryos. Together, these findings uncover a novel function of Dnmt2 in RNA-mediated epigenetic heredity.

  12. Regulation of expression and activity of DNA (cytosine-5) methyltransferases in mammalian cells.

    Science.gov (United States)

    Kinney, Shannon R Morey; Pradhan, Sriharsa

    2011-01-01

    Three active DNA (cytosine-5) methyltransferases (DNMTs) have been identified in mammalian cells, Dnmt1, Dnmt3a, and Dnmt3b. DNMT1 is primarily a maintenance methyltransferase, as it prefers to methylate hemimethylated DNA during DNA replication and in vitro. DNMT3A and DNMT3B are de novo methyltransferases and show similar activity on unmethylated and hemimethylated DNA. DNMT3L, which lacks the catalytic domain, binds to DNMT3A and DNMT3B variants and facilitates their chromatin targeting, presumably for de novo methylation. There are several mechanisms by which mammalian cells regulate DNMT levels, including varied transcriptional activation of the respective genes and posttranslational modifications of the enzymes that can affect catalytic activity, targeting, and enzyme degradation. In addition, binding of miRNAs or RNA-binding proteins can also alter the expression of DNMTs. These regulatory processes can be disrupted in disease or by environmental factors, resulting in altered DNMT expression and aberrant DNA methylation patterns.

  13. A computational NQR study on the hydrogen-bonded lattice of cytosine-5-acetic acid.

    Science.gov (United States)

    Mirzaei, Mahmoud; Hadipour, Nasser L

    2008-04-15

    A computational study at the level of density functional theory (DFT) employing 6-311++G** standard basis set was carried out to evaluate nuclear quadrupole resonance (NQR) spectroscopy parameters in cytosine-5-acetic acid (C5AA). Since the electric field gradient (EFG) tensors are very sensitive to the electrostatic environment at the sites of quadruple nuclei, the most possible interacting molecules with the target one were considered in a five-molecule model system of C5AA using X-ray coordinates transforming. The hydrogen atoms positions were optimized and two model systems of original and H-optimized C5AA were considered in NQR calculations. The calculated EFG tensors at the sites of (17)O, (14)N, and (2)H nuclei were converted to their experimentally measurable parameters, quadrupole coupling constants and asymmetry parameters. The evaluated NQR parameters reveal that the nuclei in original and H-optimized systems contribute to different hydrogen bonding (HB) interaction. The comparison of calculated parameters between optimized isolated gas-phase and crystalline monomer also shows the relationship between the structural deformation and NQR parameters in C5AA. The basis set superposition error (BSSE) calculations yielded no significant errors for employed basis set in the evaluation of NQR parameters. All the calculations were performed by Gaussian 98 package of program.

  14. [Molecular mechanisms of transitions induced by cytosine analogue: comparative quantum-chemical study].

    Science.gov (United States)

    Brovarets', O O; Govorun, D M

    2010-01-01

    Using the simplest molecular models at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of the theory it has been shown for the first time that in addition to traditional incorporational errors caused by facilitated (compared with the canonical DNA bases cytosine (Cyt)) tautomerization of 6-(2-deoxy-beta-D-ribofuranosyl)-3,4-dihydro-6H,8H-pyrimido[4,5-c][1,2]oxazin-7-one (DCyt), this mutagen causes the replication errors, increasing one million times the population of mispair Gua.DCyt* (asterisk marked mutagenic tautomer) as compared with mispair Gua.Cyt*. It is also proved that DCyt in addition to traditional incorporational errors also induces similar errors by an additional mechanism - due to a facilitated tautomerization of the wobble base pair Ade.DCyt (compared to the same pair Ade.Cyt) to a mispair Ade.DCyt* which is quasirisomorphic Watson-Crick base pair. Moreover, the obtained results allowed interpreting non-inconsistently the existing experimental NMR data.

  15. 5'-Cytosine-phosphoguanine (CpG) methylation impacts the activity of natural and engineered meganucleases.

    Science.gov (United States)

    Valton, Julien; Daboussi, Fayza; Leduc, Sophie; Molina, Rafael; Redondo, Pilar; Macmaster, Rachel; Montoya, Guillermo; Duchateau, Philippe

    2012-08-31

    In this study, we asked whether CpG methylation could influence the DNA binding affinity and activity of meganucleases used for genome engineering applications. A combination of biochemical and structural approaches enabled us to demonstrate that CpG methylation decreases I-CreI DNA binding affinity and inhibits its endonuclease activity in vitro. This inhibition depends on the position of the methylated cytosine within the DNA target and was almost total when it is located inside the central tetrabase. Crystal structures of I-CreI bound to methylated cognate target DNA suggested a molecular basis for such inhibition, although the precise mechanism still has to be specified. Finally, we demonstrated that the efficacy of engineered meganucleases can be diminished by CpG methylation of the targeted endogenous site, and we proposed a rational design of the meganuclease DNA binding domain to alleviate such an effect. We conclude that although activity and sequence specificity of engineered meganucleases are crucial parameters, target DNA epigenetic modifications need to be considered for successful gene editions.

  16. Theoretical Studies on the Interaction between Metal Cations and Cytosine, Guanine

    Institute of Scientific and Technical Information of China (English)

    ZHAO Ya-Ying; ZHOU Li-Xin; WAN Hua-Ping

    2005-01-01

    The interaction of tetra- and hexa-coordinated compounds of cytosine(C) and guanine(G) with metal cations Ca2+, Mg2+, Mn2+, Ni2+, Cu2+, and Zn2+ have been calculated by using the B3LYP/6-31G method at the 6-31G(d, p) basis set, while the remaining coordination bonds are saturated by water molecules ((H2O)4).All geometries were optimized without symmetry restrictions.Comparing the interaction energies we obtained the orders of selectivity of C and G for the above metal ions as follows: aCu2+>aNi2+>aZn2+>aMg2+>bCu2+>aMn2+>bZn2+>bNi2+ and aCu2+> aNi2+>aZn2+>aMg2+>bCu2+>aMn2+>bZn2+>bNi2, respectively (a, b represent tetra- and hexa-coordinated, respectively), which are in good agreement with the experimental facts.Interaction energies of complexes provide a comparatively reliable quantification of the selectivity of dimethyl phosphate anion for the studied metal ions.In addition, the influence of coordination number and coordination structure on the interaction energy and the variation of ionic energy were discussed sufficiently.After analyzing the interaction energies of two kinds of complexes, the "mutual selectivity"as well as the nature of the interaction between metal ions and ligands was revealed.

  17. Dual targeting of tumor angiogenesis and chemotherapy by endostatin-cytosine deaminase-uracil phosphoribosyltransferase.

    Science.gov (United States)

    Chen, Chun-Te; Yamaguchi, Hirohito; Lee, Hong-Jen; Du, Yi; Lee, Heng-Huan; Xia, Weiya; Yu, Wen-Hsuan; Hsu, Jennifer L; Yen, Chia-Jui; Sun, Hui-Lung; Wang, Yan; Yeh, Edward T H; Hortobagyi, Gabriel N; Hung, Mien-Chie

    2011-08-01

    Several antiangiogenic drugs targeting VEGF/VEGF receptor (VEGFR) that were approved by the Food and Drug Administration for many cancer types, including colorectal and lung cancer, can effectively reduce tumor growth. However, targeting the VEGF signaling pathway will probably influence the normal function of endothelial cells in maintaining homeostasis and can cause unwanted adverse effects. Indeed, emerging experimental evidence suggests that VEGF-targeting therapy induced less tumor cell-specific cytotoxicity, allowing residual cells to become more resistant and eventually develop a more malignant phenotype. We report an antitumor therapeutic EndoCD fusion protein developed by linking endostatin (Endo) to cytosine deaminase and uracil phosphoribosyltransferase (CD). Specifically, Endo possesses tumor antiangiogenesis activity that targets tumor endothelial cells, followed by CD, which converts the nontoxic prodrug 5-fluorocytosine (5-FC) to the cytotoxic antitumor drug 5-fluorouracil (5-FU) in the local tumor area. Moreover, selective targeting of tumor sites allows an increasing local intratumoral concentration of 5-FU, thus providing high levels of cytotoxic activity. We showed that treatment with EndoCD plus 5-FC, compared with bevacizumab plus 5-FU treatment, significantly increased the 5-FU concentration around tumor sites and suppressed tumor growth and metastasis in human breast and colorectal orthotropic animal models. In addition, in contrast to treatment with bevacizumab/5-FU, EndoCD/5-FC did not induce cardiotoxicity leading to heart failure in mice after long-term treatment. Our results showed that, compared with currently used antiangiogenic drugs, EndoCD possesses potent anticancer activity with virtually no toxic effects and does not increase tumor invasion or metastasis. Together, these findings suggest that EndoCD/5-FC could become an alternative option for future antiangiogenesis therapy.

  18. [Synthese of 1-(5-deoxy-beta-D-ribo-hexofuranosyl)cytosine and 1-(2,5-dideoxy-beta-D-erythro-hexofuranosyl)cytosine, and their phosphates. Specificity of an mammalian (rat) ribonucleotide-reductase].

    Science.gov (United States)

    David, S; de Sennyey, G

    1979-12-01

    Mild, acidic hydrolysis of 3-O-benzoyl-1,2,:5,6-di-O-isopropylidene-alpha-D-allofuranose gave a diol that was selectively benzoylated at O-6 in high yield by intermediate conversion to the stannylene derivative. The 3,6-dibenzoate was converted to the 5-O-tosyl derivative and thence to a mixture of iodides, which were reduced with tributylstannane to 3,6-di-O-benzoyl-1,2-O-isopropylidene-alpha-D-ribo-hexofuranose (6). Acetolysis gave an anomeric mixture of diacetates, which, when treated with N-acetylbis(trimethylsilyl)cytosine gave the protected nucleoside, which was deprotected to free "homocytidine", 1-(5-deoxy-beta-D-ribo-hexofuranosyl)cytosine (11), by alklaine methanolysis. This was N-acetylated and then treated with acetone to give a protected nucleoside, which was labelled by oxidation to the aldehyde, reduction with sodium borotritide, and deprotection. Acidic methanolysis of 6 gave a mixture of methyl 2,6- and 3,6-di-O-benzoylfuranosides, the hydroxyl groups of which were treated by the tetrachloromethane-triphenylphosphine reagent to give the 2-chloro-2-deoxy (21) and 3-chloro-3-deoxy derivatives. Reduction of 21 gave methyl 3,6-di-O-benzoyl-2,5-dideoxy-D-erythro-furanoside, further transformed in 1-(2,5-dideoxy-beta-D-erythro-hexofuranosyl)cytosine mixed with the alpha anomer. Phosphates and diphosphates of the nucleosides were prepared by extensions of known methods. The phosphate and the diphosphate of 11 act neither as substrates nor as inhibitors of a ribonucleotide-reductase from rat asicites tumor.

  19. Effect of C5-Methylation of Cytosine on the UV-Induced Reactivity of Duplex DNA: Conformational and Electronic Factors.

    Science.gov (United States)

    Banyasz, Akos; Esposito, Luciana; Douki, Thierry; Perron, Marion; Lepori, Clément; Improta, Roberto; Markovitsi, Dimitra

    2016-05-12

    C5-methylation of cytosines is strongly correlated with UV-induced mutations detected in skin cancers. Mutational hot-spots appearing at TCG sites are due to the formation of pyrimidine cyclobutane dimers (CPDs). The present study, performed for the model DNA duplex (TCGTA)3·(TACGA)3 and the constitutive single strands, examines the factors underlying the effect of C5-methylation on pyrimidine dimerization at TCG sites. This effect is quantified for the first time by quantum yields ϕ. They were determined following irradiation at 255, 267, and 282 nm and subsequent photoproduct analysis using HPLC coupled to mass spectrometry. C5-methylation leads to an increase of the CPD quantum yield up to 80% with concomitant decrease of that of pyrimidine(6-4) pyrimidone adducts (64PPs) by at least a factor of 3. The obtained ϕ values cannot be explained only by the change of the cytosine absorption spectrum upon C5-methylation. The conformational and electronic factors that may affect the dimerization reaction are discussed in light of results obtained by fluorescence spectroscopy, molecular dynamics simulations, and quantum mechanical calculations. Thus, it appears that the presence of an extra methyl on cytosine affects the sugar puckering, thereby enhancing conformations of the TC step that are prone to CPD formation but less favorable to 64PPs. In addition, C5-methylation diminishes the amplitude of conformational motions in duplexes; in the resulting stiffer structure, ππ* excitations may be transferred from initially populated exciton states to reactive pyrimidines giving rise to CPDs.

  20. Quantum chemical investigation of the electronic spectra of the keto, enol, and keto-imine tautomers of cytosine.

    Science.gov (United States)

    Tomić, Katarina; Tatchen, Jörg; Marian, Christel M

    2005-09-22

    The low-lying excited singlet states of the keto, enol, and keto-imine tautomers of cytosine have been investigated employing a combined density functional/multireference configuration interaction (DFT/MRCI) method. Unconstrained geometry optimizations have yielded out-of-plain distorted structures of the pi --> pi and n --> pi excited states of all cytosine forms. For the keto tautomer, the DFT/MRCI adiabatic excitation energy of the pi --> pi state (4.06 eV including zero-point vibrational energy corrections) supports the resonant two-photon ionization (R2PI) spectrum (Nir et al. Phys. Chem. Chem. Phys. 2002, 5, 4780). On its S1 potential energy surface, a conical intersection between the 1pipi state and the electronic ground state has been identified. The barrier height of the reaction along a constrained minimum energy path amounts to merely 0.2 eV above the origin and explains the break-off of the R2PI spectrum. The 1pipi minimum of the enol tautomer is found at considerably higher excitation energies (4.50 eV). Because of significant geometry shifts with respect to the ground state, long vibrational progressions are expected, in accord with experimental observations. For the keto-imine tautomer, a crossing of the 1pipi potential energy surface with the ground-state surface has been found, too. Its n --> pi minimum (3.27 eV) is located well below the conical intersection between the pi --> pi and S0 states, but it will be difficult to observe because of its small transition moment. The identified conical intersections of the pi --> pi excited states of the keto cytosine tautomers are made responsible for the ultrafast decay to the electronic ground states and thus may explain their subpicoseconds lifetimes.

  1. Intersystem crossing rates of S1 state keto-amino cytosine at low excess energy

    Science.gov (United States)

    Lobsiger, Simon; Etinski, Mihajlo; Blaser, Susan; Frey, Hans-Martin; Marian, Christel; Leutwyler, Samuel

    2015-12-01

    The amino-keto tautomer of supersonic jet-cooled cytosine undergoes intersystem crossing (ISC) from the v = 0 and low-lying vibronic levels of its S1(1ππ∗) state. We investigate these ISC rates experimentally and theoretically as a function of S1 state vibrational excess energy Eexc. The S1 vibronic levels are pumped with a ˜5 ns UV laser, the S1 and triplet state ion signals are separated by prompt or delayed ionization with a second UV laser pulse. After correcting the raw ISC yields for the relative S1 and T1 ionization cross sections, we obtain energy dependent ISC quantum yields QISC corr = 1 % -5%. These are combined with previously measured vibronic state-specific decay rates, giving ISC rates kISC = 0.4-1.5 ṡ 109 s-1, the corresponding S1⇝S0 internal conversion (IC) rates are 30-100 times larger. Theoretical ISC rates are computed using SCS-CC2 methods, which predict rapid ISC from the S1; v = 0 state with kISC = 3 ṡ 109 s-1 to the T1(3ππ∗) triplet state. The surprisingly high rate of this El Sayed-forbidden transition is caused by a substantial admixture of 1nOπ∗ character into the S1(1ππ∗) wave function at its non-planar minimum geometry. The combination of experiment and theory implies that (1) below Eexc = 550 cm-1 in the S1 state, S1⇝S0 internal conversion dominates the nonradiative decay with kIC ≥ 2 ṡ 1010 s-1, (2) the calculated S1⇝T1 (1ππ∗⇝3ππ∗) ISC rate is in good agreement with experiment, (3) being El-Sayed forbidden, the S1⇝T1 ISC is moderately fast (kISC = 3 ṡ 109 s-1), and not ultrafast, as claimed by other calculations, and (4) at Eexc ˜ 550 cm-1 the IC rate increases by ˜50 times, probably by accessing the lowest conical intersection (the C5-twist CI) and thereby effectively switching off the ISC decay channels.

  2. Pulsed magnetic field from video display terminals enhances teratogenic effects of cytosine arabinoside in mice

    Energy Technology Data Exchange (ETDEWEB)

    Chiang, H.; Wu, R.Y.; Shao, B.J.; Fu, Y.D.; Yao, G.D.; Lu, D.J. [Zhejiang Medical Univ. (China)

    1995-05-01

    Eighty-nine Swiss Webster mice were randomly divided into four groups: a control group, a pulsed magnetic field (PMF) group, a cytosine arabinoside (ara-C, a teratogen) group, and a combined PMF + ara-C group. Mice in the PMF and PMF + ara-C groups were irradiated with a PMF (a sawtooth waveform with 52 {mu}s rise time, 12{mu}s decay time, and 15.6 kHz frequency) at a peak magnetic flux density of 40 {mu}T for 4 hours daily on days 6-17 of gestation. The mice in the ara-C and the PMF + ara-C groups were injected intraperitoneally on day 9 of gestation with 10 mg/kg of ara-C. The incidence of resorption and dead fetuses was not affected by PMF but was increased by ara-C injection. The malformation incidence of cleft palate (CP) and/or cleft lip (CL) was significantly higher in all three of the treated groups than in the control group (P < 0.05). If, however, statistical analyses had been done on litters rather than on individual fetuses, they would show that the incidence of CP and/or CL in the PMF group is not significantly greater than that in the control group. A significantly higher incidence of CP and/or CL was found in the PMF + ara-C group (49%) than the ara-C alone group (26.1%). These data suggest that PMF might enhance the development of ara-C-induced CP and/or CL. The incidence of minor variations in skeletal development, including reduction of skeletal calcification and loss of skeleton, was not statistically significant in the PMF group. However, it was higher in the two ara-C-treated groups, and there was no significant difference between the ara-C alone group and the ara-C + PMF group. From these results it is concluded that the very weak embryotoxic effects of PMF exposure may be revealed and enhanced in combination with a teratogenic agent.

  3. IR Vibrational spectra of H-bonded complexes of adenine, 2-aminopurine and 2-aminopurine+ with cytosine and thymine: Quantum-chemical study

    Science.gov (United States)

    Brovarets', O. O.; Hovorun, D. M.

    2011-11-01

    Using theoretical study on the B3LYP/6-311++G(d,p) level of theory, we have compared vibrational spectra of 2-aminopurine (as neutral or protonated at N1 atom species) with adenine and H-bonded complexes of 2-aminopurine (as neutral or protoned at N1 atom species) · cytosine or 2-aminopurine · thymine with adenine · cytosine and adenine · thymine base pairs. The nature of the base pairing between adenine, 2-aminopurine, 2-aminopurine+ and cytosine or thymine have been investigated by means of quantum-mechanical calculations. We have investigated the effect of the hydrogen bond formation on the vibrational spectra of the investigated base pairs. The main differences in the vibrational spectra as for bases so for base pairs have been observed in the high-frequency region.

  4. First-In-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ming; Shandilya, Shivender M.D.; Carpenter, Michael A.; Rathore, Anurag; Brown, William L.; Perkins, Angela L.; Harki, Daniel A.; Solberg, Jonathan; Hook, Derek J.; Pandey, Krishan K.; Parniak, Michael A.; Johnson, Jeffrey R.; Krogan, Nevan J.; Somasundaran, Mohan; Ali, Akbar; Schiffer, Celia A.; Harris, Reuben S. (Pitt); (UMASS, MED); (SLUHSC); (UCSF); (UMM)

    2012-04-04

    APOBEC3G is a single-stranded DNA cytosine deaminase that comprises part of the innate immune response to viruses and transposons. Although APOBEC3G is the prototype for understanding the larger mammalian polynucleotide deaminase family, no specific chemical inhibitors exist to modulate its activity. High-throughput screening identified 34 compounds that inhibit APOBEC3G catalytic activity. Twenty of 34 small molecules contained catechol moieties, which are known to be sulfhydryl reactive following oxidation to the orthoquinone. Located proximal to the active site, C321 was identified as the binding site for the inhibitors by a combination of mutational screening, structural analysis, and mass spectrometry. Bulkier substitutions C321-to-L, F, Y, or W mimicked chemical inhibition. A strong specificity for APOBEC3G was evident, as most compounds failed to inhibit the related APOBEC3A enzyme or the unrelated enzymes E. coli uracil DNA glycosylase, HIV-1 RNase H, or HIV-1 integrase. Partial, but not complete, sensitivity could be conferred to APOBEC3A by introducing the entire C321 loop from APOBEC3G. Thus, a structural model is presented in which the mechanism of inhibition is both specific and competitive, by binding a pocket adjacent to the APOBEC3G active site, reacting with C321, and blocking access to substrate DNA cytosines.

  5. Induced Pib Expression and Resistance to Magnaporthe grisea are Compromised by Cytosine Demethylation at Critical Promoter Regions in Rice.

    Science.gov (United States)

    Li, Yuan; Xia, Qiong; Kou, Hongping; Wang, Dan; Lin, Xiuyun; Wu, Ying; Xu, Chunming; Xing, Shaochen; Liu, Bao

    2011-10-01

    Pib is a well-characterized rice blast-resistance gene belonging to the nucleotide binding site (NBS) and leucine-rich repeat (LRR) superfamily. Expression of Pib was low under non-challenged conditions, but strongly induced by the blast-causing fungal pathogen Magnaporthe grisea, thereby conferring resistance to the pathogen. It is generally established that cytosine methylation of the promoter-region often plays a repressive role in modulating expression of the gene in question. We report here that two critical regions of the Pib promoter were heavily CG cytosine-methylated in both cultivars studied. Surprisingly, induced expression of Pib by M. grisea infection did not entail its promoter demethylation, and partial demethylation by 5-azacytidine-treatment actually reduced Pib expression relative to wild-type plants. Accordingly, the blast disease-resistance was compromised in the 5'-azaC-treated plants relative to wild-type. In contrast, the disease susceptibility was not affected by the 5'-azaC treatment in another two rice cultivars that did not contain the Pib gene, ruling out effects of other R genes and non-specific genotoxic effects by the drug-treatment as a cause for the compromised Pib-conditioned blast-resistance. Taken together, our results suggest that promoter DNA methylation plays a novel enhancing role in conditioning high-level of induced expression of the Pib gene in times of M. grisea infection, and its conferred resistance to the pathogen.

  6. Killing effect of adenoviral mediated cytosine deaminase gene on human pancreatic cancer cell line PaTu 8988

    Institute of Scientific and Technical Information of China (English)

    PAN Xue; LI Zhao-shen; XU Guo-ming; CUI Long; ZHANG Su-zhen; GONG Yan-fang; TU Zhen-xing

    2001-01-01

    Objective: To evaluate the in vitro killing effects of cytosine deaminase gene mediated by adenovirus vector on human pancreatic carcinoma. Methods: Cytosine Deaminase (CD) gene was cloned into pAdTrack-CMV-CD, pAdTrack-CMV-CD and pAdEasy-1 were recombined in bacteria, and the products containing green fluorescent protein (GFP)were propagated in 293 cells and purified by cesium chloride gradient centrifugation. Human pancreatic carcinoma cell line 8988 were infected with this virus, then 5-FC was added; XTT assay was used to estimate the relative numbers of viable cells. Results: The positive clones were confirmed by using endonuclease digestion, and the titer of the virus containing CD gene was 2 × 1011 pfu/ml. It was found that 5-FC possessed significant cytotoxic activities for CD gene transfected 8988cell line, but had little effects on non-transfected pancreatic carcinoma cells. Conclusion: CD gene mediated by adenovirus has a high infectivity and is efficient for killing cultured pancreatic carcinoma cells, indicating suicide gene may be effective for pancreatic cancer in furure.

  7. Synthesis, Characterization, and Physicochemical Studies of Mixed Ligand Complexes of Inner Transition Metals with Lansoprazole and Cytosine

    Directory of Open Access Journals (Sweden)

    Sarika Verma

    2013-01-01

    Full Text Available Few complexes of inner transition metals [Th(IV, Ce(IV, Nd(III, Gd(III] have been synthesized by reacting their metal salts with lansoprazole, 2-([3-methyl-4-(2,2,2-trifluoroethoxypyridin-2-yl]methylsulfinyl-1H-benzoimidazole and cytosine. All the complexes were synthesized in ethanolic medium. The yield percentage rangs from 80 to 90%. The complexes are coloured solids. The complexes were characterized through elemental analyses, conductance measurements, and spectroscopic methods (FT IR, FAB Mass, 1H NMR and UV. An IR spectrum indicates that the ligand behaves as bidentate ligands. The metal complexes have been screened for their antifungal activity towards Aspergillus niger fungi. The interaction of inner transition metals with lansoprazole, in presence of cytosine, has also been investigated potentiometrically at two different temperatures 26±1°C and 36±1°C and at 0.1 M (KNO3 ionic strength. The stability constants of ternary complexes indicate the stability order as Th(IV < Ce(IV < Gd(III < Nd(III. logK values obtained are positive and suggest greater stabilization of ternary complexes. The values of thermodynamic parameters (free energy (ΔG, enthalpy (ΔH, and entropy (ΔS are also calculated.

  8. Killing effect of coexpressing cytosine deaminase and thymidine kinase on rat vascular smooth muscle cells

    Institute of Scientific and Technical Information of China (English)

    曹慧青; 孟宪敏; 刘冬青; 赵秀文; 丁金凤

    2004-01-01

    Background Vascular smooth muscle cell (VSMC) proliferation following arterial injury plays a critical role in a variety of vascular proliferative disorders, such as atherosclerosis and restenosis after balloon angioplasty. Herpes simplex virus-thymidine kinase (HSV-TK)/ganciclovir (GCV) and E.coli cytosine deaminase (CD)/5-fluorocytosine (5-Fc) suicide gene systems have been successfully employed in cardiovascular gene therapy, respectively. We reasoned that coexpression of both HSV-TK with CD suicide genes would lead to increased cell killing. To test this imagine, the adenoviral vectors expressing TK and/or CD genes were developed and tested on vascular smooth muscle cells. Methods Adenoviral vectors, including Ad-EF1α-CD-cytomegolovirus (CMV)-TK coexpressing both CD and TK double suicide genes, Ad-EF1α-CD and Ad-CMV-TK expressing CD and TK respectively, and control vector Ad-CMV-LacZ, were constructed and prepared with homologous recombination in RecA+E.coli cells. Integration and expression of CD and/or TK gene were identified by PCR and Western blot. Primary cultured VSMCs were infected at a multiplicity of infection (MOI) of 20 with exposure to their matching prodrugs 5-Fc and GCV. Cell mortality was measured by methyl thiazolyl tetrazolium (MTT) assays. Flow cytometry analysis was used to detect cell death. Apoptotic cells were analyzed using Hoechst 33342 fluorescence dye as a DNA probe. Genomic DNA cleavage of apoptotic VSMCs was tested by agarose gel electrophoresis. Results Recombinant adenovirus expressing CD and/or TK suicide genes were successfully constructed. Both single and double suicide genes could be integrated into adenoviral genome and expressed. Cytotoxic effects of Ad-EF1α-CD-CMV-TK double suicide genes combined with 5-Fc and GCV were higher than those of Ad-CMV-TK and Ad-EF1α-CD single gene groups. The rate of cell survival was only (9±3)% in the Ad-EF1α-CD-CMV-TK group, but (37±3)% in the Ad-CMV-TK and (46±4)% in the Ad-EF1

  9. Sensitization of prostate cancer cell lines to 5-fluorocytosine induced by a replication incompetent adenoviral vector carrying a cytosine deaminase transcription unit

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    AIM: To investigate the efficiency of cytosine deaminase adenoviral/5-fluorocytosine system on prostate cancer cell lines. METHODS: Cell culture, infectivity test and sensitivity test, observing the bystander effect and animal model experiment were carried out. RESULTS: All the established prostate cancer cell lines were eventually infectable, but ratio of vector/cell and time of exposed at which infection occurs was dependent on the cell lines. The expression of transfered cytosine deaminase gene peaked at different days, but persisted beyond 11 days. The prostate cell lines were sensitized to the 5-fluorocytosine by infection with the cytosine deaminase gene adenoviral vector, and only 5% of the LNCap and 10% of the RM-1 cells infected were required for 100% cell death. In the animal model, there was significant eradiation of tumor growth at the ratio of 400 vector particles/cell and with the systematic treatment of 5-fluorocytosine. CONCLUSION: The adenoviral vector carrying a cytosine deaminase transcription unit can sensitize the prostate cancer cell lines to 5-fluorocytosine, and the system can significantly inhibit the growth of prostatic tumor in mice.

  10. Bacillus halodurans Strain C125 Encodes and Synthesizes Enzymes from Both Known Pathways To Form dUMP Directly from Cytosine Deoxyribonucleotides

    DEFF Research Database (Denmark)

    Oehlenschlæger, Christian Berg; Løvgreen, Monika Nøhr; Reinauer, Eva

    2015-01-01

    Analysis of the genome of Bacillus halodurans strain C125 indicated that two pathways leading from a cytosine deoxyribonucleotide to dUMP, used for dTMP synthesis, were encoded by the genome of the bacterium. The genes that were responsible, the comEB gene and the dcdB gene, encoding dCMP deaminase...

  11. Interaction of Cu+ with cytosine and formation of i-motif-like C-M+-C complexes: alkali versus coinage metals

    NARCIS (Netherlands)

    J. Gao; G. Berden; M.T. Rodgers; J. Oomens

    2016-01-01

    The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton

  12. Targeted cytosine deaminase-uracil phosphoribosyl transferase suicide gene therapy induces small cell lung cancer-specific cytotoxicity and tumor growth delay

    DEFF Research Database (Denmark)

    Christensen, Camilla L; Gjetting, Torben; Poulsen, Thomas Tuxen

    2010-01-01

    Small cell lung cancer (SCLC) is a highly malignant cancer for which there is no curable treatment. Novel therapies are therefore in great demand. In the present study we investigated the therapeutic effect of transcriptionally targeted suicide gene therapy for SCLC based on the yeast cytosine de...

  13. Electronic Excited State and Vibrational Dynamics of Water Solution of Cytosine Observed by Time-resolved Transient Absorption Spectroscopy with Sub-10fs Deep Ultraviolet Laser Pules

    Directory of Open Access Journals (Sweden)

    Kobayashi Takayoshi.

    2013-03-01

    Full Text Available Time-resolved transient absorption spectroscopy for water solution of cytosine with sub-10fs deep ultraviolet laser pulse is reported. Ultrafast electronic excited state dynamics and coherent molecular vibrational dynamics are simultaneously observed and their relaxation mechanisms are discussed.

  14. Crystal structure of the DNA cytosine deaminase APOBEC3F: the catalytically active and HIV-1 Vif-binding domain.

    Science.gov (United States)

    Bohn, Markus-Frederik; Shandilya, Shivender M D; Albin, John S; Kouno, Takahide; Anderson, Brett D; McDougle, Rebecca M; Carpenter, Michael A; Rathore, Anurag; Evans, Leah; Davis, Ahkillah N; Zhang, Jingying; Lu, Yongjian; Somasundaran, Mohan; Matsuo, Hiroshi; Harris, Reuben S; Schiffer, Celia A

    2013-06-04

    Human APOBEC3F is an antiretroviral single-strand DNA cytosine deaminase, susceptible to degradation by the HIV-1 protein Vif. In this study the crystal structure of the HIV Vif binding, catalytically active, C-terminal domain of APOBEC3F (A3F-CTD) was determined. The A3F-CTD shares structural motifs with portions of APOBEC3G-CTD, APOBEC3C, and APOBEC2. Residues identified to be critical for Vif-dependent degradation of APOBEC3F all fit within a predominantly negatively charged contiguous region on the surface of A3F-CTD. Specific sequence motifs, previously shown to play a role in Vif susceptibility and virion encapsidation, are conserved across APOBEC3s and between APOBEC3s and HIV-1 Vif. In this structure these motifs pack against each other at intermolecular interfaces, providing potential insights both into APOBEC3 oligomerization and Vif interactions.

  15. Spectroscopic (UV/VIS, Raman) and Electrophoresis Study of Cytosine-Guanine Oligonucleotide DNA Influenced by Magnetic Field.

    Science.gov (United States)

    Banihashemian, Seyedeh Maryam; Periasamy, Vengadesh; Boon Tong, Goh; Abdul Rahman, Saadah

    2016-01-01

    Studying the effect of a magnetic field on oligonucleotide DNA can provide a novel DNA manipulation technique for potential application in bioengineering and medicine. In this work, the optical and electrochemical response of a 100 bases oligonucleotides DNA, cytosine-guanine (CG100), is investigated via exposure to different magnetic fields (250, 500, 750, and 1000 mT). As a result of the optical response of CG100 to the magnetic field, the ultra-violet-visible spectrum indicated a slight variation in the band gap of CG100 of about 0.3 eV. Raman spectroscopy showed a significant deviation in hydrogen and phosphate bonds' vibration after exposure to the magnetic field. Oligonucleotide DNA mobility was investigated in the external electric field using the gel electrophoresis technique, which revealed a small decrease in the migration of CG100 after exposure to the magnetic field.

  16. Crystallization and preliminary crystallographic analysis of a DNA (cytosine-5)-methyltransferase from Haemophilus aegyptius bound covalently to DNA.

    Science.gov (United States)

    Reinisch, K M; Chen, L; Verdine, G L; Lipscomb, W N

    1994-05-13

    A DNA (cytosine)-5-methyltransferase from Haemophilus aegyptius (M.Hae III), which catalyzes methyl transfer from S-adenosyl-L-methionine to DNA, has been crystallized as a covalent complex with a suicide oligonucleotide substrate. Crystals of the co-complex were grown by vapor diffusion with hanging droplets, using polyethylene glycol 3500 as the precipitant. The crystals belong to the orthorhombic space group P2(1)2(1)2(1); the unit cell parameters are a = 57.6 A, b = 108.0 A, c = 155.8 A with two protein-DNA complexes in the asymmetric unit. Complete sets of native and derivative data have been collected to 2.7 A using a laboratory source.

  17. Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines

    Directory of Open Access Journals (Sweden)

    Ke Tang

    2016-06-01

    Full Text Available Gene expression is a complex and quantitative trait that is influenced by both genetic and non-genetic regulators including environmental factors. Evaluating the contribution of environment to gene expression regulation and identifying which genes are more likely to be influenced by environmental factors are important for understanding human complex traits. We hypothesize that by living together as couples, there can be commonly co-regulated genes that may reflect the shared living environment (e.g., diet, indoor air pollutants, behavioral lifestyle. The lymphoblastoid cell lines (LCLs derived from unrelated couples of African ancestry (YRI, Yoruba people from Ibadan, Nigeria from the International HapMap Project provided a unique model for us to characterize gene expression pattern in couples by comparing gene expression levels between husbands and wives. Strikingly, 778 genes were found to show much smaller variances in couples than random pairs of individuals at a false discovery rate (FDR of 5%. Since genetic variation between unrelated family members in a general population is expected to be the same assuming a random-mating society, non-genetic factors (e.g., epigenetic systems are more likely to be the mediators for the observed transcriptional similarity in couples. We thus evaluated the contribution of modified cytosines to those genes showing transcriptional similarity in couples as well as the relationships these CpG sites with other gene regulatory elements, such as transcription factor binding sites (TFBS. Our findings suggested that transcriptional similarity in couples likely reflected shared common environment partially mediated through cytosine modifications.

  18. Induced Pib Expression and Resistance to Magnaporthe grisea are Compromised by Cytosine Demethylation at Critical Promoter Regions in Rice

    Institute of Scientific and Technical Information of China (English)

    Yuan Li; Qiong Xia; Hongping Kou; Dan Wang; Xiuyun Lin; Ying Wu; Chunming Xu; Shaochen Xing

    2011-01-01

    Pib is a well-characterized rice blast-resistance gene belonging to the nucleotide binding site (NBS) and leucine-rich repeat (LRR) superfamily.Expression of Pib was low under non-challenged conditions,but strongly induced by the blast-causing fungal pathogen Magnaporthe grisea,thereby conferring resistance to the pathogen.It is generally established that cytosine methylation of the promoter-region often plays a repressive role in modulating expression of the gene in question.We report here that two critical regions of the Pib promoter were heavily CG cytosine-methylated in both cultivars studied.Surprisingly,induced expression of Pib by M.grisea infection did not entail its promoter demethylation,and partial demethylation by 5-azacytidine-treatment actually reduced Pib expression relative to wildtype plants.Accordingly,the blast disease-resistance was compromised in the 5’-azaC-treated plants relative to wild-type.In contrast,the disease susceptibility was not affected by the 5’-azaC treatment in another two rice cultivars that did not contain the Pib gene,ruling out effects of other R genes and non-specific genotoxic effects by the drug-treatment as a cause for the compromised Pib-conditioned blast-resistance.Taken together,our results suggest that promoter DNA methylation plays a novel enhancing role in conditioning high-level of induced expression of the Pib gene in times of M.grisea infection,and its conferred resistance to the pathogen.

  19. Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines.

    Science.gov (United States)

    Tang, Ke; Zhang, Wei

    2016-01-01

    Gene expression is a complex and quantitative trait that is influenced by both genetic and non-genetic regulators including environmental factors. Evaluating the contribution of environment to gene expression regulation and identifying which genes are more likely to be influenced by environmental factors are important for understanding human complex traits. We hypothesize that by living together as couples, there can be commonly co-regulated genes that may reflect the shared living environment (e.g., diet, indoor air pollutants, behavioral lifestyle). The lymphoblastoid cell lines (LCLs) derived from unrelated couples of African ancestry (YRI, Yoruba people from Ibadan, Nigeria) from the International HapMap Project provided a unique model for us to characterize gene expression pattern in couples by comparing gene expression levels between husbands and wives. Strikingly, 778 genes were found to show much smaller variances in couples than random pairs of individuals at a false discovery rate (FDR) of 5%. Since genetic variation between unrelated family members in a general population is expected to be the same assuming a random-mating society, non-genetic factors (e.g., epigenetic systems) are more likely to be the mediators for the observed transcriptional similarity in couples. We thus evaluated the contribution of modified cytosines to those genes showing transcriptional similarity in couples as well as the relationships these CpG sites with other gene regulatory elements, such as transcription factor binding sites (TFBS). Our findings suggested that transcriptional similarity in couples likely reflected shared common environment partially mediated through cytosine modifications.

  20. Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

    Directory of Open Access Journals (Sweden)

    Vining Kelly J

    2012-01-01

    Full Text Available Abstract Background DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood. Results We surveyed DNA methylation from seven distinct tissue types (vegetative bud, male inflorescence [catkin], female catkin, leaf, root, xylem, phloem in the reference tree species black cottonwood (Populus trichocarpa. Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq, we mapped a total of 129,360,151 36- or 32-mer reads to the P. trichocarpa reference genome. We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data. Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation" had even lower expression than genes with promoter methylation. Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation. Conclusions We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.

  1. Structure and dynamics of H. pylori 98-10 C5-cytosine specific DNA methyltransferase in complex with S-adenosyl-l-methionine and DNA.

    Science.gov (United States)

    Singh, Swati; Tanneeru, Karunakar; Guruprasad, Lalitha

    2016-10-20

    Helicobacter pylori is a Gram-negative bacterium that inhabits the human gastrointestinal tract, and some strains of this bacterium cause gastric ulcers and cancer. DNA methyltransferases (MTases) are promising drug targets for the treatment of cancer and other diseases that are also caused by epigenetic alternations of the genome. The C5-cytosine specific DNA methyltransferase from H. pylori (M. Hpy C5mC) catalyzes the transfer of the methyl group from the cofactor S-adenosyl-l-methionine (AdoMet) to the flipped cytosine of the substrate DNA. Herein we report the sequence analyses, 3-D structure modeling and molecular dynamics simulations of M. Hpy C5mC, when complexed with AdoMet as well as DNA. We analyzed the protein-DNA interactions prominently established by the flipped cytosine and the interactions between the protein and cofactor in the active site. We propose that the contacts made by cytosine O2 with Arg155 and Arg157, and the water-mediated interactions with cytosine N3 may be essential for the activity of methyl transfer as well as the deprotonation at the C5 position in our C5mC model. Specific recognition of DNA was mediated mainly by residues from Ser221-Arg229 and Ser243-Gln246 of the target recognition domain (TRD) and some residues of the loop Ser75-Lys83 from the large domain. These findings are further supported by alanine scanning mutagenesis studies. The results reported here explain the sequence, structure and binding features necessary for the recognition between the cofactor and the substrate by the key epigenetic enzyme, M. Hpy C5mC.

  2. Investigating the Co-Adsorption Behavior of Nucleic-Acid Base (Thymine and Cytosine) and Melamine at Liquid/Solid Interface

    Science.gov (United States)

    Zhao, Huiling; Li, Yinli; Chen, Dong; Liu, Bo

    2016-12-01

    The co-adsorption behavior of nucleic-acid base (thymine; cytosine) and melamine was investigated by scanning tunneling microscopy (STM) technique at liquid/solid (1-octanol/graphite) interface. STM characterization results indicate that phase separation happened after dropping the mixed solution of thymine-melamine onto highly oriented pyrolytic graphite (HOPG) surface, while the hetero-component cluster-like structure was observed when cytosine-melamine binary assembly system is used. From the viewpoints of non-covalent interactions calculated by using density functional theory (DFT) method, the formation mechanisms of these assembled structures were explored in detail. This work will supply a methodology to design the supramolecular assembled structures and the hetero-component materials composed by biological and chemical compound.

  3. 〈生命科学科〉胎生期にcytosine arabinoside を曝露されたマウスに誘発された行動異常

    OpenAIRE

    2013-01-01

    It has been reported in epidemiological studies that prenatal exposure to chemicals such as polychlorinated biphenyl, valproic acid and nicotine during pregnancy increases the risk of developmental disabilities in childhood. In this study, we examined neurobehavioral characteristics in offspring naturally delivered from dams treated with cytosine arabinoside (cytosine-β-D-arabino furanoside ; Ara-C) to elucidate the association between the prenatal exposure to chemicals and the behavioral dis...

  4. Hydration properties of natural and synthetic DNA sequences with methylated adenine or cytosine bases in the R.DpnI target and BDNF promoter studied by molecular dynamics simulations

    Science.gov (United States)

    Shanak, Siba; Helms, Volkhard

    2014-12-01

    Adenine and cytosine methylation are two important epigenetic modifications of DNA sequences at the levels of the genome and transcriptome. To characterize the differential roles of methylating adenine or cytosine with respect to their hydration properties, we performed conventional MD simulations and free energy perturbation calculations for two particular DNA sequences, namely the brain-derived neurotrophic factor (BDNF) promoter and the R.DpnI-bound DNA that are known to undergo methylation of C5-methyl cytosine and N6-methyl adenine, respectively. We found that a single methylated cytosine has a clearly favorable hydration free energy over cytosine since the attached methyl group has a slightly polar character. In contrast, capping the strongly polar N6 of adenine with a methyl group gives a slightly unfavorable contribution to its free energy of solvation. Performing the same demethylation in the context of a DNA double-strand gave quite similar results for the more solvent-accessible cytosine but much more unfavorable results for the rather buried adenine. Interestingly, the same demethylation reactions are far more unfavorable when performed in the context of the opposite (BDNF or R.DpnI target) sequence. This suggests a natural preference for methylation in a specific sequence context. In addition, free energy calculations for demethylating adenine or cytosine in the context of B-DNA vs. Z-DNA suggest that the conformational B-Z transition of DNA transition is rather a property of cytosine methylated sequences but is not preferable for the adenine-methylated sequences investigated here.

  5. Accurate CpG and non-CpG cytosine methylation analysis by high-throughput locus-specific pyrosequencing in plants.

    Science.gov (United States)

    How-Kit, Alexandre; Daunay, Antoine; Mazaleyrat, Nicolas; Busato, Florence; Daviaud, Christian; Teyssier, Emeline; Deleuze, Jean-François; Gallusci, Philippe; Tost, Jörg

    2015-07-01

    Pyrosequencing permits accurate quantification of DNA methylation of specific regions where the proportions of the C/T polymorphism induced by sodium bisulfite treatment of DNA reflects the DNA methylation level. The commercially available high-throughput locus-specific pyrosequencing instruments allow for the simultaneous analysis of 96 samples, but restrict the DNA methylation analysis to CpG dinucleotide sites, which can be limiting in many biological systems. In contrast to mammals where DNA methylation occurs nearly exclusively on CpG dinucleotides, plants genomes harbor DNA methylation also in other sequence contexts including CHG and CHH motives, which cannot be evaluated by these pyrosequencing instruments due to software limitations. Here, we present a complete pipeline for accurate CpG and non-CpG cytosine methylation analysis at single base-resolution using high-throughput locus-specific pyrosequencing. The devised approach includes the design and validation of PCR amplification on bisulfite-treated DNA and pyrosequencing assays as well as the quantification of the methylation level at every cytosine from the raw peak intensities of the Pyrograms by two newly developed Visual Basic Applications. Our method presents accurate and reproducible results as exemplified by the cytosine methylation analysis of the promoter regions of two Tomato genes (NOR and CNR) encoding transcription regulators of fruit ripening during different stages of fruit development. Our results confirmed a significant and temporally coordinated loss of DNA methylation on specific cytosines during the early stages of fruit development in both promoters as previously shown by WGBS. The manuscript describes thus the first high-throughput locus-specific DNA methylation analysis in plants using pyrosequencing.

  6. DNA methylation at the C-5 position of cytosine by methyl radicals: a possible role for epigenetic change during carcinogenesis by environmental agents.

    Science.gov (United States)

    Kasai, Hiroshi; Kawai, Kazuaki

    2009-06-01

    During carcinogenesis, methylation of the C-5 position of cytosines in the promoter region of tumor suppressor genes is often observed. Enzymatic DNA methylation is a widely accepted mechanism for this phenomenon. It is interesting to propose a free radical mechanism for 5-methyldeoxycytidine (m(5)dC) production, because the C-5 position of cytosine is an active site for free radical reactions. When deoxycytidine (dC) and cumene hydroperoxide (CuOOH), a tumor promoter and a methyl radical producer, were reacted in the presence of ferrous ion at pH 7.4, the formation of m(5)dC was observed. The same reaction also proceeded with t-butyl hydroperoxide (BuOOH). The formation of m(5)dC was also observed in DNA by the CuOOH treatment. This is the first report of chemical DNA methylation at cytosine C-5 by environmental tumor promoters. We propose here that this reaction is one of the important mechanisms of de novo DNA methylation during carcinogenesis, because methyl radicals are produced by the biotransformation of various endogenous and exogenous compounds.

  7. Exposure of JB-6 mouse epidermal cells to 12-O-tetradecanoyl-phorbol-13-acetate is not accompanied by a significant change in total DNA-cytosine methylation.

    Science.gov (United States)

    Bondy, G P; Denhardt, D T

    1983-12-01

    The extent of methylation of the cytosine bases in DNA is believed to be a major factor influencing gene expression in eukaryotic cells. We have asked whether the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) alters the amount of 5-methylcytosine in DNA. The amount and relative distribution of 5-methylcytosine in the DNA of two subclones of the JB-6 mouse epidermal cell line were determined respectively by high performance liquid chromatography and digestion with the restriction enzymes MspI and HpaII. Exposure to TPA for up to several cell generations had no detectable effect on the degree of DNA methylation (3.9% of the total cytosine) in the two JB-6 lines or Friend erythroleukemia cells. Reduced methylation was readily detected in DNA extracted from cells exposed to 5-azacytidine. The data suggest that tumor promotion (at least that induced by TPA) is likely not the consequence of a generalized elevation or reduction in the amount of 5-methyl-cytosine in the DNA.

  8. Antitumor effects and radiosensitization of cytosine deaminase and thymidine kinase fusion suicide gene on colorectal carcinoma cells

    Institute of Scientific and Technical Information of China (English)

    De-Hua Wu; Li Liu; Long-Hua Chen

    2005-01-01

    AIM: To investigate the killing effect and radiosensitization of double suicide gene mediated by adenovirus on colorectal carcinoma cells.METHODS: Colorectal carcinoma cell line SW480 was transfected with adenovirus expression vector containing cytosine deaminase (CD) and thymidine kinase (Tk) fusion gene. The expression of CD-TK fusion gene was detected by reverse transcriptase-polymerase chain reaction. The toxic effect of ganciclovir (GCV) and 5-fiuorocytosine (5FC) on infected cells was determined by MTT assay. The radiosensitization of double suicide gene was evaluated by clonogenic assay.RESULTS: After prodrugs were used, the survival rate of colorectal carcinoma cells was markedly decreased. When GCV and 5-FC were used in combination, the cytotoxicity and bystandereffect were markedly superior to a single prodrug (x2 = 30.371, P<0.01). Both GCV and 5-FC could sensitize colorectal carcinoma cells to the toxic effect of radiation, and greater radiosensitization was achieved when both prodrug were used in combination. CONCLUSION: CD-TK double suicide gene can kill and radiosensitize colorectal carcinoma cells.

  9. Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice.

    Science.gov (United States)

    Yan, Huihuang; Kikuchi, Shinji; Neumann, Pavel; Zhang, Wenli; Wu, Yufeng; Chen, Feng; Jiang, Jiming

    2010-08-01

    We conducted genome-wide mapping of cytosine methylation using methylcytosine immunoprecipitation combined with Illumina sequencing. The chromosomal distribution pattern of methylated DNA is similar to the heterochromatin distribution pattern on rice chromosomes. The DNA methylation patterns of rice genes are similar to those in Arabidopsis thaliana, including distinct methylation patterns asssociated with gene bodies and promoters. The DNA sequences in the core domains of rice Cen4, Cen5 and Cen8 showed elevated methylation levels compared with sequences in the pericentromeric regions. In addition, elevated methylation levels were associated with the DNA sequences in the CENH3-binding subdomains, compared with the sequences in the flanking H3 subdomains. In contrast, the centromeric domain of Cen11, which is composed exclusively of centromeric satellite DNA, is hypomethylated compared with the pericentromeric domains. Thus, the DNA sequences associated with functional centromeres can be either hypomethylated or hypermethylated. The methylation patterns of centromeric DNA appear to be correlated with the composition of the associated DNA sequences. We propose that both hypomethylation and hypermethylation of CENH3-associated DNA sequences can serve as epigenetic marks to distinguish where CENH3 deposition will occur within the surrounding H3 chromatin.

  10. Raman spectroscopy and quantum-mechanical analysis of tautomeric forms in cytosine and 5-methylcytosine on gold surfaces

    Science.gov (United States)

    Nguyen, Dinh Bao; Nguyen, Thanh Danh; Kim, Sangsoo; Joo, Sang-Woo

    2017-03-01

    Spectral differences between cytosine (Cyt) and 5-methylcytosine (5MC) were investigated by means of Raman spectroscopy with a combination of density functional theory (DFT) calculations. Surface-enhanced Raman scattering (SERS) revealed discriminating peaks of 5MC from those of Cyt upon adsorption on gold nanoparticles (AuNPs). Among the notable features, the multiple bands between 850 and 700 cm- 1 for the ring-breathing modes of 5MC and Cyt could be correlated well with the simulated spectra based on the DFT calculations of the adsorbates on the gold cluster atoms. The relative energetic stabilities of the enol/keto and the amino/imino tautomeric forms of Cyt and 5MC have been estimated using DFT calculations, before and after binding six atom gold clusters. Among the six tautomeric forms, the 7H keto amino and the 4H imino trans forms are expected to be predominant in binding gold atoms, whereas the enol trans/cis conformers would coexist in the free gas phase. Our approach may provide useful theoretical guidelines for identifying 5MC from Cyt by analyzing Raman spectra on gold surfaces on the basis of quantum-mechanical calculations.

  11. Improved survival in young children with acute granulocytic leukemia treated with combination therapy using cyclophosphamide, oncovin, cytosine arabinoside, and prednisone.

    Science.gov (United States)

    Madanat, F F; Sullivan, M P

    1979-09-01

    Seven of 17 children (41%) under 5 years of age with acute granulocytic leukemia (AGL) treated with either cytosine arabinoside-cytoxan (CA-CYT) or Mini-COAP (CA-CYT with vincristine sulfate [VCR] and prednisone) have been in continuous complete remission 4 years or more. CA and CYT were each given in the dosage of 120 mg/m2 intravenously, daily in 3 divided doses, for 4 days. Induction consisted of two courses given at intervals of 2 weeks; during maintenance the courses were repeated at intervals of 4 weeks. In the Mini-COAP regimen, standard 28-day VCR-prednisone therapy was superimposed on CA-CYT induction and 4-day VCR-prednisone pulses were superimposed on CA-CYT maintenance. Transient moderate to severe myelosuppression was frequent; other manifestations of toxicity were mild. Administration of drugs at home was feasible in many instances. Mini-COAP was proved to be an effective therapeutic regimen for young children with AGL and should be considered as initial therapy.

  12. A new rapid amplification of cDNA ends method for extremely guanine plus cytosine-rich genes.

    Science.gov (United States)

    Shi, Xianzong; Jarvis, Donald L

    2006-09-15

    Rapid amplification of cDNA ends (RACE) is widely used to determine the 5'- and 3'-terminal nucleotide sequences of genes. Many different RACE methods have been developed to meet various requirements, but none addresses the difficult problems that arise when trying to isolate the ends of extremely guanine plus cytosine (GC)-rich genes. In this study, we found that we were unable to isolate the correct 5' or 3' end of an insect gene, which appeared to include extremely GC-rich sequences, using current RACE methods. Thus, we developed a new RACE method that can be used for this purpose. This new method entails first-strand cDNA synthesis at 70 degrees C with Thermo-X reverse transcriptase in the presence of homoectoine, followed by a polymerase chain reaction with 98 degrees C denaturation steps and Phusion DNA polymerase in the presence of 1M betaine and 5% dimethyl sulfoxide (DMSO). The use of these conditions yielded 5'- and 3'-RACE products that were approximately 80% GC over 213 and 162bp, respectively, and included shorter internal regions of 82 to 89% GC.

  13. Evidence that Natural Selection is the Primary Cause of the Guanine-cytosine Content Variation in Rice Genes

    Institute of Scientific and Technical Information of China (English)

    Xiaoli Shi; Xiyin Wang; Zhe Li; Qihui Zhu; Ji Yang; Song Ge; Jingchu Luo

    2007-01-01

    Cereal genes are classified into two distinct classes according to the guanine-cytosine (GC) content at the third codon sites (GC3). Natural selection and mutation bias have been proposed to affect the GC content. However, there has been controversy about the cause of GC variation. Here, we characterized the GC content of 1 092 paralogs and other single-copy genes in the duplicated chromosomal regions of the rice genome (ssp. indica) and classified the paralogs into GC3-rich and GC3-poor groups. By referring to out-group sequences from Arabidopsis and maize, we confirmed that the average synonymous substitution rate of the GC3-rich genes is significantly lower than that of the GC3-poor genes. Furthermore,we explored the other possible factors corresponding to the GC variation including the length of coding sequences, the number of exons in each gene, the number of genes in each family, the location of genes on chromosomes and the protein functions. Consequently, we propose that natural selection rather than mutation bias was the primary cause of the GC variation.

  14. Micronucleated Erythrocytes in Peripheral Blood from Neonate Rats Exposed by Breastfeeding to Cyclophosphamide, Colchicine, or Cytosine-Arabinoside

    Science.gov (United States)

    Bañales-Martínez, Luis R.; Lemus-Varela, María de Lourdes; Trujillo, Xóchitl; Sánchez-Parada, María G.; Armendáriz-Borunda, Juan; Zúñiga-González, Guillermo M.

    2016-01-01

    Genotoxic exposure to chemical substances is common, and nursing mothers could transmit harmful substances or their metabolites to their offspring through breast milk. We explored the possibility of determining genotoxic effects in the erythrocytes of breastfeeding rat pups whose mothers received a genotoxic compound while nursing. Ten groups of female rats and five pups per dam were studied. The control group received sterile water, and the experimental groups received one of three different doses of cyclophosphamide, colchicine, or cytosine-arabinoside. Blood smears were prepared from samples taken from each dam and pup every 24 h for six days. There were increased numbers of micronucleated erythrocytes (MNEs) and micronucleated polychromatic erythrocytes (MNPCEs) in the samples from pups in the experimental groups (P < 0.02) and increased MNPCE frequencies in the samples from the dams (P < 0.05). These results demonstrate the vertical transmission of the genotoxic effect of the compounds tested. In conclusion, assessing MNEs in breastfeeding neonate rats to assess DNA damage may be a useful approach for identifying genotoxic compounds and/or cytotoxic effects. This strategy could help in screening for therapeutic approaches that are genotoxic during the lactation stage and these assessments might also be helpful for developing preventive strategies to counteract harmful effects. PMID:28018917

  15. The differentiation effect of low-dose cytosine arabinoside is disturbed in PU.1-knockdown K562 cells.

    Science.gov (United States)

    Nakano, Hiroko; Yanagita, Akane; Takahashi, Shinichiro

    2014-07-01

    We recently demonstrated by using PU.1-knockdown K562 (K562 PU.1KD) cells stably expressing PU.1 short inhibitory RNAs and PU.1-overexpressing K562 (K562 PU.1OE) cells, that therapeutic concentrations of 5-aza-2'-deoxycytidine (5-azadC) induce erythroid differentiation of these cells and that the PU.1 expression level is closely associated with the differentiating and apoptotic effects of 5-azadC on K562 cells. In this study, we investigated whether the effects of low-dose cytosine arabinoside (Ara-C), which is another erythroid differentiation inducer in K562 cells, is associated with the expression level of PU.1 in these cells. As a result, we demonstrated that the effect of Ara-C on cell viability and differentiation, as determined by the WST-8 assay and β-globin mRNA expression analysis, respectively, was suppressed in K562 PU.1KD cells compared to their controls. Collectively, these findings suggest that sufficient expression of PU.1 is indispensable for the erythroid differentiation of K562 cells.

  16. Generation and characterization of a human single-chain fragment variable (scFv antibody against cytosine deaminase from Yeast

    Directory of Open Access Journals (Sweden)

    Tombesi Marina

    2008-09-01

    Full Text Available Abstract Background The ability of cytosine deaminase (CD to convert the antifungal agent 5-fluorocytosine (5-FC into one of the most potent and largely used anticancer compound such as 5-fluorouracil (5-FU raised considerable interest in this enzyme to model gene or antibody – directed enzyme-prodrug therapy (GDEPT/ADEPT aiming to improve the therapeutic ratio (benefit versus toxic side-effects of cancer chemotherapy. The selection and characterization of a human monoclonal antibody in single chain fragment (scFv format represents a powerful reagent to allow in in vitro and in vivo detection of CD expression in GDEPT/ADEPT studies. Results An enzymatic active recombinant CD from yeast (yCD was expressed in E. coli system and used as antigen for biopanning approach of the large semi-synthetic ETH-2 antibody phage library. Several scFvs were isolated and specificity towards yCD was confirmed by Western blot and ELISA. Further, biochemical and functional investigations demonstrated that the binding of specific scFv with yCD did not interfere with the activity of the enzyme in converting 5-FC into 5-FU. Conclusion The construction of libraries of recombinant antibody fragments that are displayed on the surface of filamentous phage, and the selection of phage antibodies against target antigens, have become an important biotechnological tool in generating new monoclonal antibodies for research and clinical applications. The scFvH5 generated by this method is the first human antibody which is able to detect yCD in routinary laboratory techniques without interfering with its enzymatic function.

  17. Potential benefits of combining cytosine deaminase/5-fluorocytosine gene therapy and irradiation for prostate cancer. Experimental study

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Hiroaki; Koshida, Kiyoshi; Yokoyama, Kunihiko; Mizokami, Atsushi; Namiki, Mikio [Kanazawa Univ. (Japan). School of Medicine

    2002-10-01

    The purpose of this study was to investigate the potential of combining cytosine deaminase/5-fluorocytosine (CD/5-FC) gene therapy and radiation therapy (either external beam radiation or radioimmunotherapy [RIT]), for the treatment of prostate cancer. Tumor xenografts of CD-transduced LNCaP cells grown in the testes of severe combined immunodeficiency (SCID) mice were used to evaluate antitumor effect. The mice were injected intraperitoneally with 500 mg/kg of 5-FC, or with 5, 15 or 30 mg/kg of 5-fluorouracil (5-FU), for 9 days. The tumors were treated with fractionated radiation at a dose of 1 or 3 Gy/day for 3 days, or I-131 labelled anti-prostate specific antigen (anti-PSA) monoclonal antibody (mAb) administration at a subtherapeutic dose of 20 or 80 {mu}Ci. Intratumoral and serum concentrations of 5-FU were measured using high performance liquid chromatography. Mice treated with CD/5-FC gene therapy presented a significant tumor growth inhibition comparable to that obtained with 15 mg/kg, 5-FU systemic administration without marked weight loss. Treatment with CD/5-FC gene therapy resulted in higher tumor but lower serum concentrations of 5-FU than treatment with systemic 5-FU chemotherapy. An additive antitumor effect was obtained when CD/5-FC therapy was combined with 1 Gy irradiation, which by itself did not produce a significant antitumor effect. However, the efficacy of CD/5-FC therapy was not enhanced when combined with RIT, probably due to poor accumulation of the mAb as the tumor/blood ratio never exceeded 1. These findings indicate that CD/5-FC gene therapy for prostate cancer may function with enhanced antitumor effect when combined with external beam radiation. However, combining CD/5-FC gene therapy and RIT using an anti-PSA mAb may not be effective because of insufficient accumulation of the mAb at the target tumors. (author)

  18. Sequential regimen of clofarabine, cytosine arabinoside and reduced-intensity conditioned transplantation for primary refractory acute myeloid leukemia

    Science.gov (United States)

    Mohty, Mohamad; Malard, Florent; Blaise, Didier; Milpied, Noel; Socié, Gérard; Huynh, Anne; Reman, Oumédaly; Yakoub-Agha, Ibrahim; Furst, Sabine; Guillaume, Thierry; Tabrizi, Resa; Vigouroux, Stéphane; Peterlin, Pierre; El-Cheikh, Jean; Moreau, Philippe; Labopin, Myriam; Chevallier, Patrice

    2017-01-01

    The prognosis of patients with acute myeloid leukemia in whom primary treatment fails remains very poor. In order to improve such patients’ outcome, we conducted a phase 2, prospective, multicenter trial to test the feasibility of a new sequential regimen, combining a short course of intensive chemotherapy and a reduced intensity-conditioning regimen, before allogeneic stem-cell transplantation. Twenty-four patients (median age, 47 years) with acute myeloid leukemia in primary treatment failure were included. Cytogenetic risk was poor in 15 patients (62%) and intermediate in nine (38%). The sequential regimen consisted of clofarabine (30 mg/m2/day) and cytosine arabinoside (1 g/m2/day) for 5 days, followed, after a 3-day rest, by reduced-intensity conditioning and allogeneic stem-cell transplantation combining cyclophosphamide (60 mg/kg), intravenous busulfan (3.2 mg/kg/day) for 2 days and anti-thymocyte globulin (2.5 mg/kg/day) for 2 days. Patients in complete remission at day +120 received prophylactic donor lymphocyte infusion. Eighteen patients (75%) achieved complete remission. With a median follow-up of 24.6 months, the Kaplan-Meier estimate of overall survival was 54% (95% CI: 33–71) at 1 year and 38% (95% CI: 18–46) at 2 years. The Kaplan-Meier estimate of leukemia-free survival was 46% (95% CI: 26–64) at 1 year and 29% (95% CI: 13–48) at 2 years. The cumulative incidence of non-relapse mortality was 8% (95% CI: 1–24) at 1 year and 12% (95% CI: 3–19) at 2 years. Results from this phase 2 prospective multicenter trial endorsed the safety and efficacy of a clofarabine-based sequential reduced-toxicity conditioning regimen, which warrants further investigation. This study was registered at www.clinicaltrials.gov, identifier number: NCT01188174. PMID:27561720

  19. Effect of a constant rate infusion of cytosine arabinoside on mortality in dogs with meningoencephalitis of unknown origin.

    Science.gov (United States)

    Lowrie, M; Thomson, S; Smith, P; Garosi, L

    2016-07-01

    Administration of cytosine arabinoside (CA) by continuous rate infusion (CRI) has pharmacokinetic and pharmacodynamic advantages over traditional intermittent dosing. Whether these advantages translate into clinical efficacy remains unknown. The aim of this study was to assess the efficacy and safety of CRI of CA in dogs with meningoencephalitis of unknown origin (MUO) and to compare outcomes with a group of historical control dogs treated with conventional intermittent subcutaneous (SC) administration of CA; both groups received adjunctive prednisolone. It was hypothesised that a CRI of CA for 24 h at 100 mg/m(2) would improve survival and lesion resolution compared with conventional SC delivery of 50 mg/m(2) every 12 h for 48 h. Eighty dogs with suspected MUO were recruited from consecutive dogs presenting with suspected MUO from 2006 to 2015. All dogs underwent routine clinical evaluation, magnetic resonance imaging of the brain and cerebrospinal fluid analysis. There were 39 dogs in the SC group and 41 dogs in the CRI group; baseline characteristics were similar in both groups. Survival at 3 months was 22/39 (44%) with SC delivery versus 37/41 (90%) with CRI. No dose-limiting toxicities were noted for either group. The resolution rate of magnetic resonance imaging and cerebrospinal fluid abnormalities at the 3 month re-examination were substantially improved in the CRI group versus the SC group. The CRI regimen produced a survival advantage over the SC route of administration without clinically significant toxicity. These data supports the routine use of CRI at first presentation for the treatment of MUO in dogs.

  20. Cytosine arabinoside-metabolizing enzyme genes are underexpressed in children with MLL gene-rearranged acute lymphoblastic leukemia

    Directory of Open Access Journals (Sweden)

    J.F. Mata

    2006-11-01

    Full Text Available Infant acute lymphoblastic leukemia (IALL is characterized by mixed lineage leukemia (MLL gene rearrangements, unique gene expression profiles, poor prognosis, and drug resistance. One exception is cytosine arabinoside (Ara-C to which IALL cells seem to be more sensitive. We quantified mRNA expression of Ara-C key enzymes in leukemic lymphoblasts from 64 Brazilian ALL children, 15 of them presenting MLL gene rearrangement, and correlated it with clinical and biological features. The diagnosis was based on morphological criteria and immunophenotyping using monoclonal antibodies. MLL gene rearrangements were detected by conventional cytogenetic analysis, RT-PCR and/or fluorescence in situ hybridization. The DCK and HENT1 expression levels were determined by real-time quantitative PCR using SYBR Green I. Relative quantification was made by the standard curve method. The results were analyzed by Mann-Whitney and Fisher exact tests. A P value of £0.05 was considered to be statistically significant. DCK and HENT1 expression levels were significantly lower in children with MLL gene-rearranged ALL compared to children with MLL germ line ALL (P = 0.0003 and 0.03, respectively. Our results differ from previous ones concerning HENT1 mRNA expression that observed a higher expression level in MLL gene-rearranged leukemias. In conclusion, the expression of the genes related to Ara-C metabolism was lower in MLL-positive children in the sample studied, suggesting the presence of population differences in the expression profile of these genes especially for HENT1.

  1. Antitumor effect of cytosine deaminase/5-fluorocytosine suicide gene therapy system mediated by Bifidobacterium infantis on melanoma

    Institute of Scientific and Technical Information of China (English)

    Cheng YI; Ying HUANG; Zhi-ying GUO; Shu-ren WANG

    2005-01-01

    Aim: To construct a Bifidobacterium infantis/CD targeting gene therapy system and observe the antitumor effect of cytosine deaminase/5-fluorocytosine (CD/5-FC) suicide gene therapy system mediated by Bifidobacterium infantis on melanoma in vitro and in vivo. Methods: A recombinant CD/pGEX- 1LamdaT plasmid was transfected into Bifidobacterium infantis by electroporation. Bifidobac terium infantis transfected by recombinant CD/pGEX-1LamdaT plasmid was in cubated with 5-FC anaerobically. Then the supernatant fluid was collected and added to melanoma B16-F10 cells to observe the killing effect for B16-F10 cells.Mice were inoculated with melanoma B 16-F10 cells to establish animal models.The mice were then injected with 5-FC and Bifidobacterium infantis transfected by recombinant CD/pGEX-1LamdaT plasmid. Results:Two segments of approxi mate 4.9 kb and 1.3 kb were extracted from the 6.2 kb recombinant plasmid, which were equal to the size of the pGEX-1LamdaT plasmid and CD gene, respectively.Sequencing results showed that the full length and sequence of nucleotide acid of the inserted gene in extracted recombinant plasmid was completely identical to the CD gene. In vitro, B 16-F10 cells treated by supernatant fluid were remarkably damaged morphologically, and the cell growth was significantly inhibited. Experi ments on the mice melanoma model showed that after treatment with a combination of transfected Bifidobacterium infantis and 5-FC, the tumor volume was significantly inhibited compared with controls. Conclusion: The foreign gene,CD gene, was correctly inserted into pGEX-1LambdaT plasmid and transferred into Bifidobacterium infantis. CD/5-FC suicide gene therapy system mediated by Bifidobacterium infantis demonstrated a good antitumor effect on melanoma in vitro and in vivo.

  2. Infection with a Virulent Strain of Wolbachia Disrupts Genome Wide-Patterns of Cytosine Methylation in the Mosquito Aedes aegypti.

    Directory of Open Access Journals (Sweden)

    Yixin H Ye

    Full Text Available Cytosine methylation is one of several reversible epigenetic modifications of DNA that allow a greater flexibility in the relationship between genotype and phenotype. Methylation in the simplest models dampens gene expression by modifying regions of DNA critical for transcription factor binding. The capacity to methylate DNA is variable in the insects due to diverse histories of gene loss and duplication of DNA methylases. Mosquitoes like Drosophila melanogaster possess only a single methylase, DNMT2.Here we characterise the methylome of the mosquito Aedes aegypti and examine its relationship to transcription and test the effects of infection with a virulent strain of the endosymbiont Wolbachia on the stability of methylation patterns.We see that methylation in the A. aegypti genome is associated with reduced transcription and is most common in the promoters of genes relating to regulation of transcription and metabolism. Similar gene classes are also methylated in aphids and honeybees, suggesting either conservation or convergence of methylation patterns. In addition to this evidence of evolutionary stability, we also show that infection with the virulent wMelPop Wolbachia strain induces additional methylation and demethylation events in the genome. While most of these changes seem random with respect to gene function and have no detected effect on transcription, there does appear to be enrichment of genes associated with membrane function. Given that Wolbachia lives within a membrane-bound vacuole of host origin and retains a large number of genes for transporting host amino acids, inorganic ions and ATP despite a severely reduced genome, these changes might represent an evolved strategy for manipulating the host environments for its own gain. Testing for a direct link between these methylation changes and expression, however, will require study across a broader range of developmental stages and tissues with methods that detect splice variants.

  3. Modification of the cerebral perfusion during a chemotherapy by arabinoside cytosine (A.R.A.C.) among patients suffering of an acute myelo-blastic leukemia (A.M.L.); Modification de la perfusion cerebrale au cours d'une chimiotherapie par cytosine arabinoside (ARAC) chez les patients atteints d'une leucemie aigue myeloblastique (LAM)

    Energy Technology Data Exchange (ETDEWEB)

    Modzelewski, R.; Vera, P. [Universite de Medecine de Rouen, QUANT.I.F-LITIS EA4108, departement de medecine nucleaire, 76 (France); Lepretre, S.; Tilly, H. [Centre Henri-Becquerel, departement d' hematologie, 76 - Rouen (France); Martinaud, O.; Hannequin, D. [CHU de Rouen, departement de neurologie, 76 (France); Habert, M.O. [CHU de la Pitie-Salpetriere, departement de medecine nucleaire, 75 - Paris (France)

    2010-07-01

    Cytosine arabinoside in high doses is a major treatment in acute myelo-blastic leukemia (A.M.L.). This treatment leads to neurological complications in 3-16% of cases, but the EEG, CT or MRI are normal.This prospective study examines brain perfusion in single photon emission tomography (SPECT) for patients receiving high dose arabinoside cytosine (H.D. A.R.A.C.). The SPECT of perfusion with hexamethyl propylene amine oxime (H.M.P.A.O.) for patients suffering of A.M.L. allowed to show a reduction of perfusion at the cerebellum level, of the occipito-parietal cortex and thalami, after conventional doses of A.R.A.C., while the patients had not any neurological accidents. (N.C.)

  4. Effect of C5-methylation of cytosine on the photoreactivity of DNA: a joint experimental and computational study of TCG trinucleotides.

    Science.gov (United States)

    Esposito, Luciana; Banyasz, Akos; Douki, Thierry; Perron, Marion; Markovitsi, Dimitra; Improta, Roberto

    2014-08-06

    DNA methylation, occurring at the 5 position of cytosine, is a natural process associated with mutational hotspots in skin tumors. By combining experimental techniques (optical spectroscopy, HPLC coupled to mass spectrometry) with theoretical methods (molecular dynamics, DFT/TD-DFT calculations in solution), we study trinucleotides with key sequences (TCG/T5mCG) in the UV-induced DNA damage. We show how the extra methyl, affecting the conformational equilibria and, hence, the electronic excited states, increases the quantum yield for the formation of cyclobutane dimers while reducing that of (6-4) adducts.

  5. Targeted cytosine deaminase-uracil phosphoribosyl transferase suicide gene therapy induces small cell lung cancer-specific cytotoxicity and tumor growth delay

    DEFF Research Database (Denmark)

    Christensen, Camilla L; Gjetting, Torben; Poulsen, Thomas Tuxen

    2010-01-01

    Small cell lung cancer (SCLC) is a highly malignant cancer for which there is no curable treatment. Novel therapies are therefore in great demand. In the present study we investigated the therapeutic effect of transcriptionally targeted suicide gene therapy for SCLC based on the yeast cytosine...... deaminase (YCD) gene alone or fused with the yeast uracil phosphoribosyl transferase (YUPRT) gene followed by administration of 5-fluorocytosine (5-FC) prodrug. Experimental design: The YCD gene or the YCD-YUPRT gene was placed under regulation of the SCLC-specific promoter insulinoma-associated 1 (INSM1...

  6. Crystal structure of tetra­kis­[μ2-2-(di­methyl­amino)­ethano­lato-κ3 N,O:O]di-μ3-hydroxido-di­thio­cyanato-κ2 N-dichromium(III)dilead(II) di­thio­cyanate aceto­nitrile monosolvate

    Science.gov (United States)

    Rusanova, Julia A.; Semenaka, Valentyna V.; Omelchenko, Irina V.

    2016-01-01

    The tetra­nuclear complex cation of the title compound, [Cr2Pb2(NCS)2(OH)2(C4H10NO)4](SCN)2·CH3CN, lies on an inversion centre. The main structural feature of the cation is a distorted seco-norcubane Pb2Cr2O6 cage with a central four-membered Cr2O2 ring. The CrIII ion is coordinated in a distorted octa­hedron, which involves two N atoms of one bidentate ligand and one thio­cyanate anion, two μ2-O atoms of 2-(di­methyl­amino)­ethano­late ligands and two μ3-O atoms of hydroxide ions. The coordination geometry of the PbII ion is a distorted disphenoid, which involves one N atom, two μ2-O atoms and one μ3-O atom. In addition, weak Pb⋯S inter­actions involving the coordinating and non-coordinating thio­cyanate anions are observed. In the crystal, the complex cations are linked through the thio­cyanate anions via the Pb⋯S inter­actions and O—H⋯N hydrogen bonds into chains along the c axis. The chains are further linked together via S⋯S contacts. The contribution of the disordered solvent aceto­nitrile mol­ecule was removed with the SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9–18] procedure in PLATON. The solvent is included in the reported mol­ecular formula, weight and density. PMID:27375871

  7. Crystal structure of tetra-kis-[μ2-2-(di-methyl-amino)-ethano-lato-κ(3) N,O:O]di-μ3-hydroxido-di-thio-cyanato-κ(2) N-dichromium(III)dilead(II) di-thio-cyanate aceto-nitrile monosolvate.

    Science.gov (United States)

    Rusanova, Julia A; Semenaka, Valentyna V; Omelchenko, Irina V

    2016-04-01

    The tetra-nuclear complex cation of the title compound, [Cr2Pb2(NCS)2(OH)2(C4H10NO)4](SCN)2·CH3CN, lies on an inversion centre. The main structural feature of the cation is a distorted seco-norcubane Pb2Cr2O6 cage with a central four-membered Cr2O2 ring. The Cr(III) ion is coordinated in a distorted octa-hedron, which involves two N atoms of one bidentate ligand and one thio-cyanate anion, two μ2-O atoms of 2-(di-methyl-amino)-ethano-late ligands and two μ3-O atoms of hydroxide ions. The coordination geometry of the Pb(II) ion is a distorted disphenoid, which involves one N atom, two μ2-O atoms and one μ3-O atom. In addition, weak Pb⋯S inter-actions involving the coordinating and non-coordinating thio-cyanate anions are observed. In the crystal, the complex cations are linked through the thio-cyanate anions via the Pb⋯S inter-actions and O-H⋯N hydrogen bonds into chains along the c axis. The chains are further linked together via S⋯S contacts. The contribution of the disordered solvent aceto-nitrile mol-ecule was removed with the SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9-18] procedure in PLATON. The solvent is included in the reported mol-ecular formula, weight and density.

  8. Association of polymorphisms of cytosine arabinoside-metabolizing enzyme gene with therapeutic efficacy for acute myeloid leukemia

    Institute of Scientific and Technical Information of China (English)

    XU Pei-pei; WANG Xue-mei; XU Ke; Margaret Schultz; CHEN Bao-an; FENG Ji-feng; CHENG Lu; XIA Guo-hua; LI Yu-feng; QIAN Jun; DING Jia-hua; LU Zu-hong

    2012-01-01

    Background The cytosine arabinoside (Ara-C)-based chemotherapy is the major remedial measure for acute myeloid leukemia (AML).Deoxycytidine kinase (DCK) and cytidine deaminase (CDA) are the key enzymes in the metabolism ofAra-C.Many single nucleotide polymorphisms (SNPs) and haplotypes of DCK and CDA,which contribute to susceptibility to Ara-C,have been identified in Africans and Europeans.However,there has been no report about the relation among three SNPs in DCK (rs115543896,rs72552079,and rs111454937) and two SNPs in CDA (rs2072671 and rs60369023),and their clinical response to Ara-C for a Chinese population.In this study,we aimed to investigate whether these five SNPs are associated with the therapeutic outcomes of Ara-C-based chemotherapy regimens in patients with AML.Methods A total of 151 Chinese patients with AML were enrolled in our study.SNPs genotyping were performed using the MassARRAY system by means of the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) method.Results The results illustrated that DCKrs111454937 AA genotype was more frequent in patients with higher platelet count,and A allele frequency was significantly higher in the group ≤40 years,lower white blood ceil (WBC) count patients group and the group with platelet counts >60×109/L.Meanwhile,both DCKrs72552079 TC (OR=1.225,95% Cl=1.225-9.851,P=0.0192) and CDArs60369023 GA (OR=9.851,95% Cl=1.31-77.93,P=0.0263) significantly improved Ara-C-based chemotherapy response.While DCKrs11554389 AA (OR=0.147,95% Cl=0.027-0.801,P=0.0267) wasassociated with the decrease of Ara-C-based chemotherapy response.Conclusion It is evident that the DCK and CDA polymorphisms might be the important markers for the AML patients' therapy outcomes in a Chinese population.

  9. Signature-based small molecule screening identifies cytosine arabinoside as an EWS/FLI modulator in Ewing sarcoma.

    Directory of Open Access Journals (Sweden)

    Kimberly Stegmaier

    2007-04-01

    Full Text Available BACKGROUND: The presence of tumor-specific mutations in the cancer genome represents a potential opportunity for pharmacologic intervention to therapeutic benefit. Unfortunately, many classes of oncoproteins (e.g., transcription factors are not amenable to conventional small-molecule screening. Despite the identification of tumor-specific somatic mutations, most cancer therapy still utilizes nonspecific, cytotoxic drugs. One illustrative example is the treatment of Ewing sarcoma. Although the EWS/FLI oncoprotein, present in the vast majority of Ewing tumors, was characterized over ten years ago, it has never been exploited as a target of therapy. Previously, this target has been intractable to modulation with traditional small-molecule library screening approaches. Here we describe a gene expression-based approach to identify compounds that induce a signature of EWS/FLI attenuation. We hypothesize that screening small-molecule libraries highly enriched for FDA-approved drugs will provide a more rapid path to clinical application. METHODS AND FINDINGS: A gene expression signature for the EWS/FLI off state was determined with microarray expression profiling of Ewing sarcoma cell lines with EWS/FLI-directed RNA interference. A small-molecule library enriched for FDA-approved drugs was screened with a high-throughput, ligation-mediated amplification assay with a fluorescent, bead-based detection. Screening identified cytosine arabinoside (ARA-C as a modulator of EWS/FLI. ARA-C reduced EWS/FLI protein abundance and accordingly diminished cell viability and transformation and abrogated tumor growth in a xenograft model. Given the poor outcomes of many patients with Ewing sarcoma and the well-established ARA-C safety profile, clinical trials testing ARA-C are warranted. CONCLUSIONS: We demonstrate that a gene expression-based approach to small-molecule library screening can identify, for rapid clinical testing, candidate drugs that modulate previously

  10. Targeting the immune system to fight cancer using chemical receptor homing vectors carrying Poly Inosine/Cytosine (PolyIC

    Directory of Open Access Journals (Sweden)

    Alexander eLevitzki

    2012-02-01

    Full Text Available Cancer researchers have been looking for ways to harness the immune system and to reinstate immune surveillance, to kill cancer cells without collateral damage. Here we scan current approaches to targeting the immune system against cancer, and emphasize our own approach. We are using chemical vectors attached to a specific ligand, to introduce synthetic dsRNA, poly Inosine/Cytosine (polyIC, into tumors. The ligand binds to a receptor protein that is overexpressed on the surface of the tumor cells. Upon ligand binding, the receptor complex is internalized, introducing the polyIC into the cell. In this fashion a large amount of synthetic dsRNA can be internalized, leading to the activation of dsRNA binding proteins, such as dsRNA dependent protein kinase (PKR, Toll-3 receptor (TLR3, retinoic acid–inducible gene I (RIG-1 and melanoma differentiation–associated gene 5 (MDA5. The simultaneous activation of these signaling proteins leads to the rapid demise of the targeted cell and to cytokine secretion. The cytokines lead to a strong bystander effect and to the recruitment of immune cells that converge upon the targeted cells. The bystander effects lead to the destruction of neighboring tumor cells not targeted themselves by the vector. Normal cells, being more robust than tumor cells, survive. This strategy has several advantages: (1 Recruitment of the immune system is localized to the tumor. (2 The response is rapid, leading to fast tumor eradication. (3 The bystander effects lead to the eradication of tumor cells not harboring the target. (4 The multiplicity of pro-death signaling pathways elicited by PolyIC minimizes the likelihood of the emergence of resistance. In this chapter we focus on EGFR as the targeted receptor, which is overexpressed in many tumors. In principle, the strategy can be extended to other tumors that overexpress a protein that can be internalized by a ligand, which be a small molecule, a single chain antibody or an

  11. Targeting the Immune System to Fight Cancer Using Chemical Receptor Homing Vectors Carrying Polyinosine/Cytosine (PolyIC).

    Science.gov (United States)

    Levitzki, Alexander

    2012-01-01

    Cancer researchers have been looking for ways to harness the immune system and to reinstate immune surveillance, to kill cancer cells without collateral damage. Here we scan current approaches to targeting the immune system against cancer, and emphasize our own approach. We are using chemical vectors attached to a specific ligand, to introduce synthetic dsRNA, polyinosine/cytosine (polyIC), into tumors. The ligand binds to a receptor protein that is overexpressed on the surface of the tumor cells. Upon ligand binding, the receptor complex is internalized, introducing the polyIC into the cell. In this fashion a large amount of synthetic dsRNA can be internalized, leading to the activation of dsRNA-binding proteins, such as dsRNA dependent protein kinase (PKR), Toll-like receptor 3 (TLR3), retinoic acid-inducible gene I (RIG-1), and melanoma differentiation-associated gene 5 (MDA5). The simultaneous activation of these signaling proteins leads to the rapid demise of the targeted cell and to cytokine secretion. The cytokines lead to a strong bystander effect and to the recruitment of immune cells that converge upon the targeted cells. The bystander effects lead to the destruction of neighboring tumor cells not targeted themselves by the vector. Normal cells, being more robust than tumor cells, survive. This strategy has several advantages: (1) recruitment of the immune system is localized to the tumor. (2) The response is rapid, leading to fast tumor eradication. (3) The bystander effects lead to the eradication of tumor cells not harboring the target. (4) The multiplicity of pro-death signaling pathways elicited by PolyIC minimizes the likelihood of the emergence of resistance. In this chapter we focus on EGFR as the targeted receptor, which is overexpressed in many tumors. In principle, the strategy can be extended to other tumors that overexpress a protein that can be internalized by a ligand, which can be a small molecule, a single chain antibody, or an affibody.

  12. Specific and nonspecific metal ion-nucleotide interactions at aqueous/solid interfaces functionalized with adenine, thymine, guanine, and cytosine oligomers.

    Science.gov (United States)

    Holland, Joseph G; Malin, Jessica N; Jordan, David S; Morales, Esmeralda; Geiger, Franz M

    2011-03-02

    This article reports nonlinear optical measurements that quantify, for the first time directly and without labels, how many Mg(2+) cations are bound to DNA 21-mers covalently linked to fused silica/water interfaces maintained at pH 7 and 10 mM NaCl, and what the thermodynamics are of these interactions. The overall interaction of Mg(2+) with adenine, thymine, guanine, and cytosine is found to involve -10.0 ± 0.3, -11.2 ± 0.3, -14.0 ± 0.4, and -14.9 ± 0.4 kJ/mol, and nonspecific interactions with the phosphate and sugar backbone are found to contribute -21.0 ± 0.6 kJ/mol for each Mg(2+) ion bound. The specific and nonspecific contributions to the interaction energy of Mg(2+) with oligonucleotide single strands is found to be additive, which suggests that within the uncertainty of these surface-specific experiments, the Mg(2+) ions are evenly distributed over the oligomers and not isolated to the most strongly binding nucleobase. The nucleobases adenine and thymine are found to bind only three Mg(2+) ions per 21-mer oligonucleotide, while the bases cytosine and guanine are found to bind eleven Mg(2+) ions per 21-mer oligonucleotide.

  13. Interaction of Cu(+) with cytosine and formation of i-motif-like C-M(+)-C complexes: alkali versus coinage metals.

    Science.gov (United States)

    Gao, Juehan; Berden, Giel; Rodgers, M T; Oomens, Jos

    2016-03-14

    The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.

  14. Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase

    Energy Technology Data Exchange (ETDEWEB)

    Reha-Krantz, Linda J.; Hariharan, Chithra; Subuddhi, Usharani; Xia, Shuangluo; Zhao, Chao; Beckman, Jeff; Christian, Thomas; Konigsberg, William (Yale); (Alberta)

    2011-11-21

    The adenine base analogue 2-aminopurine (2AP) is a potent base substitution mutagen in prokaryotes because of its enhanceed ability to form a mutagenic base pair with an incoming dCTP. Despite more than 50 years of research, the structure of the 2AP-C base pair remains unclear. We report the structure of the 2AP-dCTP base pair formed within the polymerase active site of the RB69 Y567A-DNA polymerase. A modified wobble 2AP-C base pair was detected with one H-bond between N1 of 2AP and a proton from the C4 amino group of cytosine and an apparent bifurcated H-bond between a proton on the 2-amino group of 2-aminopurine and the ring N3 and O2 atoms of cytosine. Interestingly, a primer-terminal region rich in AT base pairs, compared to GC base pairs, facilitated dCTP binding opposite template 2AP. We propose that the increased flexibility of the nucleotide binding pocket formed in the Y567A-DNA polymerase and increased 'breathing' at the primer-terminal junction of A+T-rich DNA facilitate dCTP binding opposite template 2AP. Thus, interactions between DNA polymerase residues with a dynamic primer-terminal junction play a role in determining base selectivity within the polymerase active site of RB69 DNA polymerase.

  15. A G4-DNA/B-DNA junction at codon 12 of c-Ha-ras is actively and asymmetrically methylated by DNA(cytosine-5)methyltransferase.

    Science.gov (United States)

    Smith, S S; Baker, D J; Jardines, L A

    1989-05-15

    Oligodeoxynucleotides spanning codon 12 of the human c-Ha-ras gene were found to be exceptionally good substrates for de novo methylation by human DNA(cytosine-5)methyltransferase. In the complex formed by two complementary 30mers, only the C-rich strand was methylated by the enzyme. Guanines at the 3' end of the G-rich strand of the complex could not be completely modified by dimethyl sulfate [corrected] suggesting tetrameric bonding at these G-residues. An eight-stranded structure, composed of four duplex DNAs at one end, joined to a G4-DNA segment at the other with the junction between the two DNA forms at codon 12, can account for our results.

  16. Pleiotropic phenotypes of the salt-tolerant and cytosine hypomethylated leafless inflorescence, evergreen dwarf and irregular leaf lamina mutants of Catharanthus roseus possessing Mendelian inheritance

    Indian Academy of Sciences (India)

    Renu Kumari; Vishakha Sharma; Vinay Sharma; Sushil Kumar

    2013-12-01

    In Catharanthus roseus, three morphological cum salt-tolerant chemically induced mutants ofMendelian inheritance and their wild-type parent cv Nirmal were characterized for overall cytosine methylation at DNA repeats, expression of 119 protein-coding and seven miRNA-coding genes and 50 quantitative traits. The mutants, named after their principal morphological feature(s), were leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill). The Southern-blot analysis of MspI digested DNAs of mutants probed with centromeric and 5S and 18S rDNA probes indicated that, in comparison to wild type, the mutants were extensively demethylated at cytosine sites. Among the 126 genes investigated for transcriptional expression, 85 were upregulated and 41 were downregulated in mutants. All of the five genes known to be stress responsive had increased expression in mutants. Several miRNA genes showed either increased or decreased expression in mutants. The C. roseus counterparts of CMT3, DRM2 and RDR2 were downregulated in mutants. Among the cell, organ and plant size, photosynthesis and metabolism related traits studied, 28 traits were similarly affected in mutants as compared to wild type. Each of the mutants also expressed some traits distinctively. The egd mutant possessed superior photosynthesis and water retention abilities. Biomass was hyperaccumulated in roots, stems, leaves and seeds of the lli mutant. The ill mutant was richest in the pharmaceutical alkaloids catharanthine, vindoline, vincristine and vinblastine. The nature of mutations, origins of mutant phenotypes and evolutionary importance of these mutants are discussed.

  17. Determination of cytosine using differential pulse voltammetry at a bismuth film electrode%铋膜修饰电极示差脉冲伏安法测定胞嘧啶

    Institute of Scientific and Technical Information of China (English)

    吴淑芳; 梁玲; 徐茂田

    2013-01-01

    In this paper , the direct electrochemical behavior of cytosine is studied at a bismuth film electrode . Cytosine gives a well -defined oxidation peak at ca.-0.23V in a 0.1M PBS buffer (pH6.64).The peak currents increase linearly with the increasement of cytosine concentration ranging from 4.98 ×10 -6 mol/L to 3.38 ×10 -5 mol/L.The detection limit of cytosine is 5.6 ×10 -7 mol/L.The results show that the method has good selectivity to determine cytosine .%利用铋膜修饰电极对胞嘧啶的电化学行为进行了研究.结果表明,在0.1mol/L 的PBS 缓冲溶液( pH6.64)中,胞嘧啶于-0.23 V电位处有一良好的氧化峰,峰电流与胞嘧啶在4.98×10-6~3.38×10-5 mol/L浓度范围内呈良好的线性关系,检出限为5.6×10-7 mol/L.实验显示,铋膜修饰电极性质稳定,对胞嘧啶的测定具有良好的选择性.

  18. Cytosine deaminase adenoviral vector and 5-fluorocytosine selectively reduce breast cancer cells 1 million-fold when they contaminate hematopoietic cells: a potential purging method for autologous transplantation.

    Science.gov (United States)

    Garcia-Sanchez, F; Pizzorno, G; Fu, S Q; Nanakorn, T; Krause, D S; Liang, J; Adams, E; Leffert, J J; Yin, L H; Cooperberg, M R; Hanania, E; Wang, W L; Won, J H; Peng, X Y; Cote, R; Brown, R; Burtness, B; Giles, R; Crystal, R; Deisseroth, A B

    1998-07-15

    Ad.CMV-CD is a replication incompetent adenoviral vector carrying a cytomegalovirus (CMV)-driven transcription unit of the cytosine deaminase (CD) gene. The CD transcription unit in this vector catalyzes the deamination of the nontoxic pro-drug, 5-fluorocytosine (5-FC), thus converting it to the cytotoxic drug 5-fluorouracil (5-FU). This adenoviral vector prodrug activation system has been proposed for use in selectively sensitizing breast cancer cells, which may contaminate collections of autologous stem cells products from breast cancer patients, to the toxic effects of 5-FC, without damaging the reconstitutive capability of the normal hematopoietic cells. This system could conceivably kill even the nondividing breast cancer cells, because the levels of 5-FU generated by this system are 10 to 30 times that associated with systemic administration of 5-FU. The incorporation of 5-FU into mRNA at these high levels is sufficient to disrupt mRNA processing and protein synthesis so that even nondividing cells die of protein starvation. To test if the CD adenoviral vector sensitizes breast cancer cells to 5-FC, we exposed primary explants of normal human mammary epithelial cells (HMECs) and the established breast cancer cell (BCC) lines MCF-7 and MDA-MB-453 to the Ad.CMV-CD for 90 minutes. This produced a 100-fold sensitization of these epithelial cells to the effects of 48 hours of exposure to 5-FC. We next tested the selectivity of this system for BCC. When peripheral blood mononuclear cells (PBMCs), collected from cancer patients during the recovery phase from conventional dose chemotherapy-induced myelosuppression, were exposed to the Ad.CMV-CD for 90 minutes in serum-free conditions, little or no detectable conversion of 5-FC into 5-FU was seen even after 48 hours of exposure to high doses of 5-FC. In contrast, 70% of 5-FC was converted into the cytotoxic agent 5-FU when MCF-7 breast cancer cells (BCCs) were exposed to the same Ad.CMV-CD vector followed by 5-FC for

  19. A systematic investigation of hydrogen-bonding effects on the 17O, 14N, and 2H nuclear quadrupole resonance parameters of anhydrous and monohydrated cytosine crystalline structures: a density functional theory study.

    Science.gov (United States)

    Mirzaei, Mahmoud; Elmi, Fatemeh; Hadipour, Nasser L

    2006-06-08

    A systematic computational study was carried out to characterize the 17O, 14N, and 2H nuclear quadrupole resonance (NQR) parameters in the anhydrous and monohydrated cytosine crystalline structures. To include the hydrogen-bonding effects in the calculations, the most probable interacting molecules with the central molecule in the crystalline phase were considered in the pentameric clusters of both structures. To calculate the parameters, couples of the methods B3LYP and B3PW91 and the basis sets 6-311++G** and CC-pVTZ were employed. The mentioned methods calculated reliable values of 17O, 14N, and 2H NQR tensors in the pentameric clusters, which are in good agreements with the experiment. The different influences of various hydrogen-bonding interactions types, N-H...N, N-H...O, and O-H...O, were observed on the 17O, 14N, and 2H NQR tensors. Lower values of quadrupole coupling constants and higher values of asymmetry parameters in the crystalline monohydrated cytosine indicate the presence of stronger hydrogen-bonding interactions in the monohydrated form rather than that of crystalline anhydrous cytosine.

  20. Treatment of colon cancer cells using the cytosine deaminase/5-fluorocytosine suicide system induces apoptosis, modulation of the proteome, and Hsp90beta phosphorylation.

    Science.gov (United States)

    Negroni, Luc; Samson, Michel; Guigonis, Jean-Marie; Rossi, Bernard; Pierrefite-Carle, Valérie; Baudoin, Christian

    2007-10-01

    The bacterial cytosine deaminase (CD) gene, associated with the 5-fluorocytosine (5FC) prodrug, is one of the most widely used suicide systems in gene therapy. Introduction of the CD gene within a tumor induces, after 5FC treatment of the animal, a local production of 5-fluorouracil resulting in intratumor chemotherapy. Destruction of the gene-modified tumor is then followed by the triggering of an antitumor immune reaction resulting in the regression of distant wild-type metastasis. The global effects of 5FC on colorectal adenocarcinoma cells expressing the CD gene were analyzed using the proteomic method. Application of 5FC induced apoptosis and 19 proteins showed a significant change in 5FC-treated cells compared with control cells. The up-regulated and down-regulated proteins include cytoskeletal proteins, chaperones, and proteins involved in protein synthesis, the antioxidative network, and detoxification. Most of these proteins are involved in resistance to anticancer drugs and resistance to apoptosis. In addition, we show that the heat shock protein Hsp90beta is phosphorylated on serine 254 upon 5FC treatment. Our results suggest that activation of Hsp90beta by phosphorylation might contribute to tumor regression and tumor immunogenicity. Our findings bring new insights into the mechanism of the anticancer effects induced by CD/5FC treatment.

  1. Methylation by a unique α-class N4-cytosine methyltransferase is required for DNA transformation of Caldicellulosiruptor bescii DSM6725.

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    Daehwan Chung

    Full Text Available Thermophilic microorganisms capable of using complex substrates offer special advantages for the conversion of lignocellulosic biomass to biofuels and bioproducts. Members of the gram-positive bacterial genus Caldicellulosiruptor are anaerobic thermophiles with optimum growth temperatures between 65°C and 78°C and are the most thermophilic cellulolytic organisms known. In fact, they efficiently use biomass non-pretreated as their sole carbon source and in successive rounds of application digest 70% of total switchgrass substrate. The ability to genetically manipulate these organisms is a prerequisite to engineering them for use in conversion of these complex substrates to products of interest as well as identifying gene products critical for their ability to utilize non-pretreated biomass. Here, we report the first example of DNA transformation of a member of this genus, C. bescii. We show that restriction of DNA is a major barrier to transformation (in this case apparently absolute and that methylation with an endogenous unique α-class N4-Cytosine methyltransferase is required for transformation of DNA isolated from E. coli. The use of modified DNA leads to the development of an efficient and reproducible method for DNA transformation and the combined frequencies of transformation and recombination allow marker replacement between non-replicating plasmids and chromosomal genes providing the basis for rapid and efficient methods of genetic manipulation.

  2. Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.

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    Gresh, Nohad; Sponer, Judit E; Devereux, Mike; Gkionis, Konstantinos; de Courcy, Benoit; Piquemal, Jean-Philip; Sponer, Jiri

    2015-07-30

    Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well calibrated but conceptually simple pair-additive empirical potentials (force fields). Although such simulations provided many valuable results, it is well established that simple force fields also introduce errors into the description, underlying the need for development of alternative anisotropic, polarizable molecular mechanics (APMM) potentials. One of the most abundant forces in all kinds of nucleic acids topologies is base stacking. Intra- and interstrand stacking is assumed to be the most essential factor affecting local conformational variations of B-DNA. However, stacking also contributes to formation of all kinds of noncanonical nucleic acids structures, such as quadruplexes or folded RNAs. The present study focuses on 14 stacked cytosine (Cyt) dimers and the doubly H-bonded dimer. We evaluate the extent to which an APMM procedure, SIBFA, could account quantitatively for the results of high-level quantum chemistry (QC) on the total interaction energies, and the individual energy contributions and their nonisotropic behaviors. Good agreements are found at both uncorrelated HF and correlated DFT and CCSD(T) levels. Resorting in SIBFA to distributed QC multipoles and to an explicit representation of the lone pairs is essential to respectively account for the anisotropies of the Coulomb and of the exchange-repulsion QC contributions.

  3. In Vivo Spectrum of UVC-induced Mutation in Mouse Skin Epidermis May Reflect the Cytosine Deamination Propensity of Cyclobutane Pyrimidine Dimers.

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    Ikehata, Hironobu; Mori, Toshio; Yamamoto, Masayuki

    2015-11-01

    Although ultraviolet radiation (UVR) has a genotoxicity for inducing skin cancers, the skin may tolerate UVC component because the epidermal layer prevents this short wavelength range from passing through. Here, UVC genotoxicity for mouse skin was evaluated in terms of DNA damage formation and mutagenicity. UVC induced UVR photolesions and mutations remarkably in the epidermis but poorly in the dermis, confirming the barrier ability of the epidermis against shorter UVR wavelengths. Moreover, the epidermis itself responded to UVC mutagenicity with mutation induction suppression, which suppressed the mutant frequencies to a remarkably low, constant level regardless of UVC dose. The mutation spectrum observed in UVC-exposed epidermis showed a predominance of UV-signature mutation, which occurred frequently in 5'-TCG-3', 5'-TCA-3' and 5'-CCA-3' contexts. Especially, for the former two contexts, the mutations recurred at several sites with more remarkable recurrences at the 5'-TCG-3' sites. Comparison of the UVC mutation spectrum with those observed in longer UVR wavelength ranges led us to a mechanism that explains why the sequence context preference of UV-signature mutation changes according to the wavelength, which is based on the difference in the mCpG preference of cyclobutane pyrimidine dimer (CPD) formation among UVR ranges and the sequence context-dependent cytosine deamination propensity of CPD.

  4. A new nuclear function of the Entamoeba histolytica glycolytic enzyme enolase: the metabolic regulation of cytosine-5 methyltransferase 2 (Dnmt2 activity.

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    Ayala Tovy

    2010-02-01

    Full Text Available Cytosine-5 methyltransferases of the Dnmt2 family function as DNA and tRNA methyltransferases. Insight into the role and biological significance of Dnmt2 is greatly hampered by a lack of knowledge about its protein interactions. In this report, we address the subject of protein interaction by identifying enolase through a yeast two-hybrid screen as a Dnmt2-binding protein. Enolase, which is known to catalyze the conversion of 2-phosphoglycerate (2-PG to phosphoenolpyruvate (PEP, was shown to have both a cytoplasmatic and a nuclear localization in the parasite Entamoeba histolytica. We discovered that enolase acts as a Dnmt2 inhibitor. This unexpected inhibitory activity was antagonized by 2-PG, which suggests that glucose metabolism controls the non-glycolytic function of enolase. Interestingly, glucose starvation drives enolase to accumulate within the nucleus, which in turn leads to the formation of additional enolase-E.histolytica DNMT2 homolog (Ehmeth complex, and to a significant reduction of the tRNA(Asp methylation in the parasite. The crucial role of enolase as a Dnmt2 inhibitor was also demonstrated in E.histolytica expressing a nuclear localization signal (NLS-fused-enolase. These results establish enolase as the first Dnmt2 interacting protein, and highlight an unexpected role of a glycolytic enzyme in the modulation of Dnmt2 activity.

  5. Intradermal cytosine-phosphate-guanosine treatment reduces lung inflammation but induces IFN-γ-mediated airway hyperreactivity in a murine model of natural rubber latex allergy.

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    Haapakoski, Rita; Karisola, Piia; Fyhrquist, Nanna; Savinko, Terhi; Wolff, Henrik; Turjanmaa, Kristiina; Palosuo, Timo; Reunala, Timo; Lauerma, Antti; Alenius, Harri

    2011-05-01

    Asthma and other allergic diseases are continuously increasing, causing considerable economic and sociologic burden to society. The hygiene hypothesis proposes that lack of microbial T helper (Th) 1-like stimulation during early childhood leads to increased Th2-driven allergic disorders later in life. Immunostimulatory cytosine-phosphate-guanosine (CpG)-oligodeoxynucleotide motifs are candidate molecules for immunotherapeutic studies, as they have been shown to shift the Th2 response toward the Th1 direction and reduce allergic symptoms. Using natural rubber latex (NRL)-induced murine model of asthma, we demonstrated that intradermal CpG administration with allergen reduced pulmonary eosinophilia, mucus production, and Th2-type cytokines, but unexpectedly induced airway hyperreactivity (AHR) to inhaled methacholine, one of the hallmarks of asthma. We found that induction in AHR was dependent on STAT4, but independent of STAT6 signaling. CpG treatment increased production of IFN-γ in the airways and shifted the ratio of CD4(+):CD8(+) T cells toward CD8(+) dominance. By blocking soluble IFN-γ with neutralizing antibody, AHR diminished and the CD4(+):CD8(+) ratio returned to CD4(+) dominance. These results indicate that increased production of IFN-γ in the lungs may lead to severe side effects, such as enhancement of bronchial hyperreactivity to inhaled allergen. This finding should be taken into consideration when planning prophylaxis treatment of asthma with intradermal CpG injections.

  6. Cytosine deaminase as a negative selectable marker for the microalgal chloroplast: a strategy for the isolation of nuclear mutations that affect chloroplast gene expression.

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    Young, Rosanna E B; Purton, Saul

    2014-12-01

    Negative selectable markers are useful tools for forward-genetic screens aimed at identifying trans-acting factors that are required for expression of specific genes. Transgenic lines harbouring the marker fused to a gene element, such as a promoter, may be mutagenized to isolate loss-of-function mutants able to survive under selection. Such a strategy allows the molecular dissection of factors that are essential for expression of the gene. Expression of individual chloroplast genes in plants and algae typically requires one or more nuclear-encoded factors that act at the post-transcriptional level, often through interaction with the 5' UTR of the mRNA. To study such nuclear control further, we have developed the Escherichia coli cytosine deaminase gene codA as a conditional negative selectable marker for use in the model green alga Chlamydomonas reinhardtii. We show that a codon-optimized variant of codA with three amino acid substitutions confers sensitivity to 5-fluorocytosine (5-FC) when expressed in the chloroplast under the control of endogenous promoter/5' UTR elements from the photosynthetic genes psaA or petA. UV mutagenesis of the psaA transgenic line allowed recovery of 5-FC-resistant, photosynthetically deficient lines harbouring mutations in the nuclear gene for the factor TAA1 that is required for psaA translation. Similarly, the petA line was used to isolate mutants of the petA mRNA stability factor MCA1 and the translation factor TCA1. The codA marker may be used to identify critical residues in known nuclear factors and to aid the discovery of additional factors required for expression of chloroplast genes.

  7. Benzo[a]pyrene diol epoxide suppresses retinoic acid receptor-β2 expression by recruiting DNA (cytosine-5--methyltransferase 3A

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    Xu Xiao-Chun

    2010-04-01

    Full Text Available Abstract Tobacco smoke is an important risk factor for various human cancers, including esophageal cancer. How benzo [a]pyrene diol epoxide (BPDE, a carcinogen present in tobacco smoke as well as in environmental pollution, induces esophageal carcinogenesis has yet to be defined. In this study, we investigated the molecular mechanism responsible for BPDE-suppressed expression of retinoic acid receptor-beta2 (RAR-β2 in esophageal cancer cells. We treated esophageal cancer cells with BPDE before performing methylation-specific polymerase chain reaction (MSP to find that BPDE induced methylation of the RAR-β2 gene promoter. We then performed chromatin immunoprecipitation (ChIP assays to find that BPDE recruited genes of the methylation machinery into the RAR-β2 gene promoter. We found that BPDE recruited DNA (cytosine-5--methyltransferase 3 alpha (DNMT3A, but not beta (DNMT3B, in a time-dependent manner to methylate the RAR-β2 gene promoter, which we confirmed by reverse transcription-polymerase chain reaction (RT-PCR analysis of the reduced RAR-β2 expression in these BPDE-treated esophageal cancer cell lines. However, BPDE did not significantly change DNMT3A expression, but it slightly reduced DNMT3B expression. DNA methylase inhibitor 5-aza-2'-deoxycytidine (5-Aza and DNMT3A small hairpin RNA (shRNA vector antagonized the effects of BPDE on RAR-β2 expressions. Transient transfection of the DNMT3A shRNA vector also antagonized BPDE's effects on expression of RAR-β2, c-Jun, phosphorylated extracellular signal-regulated protein kinases 1/2 (ERK1/2, and cyclooxygenase-2 (COX-2, suggesting a possible therapeutic effect. The results of this study form the link between the esophageal cancer risk factor BPDE and the reduced RAR-β2 expression.

  8. A novel polymorphism in human cytosine DNA-methyltransferase-3B promoter is associated with an increased risk of lung cancer.

    Science.gov (United States)

    Shen, Hongbing; Wang, Luo; Spitz, Margaret R; Hong, Waun K; Mao, Li; Wei, Qingyi

    2002-09-01

    DNA repair is central to genomic integrity. Reduced expression of several nucleotide excision repair genes has been demonstrated to be associated with increased risk of lung cancer. Because methylation of gene promoters is one of the major regulatory mechanisms of gene expression and most nucleotide excision repair gene promoters have not been fully characterized, we hypothesized that genetic variants of the genes that are responsible for regulating genomic methylation are associated with increased risk of lung cancer. Recently, we identified a C-->T transition at a novel promoter region of cytosine DNA-methyltransferase-3B (DNMT3B) and found that this polymorphic transition significantly increases the promoter activity. In this hospital-based case-control study of 319 patients with incident lung cancer and 340 healthy controls frequency matched on age (+/-5 years), sex, ethnicity, and smoking status, we genotyped subjects for this DNMT3B promoter polymorphism to determine the association between this genetic variant and risk of lung cancer. Compared with CC homozygotes, CT heterozygotes had a >2-fold increased risk of lung cancer [adjusted odds ratio (OR), 2.13; 95% confidence interval (CI), 1.47-3.08] and TT homozygotes an OR of 1.42 (95% CI, 0.91-2.21). The combined variant genotype (CT + TT) was associated with a nearly 2-fold increased risk (adjusted OR, 1.88; 95% CI, 1.32-2.66). These results suggest that this novel variant of DNMT3B is associated with increased risk of lung cancer and may contribute to identifying individuals genetically susceptible to tobacco-induced cancers. Additional studies on the underlying molecular mechanism of this polymorphism are warranted.

  9. Atypical epigenetic mark in an atypical location: cytosine methylation at asymmetric (CNN sites within the body of a non-repetitive tomato gene

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    Iusem Norberto D

    2011-05-01

    Full Text Available Abstract Background Eukaryotic DNA methylation is one of the most studied epigenetic processes, as it results in a direct and heritable covalent modification triggered by external stimuli. In contrast to mammals, plant DNA methylation, which is stimulated by external cues exemplified by various abiotic types of stress, is often found not only at CG sites but also at CNG (N denoting A, C or T and CNN (asymmetric sites. A genome-wide analysis of DNA methylation in Arabidopsis has shown that CNN methylation is preferentially concentrated in transposon genes and non-coding repetitive elements. We are particularly interested in investigating the epigenetics of plant species with larger and more complex genomes than Arabidopsis, particularly with regards to the associated alterations elicited by abiotic stress. Results We describe the existence of CNN-methylated epialleles that span Asr1, a non-transposon, protein-coding gene from tomato plants that lacks an orthologous counterpart in Arabidopsis. In addition, to test the hypothesis of a link between epigenetics modifications and the adaptation of crop plants to abiotic stress, we exhaustively explored the cytosine methylation status in leaf Asr1 DNA, a model gene in our system, resulting from water-deficit stress conditions imposed on tomato plants. We found that drought conditions brought about removal of methyl marks at approximately 75 of the 110 asymmetric (CNN sites analysed, concomitantly with a decrease of the repressive H3K27me3 epigenetic mark and a large induction of expression at the RNA level. When pinpointing those sites, we observed that demethylation occurred mostly in the intronic region. Conclusions These results demonstrate a novel genomic distribution of CNN methylation, namely in the transcribed region of a protein-coding, non-repetitive gene, and the changes in those epigenetic marks that are caused by water stress. These findings may represent a general mechanism for the

  10. Synergistic effect of therapeutic stem cells expressing cytosine deaminase and interferon-beta via apoptotic pathway in the metastatic mouse model of breast cancer.

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    Yi, Bo-Rim; Kim, Seung U; Choi, Kyung-Chul

    2016-02-01

    As an approach to improve treatment of breast cancer metastasis to the brain, we employed genetically engineered stem cells (GESTECs, HB1.F3 cells) consisting of neural stem cells (NSCs) expressing cytosine deaminase and the interferon-beta genes, HB1.F3.CD and HB1.F3.CD.IFN-β. In this model, MDA-MB-231/Luc breast cancer cells were implanted in the right hemisphere of the mouse brain, while pre-stained GESTECs with redfluorescence were implanted in the contralateral brain. Two days after stem cells injection, 5-fluorocytosine (5-FC) was administrated via intraperitoneal injection. Histological analysis of extracted brain confirmed the therapeutic efficacy of GESTECs in the presence of 5-FC based on reductions in density and aggressive tendency of breast cancer cells, as well as pyknosis, karyorrhexis, and karyolysis relative to a negative control. Additionally, expression of PCNA decreased in the stem cells treated group. Treatment of breast cancer cells with 5-fluorouracil (5-FU) increased the expression of pro-apoptotic and anti-proliferative factor, BAX and p21 protein through phosphorylation of p53 and p38. Moreover, analysis of stem cell migratory ability revealed that MDA-MB-231 cells endogenously secreted VEGF, and stem cells expressed their receptor (VEGFR2). To confirm the role of VEGF/VEGFR2 signaling in tumor tropism of stem cells, samples were treated with the VEGFR2 inhibitor, KRN633. The number of migrated stem cells decreased significantly in response to KRN633 due to Erk1/2 activation and PI3K/Akt inhibition. Taken together, these results indicate that treatment with GESTECs, particularly HB1.F3.CD.IFN-β co-expressing CD.IFN-β, may be a useful strategy for treating breast cancer metastasis to the brain in the presence of a prodrug.

  11. Dihydropyrimidine Dehydrogenase Is a Prognostic Marker for Mesenchymal Stem Cell-Mediated Cytosine Deaminase Gene and 5-Fluorocytosine Prodrug Therapy for the Treatment of Recurrent Gliomas.

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    Chung, Taemoon; Na, Juri; Kim, Young-Il; Chang, Da-Young; Kim, Young Il; Kim, Hyeonjin; Moon, Ho Eun; Kang, Keon Wook; Lee, Dong Soo; Chung, June-Key; Kim, Sung-Soo; Suh-Kim, Haeyoung; Paek, Sun Ha; Youn, Hyewon

    2016-01-01

    We investigated a therapeutic strategy for recurrent malignant gliomas using mesenchymal stem cells (MSC), expressing cytosine deaminase (CD), and prodrug 5-Fluorocytosine (5-FC) as a more specific and less toxic option. MSCs are emerging as a novel cell therapeutic agent with a cancer-targeting property, and CD is considered a promising enzyme in cancer gene therapy which can convert non-toxic 5-FC to toxic 5-Fluorouracil (5-FU). Therefore, use of prodrug 5-FC can minimize normal cell toxicity. Analyses of microarrays revealed that targeting DNA damage and its repair is a selectable option for gliomas after the standard chemo/radio-therapy. 5-FU is the most frequently used anti-cancer drug, which induces DNA breaks. Because dihydropyrimidine dehydrogenase (DPD) was reported to be involved in 5-FU metabolism to block DNA damage, we compared the survival rate with 5-FU treatment and the level of DPD expression in 15 different glioma cell lines. DPD-deficient cells showed higher sensitivity to 5-FU, and the regulation of DPD level by either siRNA or overexpression was directly related to the 5-FU sensitivity. For MSC/CD with 5-FC therapy, DPD-deficient cells such as U87MG, GBM28, and GBM37 showed higher sensitivity compared to DPD-high U373 cells. Effective inhibition of tumor growth was also observed in an orthotopic mouse model using DPD- deficient U87MG, indicating that DPD gene expression is indeed closely related to the efficacy of MSC/CD-mediated 5-FC therapy. Our results suggested that DPD can be used as a biomarker for selecting glioma patients who may possibly benefit from this therapy.

  12. Cytosine-Phosphorothionate-Guanine Oligodeoxynucleotides Exacerbates Hemophagocytosis by Inducing Tumor Necrosis Factor-Alpha Production in Mice after Bone Marrow Transplantation.

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    Liu, Jiajia; Guo, Yong-Mei; Onai, Nobuyuki; Ohyagi, Hideaki; Hirokawa, Makoto; Takahashi, Naoto; Tagawa, Hiroyuki; Ubukawa, Kumi; Kobayashi, Isuzu; Tezuka, Hiroyuki; Minamiya, Yoshihiro; Ohteki, Toshiaki; Sawada, Kenichi

    2016-04-01

    Hemophagocytic syndrome (HPS) is frequently associated with hematopoietic stem cell transplantation and is treated with some benefit derived from TNF-α inhibitors. However, the mechanisms of how HPS occurs and how a TNF-α inhibitor exerts some benefit to HPS management have remained unclear. We evaluated the effect of toll-like receptor (TLR) ligands, especially focusing on cytosine-phosphorothionate-guanine oligodeoxynucleotide (CpG), a TLR9 ligand, on HPS in mice that underwent transplantation with syngeneic or allogeneic bone marrow (BM) cells (Syn-BMT, Allo-BMT), or with allogeneic BM cells plus splenocytes to promote graft-versus-host disease (GVHD mice). Hemophagocytosis was a common feature early after all BMT, but it subsided in Syn-BMT and Allo-BMT mice. In GVHD mice, however, hemophagocytosis persisted and was accompanied by upregulated production of IFN-γ but not TNF-α, and it was suppressed by blockade of IFN-γ but not TNF-α. A single injection of the TLR9 ligand CpG promoted HPS in all BMT mice and was lethal in GVHD mice, accompanied by greatly upregulated production of TNF-α, IL-6, and IFN-γ. Blocking of TNF-α, but not IL-6 or IFN-γ, suppressed CpG-induced HPS in all BMT mice and rescued GVHD mice from CpG-induced mortality. Thus, TLR9 signaling mediates TNF-α-driven HPS in BMT mice and is effectively treated through TNF-α inhibition.

  13. Tomato yellow leaf curl virus resistance by Ty-1 involves increased cytosine methylation of viral genomes and is compromised by cucumber mosaic virus infection.

    Science.gov (United States)

    Butterbach, Patrick; Verlaan, Maarten G; Dullemans, Annette; Lohuis, Dick; Visser, Richard G F; Bai, Yuling; Kormelink, Richard

    2014-09-02

    Tomato yellow leaf curl virus (TYLCV) and related begomoviruses are a major threat to tomato production worldwide and, to protect against these viruses, resistance genes from different wild tomato species are introgressed. Recently, the Ty-1 resistance gene was identified, shown to code for an RNA-dependent RNA polymerase and to be allelic with Ty-3. Here we show that upon TYLCV challenging of resistant lines carrying Ty-1 or Ty-3, low virus titers were detected concomitant with the production of relatively high levels of siRNAs whereas, in contrast, susceptible tomato Moneymaker (MM) revealed higher virus titers but lower amounts of siRNAs. Comparative analysis of the spatial genomic siRNA distribution showed a consistent and subtle enrichment for siRNAs derived from the V1 and C3 genes in Ty-1 and Ty-3. In plants containing Ty-2 resistance the virus was hardly detectable, but the siRNA profile resembled the one observed in TYLCV-challenged susceptible tomato (MM). Furthermore, a relative hypermethylation of the TYLCV V1 promoter region was observed in genomic DNA collected from Ty-1 compared with that from (MM). The resistance conferred by Ty-1 was also effective against the bipartite tomato severe rugose begomovirus, where a similar genome hypermethylation of the V1 promoter region was discerned. However, a mixed infection of TYLCV with cucumber mosaic virus compromised the resistance. The results indicate that Ty-1 confers resistance to geminiviruses by increasing cytosine methylation of viral genomes, suggestive of enhanced transcriptional gene silencing. The mechanism of resistance and its durability toward geminiviruses under natural field conditions is discussed.

  14. The effect of haemopoietic growth factors on the cell cycle of AML progenitors and their sensitivity to cytosine arabinoside in vitro.

    Science.gov (United States)

    Smith, M A; Singer, C R; Pallister, C J; Smith, J G

    1995-08-01

    This study examines the effect of pretreatment in liquid culture of acute myeloid leukaemic (AML) progenitors with recombinant human IL-3 or G and GM-CSF. Prior to and following cytokine priming, the sensitivity of cells to cytosine arabinoside (Ara-C) at concentrations ranging from 10(-12) to 10(-4) M was assessed in clonogenic culture. In addition, the initial percentage of AML cells in S phase was assessed and their subsequent kinetic response to cytokine treatment evaluated by FACScan analysis. Light-density marrow cells (LDMCs) from 19 AML patients were initially T-cell and monocyte depleted in order to remove potential sources of endogenous cytokine production prior to in vitro investigation. LDMCs were incubated in liquid phase for 7 d in a chemically defined complete medium with or without cytokines. Clonogenic data from fresh AML LDMCs not pretreated with growth factors demonstrated a heterogenous response to Ara-C. In only 4/15 marrows tested clonogenically was there any improvement in sensitivity to Ara-C following cytokine priming. S-phase data on all 19 marrows were similarly variable either before or after cytokine preincubation. There was no discernible correlation between clonogenic and kinetic data, nor could any relationship be established between in vitro findings and the FAB subtypes of patients or clinical outcomes. In summary, it would appear that the cell-cycle status of AML cells is likely to be only one of many contributory factors governing the sensitivity of AML progenitors to Ara-C. The clinical response of AML patients to cytokine therapy in association with cell-cycle-specific cytotoxic agents may therefore be variable and unpredictable.

  15. Enhancing mucosal immunity in mice by recombinant adenovirus expressing major epitopes of porcine circovirus-2 capsid protein delivered with cytosine-phosphate-guanosine oligodeoxynucleotides.

    Science.gov (United States)

    Chang, Hong-Tao; He, Xiu-Yuan; Liu, Yu-Feng; Chen, Lu; Guo, Quan-Hai; Yu, Qiu-Ying; Zhao, Jun; Wang, Xin-Wei; Yang, Xia; Wang, Chuan-Qing

    2014-01-01

    A recombinant replication-defective adenovirus expressing the major epitopes of porcine circovirus-2 (PCV-2) capsid protein (rAd/Cap/518) was previously constructed and shown to induce mucosal immunity in mice following intranasal delivery. In the present study, immune responses induced by intranasal immunization with a combination of rAd/Cap/518 and cytosine-phosphate-guanosine oligodeoxynucleotides (CpG ODN) were evaluated in mice. The levels of PCV-2-specific IgG in serum and IgA in saliva, lung, and intestinal fluids were significantly higher in the group immunized with rAd/Cap/518 and CpG ODN than animals immunized with rAd/Cap/518 alone. The frequencies of IL-2-secreting CD4⁺ T cells and IFN-γ-producing CD8⁺ T cells were significantly higher in the combined immunization group than mice immunized with rAd/Cap/518 alone. The frequencies of CD3⁺, CD3⁺CD4⁺CD8⁻, and CD3⁺CD4⁻CD8⁺ T cells in the combined immunization group were similar to that treated with CpG ODN alone, but significantly higher than mice that did not receive CpG ODN. PCV-2 load after challenge in the combined immunization group was significantly lower than that in the phosphate-buffered saline placebo group and approximately 7-fold lower in the group treated with CpG ODN alone. These results indicate that rAd/Cap/518 combined with CpG ODN can enhance systemic and local mucosal immunity in mice, and represent a promising synergetic mucosal vaccine against PCV-2.

  16. Mechanism of action of a new antitumor ribonucleoside, 1-(3-C-ethynyl-beta-D-ribo-pentofuranosyl)cytosine (ECyd, TAS-106), differs from that of 5-fluorouracil.

    Science.gov (United States)

    Kazuno, Hiromi; Shimamoto, Yuji; Tsujimoto, Hiroaki; Fukushima, Masakazu; Matsuda, Akira; Sasaki, Takuma

    2007-06-01

    1-(3-C-ethynyl-beta-D-ribo-pentofuranosyl)cytosine (ECyd, TAS-106), is a new antitumor cytidine analogue, inhibiting RNA synthesis. In this study we investigated the cellular growth inhibition, intracellular metabolism, cell cycle phase specificity, and RNA synthesis of TAS-106 compared with those of 5-fluorouracil (5-FU), known to possess both DNA- (inhibition of thymidylate synthase activity) and RNA-synthesis-inhibiting activity (inhibition of RNA function). The IC50 values of TAS-106 and 5-FU ranged from 0.0173 to 3.11 microM, and from 6.80 to >1,000 microM, respectively, in a panel of 10 human tumor cells, indicating that TAS-106 possesses greater cytotoxicity than 5-FU. Using excess thymidine-synchronized cells, TAS-106 and 5-FU appeared to exert their cytotoxic effects independently of the cell cycle. The intracellular metabolism and the effect on pre-rRNA processing of TAS-106 differed from those of 5-FU. More than 50% of 5-FU incorporated into the cells was in the unchanged form, while 5-FU incorporated into RNA was approximately 20%. On the other hand, TAS-106 was incorporated in a time-dependent manner into the cells and rapidly converted to its mono-, di- and tri-phosphate form, however, the amount incorporated into RNA fraction was very small. 5-FU incorporated into RNA was confirmed to impair the normal processing of ribosomal RNA (formation of 34/32S RNA from 45S RNA), however, TAS-106 did not affect pre-rRNA processing and may be involved in the inhibition of the synthesis of ribosomal RNA. We concluded that intracellular accumulation and retention of the active metabolite of TAS-106, 3'-ethynylcytidine 5'-triphosphate (ECTP), may contribute to its potent cytotoxicity. The unique mechanism of antitumor activity and intensive cellular metabolism of TAS-106 could contribute to cancer chemotherapy through the pathways different from those of 5-FU or other antitumor nucleosides.

  17. A Ser29Leu substitution in the cytosine deaminase Fca1p is responsible for clade-specific flucytosine resistance in Candida dubliniensis.

    LENUS (Irish Health Repository)

    McManus, Brenda A

    2009-11-01

    The population structure of the opportunistic yeast pathogen Candida dubliniensis is composed of three main multilocus sequence typing clades (clades C1 to C3), and clade C3 predominantly consists of isolates from the Middle East that exhibit high-level resistance (MIC(50) > or = 128 microg\\/ml) to the fungicidal agent flucytosine (5FC). The close relative of C. dubliniensis, C. albicans, also exhibits clade-specific resistance to 5FC, and resistance is most commonly mediated by an Arg101Cys substitution in the FUR1 gene encoding uracil phosphoribosyltransferase. Broth microdilution assays with fluorouracil (5FU), the toxic deaminated form of 5FC, showed that both 5FC-resistant and 5FC-susceptible C. dubliniensis isolates exhibited similar 5FU MICs, suggesting that the C. dubliniensis cytosine deaminase (Fca1p) encoded by C. dubliniensis FCA1 (CdFCA1) may play a role in mediating C. dubliniensis clade-specific 5FC resistance. Amino acid sequence analysis of the CdFCA1 open reading frame (ORF) identified a homozygous Ser29Leu substitution in all 12 5FC-resistant isolates investigated which was not present in any of the 9 5FC-susceptible isolates examined. The tetracycline-inducible expression of the CdFCA1 ORF from a 5FC-susceptible C. dubliniensis isolate in two separate 5FC-resistant clade C3 isolates restored susceptibility to 5FC, demonstrating that the Ser29Leu substitution was responsible for the clade-specific 5FC resistance and that the 5FC resistance encoded by FCA1 genes with the Ser29Leu transition is recessive. Quantitative real-time PCR analysis showed no significant difference in CdFCA1 expression between 5FC-susceptible and 5FC-resistant isolates in either the presence or the absence of subinhibitory concentrations of 5FC, suggesting that the Ser29Leu substitution in the CdFCA1 ORF is the sole cause of 5FC resistance in clade C3 C. dubliniensis isolates.

  18. Cytosine arabinoside, vinblastine, diethylstilboestrol and 2-aminoanthracene tested in the in vitro human TK6 cell line micronucleus test (MNvit) at Institut Pasteur de Lille in support of OECD draft test guideline 487.

    Science.gov (United States)

    Nesslany, Fabrice; Marzin, Daniel

    2010-10-29

    The reference genotoxic agents Cytosine arabinoside, Vinblastine, Diethylstilboestrol and 2-Aminoanthracene were tested in the in vitro micronucleus assay, in human lymphoblastoid TK6 cells, without cytokinesis block, at the laboratories of Institut Pasteur de Lille, France. This was done in support of the toxicity measures recommended in the late 2007 version of the draft OECD Test Guideline 487 for the testing of chemicals. All four reference agents were positive in the assay at concentrations giving approximately 50% toxicity or less as assessed by draft Test Guideline 487 recommended measures, relative population doublings and relative increase in cell counts. Accordingly, this work supports the premise that relative population doublings and relative increase in cell counts are appropriate measures of toxicity for the non-cytokinesis blocked in vitro micronucleus assay.

  19. Remarkable induction of UV-signature mutations at the 3'-cytosine of dipyrimidine sites except at 5'-TCG-3' in the UVB-exposed skin epidermis of xeroderma pigmentosum variant model mice.

    Science.gov (United States)

    Ikehata, Hironobu; Chang, Yumin; Yokoi, Masayuki; Yamamoto, Masayuki; Hanaoka, Fumio

    2014-10-01

    The human POLH gene is responsible for the variant form of xeroderma pigmentosum (XP-V), a genetic disease highly susceptible to cancer on sun-exposed skin areas, and encodes DNA polymerase η (polη), which is specialized for translesion DNA synthesis (TLS) of UV-induced DNA photolesions. We constructed polη-deficient mice transgenic with lacZ mutational reporter genes to study the effect of Polh null mutation (Polh(-/-)) on mutagenesis in the skin after UVB irradiation. UVB induced lacZ mutations with remarkably higher frequency in the Polh(-/-) epidermis and dermis than in the wild-type (Polh(+/+)) and heterozygote. DNA sequences of a hundred lacZ mutants isolated from the epidermis of four UVB-exposed Polh(-/-) mice were determined and compared with mutant sequences from irradiated Polh(+)(/)(+) mice. The spectra of the mutations in the two genotypes were both highly UV-specific and dominated by C→T transitions at dipyrimidines, namely UV-signature mutations. However, sequence preferences of the occurrence of UV-signature mutations were quite different between the two genotypes: the mutations occurred at a higher frequency preferentially at the 5'-TCG-3' sequence context than at the other dipyrimidine contexts in the Polh(+/+) epidermis, whereas the mutations were induced remarkably and exclusively at the 3'-cytosine of almost all dipyrimidine contexts with no preference for 5'-TCG-3' in the Polh(-/-) epidermis. In addition, in Polh(-/-) mice, a small but remarkable fraction of G→T transversions was also observed exclusively at the 3'-cytosine of dipyrimidine sites, strongly suggesting that these transversions resulted not from oxidative damage but from UV photolesions. These results would reflect the characteristics of the error-prone TLS functioning in the bypass of UV photolesions in the absence of polη, which would be mediated by mechanisms based on the two-step model of TLS. On the other hand, the deamination model would explain well the mutation

  20. Self-assembling of cytosine nucleoside into triply-bound dimers in acid media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry, X-rays diffractometry, and theoretical calculations.

    Science.gov (United States)

    Armentano, Donatella; De Munno, Giovanni; Di Donna, Leonardo; Sindona, Giovanni; Giorgi, Gianluca; Salvini, Laura; Napoli, Anna

    2004-02-01

    Electrospray tandem mass spectrometry (ESI-MS/MS) is used to evaluate the assembling of cytosine and thymine nucleosides in the gas phase, through the formation of hydrogen bonded supermolecules. Mixtures of cytidine analogues and homologues deliver in the gas phase proton-bound heterodimers stabilized by multiple interactions, as proven by the kinetics of their dissociation into the corresponding protonated monomers. Theoretical calculations, performed on initial structures of methylcytosine homodimers available in the literature, converged to a minimized structure whereby the two pyrimidine rings interact through the formation of three hydrogen bonds of similar energy. The crystallographic data here reported show the equivalency of the two interacting pyrimidines which is attributable to the presence of an inversion center. Thymine and uracil pyrimidyl nucleosides form, by ESI, gaseous proton-bound dimers. The kinetic of their dissociation into the related protonated monomers shows that the nucleobases are weekly interacting through a single hydrogen bond. The minimized structure of the protonated heterodimer formed by thymine and N-1-methylthymine confirmed the existence of mainly one hydrogen bond which links the two nucleobases through the O4 oxygens. No crystallographic data exists on thymine proton-bound species, nor have we been able to obtain these aggregates in the solid phase. The gaseous phase, under high vacuum conditions, seems therefore a suitable environment where vanishing structures produced by ESI can be studied with a good degree of approximation.

  1. Estrogen receptors bind to and activate the HOXC4/HoxC4 promoter to potentiate HoxC4-mediated activation-induced cytosine deaminase induction, immunoglobulin class switch DNA recombination, and somatic hypermutation.

    Science.gov (United States)

    Mai, Thach; Zan, Hong; Zhang, Jinsong; Hawkins, J Seth; Xu, Zhenming; Casali, Paolo

    2010-11-26

    Estrogen enhances antibody and autoantibody responses through yet to be defined mechanisms. It has been suggested that estrogen up-regulates the expression of activation-induced cytosine deaminase (AID), which is critical for antibody class switch DNA recombination (CSR) and somatic hypermutation (SHM), through direct activation of this gene. AID, as we have shown, is induced by the HoxC4 homeodomain transcription factor, which binds to a conserved HoxC4/Oct site in the AICDA/Aicda promoter. Here we show that estrogen-estrogen receptor (ER) complexes do not directly activate the AID gene promoter in B cells undergoing CSR. Rather, they bind to three evolutionarily conserved and cooperative estrogen response elements (EREs) we identified in the HOXC4/HoxC4 promoter. By binding to these EREs, ERs synergized with CD154 or LPS and IL-4 signaling to up-regulate HoxC4 expression, thereby inducing AID and CSR without affecting B cell proliferation or plasmacytoid differentiation. Estrogen administration in vivo significantly potentiated CSR and SHM in the specific antibody response to the 4-hydroxy-3-nitrophenylacetyl hapten conjugated with chicken γ-globulin. Ablation of HoxC4 (HoxC4(-/-)) abrogated the estrogen-mediated enhancement of AID gene expression and decreased CSR and SHM. Thus, estrogen enhances AID expression by activating the HOXC4/HoxC4 promoter and inducing the critical AID gene activator, HoxC4.

  2. Therapeutic trial of intensified conditioning regimen with high-dose cytosine arabinoside, cyclophosphamide and either total body irradiation or busulfan followed by allogeneic bone marrow transplantation for myelodysplastic syndrome in children

    Energy Technology Data Exchange (ETDEWEB)

    Nagatoshi, Yoshihisa; Okamura, Jun; Ikuno, Yoshiko; Akamatsu, Minoru; Tasaka, Hideko [National Kyushu Cancer Center, Fukuoka (Japan)

    1997-04-01

    Ten children with myelodysplastic syndrome underwent an allogeneic bone marrow transplantation (BMT) with an intensified conditioning regimen. The median age of the patients was 8 years (range 2-10), and included 6 males and 4 females. The subtype of the disease was refractory anemia (RA) in 4, RA with excess blasts (RAEB) in 4, RAEB in transformation (RAEB-T) in 1, and juvenile chronic myelogenous leukemia (JCML) in 1. All patients were conditioned with high-dose cytosine arabinoside (12000 mg/m{sup 2}), cyclophosphamide (120 mg/kg) and either total body irradiation (10-13.2 Gy) or busulfan (16 mg/kg or 560 mg/m{sup 2}). Cyclosporine A and/or methotrexate were used for the prophylaxis of graft-versus-host disease (GVHD). Engraftment was prompt in all but one patient. Severe acute GVHD (grade 3) (n=1), interstitial pneumonitis (n=1) and veno-occlusive disease of the liver (n=1) occurred. The disease relapsed in one patient with RAEB-T. Seven of the 10 patients were alive and disease free 2-74 months after BMT. The disease-free survival rate at 4 years was 69{+-}15%. All surviving patients were in the full performance status. The examined children with MDS tolerated this intensified conditioning regimen well. (author)

  3. Using a Fluorescent Cytosine Analogue tC[superscript o] To Probe the Effect of the Y567 to Ala Substitution on the Preinsertion Steps of dNMP Incorporation by RB69 DNA Polymerase

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Shuangluo; Beckman, Jeff; Wang, Jimin; Konigsberg, William H. (Yale)

    2012-10-10

    Residues in the nascent base pair binding pocket (NBP) of bacteriophage RB69 DNA polymerase (RB69pol) are responsible for base discrimination. Replacing Tyr567 with Ala leads to greater flexibility in the NBP, increasing the probability of misincorporation. We used the fluorescent cytosine analogue, 1,3-diaza-2-oxophenoxazine (tC{sup o}), to identify preinsertion step(s) altered by NBP flexibility. When tC{sup o} is the templating base in a wild-type (wt) RB69pol ternary complex, its fluorescence is quenched only in the presence of dGTP. However, with the RB69pol Y567A mutant, the fluorescence of tC{sup o} is also quenched in the presence of dATP. We determined the crystal structure of the dATP/tC{sup o}-containing ternary complex of the RB69pol Y567A mutant at 1.9 {angstrom} resolution and found that the incoming dATP formed two hydrogen bonds with an imino-tautomerized form of tC{sup o}. Stabilization of the dATP/tC{sup o} base pair involved movement of the tC{sup o} backbone sugar into the DNA minor groove and required tilting of the tC{sup o} tricyclic ring to prevent a steric clash with L561. This structure, together with the pre-steady-state kinetic parameters and dNTP binding affinity, estimated from equilibrium fluorescence titrations, suggested that the flexibility of the NBP, provided by the Y567 to Ala substitution, led to a more favorable forward isomerization step resulting in an increase in dNTP binding affinity.

  4. Human Sulfatase-1 Improves the Effectiveness of Cytosine Deaminase Suicide Gene Therapy with 5-Fluorocytosine Treatment on Hepatocellular Carcinoma Cell Line HepG2 In Vitro and In Vivo

    Institute of Scientific and Technical Information of China (English)

    Xiao-Ping Yang; Ling Liu; Ping Wang; Sheng-Lin Ma

    2015-01-01

    Background:Human sulfatase-1 (Hsulf-l) is an endosulfatase that selectively removes sulfate groups from heparan sulfate proteoglycans (HSPGs),altering the binding of several growth factors and cytokines to HSPG to regulate cell proliferation,cell motility,and apoptosis.We investigated the role of combined cancer gene therapy with Hsulf-l and cytosine deaminase/5-fluorocytosine (CD/5-FC) suicide gene on a hepatocellular carcinoma (HCC) cell line,HepG2,in vitro and in vivo.Methods:Reverse transcription polymerase chain reaction and immunohistochemistry were used to determine the expression of Hsulf-1 in HCC.Cell apoptosis was observed through flow cytometry instrument and mechanism of Hsulf-1 to enhance the cytotoxicity of 5-FC against HCC was analyzed in HCC by confocal microscopy.We also establish a nude mice model of HCC to address the effect of Hsulf-1 expression on the CD/5-FC suicide gene therapy in vivo.Results:A significant decrease in HepG2 cell proliferation and an increase in HepG2 cell apoptosis were observed when Hsulf-1 expression was combined with the CD/5-FC gene suicide system.A noticeable bystander effect was observed when the Hsulf-1 and CD genes were co-expressed.Intracellular calcium was also increased after HepG2 cells were infected with the Hsulf-1 gene.In vivo studies showed that the suppression of tumor growth was more pronounced in animals treated with the Hsulf-1 plus CD than those treated with either gene therapy alone,and the combined treatment resulted in a significant increase in survival.Conclusions:Hsulf-1 expression combined with the CD/5-FC gene suicide system could be an effective treatment approach for HCC.

  5. Characterization of the Escherichia coli codBA operon encoding cytosine permease and cytosine deaminase

    DEFF Research Database (Denmark)

    Danielsen, S; Kilstrup, M; Barilla, K;

    1992-01-01

    . A two-codon overlap between the two reading frames indicates that they constitute an operon. Transcription of the operon was found to be regulated by exogenous purines. Polypeptides specified by each of the two reading frames were expressed in minicells, and the codB gene product was found to be highly...

  6. Communication: Electronic UV-Vis transient spectra of the ∙OH reaction products of uracil, thymine, cytosine, and 5,6-dihydrouracil by using the complete active space self-consistent field second-order perturbation (CASPT2//CASSCF) theory.

    Science.gov (United States)

    Francés-Monerris, Antonio; Merchán, Manuela; Roca-Sanjuán, Daniel

    2013-08-21

    Addition of ∙OH radicals to pyrimidine nucleobases is a common reaction in DNA/RNA damage by reactive oxygen species. Among several experimental techniques, transient absorption spectroscopy has been during the last decades used to characterize such compounds. Discrepancies have however appeared in the assignment of the adduct or adducts responsible for the reported transient absorption UV-Vis spectra. In order to get an accurate assignment of the transient spectra and a unified description of the absorption properties of the ∙OH reaction products of pyrimidines, a systematic complete active space self-consistent field second-order perturbation (CASPT2//CASSCF) theory study has been carried out on the uracil, thymine, and cytosine ∙OH addition adducts, as well as on the 5,6-dihydrouracil hydrogen abstraction products. With the obtained findings, the C5OH contributions to the lowest-energy band can be finally discarded. Instead, a bright (2)(π2) state of the C6OH adducts is determined to be the main responsible in all compounds for the absorption band in the Vis range.

  7. Cytosine arabinoside, vinblastine, 5-fluorouracil and 2-aminoanthracene testing in the in vitro micronucleus assay with L5178Y mouse lymphoma cells at Sanofi Aventis, with different cytotoxicity measurements, in support of the draft OECD Test Guideline on In Vitro Mammalian Cell Micronucleus Test.

    Science.gov (United States)

    Cariou, Olivier; Laroche-Prigent, Nathalie; Ledieu, Sandrine; Guizon, Isabelle; Paillard, Françoise; Thybaud, Véronique

    2010-10-29

    Cytosine arabinoside (a nucleoside analogue that inhibits the gap-filling step of excision repair), vinblastine (an aneugen that inhibits tubulin polymerisation), 5-fluorouracil (a nucleoside analogue with a steep response profile), and 2-aminoanthracene (a metabolism-dependent reference genotoxin) were tested in the in vitro micronucleus assay with L5178Y mouse lymphoma cells, without cytokinesis block. The four chemicals were independently evaluated in two Sanofi Aventis laboratories, one of which used an image analyser to score micronuclei, while the other scored micronucleated cells manually. Very similar results were obtained in the two laboratories, highlighting the robustness of the assay. The four test chemicals induced significant increases in the incidence of micronucleated cells at concentrations that produced no more than a 55±5% reduction in survival growth, as measured with the three parameters recommended in the draft OECD Test Guideline on In Vitro Mammalian Cell Micronucleus Test (MNvit) for chemical testing, namely the relative increase in cell counts, relative population doubling, and the relative cell count. These results support the premise that the relative increase in cell counts and relative population doubling, that take into account both cell death and cytostasis, are appropriate measures of survival growth reduction in the in vitro micronucleus test conducted in the absence of cytokinesis block, as recommended in MNvit.

  8. [Methods for detection of methylated cytosine residues in DNA].

    Science.gov (United States)

    Smirnikhina, S A; Lavrov, A V

    2009-01-01

    The article provides analysis of common methods for DNA methylation detection. Advantages and limitations of methods used for different purposes are compared. Clue step for most common methods is bisulfite treatment of DNA samples and its protocol is described in details. Recommendations are formulated for each method best in solving specific problems.

  9. The effects of cytosine methylation on general transcription factors

    Science.gov (United States)

    Jin, Jianshi; Lian, Tengfei; Gu, Chan; Yu, Kai; Gao, Yi Qin; Su, Xiao-Dong

    2016-07-01

    DNA methylation on CpG sites is the most common epigenetic modification. Recently, methylation in a non-CpG context was found to occur widely on genomic DNA. Moreover, methylation of non-CpG sites is a highly controlled process, and its level may vary during cellular development. To study non-CpG methylation effects on DNA/protein interactions, we have chosen three human transcription factors (TFs): glucocorticoid receptor (GR), brain and muscle ARNT-like 1 (BMAL1) - circadian locomotor output cycles kaput (CLOCK) and estrogen receptor (ER) with methylated or unmethylated DNA binding sequences, using single-molecule and isothermal titration calorimetry assays. The results demonstrated that these TFs interact with methylated DNA with different effects compared with their cognate DNA sequences. The effects of non-CpG methylation on transcriptional regulation were validated by cell-based luciferase assay at protein level. The mechanisms of non-CpG methylation influencing DNA-protein interactions were investigated by crystallographic analyses and molecular dynamics simulation. With BisChIP-seq assays in HEK-293T cells, we found that GR can recognize highly methylated sites within chromatin in cells. Therefore, we conclude that non-CpG methylation of DNA can provide a mechanism for regulating gene expression through directly affecting the binding of TFs.

  10. High-Resolution Analysis of Cytosine Methylation in Ancient DNA

    OpenAIRE

    Llamas, Bastien; Holland, Michelle L.; Chen, Kefei; Jennifer E Cropley; Cooper, Alan; Suter, Catherine M

    2012-01-01

    Epigenetic changes to gene expression can result in heritable phenotypic characteristics that are not encoded in the DNA itself, but rather by biochemical modifications to the DNA or associated chromatin proteins. Interposed between genes and environment, these epigenetic modifications can be influenced by environmental factors to affect phenotype for multiple generations. This raises the possibility that epigenetic states provide a substrate for natural selection, with the potential to parti...

  11. Characterization of cytosine methylated regions and 5-cytosine DNA methyltransferase (Ehmeth) in the protozoan parasite Entamoeba histolytica.

    Science.gov (United States)

    Fisher, Ohad; Siman-Tov, Rama; Ankri, Serge

    2004-01-01

    The DNA methylation status of the protozoan parasite Entamoeba histolytica was heretofore unknown. In the present study, we developed a new technique, based on the affinity of methylated DNA to 5-methylcytosine antibodies, to identify methylated DNA in this parasite. Ribosomal DNA and ribosomal DNA circles were isolated by this method and we confirmed the validity of our approach by sodium bisulfite sequencing. We also report the identification and the characterization of a gene, Ehmeth, encoding a DNA methyltransferase strongly homologous to the human DNA methyltransferase 2 (Dnmt2). Immunofluorescence microscopy using an antibody raised against a recombinant Ehmeth showed that Ehmeth is concentrated in the nuclei of trophozoites. The recombinant Ehmeth has a weak but significant methyltransferase activity when E.histolytica genomic DNA is used as substrate. 5-Azacytidine (5-AzaC), an inhibitor of DNA methyltransferase, was used to study in vivo the role of DNA methylation in E.histolytica. Genomic DNA of trophozoites grown with 5-AzaC (23 microM) was undermethylated and the ability of 5-AzaC-treated trophozoites to kill mammalian cells or to cause liver abscess in hamsters was strongly impaired.

  12. 胞嘧啶脱氨酶/5-氟胞嘧啶自杀基因治疗系统对恶性脑胶质瘤荷瘤裸鼠的抗肿瘤作用%Antitumor efficacy of cytosine deaminase/5-fluorocytosine suicide gene therapy system against Inalignant gliomas in nude mice

    Institute of Scientific and Technical Information of China (English)

    吕胜青; 张克斌; 刘学强; 尹昌林; 邱克军; Eric E.ZHANG; 杨辉

    2008-01-01

    Objective To explore the anfitumor efficacy of cytosine deaminase/5-fluoroeytosine (CD/5-FC) suicide gene therapy system against malignant gliomas. Methods CD gene was transferred into U251 malignant glioma cell line using Lipofeetamine20OOTM-mediated method. The U251 and U251/ CD cells were seeded into the subcutaneous flank of the nude mice. After tumors appeared,5-FC (500 rag/ kg · day) was subsequently intraperitoneally injected for 10 days. The mice were sacrificed after 8 weeks, the volume and weight of tumors were evaluated. At the same time, the pathological features were analyzed for the tumor samples. Results The CD gene was successfully transferred into the U251 ceils. The in vivo animal data showed that the volume and weight of these implanted tumors were dramatically decreased from ( 1.81± 0.77) cm3 to (0.09± 0.03 )cm3, and from ( 1.63 ± 0.80) g to (0.28±0.11 ) g, respectively. Morphological observation found cell apoptosis and tumor necrosis in the transfected group. Coudusion These results indicate that the CD/5-FC suicide gene therapy system may serve as one of the main adjuvant strategies in the treatment of malignant gliomas in the future.%目的 评判胞嘧啶脱氨酶/5-氟胞嘧啶(CD/5-FC)自杀基因治疗系统对恶性脑胶质瘤的抗肿瘤效果.方法 采用Lipofectamine2000TM脂质体介导方法将CD基因转染17251恶性胶质瘤细胞系,并接种于裸鼠前臂皮下,成瘤后腹腔注射5-FC(每13500mg/kg体重)10 d,观察荷瘤鼠肿瘤的生长情况,8周后比较转染组与对照组肿瘤的体积与重量,并进行病理形态学分析.结果 U251细胞获得CD基因的成功转染,5-FC用于不同组别荷瘤裸鼠,8周后转染组肿瘤体积(0.09±0.03)cm3和重量(0.28±0.11)g明显小于对照组(1.81±0.77)cm3和(1.63±0.80)g;形态学揭示转染组肿瘤细胞出现明显的凋亡与坏死.结论 裸鼠在体实验研究表明:CD/5-FC自杀基因治疗系统是治疗恶性脑胶质瘤行之有效的手段之一.

  13. Study on the cytosine deaminases expression in human immunodeficiency virus-1 infected patients%人类免疫缺陷病毒-1感染者胞嘧啶脱氨基酶家族表达水平分析

    Institute of Scientific and Technical Information of China (English)

    王珍燕; 江雪艳; 张云智; 卢洪洲

    2010-01-01

    Objective To quantitatively investigate the expression levels of the cytosine deaminases,hA3B,hA3F and hA3G in peripheral blood mononuclear cell(PBMC)of human immunodeficiency virus(HIV)infected patients and to analyze the correlation between cytosine deaminases expression and CD4~+ T lymphocyte counts. Methods Peripheral blood samples were collected from 21 HIV-infected subjects who didn't take antiretroviral therapy(ART-),21 HIV-infected subjects receiving ART(ART+),and 10 HIV-uninfected subjects. PBMC were isolated by Ficoll density gradient centrifugation, followed by RNA extraction and cDNA synthesis.hA3B,hA3F and hA3G mRNA levels were determined by real-time fluorescent quantitative polymerase chain reaction(PCR).CD4~+ T lymphocyte counts were determined using flow cytometry. Data were analyzed by t test, t' test or Wilcoxon rank sum test. Results In HIV-infected subjects without or with ART,HIV-uninfected subjects, the levels of hA3B mRNA were 208.4,365.2 and 563.6,hA3F mRNA were 245.5,316.6 and 442.9,hA3G mRNA were 404.6,360.8 and 638.6,respectively.hA3G mRNA level in HIV-infected subjects was lower than that in HIV-uninfected controls(P=0.0131),but there was no statistical difference between ART+ and ART-groups(P=0.7342).There were no correlations between hA3B,hA3F and hA3G mRNA levels and CD4+ T lymphocyte counts in either ART-or ART+HIV-infected subjects(ART-:r=-0.0104,r=-0.0545,r=0.1623,all P>0.05;ART+:r=0.3220,r=0.2193,r=0.1455,all P>0.05).In addition,hA3B,hA3F and hA3G mRNA levels were positively correlated with one another in ART-HIV-infected subjects and HIV-uninfected controls(P<0.05),but not in ART-HIV-infected subjects(P>0.05).Conclusions hA3B,hA3F and hA3G expression levels do not directly correlate with CD4~+ T lymphocyte counts in HIV-1-infected patients,hA3B,hA3F and hA3G expression levels in PBMCs tend to he decreased after HIV-1 infection, and ART may increase hA3B and hA3F mRNA expression.%目的 定量研究HIV-1感染者外周

  14. 射频消融联合胞嘧啶鸟嘌呤寡脱氧核苷酸治疗小鼠乳腺癌皮下模型%Therapy of subcutaneous models of breast cancer in miceby radiofrequency ablation combined with peritumoral injection of cytosine phosphate guanine oligodeoxyribonucleotide

    Institute of Scientific and Technical Information of China (English)

    刘宇; 黄群爱; 刘瑞磊; 姜华; 吴珏堃; 李玺

    2015-01-01

    目的 观察射频消融联合瘤周注射胞嘧啶鸟嘌呤寡脱氧核苷酸(CpG ODN)对BALB/c小鼠皮下种植性乳腺癌的治疗作用及对荷瘤鼠免疫功能的影响.方法 32只BALB/c小鼠双侧胁肋部皮下接种乳腺癌细胞EMT-6,建立乳腺癌动物模型,随机分为4组,每组8只,分别给予左侧皮下肿瘤射频消融+瘤周注射CpG ODN、射频消融、瘤周注射CpG ODN和瘤周注射生理盐水4种处理.定期测量治疗侧及非治疗侧肿瘤大小,尾静脉取血法收集各组小鼠外周血,酶联免疫吸附试验(ELISA)法检测血清白细胞介素(IL)-12、IL-10、IL-2及干扰素(IFN)-γ含量.当非治疗侧肿瘤直径达到18mm时手术切除肿瘤,并记录为非治疗侧观察终点,当治疗侧肿瘤直径达到18 mm时或出现恶病质时处死小鼠,记录生存时间.结果 射频消融+瘤周注射CpG ODN组和射频消融组治疗侧肿瘤体积体积显著小于CpG ODN组和对照组(P<0.05).射频消融+瘤周注射CpG ODN组未治疗侧的肿瘤体积在第21天后明显小于其他各组(P<0.05).射频消融+瘤周注射CpG ODN组中位生存时间为92 d,射频消融组为84d,瘤周注射CpG ODN组为64d,对照组为60d.射频消融+瘤周注射CpG ODN组小鼠外周血中IL-12浓度为312.40 ng/L,IL-10浓度为216.34 ng/L,IL-2浓度为75.33 ng/L,IFN-γ浓度为69.32 ng/L,显著高于其他3组(P<0.05).结论 射频消融联合瘤周注射CpG ODN能激活小鼠体内的抗肿瘤免疫效应,起到抑制肿瘤生长作用.%Objective To investigate the efficacy of microwave ablation combined with peritumoral injected cytosine phosphate guanine oligodeoxyribonucleotide (CpG ODN) in inducing immunityresponse against mouse breast cancer.Methods Bilateral breast cancer model was established by subcutaneous injection EMT-6 cells underneath both sides of the BALB/c mouse rib area.According the therapy method to the left side tumor,there were 32 mice were divided randomly into four groups

  15. 高危骨髓增生异常综合征及急性髓系白血病治疗方案选择研究%Effects of Idarubicin and cytosine arabinoside on high-risk myelodysplastic syndromes and acute myeloid leukemia

    Institute of Scientific and Technical Information of China (English)

    刘惠; 刘鸿; 吴玉红; 王化泉; 邢莉民; 关晶; 王珺; 李丽娟; 付蓉; 邵宗鸿; 阮二宝; 王晓明; 王国锦; 梁勇; 瞿文; 宋嘉

    2009-01-01

    Objective To compare the therapeutic and side effects of idarubicin (IDA) with those of daunorubicin(DNR) in combination with cytosine arabinoside (CA) on high-risk myelodysplastic syndromes and acute myeloid leukemia (AML).Methods 29 patients(18 patients with AML,11 patients with high-risk MDS or AMI7MDS)were treated with IDA(12mg/m~2)for 3d and CA(150mg/m~2)for 7d(IA arm) and 26 patients with AML with DNR(45mg/m~2 )for 3d and CA( 150mg/m~2)for 7d( DA arm)as induction and consolidation therapies. Results (1) For AML patients, the effective rates( CR + PR) were 83. 3% in IA arm and 53. 8% in DA arm( P = 0.042); For patients with higher white blood cell count (≥30×10~9/L) ,the effective rates were 81. 3% in IA arm and 25% in DA arm (P =0.009) ;For elder patients ( ≥ 65y) , the effective rates were 66. 7% in IA arm and 0% in DA arm (P = 0.045);(2) Treatment with IA could also offer significant advantages to high-risk MDS or AML/MDS patients with higher effective rates(83.3%) which was similar to that of AML patients by IA(72.7%). Age and Hyperleukocytosis(≥30 ×10~9/L)could not affect the effective rates in IA arm;(3) The main toxicity of IA was longer myelosuppression with lower WBC below 4 ×10~9/L which was averagely up to (24.1 7.7)d. Hemorrhage, nausea, vomit, hepatic and renal dysfunction and heart toxicity occurred unfrequently. Con-clusion IA was superior to DA as induction and consolidation therapies for AML and also effective for high-risk MDS or MDS-develeped AML. Age and hyperleukocytosis could not affect the effects of IA. IA can be the first therapy choice for the patients with AML and high-risk MDS.%目的 评价IA方案[去甲氧柔红霉素(IDA)+阿糖胞苷(Ara-C)]和DA方案[柔红霉素(DNR)+Ara-C]治疗高危骨髓增生异常综合征(MDs)、急性髓系白血病(AML)及MDS转AML患者的疗效和不良反应.方法 应用IA方案治疗2005年2月至2008年10月天津医科大学总医院血液肿瘤科收治的AML18

  16. Effects of tissue specific cytosine deaminase/5-fluorocytosine thermotherapy on hepatic metastasis of colonic carcinoma in nude mice%组织特异性胞嘧啶脱氨酶和5-氟胞嘧啶热化疗对裸鼠结肠癌肝脏转移的影响

    Institute of Scientific and Technical Information of China (English)

    黎成金; 王羊; 王烈; 涂小煌; 王瑜; 张宝明

    2009-01-01

    目的 探讨组织特异性胞嘧啶脱氨酶/5-氟胞嘧啶(CD/5-FC)系统热化疗对裸鼠结肠癌肝脏转移的影响.方法 将45只裸鼠按随机数字表法分为3组:对照组、非热疗组、热疗组,每组15只.门静脉注射法建立结肠癌肝脏转移动物模型,3组分别给予不同的治疗方法.采用χ2检验和单因素方差分析3组肝脏肿瘤转移率、转移数目;观察各组病理学变化、肿瘤细胞凋亡指数;荧光定量RT-PCR和Westernblot检测肿瘤组织中CD基因的表达情况.结果 对照组、非热疗组、热疗组肝脏平均转移癌结节数目和转移率分别为(4.6±1.3)、(2.2±1.0)、(0.5±0.8)个和100.0%、60.0%、13.3%,3组比较差异有统计学意义(F=25.898,χ2=5.208,19.548,5.168,P<0.05);肿瘤细胞凋亡指数平均为4.6%、9.9%和17.4%.热疗组可见大量细胞空泡变性、坏死、溶解现象,有较多的凋亡小体形成.3组均可以检测到CD基因的表达.结论 组织特异性CD/5-FC系统热化疗对转CD基因结肠癌LoVo细胞裸鼠肝脏转移有明显的抑制作用.%Objective To investigate the effects of tissue specific cytosine deaminase/5-fluorocytosine (CD/5-FC) thermotherapy on hepatic metastasis of colonic carcinoma in nude mice. Methods Forty-five nude mice were randomly divided into control group, 5-FC group and 5-FC thermotherapy group according to the random number table (15 mice in each group). Mice models of hepatic metastasis of colonic carcinoma were established by portal vein injection of LoVo/CEACD cells. The hepatic metastasis rate and number of metastatic nodules of the 3 groups were compared by ehi-square test and one-way ANOVA. The pathological changes in tumor tissues and apoptotic index of tumor cells were observed. The expression of the CD gene in tumor tissues was detected by fluorescent quantitative RT-PCR and Western blot. Results The number of metastatic nodules and liver metas-tasis rate were 4.6±1.3 and 100.0% in control group, 2.2±1

  17. Study on Optimum Conditions of Catechins Extracted from Greentea with Ethano%绿茶中儿茶素的最佳提取条件研究

    Institute of Scientific and Technical Information of China (English)

    陈林

    2012-01-01

    To obtain the optimum conditions of catechins extracted from green tea with ethanol,ethanol concentration,extraction temperature and extraction time were studied.The results showed that the ethanol concentration,extraction temperature,and extraction time affected extraction efficiency.The orthogonal experiment results showed that the optimal conditions for extraction and purification of catechins as follows: ethanol concentration was 75%,extraction temperature was 88.4 ℃,extraction time was 1.5 h,and the factors affecting the effect of catechins extract as follows: 〉extraction temperature〉extraction timeethanol concentration.%为了获得儿茶素乙醇提取工艺的最佳条件,主要研究了乙醇浓度、浸提温度和浸提时间对儿茶素乙醇提取效果的影响。依据儿茶素与香荚兰素的羟醛缩合生成红色产物的显色反应原理,以无机强酸为催化剂,用分光光度法对提取物中儿茶素含量进行测定。结果表明乙醇浓度、浸提温度、浸提时间对提取效果均有影响。正交试验结果表明,儿茶素的最佳提取和纯化条件为:乙醇浓度为75%,浸提温度为88.4℃,浸提时间为1.5 h,影响儿茶素提取效果的因素依次为:浸提温度〉浸提时间〉乙醇浓度。

  18. Structural characterization of diastereoisomeric ethano adducts derived from the reaction of 2'-deoxyguanosine with trans,trans-2,4-decadienal.

    Science.gov (United States)

    Loureiro, Ana Paula M; de Arruda Campos, Ivan P; Gomes, Osmar F; di Mascio, Paolo; Medeiros, Marisa H G

    2004-05-01

    Background levels of exocyclic DNA adducts have been detected in rodent and human tissues. Several studies have focused on bifunctional electrophiles generated from lipid peroxidation as one of the endogenous sources of these lesions. We have previously shown that the reaction of 2'-deoxyguanosine (dGuo) with trans,trans-2,4-decadienal (DDE), a highly cytotoxic aldehyde generated as a product of lipid peroxidation in cell membranes, results in the formation of a number of different base derivatives. Three of these derivatives have been fully characterized as 1,N(2)-etheno-2'-deoxyguanosine adducts. In the present work, four additional adducts, designated A3-A6, were isolated from in vitro reactions by reversed-phase HPLC and fully characterized on the basis of spectroscopic measurements. Adducts A3-A6 are four diastereoisomeric 1,N(2)-hydroxyethano-2'-deoxyguanosine derivatives possessing a carbon side chain with a double bond and a hydroxyl group. The systematic name of these adducts is 6-hydroxy-3-(2'-deoxy-beta-D-erythro-pentafuranosyl)-7-((E)-1-hydroxy-oct-2-enyl)-3,5,6,7-tetrahydro-imidazo[1,2-a]purin-9-one. The proposed reaction mechanism yielding adducts A3-A6 involves DDE epoxidation at C2, followed by nucleophilic addition of the exocyclic amino group of dGuo to the C1 of the aldehyde and cyclization, via nucleophilic attack, on the C2 epoxy group by N-1. The formation of adducts A1-A6 has been investigated in acidic, neutral, and basic pH in the presence of H(2)O(2) or tert-butyl hydroperoxide. Neutral conditions, in the presence of H(2)O(2), have favored the formation of adducts A1 and A2, with minor amounts of A3-A6, which were prevalent under basic conditions. These data indicate that DDE can modify DNA bases through different oxidative pathways involving its two double bonds. It is important to structurally characterize DNA base derivatives induced by alpha,beta-unsaturated aldehydes so that the genotoxic risks associated with the lipid peroxidation process can be assessed.

  19. Dual Targeting of Tumor Angiogenesis and Chemotherapy by Endostatin-Cytosine Deaminase-Uracil Phosphoribosyl Transferase

    OpenAIRE

    Chen, Chun-Te; Yamaguchi, Hirohito; Lee, Hong-Jen; Du, Yi; Lee, Heng-Huan; Xia, Weiya; Yu, Wen-Hsuan; Hsu, Jennifer L.; Yen, Chia-Jui; Sun, Hui-Lung; Wang, Yan; Yeh, Edward T H; Hortobagyi, Gabriel N.; Hung, Mien-Chie

    2011-01-01

    Several antiangiogenic drugs targeting VEGF/VEGFR approved by the FDA for many cancer types including colorectal and lung cancer can effectively reduce tumor growth. However, targeting the VEGF signaling pathway will likely influence the normal function of endothelial cells in maintaining homeostasis and cause unwanted adverse effects. Indeed, emerging experimental evidence suggests that VEGF-targeting therapy induced less tumor cell–specific cytotoxicity, allowing residual cells to become mo...

  20. DNA binding of the p21 repressor ZBTB2 is inhibited by cytosine hydroxymethylation

    Energy Technology Data Exchange (ETDEWEB)

    Lafaye, Céline; Barbier, Ewa; Miscioscia, Audrey; Saint-Pierre, Christine [Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, UMR E_3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble F-38054 (France); Kraut, Alexandra; Couté, Yohann [Etude de la Dynamique des Protéomes, Biologie à Grande Echelle, UMR S_1038 CEA/INSERM/UJF-Grenoble 1, iRTSV, 17 rue des Martyrs, Grenoble F-38054 (France); Plo, Isabelle [INSERM, U1009, Institut Gustave Roussy, Université Paris 11, 114 rue Edouard Vaillant, Villejuif F-94805 (France); Gasparutto, Didier; Ravanat, Jean-Luc [Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, UMR E_3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble F-38054 (France); Breton, Jean, E-mail: jean.breton@cea.fr [Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, UMR E_3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble F-38054 (France)

    2014-03-28

    Highlights: • 5-hmC epigenetic modification is measurable in HeLa, SH-SY5Y and UT7-MPL cell lines. • ZBTB2 binds to DNA probes containing 5-mC but not to sequences containing 5-hmC. • This differential binding is verified with DNA sequences involved in p21 regulation. - Abstract: Recent studies have demonstrated that the modified base 5-hydroxymethylcytosine (5-hmC) is detectable at various rates in DNA extracted from human tissues. This oxidative product of 5-methylcytosine (5-mC) constitutes a new and important actor of epigenetic mechanisms. We designed a DNA pull down assay to trap and identify nuclear proteins bound to 5-hmC and/or 5-mC. We applied this strategy to three cancerous cell lines (HeLa, SH-SY5Y and UT7-MPL) in which we also measured 5-mC and 5-hmC levels by HPLC-MS/MS. We found that the putative oncoprotein Zinc finger and BTB domain-containing protein 2 (ZBTB2) is associated with methylated DNA sequences and that this interaction is inhibited by the presence of 5-hmC replacing 5-mC. As published data mention ZBTB2 recognition of p21 regulating sequences, we verified that this sequence specific binding was also alleviated by 5-hmC. ZBTB2 being considered as a multifunctional cell proliferation activator, notably through p21 repression, this work points out new epigenetic processes potentially involved in carcinogenesis.

  1. The DNA cytosine deaminase APOBEC3B promotes tamoxifen resistance in ER-positive breast cancer

    Science.gov (United States)

    Law, Emily K.; Sieuwerts, Anieta M.; LaPara, Kelly; Leonard, Brandon; Starrett, Gabriel J.; Molan, Amy M.; Temiz, Nuri A.; Vogel, Rachel Isaksson; Meijer-van Gelder, Marion E.; Sweep, Fred C. G. J.; Span, Paul N.; Foekens, John A.; Martens, John W. M.; Yee, Douglas; Harris, Reuben S.

    2016-01-01

    Breast tumors often display extreme genetic heterogeneity characterized by hundreds of gross chromosomal aberrations and tens of thousands of somatic mutations. Tumor evolution is thought to be ongoing and driven by multiple mutagenic processes. A major outstanding question is whether primary tumors have preexisting mutations for therapy resistance or whether additional DNA damage and mutagenesis are necessary. Drug resistance is a key measure of tumor evolvability. If a resistance mutation preexists at the time of primary tumor presentation, then the intended therapy is likely to fail. However, if resistance does not preexist, then ongoing mutational processes still have the potential to undermine therapeutic efficacy. The antiviral enzyme APOBEC3B (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3B) preferentially deaminates DNA C-to-U, which results in signature C-to-T and C-to-G mutations commonly observed in breast tumors. We use clinical data and xenograft experiments to ask whether APOBEC3B contributes to ongoing breast tumor evolution and resistance to the selective estrogen receptor modulator, tamoxifen. First, APOBEC3B levels in primary estrogen receptor–positive (ER+) breast tumors inversely correlate with the clinical benefit of tamoxifen in the treatment of metastatic ER+ disease. Second, APOBEC3B depletion in an ER+ breast cancer cell line results in prolonged tamoxifen responses in murine xenograft experiments. Third, APOBEC3B overexpression accelerates the development of tamoxifen resistance in murine xenograft experiments by a mechanism that requires the enzyme’s catalytic activity. These studies combine to indicate that APOBEC3B promotes drug resistance in breast cancer and that inhibiting APOBEC3B-dependent tumor evolvability may be an effective strategy to improve efficacies of targeted cancer therapies. PMID:27730215

  2. The Dnmt3L ADD Domain Controls Cytosine Methylation Establishment during Spermatogenesis

    Directory of Open Access Journals (Sweden)

    Georgios Vlachogiannis

    2015-02-01

    Full Text Available A critical aspect of mammalian gametogenesis is the reprogramming of genomic DNA methylation. The catalytically inactive adaptor Dnmt3L is essential to ensuring this occurs correctly, but the mechanism by which it functions is unclear. Using gene targeting to engineer a single-amino-acid mutation, we show that the Dnmt3L histone H3 binding domain (ADD is necessary for spermatogenesis. Genome-wide single-base-resolution DNA methylome analysis of mutant germ cells revealed overall reductions in CG methylation at repetitive sequences and non-promoter CpG islands. Strikingly, we also observe an even more severe loss of non-CG methylation, suggesting an unexpected role for the ADD in this process. These epigenetic deficiencies were coupled with defects in spermatogonia, with mutant cells displaying marked changes in gene expression and reactivation of retrotransposons. Our results demonstrate that the Dnmt3L ADD is necessary for Dnmt3L function and full reproductive fitness.

  3. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed Missael Vargas;

    2014-01-01

    Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence ...

  4. Lack of dependance of transcription-induced cytosine deaminations on protein synthesis.

    Science.gov (United States)

    Mokkapati, Sanath Kumar; Bhagwat, Ashok S

    2002-10-31

    Transcription-induced mutations (TIM) is a phenomenon in Escherichia coli in which transcription promotes C to T and other mutations in a strand-specific manner. Because the processes of transcription and translation are coupled in prokaryotes and some models regarding creating a hypermutagenic state in E. coli require new protein synthesis, we tested the possibility that TIM was dependent on efficient synthesis of proteins. We used puromycin to reversibly inhibit protein synthesis and found that it had little effect on mRNA synthesis, plasmid copy-number or TIM. Our results show that TIM is not dependent on efficient translation of mRNA and this helps eliminate certain models concerning the mechanism underlying TIM.

  5. Contrasting reactions of hydrated electron and formate radical with 2-thio analogues of cytosine and uracil.

    Science.gov (United States)

    Prasanthkumar, Kavanal P; Alvarez-Idaboy, Juan R; Kumar, Pavitra V; Singh, Beena G; Priyadarsini, K Indira

    2016-10-19

    2-Thiocytosine (TC) and 2-thiouracil (TU) were subjected to hydrated electron (eaq(-)), formate radical (CO2˙(-)) and 2-hydroxypropan-2-yl radical ((CH3)2˙COH) reactions in aqueous medium. Transients were characterized by absorption spectroscopy and the experimental findings were rationalized by DFT calculations at LC-ωPBE and M06-2X levels using a 6-311+G(d,p) basis set and SMD solvation. In eaq(-) reactions, a ring N-atom protonated radical of TC and an exocyclic O-atom protonated radical of TU were observed via addition of eaq(-) and subsequent protonation by solvent molecules. However, two competing but simultaneous mechanisms are operative in CO2˙(-) reactions with TC and TU. The first one corresponds to formations of N(O)-atom protonated radicals (similar to eaq(-) reactions); the second mechanism led to 2 center-3 electron, sulfur-sulfur bonded neutral dimer radicals, TCdim˙ and TUdim˙. DFT calculations demonstrated that H-abstraction by CO2˙(-) from TC(TU) results in S-centered radical which upon combination with TC(TU) provide the dimer radical. In some cases, DFT energy profiles were further validated by CBS-QB3//M06-2X calculations. This is the first time report for a contradictory behavior in the mechanisms of eaq(-) and CO2˙(-) reactions with any pyrimidines or their thio analogues.

  6. Patterns of DNA cytosine methylation between haploids and corresponding diploids in rice

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hongyu; PENG Hai; LI Yun; XU Peizhou; WANG Xudong; WU Xianjun

    2006-01-01

    Eighteen pairs of diploid-haploid twinseedlings were identified and screened out from special rice SARⅡ-628 population. Five pairs of them were selected and randomly designated as A, B, C, D and E. Simple sequence repeats (SSR) analysis showed that there was no difference among 310 sites,which indicated that there was no base mutation on DNA primary structure. DNA methylation plays an important role in gene expression regulation during growth and development stages in eukaryotes. A modified AFLP technique (methylation-sensitive AFLP, MSAP) was employed to detect the DNA methylation patterns in the 5'-CCGG sites of the five pairs of twin-seedlings. Although no methylation mutation was detected among the five diploids,forty-three methylation mutation sites were found from the corresponding haploids. The MSAP ratios,which were the ratios of MSAP sites to the total amplified sites, in five haploids were 18.79%, 19.35%,18.49%, 18.45% and 18.75%, respectively. And corresponding full methylation levels (5'-CmCGG in double strands) of those haploids were 10.58%,11.3%, 10.11%, 10.09% and 10.34%, respectively.Both MSAP and full methylation levels in the five haploids were higher than that of their corresponding diploids, which suggested that hypermethylation occurred in some 5'-CCGG sites. Five types of MASP patterns among the five pairs of twin-seedlings were detected as follows: (1) no changes, methylation levels were the same in both haploids and diploids; (2)demethylation, diploid was methylated but no methylation in the same site in haploid; (3) hypermethylation, the methylation level in haploid was higher than those in diploid; (4) hypomethylation, methylation in haploid was lower than those in diploid; (5)undecided pattern, change trend of methylation levels in haploids was not decided. The bands of 18 sites were reclaimed, then sequenced and searched on website to determine the sites of those sequences on rice chromosomes. The result showed that the methylation mutation involved the whole rice genome and 12 pairs of chromosomes. The mutation was site-related and there were different mutation sites for different haploids. Compared to diploids, the higher methylation level in haploids might be a readjusting reaction to the decrease in ploidy for the sake of survival.

  7. A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen

    Science.gov (United States)

    Chao, Michael C.; Zhu, Shijia; Kimura, Satoshi; Davis, Brigid M.; Schadt, Eric E.; Fang, Gang; Waldor, Matthew K.

    2015-01-01

    DNA methylation is a key epigenetic regulator in all domains of life, yet the effects of most bacterial DNA methyltransferases on cellular processes are largely undefined. Here, we used diverse techniques, including bisulfite sequencing, transcriptomics, and transposon insertion site sequencing to extensively characterize a 5-methylcytosine (5mC) methyltransferase, VchM, in the cholera pathogen, Vibrio cholerae. We have comprehensively defined VchM’s DNA targets, its genetic interactions and the gene networks that it regulates. Although VchM is a relatively new component of the V. cholerae genome, it is required for optimal V. cholerae growth in vitro and during infection. Unexpectedly, the usually essential σE cell envelope stress pathway is dispensable in ∆vchM V. cholerae, likely due to its lower activation in this mutant and the capacity for VchM methylation to limit expression of some cell envelope modifying genes. Our work illuminates how an acquired DNA methyltransferase can become integrated within complex cell circuits to control critical housekeeping processes. PMID:26588462

  8. 无水乙醇预处理提取番茄红素工艺优化%Optimization of Pretreatment Process with Anhydrous EthanoI for Lycopene Extraction

    Institute of Scientific and Technical Information of China (English)

    范少丽; 敬思群; 纵伟

    2015-01-01

    Lycopene is extracted by anhydrous ethanol pretreatment method with ethyl acetate as extraction solvent and lycopene extraction rate as index.The optimal conditions of anhydrous ethanol pretreatment are obtained through single factor and orthogonal experiments,and the results show that the anhydrous ethanol pretreatment processing time is of 20 min,the processing temperature of 50 ℃, and the solid-liquid ratio of 1 ∶ 2,the number of processing stage is 2.Under these conditions, lycopene extraction rate is up to 62.45 mg/100 g and lycopene content reaches 80.69%.The modern instrumental analysis methods such as SEM,IR and XRD are applied to characterize the product,and the results show that the characterization of lycopene product and pretreatment of anhydrous ethanol is basically in accordance with the lycopene standard.%采用无水乙醇预处理番茄酱,用乙酸乙酯提取番茄红素,以番茄红素提取得率为考察指标,通过单因素和正交实验确定无水乙醇预处理最优条件为:预处理时间20 min、处理温度50℃、料液比1∶2、二级处理,番茄红素提取得率为62.45 mg/100 g,番茄红素含量可达80.69%。同时采用 SEM,IR,XRD现代仪器分析手段对番茄红素产品进行表征,结果表明无水乙醇预处理提取得到番茄红素产品表征与番茄红素标准品基本一致。

  9. Dynamic research on the anaerobic treatment of ceIIuIosic ethanoI wastewater producing methane%厌氧处理纤维素乙醇废水产甲烷动态研究

    Institute of Scientific and Technical Information of China (English)

    张蕾; 郭宏山; 李宝忠; 陈天佐; 朱卫

    2016-01-01

    Cellulosic ethanol wastewater as the researc h target,the BMP test is carried out,under the following conditions:the mass ratio of substrate COD/inoculum VSS are 0.13,0.27,0.40,0.54,respectively,and the initial COD are 5,10,15,20 g/L,respectively. The results show that after a 30 day anaerobic fermentation,the BMP test results of various samples are 37.7,81.2,114.2,153.0 mL/gVSS,respectively,and anaerobic biodegradability RA is above 80%. The modified Gompertz model is used for the nonlinear fitting of cumulative methane production. The model can exactly predict the maximum methane production velocity,anaerobic starting lag phase,and suitable residence time,under different initial organic loading. After the BMP test,the COD removing rate obtained is higher than 80%,and both pH and alkalinity are improved remarkably.%以纤维素乙醇废水为研究对象,在底物COD与接种物VSS的质量比分别为0.13、0.27、0.40、0.54,初始COD分别为5、10、15、20 g/L的条件下进行了BMP测试。结果表明:厌氧发酵30 d后各样品的BMP测试结果分别为37.7、81.2、114.2、153.0 mL/gVSS,厌氧生物可降解率RA在80%以上。利用修正的Gompertz模型对累积产甲烷量进行非线性拟合,模型可以准确地预测出不同初始有机负荷下的最大产甲烷速率、厌氧启动延滞期以及合适的停留时间。 BMP测试结束后,测得COD去除率达到80%以上,pH和碱度均显著提高。

  10. 脱脂沙苑子乙醇提取物的体外抗氧化活性研究%Studies on antioxidant activities of ethanoic extract from defatted Semen astragali complanati in vitro

    Institute of Scientific and Technical Information of China (English)

    王莉; 刘静; 杨建雄

    2008-01-01

    通过测定脱脂沙苑子乙醇提取物(ESA)对1,1-二苯基-2-苦苯肼自由基(DPPH·)、超氧阴离子自由基(O-·2)和羟基自由基(·OH)的清除能力、对Fe2+诱导的脂质过氧化反应的抑制作用、还原力和总抗氧化力,评价ESA的体外抗氧化活性,并与公认的抗氧化剂维生素C作了对照.结果表明,ESA有一定的DPPH·清除能力(IC50=419.1μg/mL)、较强的超氧阴离子清除能力(IC50=117.9μg/mL)和羟基自由基清除能力(IC50=224.4μg/mL),能有效的抑制脂质过氧化(IC50=1.70 mg/mL),有良好的总抗氧化力,说明沙苑子具有明显的抗氧化活性.

  11. Exploring the Ribose Sub-Pocket of the Substrate-Binding Site in Escherichia coli IspE : Structure-Based Design, Synthesis, and Biological Evaluation of Cytosines and Cytosine Analogues

    NARCIS (Netherlands)

    Schuetz, Andri P.; Osawa, Sho; Mathis, Jennifer; Hirsch, Anna K. H.; Bernet, Bruno; Illarionov, Boris; Fischer, Markus; Bacher, Adelbert; Diederich, Francois; Schütz, Andri P.

    2012-01-01

    The enzymes of the non-mevalonate pathway for the isoprenoid biosynthesis are promising targets for the development of selective drugs for the treatment of important infectious diseases. This pathway is used by plants, many eubacteria, and apicomplexan protozoa, including major human pathogens such

  12. Experimental and theoretical studies on the coordination chemistry of the N1-hexyl substituted pyrimidines (uracil, 5-fluorouracil and cytosine).

    Science.gov (United States)

    Barceló-Oliver, Miquel; Baquero, Beatriz Adriana; Bauzá, Antonio; García-Raso, Angel; Vich, Roberto; Mata, Ignasi; Molins, Elies; Terrón, Angel; Frontera, Antonio

    2013-06-01

    N(1)-Hexyl substituted pyrimidines were shown to present solubility properties closer to the real bases than the commonly used methyl and ethyl derivatives, yielding bi-layered structures in the solid state. The study of their coordination capabilities, mainly with Ag(I) and Hg(II), is presented in order to prove their reactivity. A series of coordination complexes, namely, [Hg(N(1)-hexyl-5-fluorouracilate)2]4·6H2O (1), (Ag(+))·[Ag(N(1)-hexyl-5-fluorouracilate)2](-) (2), [Ag(NO3)(N(1)-hexyluracil-κO(4))4] (3), [ZnBr2(N(1)-hexylcytosine)2] (4), [CdBr2(N(1)-hexylcytosine)2] (5), [HgBr2(N(1)-hexylcytosine)2] (6) and [CoBr2(N(1)-hexylcytosine)2] (7), have been synthesized in good yields and X-ray characterized. The presence of the hexyl chains and the fluorine atoms causes the formation of interesting 3D architectures in the solid state. Their structures have been further characterized by infrared spectra (IR) and elemental analyses. In addition, DFT-D3 calculations are used to study interesting noncovalent interactions observed in the solid state, like fluorine-fluorine, fluorine-π and hydrophobic interactions.

  13. Higher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAs

    KAUST Repository

    Chawla, Mohit

    2013-10-10

    The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. 2013 The Author(s).

  14. Effects of protonation and C5 methylation on the electrophilic addition reaction of cytosine: a computational study.

    Science.gov (United States)

    Jin, Lingxia; Wang, Wenliang; Hu, Daodao; Min, Suotian

    2013-01-10

    The mechanism for the effects of protonation and C5 methylation on the electrophilic addition reaction of Cyt has been explored by means of CBS-QB3 and CBS-QB3/PCM methods. In the gas phase, three paths, two protonated paths (N3 and O2 protonated paths B and C) as well as one neutral path (path A), were mainly discussed, and the calculated results indicate that the reaction of the HSO(3)(-) group with neutral Cyt is unlikely because of its high activation free energy, whereas O2-protonated path (path C) is the most likely to occur. In the aqueous phase, path B is the most feasible mechanism to account for the fact that the activation free energy of path B decreases compared with the corresponding path in the gas phase, whereas those of paths A and C increase. The main striking results are that the HSO(3)(-) group directly interacts with the C5═C6 bond rather than the N3═C4 bond and that the C5 methylation, compared with Cyt, by decreasing values of global electrophilicity index manifests that C5 methylation forms are less electrophilic power as well as by decreasing values of NPA charges on C5 site of the intermediates make the trend of addition reaction weaken, which is in agreement with the experimental observation that the rate of 5-MeCyt reaction is approximately 2 orders of magnitude slower than that of Cyt in the presence of bisulfite. Apart from cis and trans isomers, the rare third isomer where both the CH(3) and SO(3) occupy axial positions has been first found in the reactions of neutral and protonated 5-MeCyt with the HSO(3)(-) group. Furthermore, the transformation of the third isomer from the cis isomer can occur easily.

  15. Genome-wide screen of genes imprinted in sorghum endosperm, and the roles of allelic differential cytosine methylation.

    Science.gov (United States)

    Zhang, Meishan; Li, Ning; He, Wenan; Zhang, Huakun; Yang, Wei; Liu, Bao

    2016-02-01

    Imprinting is an epigenetic phenomenon referring to allele-biased expression of certain genes depending on their parent of origin. Accumulated evidence suggests that, while imprinting is a conserved mechanism across kingdoms, the identities of the imprinted genes are largely species-specific. Using deep RNA sequencing of endosperm 14 days after pollination in sorghum, 5683 genes (29.27% of the total 19 418 expressed genes) were found to harbor diagnostic single nucleotide polymorphisms between two parental lines. The analysis of parent-of-origin expression patterns in the endosperm of a pair of reciprocal F1 hybrids between the two sorghum lines led to identification of 101 genes with ≥ fivefold allelic expression difference in both hybrids, including 85 maternal expressed genes (MEGs) and 16 paternal expressed genes (PEGs). Thirty of these genes were previously identified as imprinted in endosperm of maize (Zea mays), rice (Oryza sativa) or Arabidopsis, while the remaining 71 genes are sorghum-specific imprinted genes relative to these three plant species. Allele-biased expression of virtually all of the 14 tested imprinted genes (nine MEGs and five PEGs) was validated by pyrosequencing using independent sources of RNA from various developmental stages and dissected parts of endosperm. Forty-six imprinted genes (30 MEGs and 16 PEGs) were assayed by quantitative RT-PCR, and the majority of them showed endosperm-specific or preferential expression relative to embryo and other tissues. DNA methylation analysis of the 5' upstream region and gene body for seven imprinted genes indicated that, while three of the four PEGs were associated with hypomethylation of maternal alleles, no MEG was associated with allele-differential methylation.

  16. Potent inhibitors for the deamination of cytosine arabinoside and 5-aza-2'-deoxycytidine by human cytidine deaminase.

    Science.gov (United States)

    Laliberté, J; Marquez, V E; Momparler, R L

    1992-01-01

    Deamination of the nucleoside analogues ARA-C and 5-AZA-CdR by CR deaminase results in a loss of antileukemic activity. To prevent the inactivation of these analogues, inhibitors of CR deaminase may prove to be useful agents. In the present study we investigated the effects of the deaminase inhibitors Zebularine, 5-F-Zebularine, and diazepinone riboside on the deamination of CR, ARA-C, and 5-AZA-CdR using highly purified human CR deaminase (EC 3.5.4.5). These inhibitors produced a competitive type of inhibition with each substrate, the potency of which followed the patterns diazepinone riboside greater than 5-F-Zebularine and THU greater than Zebularine. 5-AZA-CdR was more sensitive than ARA-C to the inhibition produced by these deaminase inhibitors. The inhibition constants for diazepinone riboside lay in the range of 5-15 nM, suggesting that this inhibitor could be an excellent candidate for use in combination chemotherapy with either ARA-C or 5-AZA-CdR in patients with leukemia.

  17. [Quantum-chemical investigation of tautomerization ways of Watson-Crick DNA base pair guanine-cytosine].

    Science.gov (United States)

    Brovarets', O O; Hovorun, D M

    2010-01-01

    A novel physico-chemical mechanism of the Watson-Crick DNA base pair Gua.Cyt tautomerization Gua.Cyt*Gua.CytGua*.Cyt (mutagenic tautomers of bases are marked by asterisks) have been revealed and realized in a pathway of single proton transfer through two mutual isoenergetic transition states with Gibbs free energy of activation 30.4 and 30.6 kcal/mol and they are ion pairs stabilized by three (N2H...N3, N1H...N4- and O6+H...N4-) and five (N2H...O2, N1H...O2, N1H...N3, O6+H...N4- and 06+H...N4-) H-bonds accordingly. Stable base pairs Gua-Cyt* and Gua*.Cyt which dissociate comparably easy into monomers have acceptable relative Gibbs energies--12.9 and 14.3 kcal/mol--for the explanation of the nature of the spontaneous transitions of DNA replication. Results are obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-31 1++G(d,p) level of theory in vacuum approach.

  18. Synthesis of cis-(±)-2-Hydroxymethyl-5-(Cytosine-1'-yl)- 1,3-Oxathiolane (BCH-189)

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The target compound BCH-189 was synthesized with high yield via four steps from benzoyloxy acetylaldehyde and p-dithiane-2,5-diol as starting materials. The synthetic route is preferable to what literature reported.

  19. Chilling- and Freezing-Induced Alterations in Cytosine Methylation and Its Association with the Cold Tolerance of an Alpine Subnival Plant, Chorispora bungeana.

    Directory of Open Access Journals (Sweden)

    Yuan Song

    Full Text Available Chilling (0-18°C and freezing (<0°C are two distinct types of cold stresses. Epigenetic regulation can play an important role in plant adaptation to abiotic stresses. However, it is not yet clear whether and how epigenetic modification (i.e., DNA methylation mediates the adaptation to cold stresses in nature (e.g., in alpine regions. Especially, whether the adaptation to chilling and freezing is involved in differential epigenetic regulations in plants is largely unknown. Chorispora bungeana is an alpine subnival plant that is distributed in the freeze-thaw tundra in Asia, where chilling and freezing frequently fluctuate daily (24 h. To disentangle how C. bungeana copes with these intricate cold stresses through epigenetic modifications, plants of C. bungeana were treated at 4°C (chilling and -4°C (freezing over five periods of time (0-24 h. Methylation-sensitive amplified fragment-length polymorphism markers were used to investigate the variation in DNA methylation of C. bungeana in response to chilling and freezing. It was found that the alterations in DNA methylation of C. bungeana largely occurred over the period of chilling and freezing. Moreover, chilling and freezing appeared to gradually induce distinct DNA methylation variations, as the treatment went on (e.g., after 12 h. Forty-three cold-induced polymorphic fragments were randomly selected and further analyzed, and three of the cloned fragments were homologous to genes encoding alcohol dehydrogenase, UDP-glucosyltransferase and polygalacturonase-inhibiting protein. These candidate genes verified the existence of different expressive patterns between chilling and freezing. Our results showed that C. bungeana responded to cold stresses rapidly through the alterations of DNA methylation, and that chilling and freezing induced different DNA methylation changes. Therefore, we conclude that epigenetic modifications can potentially serve as a rapid and flexible mechanism for C. bungeana to adapt to the intricate cold stresses in the alpine areas.

  20. Beneficial response of cervical dystonia spasmodic torticollis to cidofovir, an acyclic phosphonate analog (s-1-3-hydroxy-2- phosphonylmethoxypropyl of cytosine

    Directory of Open Access Journals (Sweden)

    Lerner AM

    2014-09-01

    Full Text Available A Martin Lerner,1 Safedin Beqaj21Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA; 2Pathology Inc., Torrance, CA, USAAbstract: We report the case of a 23-year-old healthy man who had sudden onset of cervical dystonia spasmodic torticollis in October 2012. He was treated with intravenous cidofovir, which was started on February 20, 2013, followed by oral valganciclovir and famciclovir. Pulling of the neck and tilt of the head far to the left is no longer present (as at April 22, 2014. Human herpesvirus 6 total antibody titers fell from 11.27 (negative <1 on January 15, 2013 to 1.89 on August 5, 2013. To our knowledge, this is the first case of improvement in cervical dystonia spasmodic torticollis with treatment.Keywords: cidofovir, spasmodic torticollis, cervical dystonia

  1. The synergistic risk effect of apolipoprotein ε4 and DNA (cytosine-5-)-methyltransferase 3 beta (DNMT3B) haplotype for Alzheimer's disease.

    Science.gov (United States)

    de Bem, Cíntia Monique Boschmann Ens; Pezzi, Julio Carlos; Borba, Ericksen Mielle; Chaves, Marcia Lorena Fagundes; de Andrade, Fabiana Michelsen; Fiegenbaum, Marilu; Camozzato, Analuiza

    2016-07-01

    Alzheimer's disease (AD) is a complex and multifactorial disease with the contribution of several genes and polymorphisms to its development. Among these genes, the APOEε4 is the best known risk factor for AD. Methylation is associated with APOE expression and AD development. Recently, we found an association of the TGG haplotype in the DNMT3B gene, one of the catalyst enzyme for methylation, with AD. Therefore, the objective of the study was to investigate whether APOEε4 and TGG haplotype have an synergistic effect on AD. The sample was composed of 212 Caucasian individuals (108 healthy controls and 104 with AD by NINCDS-ADRDA and DSM-IV-TR criteria) from southern Brazil. The genetic analyses were performed by real time PCR for TaqMan(®) assay. Multivariate logistic regression was performed categorizing groups according to presence of APOEε4 and/or TGG haplotype as an independent variable for outcome AD. The presence of TGG haplotype plus the allele APOEε4 were strongly associated with AD [OR 11.13; 95 % CI (4.25-29.16); P DNMT3B gene with the APOEε4 in this sample of AD patients. The presence of TGG haplotype and APOEε4 significantly increased the risk of developing the disease, showing an synergistic effect.

  2. Highly efficient generation of glutamatergic/cholinergic NT2-derived postmitotic human neurons by short-term treatment with the nucleoside analogue cytosine β-d-arabinofuranoside

    Directory of Open Access Journals (Sweden)

    Imanol González-Burguera

    2016-03-01

    Taken together, our results further reinforce the notion NT2 cells are a versatile source of neuronal phenotypes and provide a new encouraging platform for studying mechanisms of neuronal differentiation and for exploring neuronal replacement strategies.

  3. Relapse in childhood acute lymphoblastic leukemia after elective cessation of initial treatment: failure of subsequent treatment with cyclophosphamide, cytosine arabinoside, vincristine and prednisone (COAP).

    Science.gov (United States)

    Sallan, S E; Hitchcock-Bryan, S

    1981-01-01

    Although the majority of children with acute lymphoblastic leukemia (ALL) can electively stop treatment after 2 1/2-5 years of continuous disease-free remission, 20-25% of those patients relapse after discontinuation of therapy. We treated 15 patients whose disease recurred after stopping treatment. Fourteen of them attained complete remission, but the median duration of disease-free survival was only 11 months. In this population, the site of initial relapse, bone marrow or testicle, did not influence subsequent outcome. Patients who relapsed within six months of stopping initial therapy had shorter second remissions than those who relapsed after six months. We conclude that the combination chemotherapy utilized in this study was inadequate for the control of relapsed ALL. Future programs will have to use different drug combinations or bone marrow transplantation.

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

    Science.gov (United States)

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

    2016-08-09

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

  5. 基于食醋中乙醇的δ13C 值对其真伪鉴别的应用初探%AppIication of the δ13C of EthanoI in Vinegar for Distinguishing the FaIse from the Genuine

    Institute of Scientific and Technical Information of China (English)

    李鑫; 陈小珍; 姜侃; 张东雷; 尚才人; 章舒祺

    2015-01-01

    The determination method of the δ13C of ethanol in vinegar is built by LC-IRMS;the operational process of the instruments is introduced, through the selection of chromatography column,the effect of other components (sugar,acid)on the δ13C of ethanol in vinegar is detected from the perspective of peak time.The δ13C of pure CO2 reference gas is calibrated via international standard substance-sugar and the determination accuracy and stability in the linear range are investigated.16 batches of representative samples are determined;the relationship of theδ13C among ethanol in vinegar,vinegar,vinegar sediment is analyzed.Theδ13C of ethanol in vinegar is -28‰~-31‰,it is different from others,less than theδ13C of vinegar,it is stated that the loss happens in the process of transformation ofδ13C.Use the analysis method to test theδ13C of a variety of alcohol which is common in market,the δ13C is-10‰ ~ -17‰ of industrial alcohol,corn edible alcohol, starch alcohol,theδ13C is -29.1‰±1.2‰ of rice alcohol,theδ13C is -17.6‰±1.3‰ of sorghum alcohol,only the rice alcohol intervals coincide with the δ13C of ethanol in vinegar,others can be easily distinguished,the determination of the δ13C of ethanol in vinegar can play the role in distinguishing the false from the genuine.%文章新建了液相色谱联用稳定同位素比率质谱(LC-IRMS)对食醋中乙醇δ13C 值进行测定的方法。简述了仪器的运行过程,通过对色谱柱的选择,从出峰时间的角度考察了其他组分(糖、酸)对乙醇δ13C 值测定的影响,使用蔗糖标准物质标定了高纯 CO2参考气的δ13C 值并考察了线性范围下的测定重复性。对16批次代表性样品进行测定,分析食醋、食醋沉淀物、食醋中乙醇三者间δ13C 值的关系,乙醇的δ13C 值基本在-28‰~-31‰,与其余二者的δ13C 值范围有所差别,低于食醋的δ13C 值,说明了在转化过程中发生了一部分的同位素损失;对市场上常见的多种酒精的δ13C 值使用该分析方法进行测定,发现工业酒精、玉米食用酒精、淀粉酒精δ13C 值在-10‰~-17‰,大米食用酒精在-29.1‰±1.2‰,高粱食用酒精在-17.6‰±1.3‰,其中仅有大米食用酒精的δ13C 值与食醋中乙醇的δ13C 值区间重合,其他均能轻易分辨出,通过测定食醋中乙醇的δ13C 值或可起到真伪鉴别的作用。

  6. NCBI nr-aa BLAST: CBRC-ACAR-01-0265 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-ACAR-01-0265 ref|YP_001062117.1| cytosine permease [Burkholderia pseudomallei ...668] ref|ZP_01765971.1| cytosine permease [Burkholderia pseudomallei 305] gb|ABN88339.1| cytosine permease [Burkholder...ia pseudomallei 668] gb|EBA49758.1| cytosine permease [Burkholderia pseudomallei 305] YP_001062117.1 0.008 27% ...

  7. A symphony on C : orchestrating DNA repair for gene expression via cytosine modification The 2012 IMB Conference: DNA Demethylation, Repair and Beyond Institute of Molecular Biology, Mainz, Germany, 18-21 October 2012

    NARCIS (Netherlands)

    Rots, Marianne G.; Petersen-Mahrt, Svend K.

    2013-01-01

    Headline-grabbing attention has been given to DNA demethylation pathways as new epigenetic mechanisms, with reviews and hypotheses outnumbering research papers. As candidate proteins for DNA demethylation include well-known DNA repair enzymes, it was timely to join epigenetics and DNA repair experts

  8. Analysis of DNA Cytosine Methylation under Salt Stress in Carthamus tinctorius Based on MSAP%盐胁迫下红花基因组DNA甲基化的MSAP分析

    Institute of Scientific and Technical Information of China (English)

    李慧; 彭立新; 于玮玮; 冯涛; 林木强; 阎国荣

    2011-01-01

    Analysis of DNA methylation status was carried out by MSAP (methylation-sensitive amplified polymorphism) method in Carthamus tinctorius L. After 200 mmol ? L"1 NaCl stress for 0,4,8 and 12 h, respectively. Totally, 3 140 genetic loci were produced by 13 pairs of selective primers. The results indicated that the corresponding total DNA methylation ratios were 31. 8%, 27. 1% 31. 0% and 31. 3% in the samples treated by NaCl stress for 0,4,8 and 12 h, respectively. Further analysis of the DNA methylation patterns suggested that demethylation adjustment was predominant in 4 h samples, however, the methylation level was got back to the level of CK in 8 and 12 h samples, and methylation adjustment was almost consistent with demethylation adjustment. These results indicated that the changes of DNA methylation status were closely associated with the responses of salt stress in Carthamus tinctorius L.%以红花幼苗为研究材料,经200 mmol·L-1 NaCl溶液分别处理4、8、12 h,以未经盐胁迫处理为对照(CK),对DNA甲基化变化特征进行MSAP(甲基化敏感扩增多态性)分析.选用13对选扩引物,共检测到3 140个基因位点.甲基化水平分析表明,CK,4、8、12 h处理样本中总甲基化率分别为31.8%、27.1%、31.0%和31.3%.进一步对不同处理时间红花基因组DNA甲基化模式的变化特征进行分析表明,NaCl处理4h后DNA的去甲基化模式调整占优势,而处理8h及12h后DNA甲基化水平恢复到CK水平,甲基化及去甲基化模式调整基本一致.上述结果显示,盐胁迫条件下红花基因组DNA甲基化状态发生了一定变化,并且这种变化与盐胁迫程度相关,推测DNA甲基化修饰可能参与了红花的盐胁迫应答.

  9. 胞嘧啶脱氨酶基因修饰的结肠癌细胞瘤苗抗肿瘤研究%Efficacy of antitumour colon cancer cell vaccine modified by eschrichia coli cytosine deaminase gene

    Institute of Scientific and Technical Information of China (English)

    沈历宗; 王建华; 王海权; 华一兵; 吴文溪

    2006-01-01

    目的 研究胞嘧啶脱氨酶(EC-CD)自杀基因修饰的结肠癌细胞瘤苗的抗肿瘤作用.方法 用含EC-CD基因的逆转录病毒质粒pLCDSN将人EC-CD基因转导入鼠结肠癌细胞株CT26,用G418进行筛选,得到抗性克隆CT26/CD,比较CT26/CD与野生型CT26的成瘤性,评价CT26/CD对野生型CT26细胞肝转移模型的治疗作用.结果 CT26/CD能在含0.6 g/L G418的培养液中稳定生长;RT-PCR证实EC-CD基因在CT26/CD中表达;CT26/CD细胞对5-氟胞嘧啶(5-FC)的敏感性明显增加(P=0.000),且具有良好的旁观者效应;CT26/CD的成瘤性与野生型CT26相似(P=0.892);CT26/CD联合5-FC对野生型CT26的肝转移有明显抑制作用,明显延长了荷瘤小鼠存活期(P=0.000).结论 EC-CD基因修饰的结肠癌细胞瘤苗有一定的抗肿瘤作用.

  10. Molecular and crystal structures of dialkylated adenines ( N6, N9-Me 2Ade, N3, N6-MeBnAde) and cytosines ( N1, N4-Me 2Cyt)

    Science.gov (United States)

    Krüger, Thomas; Wagner, Christoph; Bruhn, Clemens; Lis, Tadeusz; Steinborn, Dirk

    2008-11-01

    N6, N9-Dimethyladenine ( N6, N9-Me 2Ade, 1) and N1, N4-dimethylcytosine ( N1, N4-Me 2Cyt, 3) were obtained by conventional methods, whereas the reaction of N6-benzyladenine with MeI/NaOH resulted in the formation of N3, N6-MeBnAde ( 2a) and N6, N9-BnMeAde ( 2b). All compounds were fully characterized by microanalysis, NMR spectroscopy ( 1H, 13C) and 1, 2a·2MeOH and 3 also by single-crystal X-ray diffraction analyses. In single-crystals of 1, obtained from THF solutions, twofold N6-H···N7' hydrogen-bonded dimeric units ( N6, N9-Me 2Ade) 2 (AA1 2 type according to Jeffrey and Saenger, 1991) were found. This proved to be another modification than that obtained by crystallization N6, N9-Me 2Ade from MeOH/PhCl (Sternglanz, 1978). Crystals of 2a·2MeOH exhibited an analogous hydrogen bond pattern as found in 1. The shorter N6···N7' distance in 2a·2MeOH (2.932(2) Å) indicates slightly stronger hydrogen bonds than in 1 (3.078(3) Å). Crystals of 3 are built up from centrosymmetric dimers ( N1, N4-Me 2Cyt) 2 having a twofold N4-H···N3' hydrogen bond, thus exhibiting the CC3 2 hydrogen bond pattern. The hydrogen bonding patterns in the dialkylated nucleobase derivatives are discussed in terms of those found in crystals of the less substituted nucleobases N9-MeAde and Cyt/ N1-MeCyt, respectively.

  11. 野油菜黄单胞菌中胞嘧啶脱氨酶注释基因的功能鉴定%Functional characterization of annotated cytosine deaminase genes in Xanthomonas campestris

    Institute of Scientific and Technical Information of China (English)

    梁晓夏; 黄俊锭; 何勇强; 姜伯乐

    2009-01-01

    胞嘧啶脱氨酶广泛存在于细菌、真菌中,而植物缺乏胞嘧啶脱氨酶,提示胞嘧啶脱氨酶可作为病原细菌的潜在药物靶标.胞嘧啶脱氨酶催化胞嘧啶脱氨形成尿嘧啶和氨,是嘧啶补偿途径中的关键酶,对一些动物病原细菌的致病性至关重要.胞嘧啶脱氨酶催化5-氟胞嘧啶脱氨形成5-氟尿嘧啶和氮,而5-氟尿嘧啶对细菌是致命毒性的.在野油菜黄单胞菌野油菜致病变种(Xcc)8004菌株的基因组中,XC0670注释为胞嘧啶脱氨酶基因.BLAST和SMART分析发现,XC0670、XC1949和XC3413编码的蛋白都具有核苷脱氨酶结构域.本工作分别构建了XC0670、XC3413的缺失突变体,从Xcc 8004突变体库中调出XC1949 Tn5插入突变体.由于各个突变体与野生型一样在含5-氟胞嘧啶的MMX培养基上不能生长,在以胞嘧啶为唯一氮原的NNM培养基上都能生长,而含有XC0670、XC1949、XC3413组成型表达构建的大肠杆菌在含5-氟胞嘧啶的LA培养基上都能正常生长,GUS活性检测显示这3个基因都不受胞嘧啶诱导.研究结果表明这3个基因都不具有胞嘧啶脱氨酶活性.致病性试验和致病生化因子检测表明,XC0670、XC3413与Xcc致病性、胞外酶、胞外多糖无关,XC1949与Xcc致病性相关,而与胞外酶、胞外多糖无关.

  12. Antitumor Effect of Cytosine Deaminase Genetherapy in Situ Human Colon Carcinoma in Nude Mice%组织特异性CD/5-FC系统对大肠癌的原位基因治疗

    Institute of Scientific and Technical Information of China (English)

    黎成金; 马庆久; 涂小煌; 王烈; 李金茂

    2005-01-01

    目的探讨癌胚抗原(carcinoembryonic antigen,CEA)组织特异性胞嘧啶脱氨基酶基因对不同分泌CEA大肠癌组织的靶向杀伤作用.方法脂质体法将CEA组织特异性逆转录病毒载体G1CEACDNa在PA317细胞中进行包装,大肠癌细胞LoVo和SW480分别接种到BALB/c裸鼠大腿皮下,成瘤2周后,瘤内多点注射法行原位基因转染,每天腹腔注射500mg/kg的5-FC(5-fluorocytosine),观察治疗效果.结果病毒滴度为5.6×106CFU/L.经多次注射法转染,目的基因在肿瘤组织中能有效表达,治疗21天后,基因治疗组有明显的抑瘤作用,但对LoVo细胞肿瘤的抑瘤作用明显大于对SW480细胞肿瘤.结论 CEA组织特异性CD/5-FC系统对LoVo细胞肿瘤的抑瘤作用更明显.

  13. Nuffield Advanced Chemistry Courses Topic 10

    Science.gov (United States)

    Education in Science, 1975

    1975-01-01

    Presents an alternative series of investigations replacing the propanone-trichloromethane system (Topic 10) in the Nuffield A-Level course. A trichloromethane-ethyl ethanoate (acetate) system presented in four experiments give good results and removed the dangers arising from the other system. Topic 10 need not be re-written, just the replacement…

  14. Design, synthesis and evaluation of small molecule reactive oxygen species generators as selective Mycobacterium tuberculosis inhibitors.

    Science.gov (United States)

    Dharmaraja, Allimuthu T; Alvala, Mallika; Sriram, Dharmarajan; Yogeeswari, Perumal; Chakrapani, Harinath

    2012-10-25

    Here, we report 5-hydroxy-1,2,3,4,4a,9a-hexahydro-1,4-ethano-9,10-anthraquinone (13), a small molecule generating reactive oxygen species (ROS) in pH 7.4 buffer under ambient aerobic conditions that has selective and potent Mycobacterium tuberculosis growth inhibitory activity.

  15. 胡芦巴种子不同溶剂提取物及提取工艺对植物果实致病菌的抑菌作用初探

    Institute of Scientific and Technical Information of China (English)

    邵明昱; 王颖; 崔新仪; 杨晓君

    2011-01-01

    [ Objective ] The purpose of this writing is to expIore the antibacteriaI activity of the extract from the seeds of Trigonella foenum -graecum L. For pIant disease caused by bacteria and screen out the best soIvent extraction process. [ Method ] Extract was taken from seeds of Trigonella foenum - graecum L. By ethanoI, ethyI acetate and water to expIore the impact of colletrotrichum gloeosporioildes, Valsa mali and Jujube rotten bacteria by it. Result The different extracted soIvents from the seeds of Trigonella foenum -graecum L. Have antibacteriaI effects for colletrotrichum gloeosporioildes and Valsa mali and Jujube rotten bacteria, and the best antimicrobiaI effect is the extract by ethanoI. The best technics to extract the soIvent from the seeds of Trigonella foenum - graecum L. Is to use 80% ethanoI. The ratio of the IiGuid - soIid is l:l5 , at 60 ℃ for 2 h extraction. [ conclusion ] The extracted soIvents form the seeds of Trigonella foenum -graecum L. Have the bacteriostatic effect in the order Iike this ethanoI concentration > extraction time > extraction temperature > IiGuid - solid ratio.

  16. Gene : CBRC-TTRU-01-0557 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available -cytosine permease or related protein [Methylacidiphilum infernorum V4] gb|ACD84391.1| Purine-cytosine perme...ase or related protein [Methylacidiphilum infernorum V4] 0.069 27% MLGKFSTIISSNIFSVPFFLSSSSGTHVIRMLLCLMLSQRS

  17. NCBI nr-aa BLAST: CBRC-ACAR-01-0265 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-ACAR-01-0265 ref|YP_001024680.1| cytosine permease [Burkholderia mallei NCTC 1...0229] ref|YP_001079015.1| cytosine permease [Burkholderia mallei NCTC 10247] gb|ABN00085.1| cytosine permease [Burkholder...ia mallei NCTC 10229] gb|ABO02273.1| cytosine permease [Burkholderia mallei NCTC 10247] YP_001024680.1 0.008 27% ...

  18. Influence of short-term fixation with mixed formalin or ethanol solution on the mechanical properties of human cortical bone

    OpenAIRE

    Mick E.; Steinke H.; Wolfskämpf T.; Wieding J.; Hammer N.; Schulze M.; Souffrant R.; Bader R.

    2015-01-01

    Bone specimens obtained for biomechanical experiments are fresh-frozen for storage to slow down tissue degradation and autolysis in long-term storage. Alternatively, due to infectious risks related to the fresh tissues, fixative agents are commonly used. However, fixatives will likely change the mechanical properties of bone. Existing studies on this issue gave controversial results that are hardly comparable due to a variety of measurement approaches. For this reason, the influence of ethano...

  19. 21 CFR 184.1005 - Acetic acid.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Acetic acid. 184.1005 Section 184.1005 Food and... Substances Affirmed as GRAS § 184.1005 Acetic acid. (a) Acetic acid (C2H4O2, CAS Reg. No. 64-19-7) is known as ethanoic acid. It occurs naturally in plant and animal tissues. It is produced by fermentation...

  20. Healing, Antioxidant and Cytoprotective Properties of Indigofera truxillensis in Different Models of Gastric Ulcer in Rats

    OpenAIRE

    2012-01-01

    The present study evaluated the antiulcerogenic activity and mechanisms of the aqueous (AqF 100 mg/kg) and ethyl acetate (AcF 50 mg/kg) fractions from Indigofera truxillensis leaves. This dose was selected to assess its activity on ulcer healing and its action on gastric acid and mucus secretion, prostaglandin production and antioxidant enzyme activity (superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and glutathione reductase (GSH-Rd)). Gastric ulcer was induced by absolute ethano...

  1. Anti Bacterial and Anti Inflammatory efficacy of Zingiber officinale and Decalepis hamiltonii ? In Vitro Study

    OpenAIRE

    Arun kumar M; Tejaswi B; Susila V Anand

    2014-01-01

    Aim: To evaluate the in vitro anti bacterial and anti inflammatory potential of Zingiber Officinale and Decalepis Hamiltonii against E. faecalis. Materials and Methods: Ethanolic extract of Zingiber and Decalepis was subjected to microbiological assay to determine its Maximum zone of inhibition using Agar disk diffusion test, minimum inhibitory concentration using serial broth dilution method and anti inflammatory potential using protein denaturation assay against E. faecalis. Results: Ethano...

  2. Endogenous bufadienolide mediates pressor response to ethanol withdrawal in rats

    OpenAIRE

    Kashkin, Vladimir A.; Zvartau, Edwin E.; Fedorova, Olga V.; Bagrov, Yakov Y.; Lakatta, Edward G.; Bagrov, Alexei Y.

    2007-01-01

    An endogenous natriuretic and vasoconstrictor Na/K-ATPase inhibitor, marinobufagenin (MBG), is implicated in NaCl-induced hypertension and in ethanol addiction. In rats, MBG suppresses voluntary alcohol intake, while immunization against MBG induces alcohol-seeking behavior. Since alcohol withdrawal is associated with elevation of blood pressure (BP) and renal sodium retention, we hypothesized that MBG mediates pressor response to ethanol withdrawal. In male Sprague-Dawley rats, forced ethano...

  3. 脊髓小脑共济失调1型中等重复动态突变患者临床表型分析%Clinical analysis on the cases with intermediate Cytosine-Adenine-Guanine repeat alleles of spinocerebellar ataxia type 1

    Institute of Scientific and Technical Information of China (English)

    顾卫红; 郝莹; 王晓工; 王康; 杜皓萍; 杨斯柳; 王国相

    2008-01-01

    目的:探讨脊髓小脑共济失调1型(SCA1)中等重复动态突变患者临床表型特征.方法:采用基于CEQ8000核酸分析仪的片段分析方法对2个表型为常染色体显性遗传脊髓小脑共济失调家系进行SCA1基因CAG重复序列突变检测,并分析其临床特征.结果:所研究家系的先证者为SCA1基因CAG中等重复序列等位基因携带者,其临床表型存在共性和一定的差异.结论:本研究证实了SCA1基因CAG中等重复序列的致病性,且在不同的家系患者存在临床变异.

  4. 大梅组合中亲子代甲基化差异及其与生产性状的关系%Differences of Cytosine Methylation in Parental Lines and Hybrid F1 of Large White × Meishan and Their Effects on F1 Performance

    Institute of Scientific and Technical Information of China (English)

    蒋曹德; 邓昌彦; 熊远著

    2005-01-01

    In order to probe the effect of methylation on heterosis, methylation-sensitive AP-PCR technique was adopted to amplify pig genome DNA with 40 single arbitrary primers. The material involved parental lines and hybrid F1 of Large White × Meishan.Nineteen cdifferentially methylated sites with Rsa Ⅰ +Hpa Ⅱ digestion and 14 differentially methylated sites with Rsa Ⅰ +Msp Ⅰ digestion between parental lines and the hybrid were found. All fragments detected in this study were grouped into four classes: (1) the same level of methylation in both parental lines and the hybrid; (2) the same level of methylation in one parent and the hybrid; (3) an increased level of methylation in the hybrid compared to the parents, and (4) a decreased level of methylation in the hybrid. Five sites had significant effects on 7 traits (P <0.05). Sequence analysis showed that three sequences had their match in GenBank with high identity (greater than 87%) and two sequences had no match in the database. G.C percent of three sequences was over 50, and observed/expected CpG of all sequences was above 0.6. Furthermore, one sequences contained G/C boxes. This study has demonstrated that sites in CpG islands within a gene promoter region were differentially methylated in the hybrid compared to parental lines; methylated sites exerted differentially on F1 performance, showing heterosis could benefit from expression or repression of some genes.%为了探讨DNA甲基化对杂种优势的影响,采用了甲基化敏感随机扩增PCR技术(methylation-sensitiveAP-PCR,MS-AP-PCR),利用40条随机引物对大梅组合亲子代基因组DNA进行了扩增.结果:在RsaⅠ+HpaⅡ酶切扩增片段中,有19个位点在亲子代出现差异;在RsaⅠ+HpaⅡ酶切扩增片段中,有14个位点在亲子代出现差异.亲子代间甲基化状况可归纳为4种类型:(1)亲子代甲基化水平相同;(2)单亲与F1代甲基化水平相同;(3)同亲代相比,F1代发生甲基化;(4)同亲代相比,F1代去甲基化.5个甲基化变化位点对7个生产性状产生显著的影响(P<0.05).通过对生产性状产生显著影响的片段序列分析发现,这些序列在GenBank中有同源序列(同源性高于87%);3个片段G+C%大于50;所有片段CpG岛观测值/期望值都大于0.6;而且,有一个片段含有G/C盒.表明:基因启动子区域CpG岛甲基化在亲子代出现差异;不同甲基化位点对杂种生产性状的作用方向不同,说明杂种优势的表现既与有些基因的表达有关,也与有些基因的表达抑制有关.

  5. 癌胚抗原启动子驱动双自杀基因对裸鼠大肠癌移植瘤的作用%Cytosine deaminase and thymidine kinase double suicide gene system driven by carcinoembryonic antigen promoter for the treatment of colorectal carcinoma xenograft in nude mice

    Institute of Scientific and Technical Information of China (English)

    黄正接; 冯庆钊; 尤俊; 许林; 罗维远; 易文城; 曾岳岳; 罗琪

    2013-01-01

    Objective To explore the therapeutic efficacy of double suicide gene system driven by carcinoembryonic antigen (CEA) promoter (Cp-CDglyTK) on colorectal carcinoma xenograft in nude mice.Methods The plasmid pcDNA3.1 (-) Cp-CDglyTK was transfected into the CEA-positive SW480 and CEA-negative HeLa cells respectively.The expression of suicide gene was detected by RT-PCR.And the transfected cells were treated with 5-fluorocytosine (5-FC) and ganciclovir (GCV) at different concentrations and the cell-killing and bystander effects assayed by methyl thiazolyl tetrazolium (MTT).By a transplantation of cultivated cells,SW480 or HeLa cell lines were injected subcutaneously into right axillary of nude mice to establish 96 SW480 and 72 HeLa tumor animal models.Nude mice were completely randomized with statistical software according to tumor volume.For prodrug therapy,48 SW480-bearing mice were divided equally into 4 groups of Ⅰ-Ⅳ.At the same time,48 HeLa-bearing mice were divided equally into 4 groups of Ⅴ-Ⅷ.Groups Ⅰ & Ⅴreceived an intratumoral injection of PBS,groups Ⅱ & ⅥGCV and 5-FC intratumorally,groups Ⅲ & Ⅶ PBS intraperitoneally and groups Ⅳ & Ⅷ GCV and 5-FC intraperitoneally.Forty-eight SW480-bearing mice were divided equally into 4 groups of Ⅸ ~ Ⅻ and 24 Hela-bearing ones into groups of ⅩⅢ & ⅩⅣ in therapy experiment by suicide gene plus prodrug.Six groups received an intratumoral injection of liposome Lipofectamine (R) and plasmid CP-CDglyTK and then an intraperitoneal injection of drug.The groups of Ⅸ and ⅩⅢ received an injection of PBS,group Ⅹ GCV,group Ⅺ 5-FC and groups Ⅻ & ⅩⅣ GCV and 5-FC.The observation parameters included tumor bulk,tumor weight,survival time and treatment effect in each group.Results SW480 cells transfected by plasmid pcDNA3.1 (-) Cp-CDglyTK expressed CDglyTK gene.The inhibition rates of GCV and 5-FC were significantly higher than those of HeLa cells (59.87% ± 0.21% vs 9.90% ± 0.09%,P < 0.01).And higher inhibition rates and stronger bystander effect existed in double versus single produg (all P < 0.05).Tumor size,final tumor weight and survival time of nude mice in groups of Ⅱ,Ⅳ,Ⅵ & ⅤⅢ had no significant difference with groups of Ⅰ,Ⅲ,Ⅴ & Ⅶ (all P < 0.05).Final tumor size and weight of group Ⅻ was significantly smaller than those of groups of Ⅸ,Ⅹ and Ⅺ ((150.0 ± 3.2) vs (522.5 ± 1.9) and (256.8 ± 10.4) and (260.7 ± 2.2)mm3,(54.1 ± 10.4) vs (682.0 ± 12.O) and (251.8 ± 15.1) and (271.6 ± 17.7) mg,all P < 0.05).Meanwhile,the tumor inhibition rate and survival time of group Ⅻ (92.1% and (25.7 ±0.8)d)were significant higher and longer than group Ⅹ (63.1% and (21.8 ± 0.5)d)and group Ⅺ(60.2% and (18.0 ±0.9)d) (all P <0.05).However,no significant difference existed in tumor size,final tumor weight and survival time between groups ⅩⅢ and ⅩⅣ (all P > 0.05).The inhibition rate of group ⅩⅣ was merely 0.9%.Conclusion CDglyTK double suicide gene system driven by CEA promoter may inhibit CEA positive colorectal cancer xenograft in prodrug-treated nude mice.%目的 探讨癌胚抗原启动子(Cp)驱动的双自杀基因系统Cp-CDglyTK对裸鼠大肠癌移植瘤的治疗作用.方法 pcDNA3.1(-)Cp-CDglyTK质粒转染癌胚抗原阳性的SW480细胞和癌胚抗原阴性的HeLa细胞,反转录PCR检测目的基因的表达;给予不同浓度的前体药物5氟胞嘧啶(5-FC)及更昔洛韦(GCV)处理,用四甲基偶氮唑盐(MTT)法评估杀伤效应和旁观者效应.96只裸鼠在右侧腋窝皮下移植SW480细胞,72只移植HeLa细胞,建立大肠癌移植瘤模型.前体药物治疗实验中,取SW480和HeLa移植瘤裸鼠各48只,各分4组(Ⅰ~Ⅳ,Ⅴ~Ⅷ组,n=12),分别瘤体注射磷酸盐缓冲液(PBS)、GCV联合5-FC,腹腔注射PBS、GCV联合5-FC.自杀基因联合前体药物治疗实验中,余下48只SW480移植瘤裸鼠分为Ⅸ~Ⅻ组(n=12),24只HeLa移植瘤裸鼠分为ⅩⅢ~ⅩⅣ组(n=12),均经瘤体注射脂质体Lipofectamine(R)和质粒Cp-CDglyTK,再由腹腔注射药物(Ⅸ组:PBS,Ⅹ组GCV,Ⅺ组:5-FC,Ⅻ组:GCV联合5-FC,Ⅻ组:PBS,ⅩⅣ组:GCV联合5-FC).记录肿瘤体积、最终肿瘤重量和生存时间,比较分析各组裸鼠的治疗效果.结果 转染质粒的SW480细胞有CDglyTK基因的表达,GCV联合5-FC对转染质粒的SW480细胞的抑制率(59.87%±0.21%)明显高于HeLa细胞(9.90%±0.09%,P<0.01),GCV与5-FC联合用药对转染质粒的SW480细胞的生长抑制率和旁观者效应大于单一使用GCV或5-FC(均P<0.05).Ⅱ、Ⅳ、Ⅵ、Ⅷ组分别与对照组Ⅰ、Ⅲ、Ⅴ、Ⅶ组比较,肿瘤体积、最终瘤重和生存期差异均无统计学意义(均P >0.05).Ⅻ组最终肿瘤体积和最终瘤重均小于Ⅸ组、Ⅹ组和Ⅺ组[(150.0±3.2)比(522.5±1.9)、(256.8±10.4)和(260.7±2.2)mm3,(54.1±10.4)比(682.0±12.0)、(251.8±15.1)和(271.6±17.7) mg,均P<0.05];Ⅻ组的肿瘤生长抑制率和生存时间大于Ⅹ组和Ⅺ组[92.1%比63.1%、60.2%,(25.7±0.8)比(21.8±0.5)、(18.0±0.9)d,均P<0.05].ⅩⅣ和ⅩⅢ组肿瘤体积、最终瘤重和生存时间差异均无统计学意义(均P>0.05),ⅩⅣ组的肿瘤生长抑制率仅为0.9%.结论 Cp-CDglyTK在荷瘤裸鼠体内通过脂质体的介导,能靶向作用于癌胚抗原阳性的大肠癌细胞,并通过前体药物显著抑制裸鼠大肠癌移植瘤.

  6. 原位基因治疗联合前药热化疗治疗结肠癌肝转移的实验研究%Anti-tumor effect of cytosine deaminase genetherapy in situ combined with thermochemotherapy for colon cancer liver metastasis in nude mice

    Institute of Scientific and Technical Information of China (English)

    邹忠东; 张宝明; 黎成金; 王烈; 涂小煌

    2009-01-01

    目的:探讨胞嘧啶睨氨酶(CD)基因联合5-氟胞嘧啶(5-FC)热化疗对裸鼠结肠癌肝转移的治疗效果.方法:30只BALB/c裸鼠经门静脉注射人结肠癌Lovo细胞建立结肠癌肝转移模型,随机分为转基因组和非转基因组,每组15只.转基因组:经腹腔注射病毒上清(0.2 mL/d,共5d)进行原位基因转染;非转基因组经蝮腔注射生理盐水(0.2 mL/d,共5d),2组同时腹腔注射42℃500 mg·kg-1·d-1)5-FC.治疗21 d后将动物处死,观察肝脏转移率和转移结节数,PCR法检测目的基因在肿瘤组织的整合,RT-PCR法检测目的基因在肿瘤组织的表达,观察肿瘤病理学变化.结果:目的基因成功转染并在肿瘤组织中有效表达.转基因组与非转移基因组肝脏转移率分别为26.7%(4/15)、100.O%(15/15),2组比较差异有统计学意义(P<0.05),肝脏转移结节数分别为0.60±0.83、2.40±0.99(P<0.001).镜下转基因组肝内转移癌细胞变性,染色体消失,可见凋亡小体,而非转基因组未见明显变化.结论:原位基因治疗联合前药热化疗对裸鼠结肠癌肝转移有明显抑制作用.

  7. The models of proton assisted and the unassisted formation of CGC base triplets.

    Science.gov (United States)

    Medhi, Chitrani

    2002-01-01

    The triple helix is formed by combining a double and a single strand DNAs in low pH and dissociates in high pH. Under such conditions, protonation of cytosine in the single strand is necessary for triplex formation where cytosine-guanine-cytosine (CGC+) base triplet stabilizes the triple helix. The mechanism of CGC+ triplet formation from guanine-cytosine (GC) and a protonated cytosine (C+) shows the importance of N3 proton. Similarly in the case of CGC (unprotonated) triplet, the donor acceptor H-bond at N3 hydrogen of the cytosine analog (C) initiates the interaction with GC. The correspondence between the two models of triplets, CGC+ and CGC, unambiguously assigned that protonation at N3 cytosine in low pH to be the first step in triplet formation, but a donor acceptor triplet (CGC) can be designed without involving a proton in the Hoogsteen H-bond. Further, the bases of cytosine analogue also show the capability of forming Watson Crick (WC) H-bonds with guanine.

  8. Arabidopsis CDS blastp result: AK106879 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK106879 002-118-E09 At5g03555.1 permease, cytosine/purines, uracil, thiamine, allan...toin family protein contains Pfam PF02133: permease, cytosine/purines, uracil, thiamine, allantoin family 1e-161 ...

  9. NCBI nr-aa BLAST: CBRC-TTRU-01-1135 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-1135 ref|YP_001940988.1| Purine-cytosine permease or related protein [Methylacidiphilum inferno...rum V4] gb|ACD84391.1| Purine-cytosine permease or related protein [Methylacidiphilum infernorum V4] YP_001940988.1 0.031 23% ...

  10. NCBI nr-aa BLAST: CBRC-TTRU-01-0557 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-0557 ref|YP_001940988.1| Purine-cytosine permease or related protein [Methylacidiphilum inferno...rum V4] gb|ACD84391.1| Purine-cytosine permease or related protein [Methylacidiphilum infernorum V4] YP_001940988.1 0.069 27% ...

  11. Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells

    DEFF Research Database (Denmark)

    Rodriguez, Jairo; Vives, Laura; Jordà, Mireia

    2008-01-01

    Methylation of the cytosine is the most frequent epigenetic modification of DNA in mammalian cells. In humans, most of the methylated cytosines are found in CpG-rich sequences within tandem and interspersed repeats that make up to 45% of the human genome, being Alu repeats the most common family....

  12. Boron Nitride sheet as a novel surface for medical adsorption and drug synthesis

    OpenAIRE

    M. Zawari

    2015-01-01

    In this study we investigate Adenine, Guanine, Cytosine and Thymine moleculesadsorption on Boron Nitride by Density-functional theory (DFT). For this purpose we calculate adsorption energy (∆Ead), HOMO- LUMO energy gap(∆Eg), voltage difference (∆V) and (∆q) of Adenine, Guanine, Cytosine and Thymine molecules on different adsorption distances on Boron Nitride layer and compare them.

  13. Effects of TET2 mutations on DNA methylation in chronic myelomonocytic leukemia

    Science.gov (United States)

    TET2 enzymatically converts 5-methyl-cytosine to 5-hydroxymethyl-cytosine, possibly leading to loss of DNA methylation. TET2 mutations are common in myeloid leukemia and were proposed to contribute to leukemogenesis through DNA methylation. To expand on this concept, we studied chronic myelomonocyti...

  14. Crystal structure of intercalated four-stranded d(C3T) at 1.4 angstroms resolution

    Science.gov (United States)

    Kang, C. H.; Berger, I.; Lockshin, C.; Ratliff, R.; Moyzis, R.; Rich, A.

    1994-01-01

    The crystal structure of d(C3T), solved at 1.4 angstroms resolution, reveals that the molecule forms a four-stranded intercalated complex. It consists of two parallel-stranded duplexes, each of which is held together by cytosine-protonated cytosine base pairs. The two duplexes are intercalated with each other and have opposite strand orientation. The molecule has a flat, lath-like appearance, and the covalently bonded cytosines have a slow right-handed twist of 17.1 degrees. However, there is considerable asymmetry. On one of the flat sides, the phosphate groups are rotated away from the center of the molecule. They are held in this orientation by bridging water molecules that bind the NH of cytosine and a phosphate group of an opposite chain. There is also considerable microheterogeneity in the structure. The cytosine hemiprotonation occurs even at pH 7 where stable crystals form.

  15. Solvolysis of the Tumor-Inhibiting Ru(III)-Complex trans-Tetrachlorobis(Indazole)Ruthenate(III)

    OpenAIRE

    Pieper, Thomas; Peti, Wolfgang; Keppler, Bernhard K.

    2000-01-01

    The ruthenium(III) complex Hlnd trans-[RuCl4,(ind)2], with two trans-standing indazole (ind) ligands bound to ruthenium via nitrogen, shows remarkable activity in different tumor models in vitro and in vivo. The solvolysis of the complex trans-[RuCl4,(ind)2]- has been investigated by means of spectroscopic techniques (UV/vis, NMR)in different solvents. We investigated the indazolium as well as the sodium salt, the latter showing improved solubility in water. In aqueous acetonitrile and ethano...

  16. Analysis of difference spectra of protonated DNA: determination of degree of protonation of nitrogen bases and the fractions of disordered nucleotide pairs.

    Science.gov (United States)

    Smol'janinova, T I; Zhidkov, V A; Sokolov, G V

    1982-01-01

    The titration curves of nitrogen bases and fractions of disordered nucleotide pairs are obtained during DNA protonation. It is shown that purine bases are the first sites of the DNA double helix protonation. The cytosine protonation is due to proton-induced conformational transition within GC pairs with the sequence proton transfer from (N-7) of guanine to (N-3) of cytosine. Within DNA with unwound regions the bases are protonated in the following order: cytosine, adenine, guanine. It is shown that GC pairs are the primary centres in which the unwinding of protonated DNAs occurs. PMID:7079177

  17. Crystal structure of a four-stranded intercalated DNA: d(C4)

    Science.gov (United States)

    Chen, L.; Cai, L.; Zhang, X.; Rich, A.

    1994-01-01

    The crystal structure of d(C4) solved at 2.3-A resolution reveals a four-stranded molecule composed of two interdigitated or intercalated duplexes. The duplexes are held together by hemiprotonated cytosine-cytosine base pairs and are parallel stranded, but the two duplexes point in opposite directions. The molecule has a slow right-handed twist of 12.4 degrees between covalently linked cytosine base pairs, and the base stacking distance is 3.1 A. This is in general agreement with the NMR studies. A biological role for DNA in this conformation is suggested.

  18. Rescue of the Orphan Enzyme Isoguanine Deaminase

    Science.gov (United States)

    Hitchcock, Daniel S.; Fedorov, Alexander A.; Fedorov, Elena V.; Dangott, Lawrence J.; Almo, Steven C.; Raushel, Frank M.

    2011-01-01

    Cytosine deaminase (CDA) from Escherichia coli was shown to catalyze the deamination of isoguanine (2-oxoadenine) to xanthine. Isoguanine is an oxidation product of adenine in DNA that is mutagenic to the cell. The isoguanine deaminase activity in E. coli was partially purified by ammonium sulfate fractionation, gel filtration and anion exchange chromatography. The active protein was identified by peptide mass fingerprint analysis as cytosine deaminase. The kinetic constants for the deamination of isoguanine at pH 7.7 are kcat = 49 s-1, Km = 72 μM, and kcat/Km = 6.7 × 105 M-1 s-1. The kinetic constant for the deamination of cytosine are kcat = 45 s-1, Km = 302 μM, and kcat/Km = 1.5 × 105 M-1 s-1. Under these reaction conditions isoguanine is the better substrate for cytosine deaminase. The three dimensional structure of CDA was determined with isoguanine in the active site. PMID:21604715

  19. Ligation Bias in Illumina Next-Generation DNA Libraries

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine; Schubert, Mikkel; Clary, Joel;

    2013-01-01

    Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products,...

  20. Next-generation sequencing offers new insights into DNA degradation

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren; Orlando, Ludovic Antoine Alexandre; Willerslev, Eske

    2012-01-01

    The processes underlying DNA degradation are central to various disciplines, including cancer research, forensics and archaeology. The sequencing of ancient DNA molecules on next-generation sequencing platforms provides direct measurements of cytosine deamination, depurination and fragmentation r...

  1. Direct Base-to-Base Transitions in ssDNA Revealed by Tip-Enhanced Raman Scattering

    CERN Document Server

    Lin, Xiu-Mei; Singh, Prabha; Siegmann, Michael; Kupfer, Stephan; Zhang, Zhenglong; Gräfe, Stefanie; Deckert, Volker

    2016-01-01

    In the present contribution, specifically designed single-stranded DNA (ssDNA) sequences composed of adenine and cytosine were used as nanometric rulers to target the maximum achievable spatial resolution of tip-enhanced Raman spectroscopy (TERS) under ambient conditions. By stepping along a strand with a TERS tip, the obtained spectra allowed for a clear spectral discrimination including conformational information of the nucleobases, and even sharp adenine-cytosine transitions were detected repeatedly with a spatial resolution below 1 nm.

  2. 5-Aza-2′-deoxycytidine Induced Growth Inhibition of Leukemia Cells through Modulating Endogenous Cholesterol Biosynthesis*

    OpenAIRE

    Zhang, Fan; Dai, Xiaoxia; Wang, Yinsheng

    2012-01-01

    5-Aza-2′-deoxycytidine (5-Aza-CdR), a nucleoside analog that can inhibit DNA cytosine methylation, possesses potent antitumorigenic activities for myeloid disorders. Although 5-Aza-CdR is known to be incorporated into DNA and inhibit DNA (cytosine-5)-methyltransferases, the precise mechanisms underlying the drug's antineoplastic activity remain unclear. Here we utilized a mass spectrometry-based quantitative proteomic method to analyze the 5-Aza-CdR-induced perturbation of protein expression ...

  3. Genetic variations in the human cannabinoid receptor gene are associated with happiness.

    Directory of Open Access Journals (Sweden)

    Masahiro Matsunaga

    Full Text Available Happiness has been viewed as a temporary emotional state (e.g., pleasure and a relatively stable state of being happy (subjective happiness level. As previous studies demonstrated that individuals with high subjective happiness level rated their current affective states more positively when they experience positive events, these two aspects of happiness are interrelated. According to a recent neuroimaging study, the cytosine to thymine single-nucleotide polymorphism of the human cannabinoid receptor 1 gene is associated with sensitivity to positive emotional stimuli. Thus, we hypothesized that our genetic traits, such as the human cannabinoid receptor 1 genotypes, are closely related to the two aspects of happiness. In Experiment 1, 198 healthy volunteers were used to compare the subjective happiness level between cytosine allele carriers and thymine-thymine carriers of the human cannabinoid receptor 1 gene. In Experiment 2, we used positron emission tomography with 20 healthy participants to compare the brain responses to positive emotional stimuli of cytosine allele carriers to that of thymine-thymine carriers. Compared to thymine-thymine carriers, cytosine allele carriers have a higher subjective happiness level. Regression analysis indicated that the cytosine allele is significantly associated with subjective happiness level. The positive mood after watching a positive film was significantly higher for the cytosine allele carriers compared to the thymine-thymine carriers. Positive emotion-related brain region such as the medial prefrontal cortex was significantly activated when the cytosine allele carriers watched the positive film compared to the thymine-thymine carriers. Thus, the human cannabinoid receptor 1 genotypes are closely related to two aspects of happiness. Compared to thymine-thymine carriers, the cytosine allele carriers of the human cannabinoid receptor 1 gene, who are sensitive to positive emotional stimuli, exhibited greater

  4. Genetic variations in the human cannabinoid receptor gene are associated with happiness.

    Science.gov (United States)

    Matsunaga, Masahiro; Isowa, Tokiko; Yamakawa, Kaori; Fukuyama, Seisuke; Shinoda, Jun; Yamada, Jitsuhiro; Ohira, Hideki

    2014-01-01

    Happiness has been viewed as a temporary emotional state (e.g., pleasure) and a relatively stable state of being happy (subjective happiness level). As previous studies demonstrated that individuals with high subjective happiness level rated their current affective states more positively when they experience positive events, these two aspects of happiness are interrelated. According to a recent neuroimaging study, the cytosine to thymine single-nucleotide polymorphism of the human cannabinoid receptor 1 gene is associated with sensitivity to positive emotional stimuli. Thus, we hypothesized that our genetic traits, such as the human cannabinoid receptor 1 genotypes, are closely related to the two aspects of happiness. In Experiment 1, 198 healthy volunteers were used to compare the subjective happiness level between cytosine allele carriers and thymine-thymine carriers of the human cannabinoid receptor 1 gene. In Experiment 2, we used positron emission tomography with 20 healthy participants to compare the brain responses to positive emotional stimuli of cytosine allele carriers to that of thymine-thymine carriers. Compared to thymine-thymine carriers, cytosine allele carriers have a higher subjective happiness level. Regression analysis indicated that the cytosine allele is significantly associated with subjective happiness level. The positive mood after watching a positive film was significantly higher for the cytosine allele carriers compared to the thymine-thymine carriers. Positive emotion-related brain region such as the medial prefrontal cortex was significantly activated when the cytosine allele carriers watched the positive film compared to the thymine-thymine carriers. Thus, the human cannabinoid receptor 1 genotypes are closely related to two aspects of happiness. Compared to thymine-thymine carriers, the cytosine allele carriers of the human cannabinoid receptor 1 gene, who are sensitive to positive emotional stimuli, exhibited greater magnitude

  5. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.

    OpenAIRE

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

    2004-01-01

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

  6. Boron Nitride sheet as a novel surface for medical adsorption and drug synthesis

    Directory of Open Access Journals (Sweden)

    M. Zawari

    2015-03-01

    Full Text Available In this study we investigate Adenine, Guanine, Cytosine and Thymine moleculesadsorption on Boron Nitride by Density-functional theory (DFT. For this purpose we calculate adsorption energy (∆Ead, HOMO- LUMO energy gap(∆Eg, voltage difference (∆V and (∆q of Adenine, Guanine, Cytosine and Thymine molecules on different adsorption distances on Boron Nitride layer and compare them.

  7. Endophytic fungi found in association with Bacopa monnieri as potential producers of industrial enzymes and antimicrobial bioactive compounds

    Directory of Open Access Journals (Sweden)

    Meenu Katoch

    2014-10-01

    Full Text Available This study aimed to screen the endophytic fungal species of ethano-medicinal plant Bacopa monnieri (L. Pennell for their ability to produce antimicrobial substances against Bacillus subtilis, Pseudomonas aeroginosa, Salmonella typhimurium, Escherichia coli, Klebsiella pneumonia, Staphylococcus aureus, and Candida albicans. Endophytes were also screened for their ability to produce amylase, cellulase, protease and lipase to evaluate their ecological role within the host plant. Twenty-six endophytes were isolated and seventeen were identified. All the isolated endophytes exhibited amylolytic activity. Lipolytic, cellulolytic, proteolytic activity was shown by 98, 28 and 31% isolates, respectively. Similarly, all the endophytes (100% exhibited significant antimicrobial activity against K. pneumonia, while seventeen endophytes (89.5% were active against S. aureus. Fourteen endophytes (78.9% showed significant antimicrobial activity against B. subtilis and C. albicans. Eleven (57.8%, nine (50%, four (21% endophytes were active against S. typhimurium, E. coli and P. aeruginosa, respectively.

  8. Synthesis of new opioid derivatives with a propellane skeleton and their pharmacologies: part 3, novel propellane derivatives with pentacyclic skeletons.

    Science.gov (United States)

    Fujii, Hideaki; Nakajima, Ryo; Akiyama, Junko; Yamamoto, Naoshi; Hirayama, Shigeto; Nemoto, Toru; Gouda, Hiroaki; Hirono, Shuichi; Nagase, Hiroshi

    2012-12-15

    Previously reported propellane derivative KNT-42 preferred the κ receptor and functioned as a message part in the message-address concept, but its affinity for the κ receptor was not high. To improve affinity, we synthesized five pentacyclic propellane derivatives designed for the purpose of fixing the conformation of KNT-42. The etheno- and ethano-bridged derivatives SYK-347 and SYK-393 exhibited high affinity and selectivity for the κ receptor, whereas the other derivatives did not. These results would be due to the different ranges of movement of the basic nitrogens and less basicity of the nitrogens due to the electron withdrawing effect of the introduced hydroxy or keto group. SYK-347 and SYK-393 preferring the κ receptor were expected to be useful for designing selective ligands for opioid receptor types, especially the κ receptor.

  9. Electronic structure and biological activity of chosen DDT-type insecticides studied by 35Cl-NQR.

    Science.gov (United States)

    Jadzyn, Maciej; Nogaj, Bolesław

    2009-02-01

    A correlation between the electronic structure and biological activity of chosen dichlorodiphenyltrichloroethane (DDT)-type insecticides: 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane, 1,1-dichloro-2,2-bis(4-chlorophenyl)ethane, 2,2-bis(p-chlorophenyl)-1,1-dichloroethylene, 2,2-bis(4-chlorophenyl)ethanoic acid and 4,4'-dichlorobenzophenone (used in agriculture) has been analysed on the basis of the (35)Cl-nuclear quadrupole resonance (NQR) spectroscopy. The (35)Cl-NQR resonance frequencies measured at 77 K have been correlated with the lethal dose (LD(50)) parameter that characterises the biological activity of these insecticides.

  10. Buprenorphine.

    Science.gov (United States)

    Mazurek, Jaroslaw; Hoffmann, Marcel; Fernandez Casares, Anna; Cox, Phillip D; Minardi, Mathew D

    2014-06-01

    In the crystal structure of a semi-synthetic opioid drug buprenorphine, C29H41NO4 {systematic name: (2S)-2-[(5R,6R,7R,14S)-9α-cyclo-propyl-methyl-3-hy-droxy-6-meth-oxy-4,5-ep-oxy-6,14-ethano-morphinan-7-yl]-3,3-di-methyl-butan-2-ol}, the cyclo-propyl-methyl group is disordered over two sites with an occupancy factor of 0.611 (3) for the major component. One of the hy-droxy groups is involved in intra-molecular O-H⋯O hydrogen bond. The other hy-droxy group acts as a proton donor in an inter-molecular O-H⋯O inter-action that connects mol-ecules into a zigzag chain along the b axis.

  11. The correlation of blue shift of photoluminescence and morphology of silicon nanoporous

    Science.gov (United States)

    Al-Jumaili, Batool E. B.; Talib, Zainal A.; Josephine L., Y.; Paiman, Suriati B.; Ahmed, Naser M.; Al-Jumaily, Abdulmajeed H. J.; Ramizy, Asmiet; Abdulateef, Sinan A.; Muh'd, Ibrahim B.; Mofdal, Manahil E. E.

    2016-07-01

    Porous silicon with diameters ranging from 6.41 to 7.12 nm were synthesized via electrochemical etching by varied anodization current density in ethanoic solutions containing aqueous hydrofluoric acid up to 65mA/cm2.The luminescence properties of the nanoporous at room temperature were analyzed via photoluminescence spectroscopy. Photoluminescence PL spectra exhibit a broad emission band in the range of 360-700 nm photon energy. The PL spectrum has a blue shift in varied anodization current density; the blue shift incremented as the existing of anodization although the intensity decreased. The current blue shift is owning to alteration of silicon nanocrystal structure at the superficies. The superficial morphology of the PS layers consists of unified and orderly distribution of nanocrystalline Si structures, have high porosity around (93.75%) and high thickness 39.52 µm.

  12. Selective solid phase extraction for separation and preconcentration of palladium from Gold Ore and anode slime after complexation with a N{sub 4}O{sub 2} mixed donor ligand derivative

    Energy Technology Data Exchange (ETDEWEB)

    Bulut, Volkan Numan [Macka Vocational School, Karadeniz Technical University, Macka/ Trabzon (Turkey); Tufekci, Mehmet; Duran, Celal; Kantekin, Halit [Faculty of Arts and Sciences, Department of Chemistry, Karadeniz Technical University, Trabzon (Turkey); Soylak, Mustafa [Faculty of Science, Department of Chemistry, Erciyes University, Kayseri (Turkey)

    2010-07-15

    A selective and sensitive method for the preconcentration, separation, and determination of palladium with flame atomic absorption spectrometry using 4,15-bis[(4-methylphenyl)sulfonyl]-20,21-dinitro-2,3,4,5,6,7,9,10,12,13,14,15,16,17-tetradecahydro-8,11-ethano-1,18,4,8,11,15-benzodioxa tetraaza cycloicosine (TNACIN) on XAD-2010 was developed. TNACIN-Pd(II) complex formed acidic aqueous solution (0.075-0.100 M HNO{sub 3}) was accumulated on XAD-2010 and then eluted with 1 M HCl in acetone. The effects of some analytical parameters including pH, TNACIN amount, sample volume, eluent type, and concentration, sample flow rate and matrix ions were studied for optimization of the method. Detection limit and precision were calculated for Pd(II). This method was also verified with CRM and internal standard, and satisfactory results were obtained. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  13. Structure-activity approach in the reactivation of tabun-phosphorylated human acetylcholinesterase with bispyridinium para-aldoximes.

    Science.gov (United States)

    Kovarik, Zrinka; Calić, Maja; Sinko, Goran; Bosak, Anita

    2007-06-01

    We investigated interactions of bispyridinium para-aldoximes N,N'-(propano)bis(4-hydroxyiminomethyl) pyridinium bromide (TMB-4), N,N'-(ethano)bis(4-hydroxyiminomethyl)pyridinium methanosulphonate (DMB-4), and N,N'-(methano)bis(4-hydroxyiminomethyl)pyridinium chloride (MMB-4) with human erythrocyte acetylcholinesterase phosphorylated by tabun. We analysed aldoxime conformations to determine the flexibility of aldoxime as an important feature for binding to the acetylcholinesterase active site. Tabun-inhibited human erythrocyte acetylcholinesterase was completely reactivated only by the most flexible bispyridinium aldoxime - TMB-4 with a propylene chain between two rings. Shorter linkers than propylene (methylene or ethylene) as in MMB-4 and DMB-4 did not allow appropriate orientation in the active site, and MMB-4 and DMB-4 were not efficient reactivators of tabun-phosphorylated acetylcholinesterase. Since aldoximes are also reversible inhibitors of native acetylcholinesterase, we determined dissociation constants and their protective index against acetylcholinesterase inactivation by tabun.

  14. Measurements and analysis of excess enthalpies of ester + n-alkane using the UNIFAC model

    Energy Technology Data Exchange (ETDEWEB)

    Ortega, J. (Escuela Superior de Ingenieros Industriales, Las Palmas (Spain). Catedra de Termodinamica y Fisicoquimica); Legido, J.L.; Fernandez, J.; Pias, L.; Paz Andrade, M.I. (Universidad de Santiago de Compostela (Spain). Dept. de Fisica Aplicada)

    1991-02-01

    We present new experimental data of the excess molar enthalpies at 298.15 K for eighteen different binary mixtures of nine methyl alkanoates (ethanoate to decanoate) with n-heptane and n-undecane. The results show that all the systems are endothermic, h{sup E} values increase with the length of the n-alkane and decrease with the length of the methyl ester. The data have been analysed with a version of the UNIFAC model, and the parameters corresponding to the CH{sub 2}/COOC interaction have been recalculated using a larger base of experimental data. New values for the CH{sub 2}/COO interaction parameters have been obtained. (orig.).

  15. Potential formation of three pyrimidine bases in interstellar regions

    CERN Document Server

    Majumdar, Liton; Das, Ankan; Chakrabarti, Sandip K

    2015-01-01

    Work on the chemical evolution of pre-biotic molecules remains incomplete since the major obstacle is the lack of adequate knowledge of rate coefficients of various reactions which take place in interstellar conditions. In this work, we study the possibility of forming three pyrimidine bases, namely, cytosine, uracil and thymine in interstellar regions. Our study reveals that the synthesis of uracil from cytosine and water is quite impossible under interstellar circumstances. For the synthesis of thymine, reaction between uracil and :CH2 is investigated. Since no other relevant pathways for the formation of uracil and thymine were available in the literature, we consider a large gas-grain chemical network to study the chemical evolution of cytosine in gas and ice phases. Our modeling result shows that cytosine would be produced in cold, dense interstellar conditions. However, presence of cytosine is yet to be established. We propose that a new molecule, namely, C4N3OH5 could be observable in the interstellar ...

  16. CRISPR/Cas9-mediated phage resistance is not impeded by the DNA modifications of phage T4.

    Directory of Open Access Journals (Sweden)

    Stephanie J Yaung

    Full Text Available Bacteria rely on two known DNA-level defenses against their bacteriophage predators: restriction-modification and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-CRISPR-associated (Cas systems. Certain phages have evolved countermeasures that are known to block endonucleases. For example, phage T4 not only adds hydroxymethyl groups to all of its cytosines, but also glucosylates them, a strategy that defeats almost all restriction enzymes. We sought to determine whether these DNA modifications can similarly impede CRISPR-based defenses. In a bioinformatics search, we found naturally occurring CRISPR spacers that potentially target phages known to modify their DNA. Experimentally, we show that the Cas9 nuclease from the Type II CRISPR system of Streptococcus pyogenes can overcome a variety of DNA modifications in Escherichia coli. The levels of Cas9-mediated phage resistance to bacteriophage T4 and the mutant phage T4 gt, which contains hydroxymethylated but not glucosylated cytosines, were comparable to phages with unmodified cytosines, T7 and the T4-like phage RB49. Our results demonstrate that Cas9 is not impeded by N6-methyladenine, 5-methylcytosine, 5-hydroxymethylated cytosine, or glucosylated 5-hydroxymethylated cytosine.

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

    Science.gov (United States)

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

    2013-05-01

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

  18. Gas-phase hydration thermochemistry of sodiated and potassiated nucleic acid bases.

    Science.gov (United States)

    Wincel, Henryk

    2012-09-01

    Hydration reactions of sodiated and potassiated nucleic acid bases (uracil, thymine, cytosine, and adenine) produced by electrospray have been studied in a gas phase using the pulsed ion-beam high-pressure mass spectrometer. The thermochemical properties, ΔH(o)(n), ΔS(o)(n), and ΔG(o)(n), for the hydrated systems were obtained from hydration equilibrium measurement. The structural aspects of the hydrated complexes are discussed in conjunction with available literature data. The correlation between water binding energies in the hydrated complexes and the corresponding metal ion affinities of nucleobases suggests that a significant (if not dominant) amount of the canonical structure of cytosine undergoes tautomerization during electrospray ionization, and the thermochemical values for cationized cytosine probably correspond to a mixture of tautomeric complexes.

  19. Proton transfer studies in CGC+ assembly

    Science.gov (United States)

    Żabicki, Michał; Gudowska-Nowak, Ewa; Fischer, Sighart F.

    2009-12-01

    We have designed and analyzed a molecular model of a generic triple helix DNA base structure - the cytosine-guanine-cytosine (CGC+) assembly. The complex has been investigated for the ability of a concerted proton transfer from cytosine to guanine. Ab initio calculations have been preformed using Unrestricted Hartree-Fock (UHF) method with 6-31G ∗+ basis set. In order to determine possible reaction paths, the potential map has been constructed pointing the most stable configuration for the process to occur. Based on this observation, we have estimated a transmission coefficient for the transfer and found no support for a concerted motion. The effect of fluctuations of the barrier height on the kinetics is also discussed.

  20. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways.

    Science.gov (United States)

    Äijö, Tarmo; Huang, Yun; Mannerström, Henrik; Chavez, Lukas; Tsagaratou, Ageliki; Rao, Anjana; Lähdesmäki, Harri

    2016-03-14

    We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylase-assisted bisulfite sequencing data. Lux models all cytosine modifications (C, 5mC, 5hmC, 5fC, and 5caC) simultaneously together with experimental parameters, including bisulfite conversion and oxidation efficiencies, as well as various chemical labeling and protection steps. We show that Lux improves the quantification and comparison of cytosine modification levels and that Lux can process any oxidized methylcytosine sequencing data sets to quantify all cytosine modifications. Analysis of targeted data from Tet2-knockdown embryonic stem cells and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathways and reveals 5hmC localization in putative regulatory regions.

  1. Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine.

    Science.gov (United States)

    Wang, Hua; Guan, Shengxi; Quimby, Aine; Cohen-Karni, Devora; Pradhan, Sriharsa; Wilson, Geoffrey; Roberts, Richard J; Zhu, Zhenyu; Zheng, Yu

    2011-11-01

    PvuRts1I is a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA. Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties. At the sequence level, these proteins share a few uniquely conserved features. We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine. The distances between the cleavage sites and the modified cytosine are fixed within a narrow range, with the majority being 11-13 nt away in the top strand and 9-10 nt away in the bottom strand. The recognition sites of these enzymes generally require two cytosines on opposite strand around the cleavage sites, i.e. 5'-CN(11-13)↓N(9-10)G-3'/3'-GN(9-10)↓N(11-13)C-5', with at least one cytosine being modified for efficient cleavage. As one potential application for these enzymes is to provide useful tools for selectively mapping 5hmC sites, we have compared the relative selectivity of a few PvuRts1I family members towards different forms of modified cytosines. Our results show that the inherently different relative selectivity towards modified cytosines can have practical implications for their application. By using AbaSDFI, a PvuRts1I homolog with the highest relative selectivity towards 5ghmC, to analyze rat brain DNA, we show it is feasible to map genomic 5hmC sites close to base resolution. Our study offers unique tools for determining more accurate hydroxymethylomes in mammalian cells.

  2. The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L

    Science.gov (United States)

    Kalinka, Anna; Poter, Paulina

    2017-01-01

    Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin. MSAP analysis showed that S. sylvestre was the most distinct species among the studied rye taxa; however, the results clearly indicated that these differences were not statistically significant. The total methylation level of the studied loci was very similar in all taxa and ranged from 60% in S. strictum ssp. africanum to 66% in S. cereale ssp. segetale, which confirmed the lack of significant differences in the sequence methylation pattern between the pairs of rye taxa. The level of global cytosine methylation in the DNA was not significantly associated with the content of t-heterochromatin and did not overlap with the existing taxonomic rye relationships. The highest content of 5-methylcytosine was found in S. cereale ssp. segetale (83%), while very low in S. strictum ssp. strictum (53%), which was significantly different from the methylation state of all taxa, except for S. sylvestre. The other studied taxa of rye had a similar level of methylated cytosine ranging from 66.42% (S. vavilovii) to 74.41% in (S. cereale ssp. afghanicum). The results obtained in this study are evidence that the percentage of methylated cytosine cannot be inferred solely based on the genome size or t-heterochromatin. This is a significantly more complex issue. PMID:28149679

  3. Spontaneous Oligomerization of Nucleotide Alternatives in Aqueous Solutions

    Science.gov (United States)

    Smith, Karen E.; House, Christopher H.; Dworkin, Jason P.; Callahan, Michael P.

    2017-03-01

    On early Earth, a primitive polymer that could spontaneously form from likely available precursors may have preceded both RNA and DNA as the first genetic material. Here, we report that heated aqueous solutions containing 5-hydroxymethyluracil (HMU) result in oligomers of uracil, heated solutions containing 5-hydroxymethylcytosine (HMC) result in oligomers of cytosine, and heated solutions containing both HMU and HMC result in mixed oligomers of uracil and cytosine. Oligomerization of hydroxymethylated pyrimidines, which may have been abundant on the primitive Earth, might have been important in the development of simple informational polymers.

  4. Nucleobase Derived Monolayers of Conjugated Polymers for Nucleotide Recognition

    Institute of Scientific and Technical Information of China (English)

    CHEN Jie; BERMAN Amir

    2001-01-01

    @@ Polymerizable amphiphilic diacetylene containing monomers, (10,12 pentacosadinoyic acid, PDA) with a cytosine derived headgroup were synthesized and spread on a Langmuir film balance. Various surface dilutions of the cytosine and alcohol derivatives (PDC and PDOH, respectively) were produced and UV polymerized in situ. Films were produced in water and in a solution containing the complementary base (guanosine, G). Each dilution exhibited typical features in its compression isotherm, visible spectra, and structural organization when examined by Brewster angle microscopy, polarized light microscopy and SPM.

  5. Nucleobase Derived Monolayers of Conjugated Polymers for Nucleotide Recognition

    Institute of Scientific and Technical Information of China (English)

    CHEN; Jie

    2001-01-01

    Polymerizable amphiphilic diacetylene containing monomers, (10,12 pentacosadinoyic acid, PDA) with a cytosine derived headgroup were synthesized and spread on a Langmuir film balance. Various surface dilutions of the cytosine and alcohol derivatives (PDC and PDOH, respectively) were produced and UV polymerized in situ. Films were produced in water and in a solution containing the complementary base (guanosine, G). Each dilution exhibited typical features in its compression isotherm, visible spectra, and structural organization when examined by Brewster angle microscopy, polarized light microscopy and SPM.  ……

  6. Genome-wide gene expression profiling of testicular carcinoma in situ progression into overt tumours

    DEFF Research Database (Denmark)

    Almstrup, K; Hoei-Hansen, C E; Nielsen, J E;

    2005-01-01

    The carcinoma in situ (CIS) cell is the common precursor of nearly all testicular germ cell tumours (TGCT). In a previous study, we examined the gene expression profile of CIS cells and found many features common to embryonic stem cells indicating that initiation of neoplastic transformation into...... found that both DNMT3B (DNA (cytosine-5-)-methyltransferase 3 beta) and DNMT3L (DNA (cytosine-5-)-methyltransferase 3 like) were overexpressed in the N-SEMs, indicating the epigenetic differences between N-SEMs and classical SEM....

  7. [Successful treatment of acute promyelocytic leukemia in a pregnant patient with all-trans retinoic acid and chemotherapy resulting in a safe delivery].

    Science.gov (United States)

    Itoh, Mitsuru; Takao, Sumiko; Yago, Kazuhiro; Shimada, Hideto

    2003-06-01

    A 32-year-old woman at 21 gestational weeks was admitted because of leukocytosis with DIC. She was diagnosed as having acute promyelocytic leukemia and treated with all-trans retinoic acid (70 mg/body) in combination with daunorubicin and cytosine arabinoside. She achieved complete remission, and continuously received a second treatment with daunorubicin and cytosine arabinoside. Cesarean section was performed, and a live male infant was born in the 30th week of pregnancy. The mother and baby have progressed excellently to date. In a such case, the choice of treatment and time of birth should be considered depending on the individual situation.

  8. Evidence for non-CpG methylation in mammals

    DEFF Research Database (Denmark)

    Yan, Jie; Zierath, Juleen R; Barres, Romain

    2011-01-01

    In mammals, the existence of cytosine methylation on non-CpG sequences is controversial. Here, we adapted a LuminoMetric-based Assay (LUMA) to determine global non-CpG methylation levels in rodent and human tissues. We observed that......In mammals, the existence of cytosine methylation on non-CpG sequences is controversial. Here, we adapted a LuminoMetric-based Assay (LUMA) to determine global non-CpG methylation levels in rodent and human tissues. We observed that...

  9. Methylation-Specific PCR Unraveled

    Directory of Open Access Journals (Sweden)

    Sarah Derks

    2004-01-01

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

  10. [Progress of the SUPERMAN epigenetic mutation in Arabidopsis].

    Science.gov (United States)

    Tang, Rong-Hua; Zhang, Jun-Cheng; Zhuang, Wei-Jian; Wu, Wei-Ren

    2003-09-01

    The SUPERMAN gene in Arabidopsis has its epigenetic mutants (the clark kent alleles,clk). The phenotype of clk and its genotype and methylated patterns and the epi-mutation mechanisms of SUPERMAN were summarized in the review. Heritable but unstable sup epi-alleles are associated with nearly identical patterns of excess cytosine methylation within the SUP gene and a decreased level of SUP RNA. The methylation of cytosine at CpG and CPXPG is controlled by METHYLTRANSFERASE1(MET1) and CHROMOMETHYLASE3 (CMT3) which is regulated by KRYPTONITE gene, respectively.

  11. The self assembly of thymine at Au(110)/liquid interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Molina Contreras, J.R. [Departamento de Ingenieria Electrica y Electronica, Instituto Tecnologico de Aguascalientes, Mexico (Mexico); Smith, C.I.; Bowfield, A.; Weightman, P. [Physics Department, University of Liverpool (United Kingdom); Tillner, F. [Fachbereich Physik, Universitaet Konstanz (Germany)

    2012-06-15

    We show that thymine self-assembles into an ordered structure when adsorbed at a Au(110)/liquid interface. Reflection anisotropy spectroscopy (RAS) shows that as found for cytosine and adenine the adsorbed thymine molecules are oriented essentially vertically on the Au(110) surface with the molecule aligned along one of the principal axes of the Au(110) surface. Simulations of the RA spectra to an empirical model indicates that as found for adsorbed cytosine and adenine, thymine is aligned along the [1 anti 10] direction on the Au(110) surface. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  12. Methods for detection of methyl-CpG dinucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, John J

    2013-11-26

    The invention provides methods for enriching methyl-CpG sequences from a DNA sample. The method makes use of conversion of cytosine residues to uracil under conditions in which methyl-cytosine residues are preserved. Additional methods of the invention enable to preservation of the context of me-CpG dinucleotides. The invention also provides a recombinant, full length and substantially pure McrA protein (rMcrA) for binding and isolation of DNA fragments containing the sequence 5'-C.sup.MeCpGG-3'. Methods for making and using the rMcrA protein, and derivatives thereof are provided.

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

    Science.gov (United States)

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

    2016-10-01

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

  14. Response to Comment on "Positive Selection of Tyrosine Loss in Metazoan Evolution"

    DEFF Research Database (Denmark)

    Tan, Chris Soon Heng; Schoof, Erwin; Creixell, Pau

    2011-01-01

    Su et al. claim guanine-cytosine (GC) content variation can largely explain the observed tyrosine frequency variation, independent of adaptive evolution of cell-signaling complexity. We found that GC content variation, in the absence of selection for amino acid changes, can only maximally account...

  15. Toxic Neuronal Death by Glyeraldehyde-3-Phosphate Dehydrogenase and Mitochondria

    Science.gov (United States)

    2003-08-01

    eosinophilic inclusions in MPTP-treated monkeys. Ann Neurol, 1986. 20(4): p. 449- 55. Crossman, A.R., C.E. Clarke, S. Boyce, R.G. Robertson, and M.A. Sambrook...methylpropa rgylamine prevent apoptosis in cerebella r granu le neu- rons induced by cytosine a rabinoside but not low ext racellu la r potassium. J Neu

  16. Analysis of DNA methylation in different maize tissues

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    DNA methylation plays an important role in gene expression regulation during biological development and tissue differentiation in plants. This study adopted methylation-sensitive Amplified fragment length polymorphism (AFLP) to compare the levels of DNA cytosine methylation at CCGG sites in tassel, bracteal leaf, and ear leaf from maize inbred lines, 18 White and 18 Red, respectively, and also examined specific methylation patterns of the three tissues. Significant differences in cytosine methylation level among the three tissues and the same changing tendency in two inbred lines were detected. Both MSAP (methylation sensitive amplification polymorphism) ratio and full methylation level were the highest in bracteal leaf, and the lowest in tassel. Meanwhile, different methylation levels were observed in the same tissue from the inbred lines, 18 White and 18 Red. Full methylation of internal cytosine was the dominant type in the maize genome. The differential methylation patterns in the three tissues were observed. In addition, sequencing of nine differentially methylated fragments and the subsequent blast search revealed that the cytosine methylated 5′-CCGG-3′ sequences were distributed in repeating sequences, in the coding and noncoding regions. Southern hybridization was used to verify the methylation polymorphism. These results clearly demonstrated the power of the MSAP technique for large-scale DNA methylation detection in the maize genome, and the complexity of DNA methylation change during plant growth and development. The different methylation levels may be related to specific gene expression in various tissues.

  17. Carpal and tarsal bone development is highly sensitive to three antiproliferative teratogens in mice.

    Science.gov (United States)

    Rahman, M E; Ishikawa, H; Watanabe, Y; Endo, A

    1996-01-01

    When pregnant mice were given small doses of teratogens (cytosine arabinoside, mitomycin C, or busulfan) that did not induce anomalies of any other organs, a high incidence of carpal and tarsal bone anomalies still occurred. The carpal and tarsal bones may be used as a sensitive target for teratogenicity testing.

  18. Benzo[a]pyrene decreases global and gene specific DNA methylation during zebrafish development

    Science.gov (United States)

    DNA methylation is important for gene regulation and is vulnerable to early-life exposure to environmental contaminants. We found that direct waterborne benzo[a]pyrene (BaP) exposure at 24 'g/L from 2.5 to 96 hours post fertilization (hpf) to zebrafish embryos significantly decreased global cytosine...

  19. Global and gene specific DNA methylation changes during zebrafish development

    Science.gov (United States)

    DNA methylation is dynamic through the life of an organism. In this study, we measured the global and gene specific DNA methylation changes in zebrafish at different developmental stages. We found that the methylation percentage of cytosines was 11.75 ± 0.96% in 3.3 hour post fertilization (hpf) zeb...

  20. Epigenetic editing using programmable zinc ginger proteins : inherited silencing of endogenous gene expression by targeted DNA methylation

    NARCIS (Netherlands)

    Stolzenburg, Sabine

    2014-01-01

    Cancer development is not only the result of genetic mutations but also stems from modifications in the epigenetic code leading to an aberrant expression of genes relevant for cancer. The most studied epigenetic mark is DNA methylation of cytosines in the promoters of genes, which is associated with

  1. Huntington's Disease

    Science.gov (United States)

    ... seizures. More than 30,000 Americans have HD. Huntington’s disease is caused by a mutation in the gene for a protein called huntingtin. The defect causes the cytosine, adenine, and guanine (CAG) building blocks of DNA to repeat many more ...

  2. Molecular Data for a Biochemical Model of DNA Radiation Damage: Electron Impact Ionization and Dissociative Ionization of DNA Bases and Sugar-Phosphate Backbone

    Science.gov (United States)

    Dateo, Christopher E.; Fletcher, Graham D.

    2004-01-01

    As part of the database for building up a biochemical model of DNA radiation damage, electron impact ionization cross sections of sugar-phosphate backbone and DNA bases have been calculated using the improved binary-encounter dipole (iBED) model. It is found that the total ionization cross sections of C3'- and C5'-deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3'- and C5'-deoxyribose-phospate cross sections, differing by less than 10%. Of the four DNA bases, the ionization cross section of guanine is the largest, then in decreasing order, adenine, thymine, and cytosine. The order is in accordance with the known propensity of oxidation of the bases by ionizing radiation. Dissociative ionization (DI), a process that both ionizes and dissociates a molecule, is investigated for cytosine. The DI cross section for the formation of H and (cytosine-Hl)(+), with the cytosine ion losing H at the 1 position, is also reported. The threshold of this process is calculated to be 17.1 eV. Detailed analysis of ionization products such as in DI is important to trace the sequential steps in the biochemical process of DNA damage.

  3. OXIC AND ANOXIC GROWTH OF A NEW CITROBACTER SPECIES ON AMINO-ACIDS

    NARCIS (Netherlands)

    GERRITSE, J; GOTTSCHAL, JC

    1993-01-01

    A facultatively anaerobic bacterium, strain P-88, was enriched selectively under dual limitation by glutamate and oxygen in a chemostat. The new strain is a gram-negative motile rod. The mol% guanine plus cytosine of the DNA is 51.4 +/- 0.6 mol%. The organism grows on citrate as a sole source of car

  4. Promoter CpG island hypermethylation in the development of cutaneous melanoma

    NARCIS (Netherlands)

    Gao, Linda

    2015-01-01

    Epigenetic mechanisms such as promoter methylation affect gene expression by inducing changes in organizational structure of chromatin rather than in the DNA sequence. Increased methylation of cytosine within cystosine-guanine (CpG) dinucleotides that are located at higher density in gene promoter r

  5. Efficient N-Arylation and N-Alkenylation of the Five DNA/RNANucleobases

    DEFF Research Database (Denmark)

    Jacobsen, Mikkel Fog; Knudsen, Martin M.; Gothelf, Kurt Vesterager

    2006-01-01

    -substituted pyrimidin-2(1H)-one served as both a cytosine and a uracil precursor and was N-arylated and N-alkenylated in high yields. Adenine was efficiently and selectively N-arylated and N-alkenylated at the N9 position by employing a bis-Boc-protected adenine derivative, while a bis-Boc-protected 2-amino-6...

  6. Cancer Prevention and Control Research Manpower Development

    Science.gov (United States)

    1997-10-01

    Infectious Disease Journal, Vol. 15, Issue 4: 340-344, 1996. 18. Taylor, S.C., Shacks, S.J., Zengwei, Qu, and Wiley, Paul : Type 2 Cytosine Serum Levels in...Greif F, Klausner Y, Rozin R R. A . ; depend upon not only ER content bt :also cellularity correlation between oestrogen receptors and tumor size in

  7. Enhanced H-bonding and pi-stacking in DNA: a potent duplex-stabilizing and mismatch sensing nucleobase analogue

    DEFF Research Database (Denmark)

    Lou, Chenguang; Dallmann, Andre; Marafini, Pietro;

    2014-01-01

    X-pyrene is a new nucleic acid duplex stabilizing cytosine analogue that combines enhanced pi-stacking, hydrogen bonding and electrostatic interactions to greatly increase the stability of bulged DNA duplexes and DNA/RNA hybrids. X-pyrene is highly selective for guanine as a partner and duplex...... analogue for use in a variety of biological applications....

  8. MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy

    DEFF Research Database (Denmark)

    Neupane, Manish; Clark, Allison P.; Landini, Serena;

    2016-01-01

    An unbiased genome-scale screen for unmutated genes that drive cancer growth when overexpressed identified methyl cytosine-guanine dinucleotide (CpG) binding protein 2 (MECP2) as a novel oncogene. MECP2 resides in a region of the X-chromosome that is significantly amplified across 18% of cancers,...

  9. Role of TET enzymes in DNA methylation, development, and cancer

    DEFF Research Database (Denmark)

    Rasmussen, Kasper Dindler; Helin, Kristian

    2016-01-01

    The pattern of DNA methylation at cytosine bases in the genome is tightly linked to gene expression, and DNA methylation abnormalities are often observed in diseases. The ten eleven translocation (TET) enzymes oxidize 5-methylcytosines (5mCs) and promote locus-specific reversal of DNA methylation...

  10. Deciphering the biology of Mycobacterium tuberculosis from thecomplete genome sequence

    DEFF Research Database (Denmark)

    Cole, S.T.; Krogh, Anders Stærmose

    1998-01-01

    of the biology of this slow-growing pathogen and to help the conception of new prophylactic and therapeutic interventions. The genome comprises 4,411,529 base pairs, contains around 4,000 genes, and has a very high guanine + cytosine content that is reflected in the biased amino-acid content of the proteins. M...

  11. Microenvironmental Regulation of Biomacromolecular Therapies

    Science.gov (United States)

    2007-06-01

    Expert Opin. Biol. Ther. 4, 65–73 (2004). 23. Theys, J. et al. Specific targeting of cytosine deaminase to solid tumors by engineered Clostridium ... transgene expression of plasmid delivered by cationic liposomes. Biochim. Biophys. Acta 1445, 53–64 (1999). 110. Hanenberg, H. et al. Colocalization of

  12. BSMAP: whole genome bisulfite sequence MAPping program

    Directory of Open Access Journals (Sweden)

    Li Wei

    2009-07-01

    Full Text Available Abstract Background Bisulfite sequencing is a powerful technique to study DNA cytosine methylation. Bisulfite treatment followed by PCR amplification specifically converts unmethylated cytosines to thymine. Coupled with next generation sequencing technology, it is able to detect the methylation status of every cytosine in the genome. However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple CpG heterogeneous methylation. Results We developed an efficient bisulfite reads mapping algorithm BSMAP to address the above issues. BSMAP combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping. Compared with existing bisulfite mapping approaches, BSMAP is faster, more sensitive and more flexible. Conclusion BSMAP is the first general-purpose bisulfite mapping software. It is able to map high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage. It is freely available under GPL v3 license at http://code.google.com/p/bsmap/.

  13. Elevated APOBEC3B Correlates with Poor Outcomes for Estrogen-Receptor-Positive Breast Cancers

    NARCIS (Netherlands)

    A.M. Sieuwerts (Anieta); S. Willis (Scooter); M.J. Burns (Michael); M.P. Look (Maxime); M.E.M.-V. Gelder (Marion E. Meijer-Van); A. Schlicker (Andreas); D.A.M. Heideman (Danielle); H. Jacobs (Heinz); L. Wessels (Lodewyk); B. Leyland-Jones (Brian); K.P. Gray (Kathryn); J.A. Foekens (John); R.S. Harris (Reuben); J.W.M. Martens (John)

    2014-01-01

    textabstractRecent observations connected DNA cytosine deaminase APOBEC3B to the genetic evolution of breast cancer. We addressed whether APOBEC3B is associated with breast cancer clinical outcomes. APOBEC3B messenger RNA (mRNA) levels were related in 1,491 primary breast cancers to disease-free (DF

  14. Genomic uracil and human disease

    DEFF Research Database (Denmark)

    Hagen, Lars; Pena Diaz, Javier; Kavli, Bodil;

    2006-01-01

    , mutations resulting from uracil in DNA are prevented by error-free base excision repair. However, in B-cells uracil in DNA is also a physiological intermediate in acquired immunity. Here, activation-induced cytosine deaminase (AID) introduces template uracils that give GC to AT transition mutations...

  15. Epigenetic Vestiges of Early Developmental Adversity: Childhood Stress Exposure and DNA Methylation in Adolescence

    Science.gov (United States)

    Essex, Marilyn J.; Boyce, W. Thomas; Hertzman, Clyde; Lam, Lucia L.; Armstrong, Jeffrey M.; Neumann, Sarah M. A.; Kobor, Michael S.

    2013-01-01

    Fifteen-year-old adolescents (N = 109) in a longitudinal study of child development were recruited to examine differences in DNA methylation in relation to parent reports of adversity during the adolescents' infancy and preschool periods. Microarray technology applied to 28,000 cytosine-guanine dinucleotide sites within DNA derived from buccal…

  16. Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

    NARCIS (Netherlands)

    van der Graaf, Adriaan; Wardenaar, Renee; Neumann, Drexel A.; Taudt, Aaron; Shaw, Ruth G.; Jansen, Ritsert C.; Schmitz, Robert J.; Colome-Tatche, Maria; Johannes, Frank

    2015-01-01

    Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at

  17. Characterization of genetic miscoding lesions caused by postmortem damage

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Hansen, Anders J; Willerslev, Eske;

    2002-01-01

    The spectrum of postmortem damage in mitochondrial DNA was analyzed in a large data set of cloned sequences from ancient human specimens. The most common forms of damage observed are two complementary groups of transitions, termed "type 1" (adenine-->guanine/thymine-->cytosine) and "type 2" (cyto...

  18. Treatment of newly diagnosed acute promyelocytic leukemia (APL) : a comparison of French-Belgian-Swiss and PETHEMA results

    NARCIS (Netherlands)

    Ades, Lionel; Sanz, Miguel A.; Chevret, Sylvie; Montesinos, Pau; Chevallier, Patrice; Raffoux, Emmanuel; Vellenga, Edo; Guerci, Agnbs; Pigneux, Arnaud; Huguet, Francoise; Rayon, Consuelo; Stoppa, Anne Marie; de la Serna, Javier; Cahn, Jean-Yves; Meyer-Monard, Sandrine; Pabst, Thomas; Thomas, Xavier; de Botton, Stephane; Parody, Ricardo; Bergua, Juan; Lamy, Thierry; Vekhoff, Anne; Negri, Silvia; Ifrah, Norbert; Dombret, Herve; Ferrant, Augustin; Bron, Dominique; Degos, Laurent; Fenaux, Pierre

    2008-01-01

    All-trans retinoic acid (ATRA) plus anthracycline chemotherapy is the reference treatment of newly diagnosed acute promyelocytic leukemia (APL), whereas the role of cytosine arabinoside (AraC) remains disputed. We performed a joint analysis of patients younger than 65 years included in Programa para

  19. Physiological and biochemical contributions to the taxonomy of the genus Prototheca. II. Starch hydrolysis and base composition of DNA.

    Science.gov (United States)

    Kerfin, W; Kessler, E

    1978-01-23

    16 strains of the genus Prototheca do not produce extracellular amylolytic enzymes. The base composition of their DNA shows rather continuous values from 62% to 78% GC (guanine + cytosine). Their assignment to four species and their possible relationship with Chlorella protothecoides are discussed.

  20. TET1 is a DNA-binding protein that modulates DNA methylation and gene transcription via hydroxylation of 5-methylcytosine

    Institute of Scientific and Technical Information of China (English)

    Haikuo Zhang; Xin Zhang; Erin Clark; Michelle Mulcahey; Stephen Huang; Yujiang Geno Shi

    2010-01-01

    @@ Dear Editor, DNA methylation, which often occurs at the 5-carbon position of cytosine (5mC) located in CpG dinucleotide, is a key epigenetic hallmark and serves as a major epigenetic mechanism for establishing X-inactivation, paren tal imprinting and silencing retrotransposable elements during early embryogenesis in mammals.

  1. Rescue of TET2 Haploinsufficiency in Myelodysplastic Syndrome Patients Using Turbo Cosubstrate

    Science.gov (United States)

    2016-07-01

    protein of >90% purity in a single step (Figure 2). Since the TET2 demethylase contain cysteine-rich DNA binding domains and the structure and...different cytosine derivatives. For each parent ion nucleoside (Q1), the most intense product ion (Q3) was detected. o What opportunities for

  2. Drug: D01155 [KEGG MEDICUS

    Lifescience Database Archive (English)

    Full Text Available 0240(6240) Pyrimidine metabolism hsa00480(6240) Glutathione metabolism map07041 Antineoplastics... cellular function 42 Antineoplastics 422 Antimetabolites 4224 Cytosines D01155 Gemcitabine hydrochloride (J...807] Gemcitabine [ATC:L01BC05] D01155 Gemcitabine hydrochloride (JAN/USAN) Antineoplastics [BR:br08308] Anti

  3. Advances in DNA methylation: 5-hydroxymethylcytosine revisited

    DEFF Research Database (Denmark)

    Dahl, Christina; Grønbæk, Kirsten; Guldberg, Per

    2011-01-01

    Mammalian DNA contains two modified cytosine bases; 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Both of these have been known for decades but have received very different levels of attention in the scientific literature. 5mC has been studied extensively, and its role as an epigenet...

  4. Deciphering the four-letter code : The genetic basis of complex traits and common disease

    NARCIS (Netherlands)

    Pulit, S.L.

    2016-01-01

    Deoxyribonucleic acid (DNA) is made up of four bases: adenine (A), cytosine (C), guanine (G), and thymine (T). Assembled in a strategic fashion, these bases code for the unique genomes of all walks of life, from viruses, to rodents, to primates. The human genome, mapped completely for the first time

  5. DNA methylation of the GC box in the promoter region mediates isolation rearing-induced suppression of srd5a1 transcription in the prefrontal cortex.

    Science.gov (United States)

    Araki, Ryota; Nishida, Shoji; Hiraki, Yosuke; Matsumoto, Kinzo; Yabe, Takeshi

    2015-10-01

    The levels of allopregnanolone (ALLO), a neurosteroid, in brain and serum are related to severity of depression and anxiety. Steroid 5α-reductase type I is the rate-limiting enzyme in ALLO biosynthesis and plays an important role in control of the ALLO level in mammalian brain. In this study, we examined an epigenetic mechanism for transcriptional regulation of srd5a1, which codes for steroid 5α-reductase type I, using isolation-reared mice. The mRNA level of srd5a1 was decreased in the prefrontal cortex (PFC) in isolation-reared mice. Rearing in social isolation increased methylation of cytosines at -82 and -12 bp downstream of the transcription start site, which are located in a GC box element in the promoter region of srd5a1. Binding of Sp1, a ubiquitous transcription factor, to the GC box was decreased in the promoter region of srd5a1 in the PFC in isolation-reared mice. Site-specific methylation at cytosine -12 of a srd5a1 promoter-luciferase reporter construct, but not that of cytosine -82, downregulated the promoter activity of srd5a1. These findings suggest that transcription of srd5a1 in brain is regulated by environmental factor-induced cytosine methylation in the promoter region. This finding could contribute to development of antidepressant and anxiolytic agents.

  6. Cognition and Adaptive Skills in Myotonic Dystrophy Type 1: A Study of 55 Individuals with Congenital and Childhood Forms

    Science.gov (United States)

    Ekstrom, Anne-Berit; Hakenas-Plate, Louise; Tulinius, Mar; Wentz, Elisabet

    2009-01-01

    Aims: To investigate cognitive abilities and adaptive skills in children and adolescents with myotonic dystrophy type 1 (DM1) and correlate the findings to the cytosine-thymine-guanine (CTG) repeat expansion size. Method: Cognitive level was assessed in 55 children and adolescents with DM1 (31 males, 24 females; mean age 12y 1mo, SD 5y 1mo; range…

  7. Cardiac manifestations of myotonic dystrophy type 1

    DEFF Research Database (Denmark)

    Petri, Helle; Vissing, John; Witting, Nanna;

    2012-01-01

    To estimate the degree of cardiac involvement regarding left ventricular ejection fraction, conduction abnormalities, arrhythmia, risk of sudden cardiac death (SCD) and the associations between cardiac involvement and cytosine-thymine-guanine (CTG)-repeat, neuromuscular involvement, age and gende...... in patients with myotonic dystrophy type 1 (MD1)....

  8. A Prebiotic Chemistry Experiment on the Adsorption of Nucleic Acids Bases onto a Natural Zeolite

    Science.gov (United States)

    Anizelli, Pedro R.; Baú, João Paulo T.; Gomes, Frederico P.; da Costa, Antonio Carlos S.; Carneiro, Cristine E. A.; Zaia, Cássia Thaïs B. V.; Zaia, Dimas A. M.

    2015-09-01

    There are currently few mechanisms that can explain how nucleic acid bases were synthesized, concentrated from dilute solutions, and/or protected against degradation by UV radiation or hydrolysis on the prebiotic Earth. A natural zeolite exhibited the potential to adsorb adenine, cytosine, thymine, and uracil over a range of pH, with greater adsorption of adenine and cytosine at acidic pH. Adsorption of all nucleic acid bases was decreased in artificial seawater compared to water, likely due to cation complexation. Furthermore, adsorption of adenine appeared to protect natural zeolite from thermal degradation. The C=O groups from thymine, cytosine and uracil appeared to assist the dissolution of the mineral while the NH2 group from adenine had no effect. As shown by FT-IR spectroscopy, adenine interacted with a natural zeolite through the NH2 group, and cytosine through the C=O group. A pseudo-second-order model best described the kinetics of adenine adsorption, which occurred faster in artificial seawaters.

  9. Chromatin domains and function

    NARCIS (Netherlands)

    P. Fransz

    2009-01-01

    The inheritance of biological traits involves not only the transfer of genetic information in the form of DNA, but also epigenetic information. The latter is encrypted in a DNA component, methylation of cytosine residues, and in non-DNA components such as histone modifications, non-histone proteins,

  10. The value of fludarabine in addition to ARA-C and G-CSF in the treatment of patients with high-risk myelodysplastic syndromes and AML in elderly patients.

    NARCIS (Netherlands)

    Ossenkoppele, G.J.; Graveland, W.J.; Sonneveld, P.; Daenen, S.M.G.J.; Biesma, D.H.; Verdonck, L.F.; Schaafsma, M.R.; Westveer, P.H.; Peters, G.J.; Noordhuis, P.; Muus, P.; Selleslag, D.; Holt, B. van der; Delforge, M.; Lowenberg, B.; Verhoef, G.E.

    2004-01-01

    Fludarabine in addition to cytosine-arabinoside (ARA-C) increases the accumulation of ARA-C-5'-triphosphate (ARA-CTP), which is responsible for the cytotoxic effect in leukemic blasts. In a randomized phase 3 trial, patients with high-risk myelodysplastic syndrome (MDS) (n = 91) or elderly patients

  11. The value of fludarabine in addition to ARA-C and G-CSF in the treatment of patients with high-risk myelodysplastic syndromes and AML in elderly patients

    NARCIS (Netherlands)

    Ossenkoppele, GJ; Graveland, WJ; Sonneveld, P; Daenen, SMGJ; Biesma, DH; Verdonck, LF; Schaafsma, R; Westveer, PHM; Peters, F; Noordhuis, P; Muus, P; van der Holt, R; Delforge, M; Lowenberg, B; Verhoef, GEG

    2004-01-01

    Fludarabine in addition to cytosine-arabinoside (ARA-C) increases the accumulation of ARA-C-5'-triphosphate (ARA-CTP), which is responsible for the cytotoxic effect in leukemic blasts. In a randomized phase 3 trial, patients with high-risk myelodysplastic syndrome (MDS) (n = 91) or elderly patient's

  12. Non-canonical uracil processing in DNA gives rise to double-strand breaks and deletions

    DEFF Research Database (Denmark)

    Bregenhorn, Stephanie; Kallenberger, Lia; Artola-Borán, Mariela;

    2016-01-01

    During class switch recombination (CSR), antigen-stimulated B-cells rearrange their immunoglobulin constant heavy chain (CH) loci to generate antibodies with different effector functions. CSR is initiated by activation-induced deaminase (AID), which converts cytosines in switch (S) regions, repet...... choice in DSB repair. Given its amenability to manipulation, our system represents a powerful tool for the molecular dissection of CSR....

  13. Methods for sequencing GC-rich and CCT repeat DNA templates

    Science.gov (United States)

    Robinson, Donna L.

    2007-02-20

    The present invention is directed to a PCR-based method of cycle sequencing DNA and other polynucleotide sequences having high CG content and regions of high GC content, and includes for example DNA strands with a high Cytosine and/or Guanosine content and repeated motifs such as CCT repeats.

  14. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing.

    Directory of Open Access Journals (Sweden)

    Yun Huang

    Full Text Available BACKGROUND: We recently showed that enzymes of the TET family convert 5-mC to 5-hydroxymethylcytosine (5-hmC in DNA. 5-hmC is present at high levels in embryonic stem cells and Purkinje neurons. The methylation status of cytosines is typically assessed by reaction with sodium bisulfite followed by PCR amplification. Reaction with sodium bisulfite promotes cytosine deamination, whereas 5-methylcytosine (5-mC reacts poorly with bisulfite and is resistant to deamination. Since 5-hmC reacts with bisulfite to yield cytosine 5-methylenesulfonate (CMS, we asked how DNA containing 5-hmC behaves in bisulfite sequencing. METHODOLOGY/PRINCIPAL FINDINGS: We used synthetic oligonucleotides with different distributions of cytosine as templates for generation of DNAs containing C, 5-mC and 5-hmC. The resulting DNAs were subjected in parallel to bisulfite treatment, followed by exposure to conditions promoting cytosine deamination. The extent of conversion of 5-hmC to CMS was estimated to be 99.7%. Sequencing of PCR products showed that neither 5-mC nor 5-hmC undergo C-to-T transitions after bisulfite treatment, confirming that these two modified cytosine species are indistinguishable by the bisulfite technique. DNA in which CMS constituted a large fraction of all bases (28/201 was much less efficiently amplified than DNA in which those bases were 5-mC or uracil (the latter produced by cytosine deamination. Using a series of primer extension experiments, we traced the inefficient amplification of CMS-containing DNA to stalling of Taq polymerase at sites of CMS modification, especially when two CMS bases were either adjacent to one another or separated by 1-2 nucleotides. CONCLUSIONS: We have confirmed that the widely used bisulfite sequencing technique does not distinguish between 5-mC and 5-hmC. Moreover, we show that CMS, the product of bisulfite conversion of 5-hmC, tends to stall DNA polymerases during PCR, suggesting that densely hydroxymethylated regions

  15. Divergence of Pumilio/fem-3 mRNA binding factor (PUF) protein specificity through variations in an RNA-binding pocket.

    Science.gov (United States)

    Qiu, Chen; Kershner, Aaron; Wang, Yeming; Holley, Cynthia P; Wilinski, Daniel; Keles, Sunduz; Kimble, Judith; Wickens, Marvin; Hall, Traci M Tanaka

    2012-02-24

    mRNA control networks depend on recognition of specific RNA sequences. Pumilio-fem-3 mRNA binding factor (PUF) RNA-binding proteins achieve that specificity through variations on a conserved scaffold. Saccharomyces cerevisiae Puf3p achieves specificity through an additional binding pocket for a cytosine base upstream of the core RNA recognition site. Here we demonstrate that this chemically simple adaptation is prevalent and contributes to the diversity of RNA specificities among PUF proteins. Bioinformatics analysis shows that mRNAs associated with Caenorhabditis elegans fem-3 mRNA binding factor (FBF)-2 in vivo contain an upstream cytosine required for biological regulation. Crystal structures of FBF-2 and C. elegans PUF-6 reveal binding pockets structurally similar to that of Puf3p, whereas sequence alignments predict a pocket in PUF-11. For Puf3p, FBF-2, PUF-6, and PUF-11, the upstream pockets and a cytosine are required for maximal binding to RNA, but the quantitative impact on binding affinity varies. Furthermore, the position of the upstream cytosine relative to the core PUF recognition site can differ, which in the case of FBF-2 originally masked the identification of this consensus sequence feature. Importantly, other PUF proteins lack the pocket and so do not discriminate upstream bases. A structure-based alignment reveals that these proteins lack key residues that would contact the cytosine, and in some instances, they also present amino acid side chains that interfere with binding. Loss of the pocket requires only substitution of one serine, as appears to have occurred during the evolution of certain fungal species.

  16. Synthesis, Antibacterial and Antifungal Activity of Some New Pyrazoline and Pyrazole Derivatives

    Directory of Open Access Journals (Sweden)

    Seham Y. Hassan

    2013-02-01

    Full Text Available A series of 2-pyrazolines 5–9 have been synthesized from α,β-unsaturated ketones 2–4. New 2-pyrazoline derivatives 13–15 bearing benzenesulfonamide moieties were then synthesized by condensing the appropriate chalcones 2–4 with 4-hydrazinyl benzenesulfonamide hydrochloride. Ethyl [1,2,4] triazolo[3,4-c][1,2,4]triazino[5,6-b]-5H-indole-5-ethanoate (26 and 1-(5H-[1,2,4]triazino[5,6-b] indol-3-yl-3-methyl-1H-pyrazol-5(4H-one (32 were synthesized from 3-hydrazinyl-5H-[1,2,4]triazino[5,6-b]indole (24. On the other hand ethyl[1,2,4]triazolo[3,4-c][1,2,4]triazino[5,6-b]-5,10-dihydroquinoxaline- 5-ethanoate (27 and 1-(5,10-dihydro-[1,2,4]triazino[5,6-b]quinoxalin-3-yl-3-methyl-1H-pyrazol-5(4H-one (33 were synthesized from 3-hydrazinyl-5,10-dihydro-[1,2,4]triazino[5,6-b]quinoxaline (25 by reaction with diethyl malonate or ethyl acetoacetate, respectively. Condensation of 6,6-dimethyl-4-oxo-4,5,6,7-tetrahydro-1H-indole-2-carbaldehyde (1' with compound 24 or 25 afforded the corresponding Schiff's bases 36 and 37, respectively. Reaction of the Schiff's base 37 with benzoyl hydrazine or acetic anhydride afforded benzohydrazide derivative 39 and the cyclized compound 40, respectively. Furthermore, the pyrazole derivatives 42–44 were synthesized by cyclization of hydrazine derivative 25 with the prepared chalcones 2–4. All the newly synthesized compounds have been characterized on the basis of IR and 1H-NMR spectral data as well as physical data. Antimicrobial activity against the organisms E. coli ATCC8739 and P. aeruginosa ATCC 9027 as examples of Gram-negative bacteria, S. aureus ATCC 6583P as an example of Gram-positive bacteria and C. albicans ATCC 2091 as an example of a yeast-like fungus have been studied using the Nutrient Agar (NA and Sabouraud Dextrose Agar (SDA diffusion methods. The best performance was found for the compounds 16, 17, 19 and 20.

  17. π-Radical to σ-Radical Tautomerization in One-Electron-Oxidized 1-Methylcytosine and Its Analogs.

    Science.gov (United States)

    Adhikary, Amitava; Kumar, Anil; Bishop, Casandra T; Wiegand, Tyler J; Hindi, Ragda M; Adhikary, Ananya; Sevilla, Michael D

    2015-09-01

    In this work, iminyl σ-radical formation in several one-electron-oxidized cytosine analogs, including 1-MeC, cidofovir, 2'-deoxycytidine (dCyd), and 2'-deoxycytidine 5'-monophosphate (5'-dCMP), were investigated in homogeneous, aqueous (D2O or H2O) glassy solutions at low temperatures by employing electron spin resonance (ESR) spectroscopy. Upon employing density functional theory (DFT) (DFT/B3LYP/6-31G* method), the calculated hyperfine coupling constant (HFCC) values of iminyl σ-radical agree quite well with the experimentally observed ones, thus confirming its assignment. ESR and DFT studies show that the cytosine iminyl σ-radical is a tautomer of the deprotonated cytosine π-cation radical [cytosine π-aminyl radical, C(N4-H)(•)]. Employing 1-MeC samples at various pHs ranging from ca. 8 to 11, ESR studies show that the tautomeric equilibrium between C(N4-H)(•) and the iminyl σ-radical at low temperature is too slow to be established without added base. ESR and DFT studies agree that, in the iminyl σ-radical, the unpaired spin is localized on the exocyclic nitrogen (N4) in an in-plane pure p-orbital. This gives rise to an anisotropic nitrogen hyperfine coupling (Azz = 40 G) from N4 and a near isotropic β-nitrogen coupling of 9.7 G from the cytosine ring nitrogen at N3. Iminyl σ-radical should exist in its N3-protonated form, as the N3-protonated iminyl σ-radical is stabilized in solution by over 30 kcal/mol (ΔG = -32 kcal/mol) over its conjugate base, the N3-deprotonated form. This is the first observation of an isotropic β-hyperfine ring nitrogen coupling in an N-centered DNA radical. Our theoretical calculations predict that the cytosine iminyl σ-radical can be formed in double-stranded DNA by a radiation-induced ionization-deprotonation process that is only 10 kcal/mol above the lowest energy path.

  18. π to σ Radical Tautomerization in One-Electron Oxidized 1-Methylcytosine and its Analogs

    Science.gov (United States)

    Adhikary, Amitava; Kumar, Anil; Bishop, Casandra T.; Wiegand, Tyler J.; Hindi, Ragda M.; Adhikary, Ananya; Sevilla, Michael D.

    2015-01-01

    In this work iminyl σ-radical formation in several one-electron oxidized cytosine analogs including 1-MeC, cidofovir, 2′-deoxycytidine (dCyd), and 2′-deoxycytidine 5′-monophosphate (5′-dCMP) were investigated in homogeneous aqueous (D2O or H2O) glassy solutions at low temperatures employing electron spin resonance (ESR) spectroscopy. Employing density functional theory (DFT) (DFT/B3LYP/6-31G* method), the calculated hyperfine coupling constant (HFCC) values of iminyl σ-radical agree quite well with the experimentally observed ones thus confirming its assignment. ESR and DFT studies show that the cytosine-iminyl σ-radical is a tautomer of the deprotonated cytosine π-cation radical (cytosine π-aminyl radical, C(N4-H)•). Employing 1-MeC samples at various pHs ranging ca. 8 to ca. 11, ESR studies show that the tautomeric equilibrium between C(N4-H)• and the iminyl σ-radical at low temperature is too slow to be established without added base. ESR and DFT studies agree that in the iminyl-σ radical, the unpaired spin is localized to the exocyclic nitrogen (N4) in an in-plane pure p-orbital. This gives rise to an anisotropic nitrogen hyperfine coupling (Azz = 40 G) from N4 and a near isotropic β-nitrogen coupling of 9.7 G from the cytosine ring nitrogen at N3. Iminyl σ-radical should exist in its N3-protonated form as the N3-protonated iminyl σ-radical is stabilized in solution by over 30 kcal/mol (ΔG= −32 kcal/mol) over its conjugate base, the N3-deprotonated form. This is the first observation of an isotropic β-hyperfine ring nitrogen coupling in an N-centered DNA-radical. Our theoretical calculations predict that the cytosine iminyl σ-radical can be formed in dsDNA by a radiation-induced ionization–deprotonation process that is only 10 kcal/mol above the lowest energy path. PMID:26237072

  19. Thermodynamic study of (alkyl esters+{alpha},{omega}-alkyl dihalides) I: H{sub m}{sup E} and V{sub m}{sup E} for 25 binary mixtures {l_brace}xC{sub u-1}H{sub 2u-1}CO{sub 2}C{sub 2}H{sub 5}+(1-x){alpha},{omega}-ClCH{sub 2}(CH{sub 2}){sub v-2}CH{sub 2}C= l{r_brace}, where u=1 to 5, {alpha}=1 and v={omega}=2 to 6

    Energy Technology Data Exchange (ETDEWEB)

    Ortega, J. [Laboratorio de Termodinamica y Fisicoquimica de Fluidos, Parque Cientifico-Tecnologico, Campus Universitario Tafira, Universidad de Las Palmas de Gran Canaria, 35071-Las Palmas de Gran Canaria, Canary Islands (Spain)]. E-mail: jortega@dip.ulpgc.es; Marrero, E. [Laboratorio de Termodinamica y Fisicoquimica de Fluidos, Parque Cientifico-Tecnologico, Campus Universitario Tafira, Universidad de Las Palmas de Gran Canaria, 35071-Las Palmas de Gran Canaria, Canary Islands (Spain); Toledo, F.J. [Laboratorio de Termodinamica y Fisicoquimica de Fluidos, Parque Cientifico-Tecnologico, Campus Universitario Tafira, Universidad de Las Palmas de Gran Canaria, 35071-Las Palmas de Gran Canaria, Canary Islands (Spain); Espiau, F. [Laboratorio de Termodinamica y Fisicoquimica de Fluidos, Parque Cientifico-Tecnologico, Campus Universitario Tafira, Universidad de Las Palmas de Gran Canaria, 35071-Las Palmas de Gran Canaria, Canary Islands (Spain)

    2005-12-15

    This article presents the experimental data of H{sub m}{sup E} and V{sub m}{sup E}, obtained at atmospheric pressure and at a temperature of 298.15K, for a set of 25 binary mixtures composed of the first 5 ethyl alkanoates (methanoate to pentanoate) and five {alpha},{omega}-dichloroalkanes (1,2-dichloroethane to 1,6-dichlorohexane). Quantitatively, and with only a few exceptions, small values are obtained for the excess properties and the results imply that specific interactions exist between both types of compounds, with exothermic process for most mixtures, but with the exception of some that contain ethyl methanoate and ethanoate. The change in enthalpies with increasing length of the dichloroalkane chain for the same ester is regular, and also the change in H{sub m}{sup E} with the acid portion of the ethyl ester. However, the change in excess volumes does not present such a regular variation. A behavioural structural model is established to explain the results of the excess properties. Experimental values of H{sub m}{sup E} and V{sub m}{sup E} were correlated, as a function of ester concentration, x with a new expression which uses the so-called active fraction as a variable and which, in turn, is a function of this concentration. The application of two versions of the UNIFAC group contribution models produces no good estimations of H{sub m}{sup E}.

  20. Synthesis of Phthalyl Substituted Imidazolones and Schiff Bases as Antimicrobial Agents

    Directory of Open Access Journals (Sweden)

    Pramilla Sah

    2011-01-01

    Full Text Available A new series of phthalyl substituted imidazolones (4a–g and Schiff bases (5a–d were synthesized from 2-methyl-(m-nitro-1,3-dioxo-1,3-dihydro-(2H-isoindole-2-yl-5-amino-1,3,4-thiadiazole (3a–b. Compounds (3a–b were prepared by cyclisation of 2-(m-nitro-1,3-dioxo-1,3-dihydro-(2H-isoindole-2-ylmethyl ethanoate (2 with thiosemicarbazide. 2-(m-nitro-1,3-dioxo-1,3-dihydro-(2H-isoindole-2-ylethanoic acid (1 in presence of thionyl chloride and methanol gave the ester (2 while compound (1 was synthesized by aminolysis of phthalic anhydride with glycine. The compounds were characterized by spectral techniques of IR, 1H NMR, Mass and elemental analysis. All the synthesized compounds (4a–g and (5a–d were screened for their antibacterial activity against the pathogenic strains E. coli, P. aureus, C. freundii while antifungal activity was evaluated against A. niger, A. flavus, Penicillium sp. and C. albicans.

  1. Pharmacological properties of novel bicyclic isoquinoline analogs in isolated guinea pig atria, trachea and in human platelets: relationship to trimetoquinol.

    Science.gov (United States)

    Shams, G; Fedyna, J; Romstedt, K J; Adejare, A; Miller, D D; Roche, V F; Feller, D R

    1991-01-01

    1. Antiplatelet and beta-adrenoceptor activities of a set of secondary and tertiary N-methyl substituted amine analogs of trimetoquinol (TMQ, I and II, respectively) and 5,8-ethano-l-(p-methoxybenzyl)-1,2,3,4,5,6,7,8-octahydroisoquin oline (bicyclic isoquinoline compounds III and IV, respectively) were examined. 2. Compounds III and IV induced relaxations of guinea pig trachea which were blocked by propranolol whereas neither compound acted as an agonist nor antagonist of beta-adrenoceptors (chronotropy) in guinea pig atria. TMQ analogs (I and II) were agonists in both beta-adrenoceptor systems. 3. When tested in human platelets, compounds III and IV, like the TMQ analogs, blocked several inducers of the prostaglandin-dependent and -independent pathways, and the alpha 2-adrenoceptor-mediated pathway of platelet activation. 4. The bicyclic isoquinoline analogs (III and IV) possessed more selective beta 2-adrenoceptor stimulatory activity and equal or greater inhibitory activity against inducers of the prostaglandin-independent pathways of platelet function than the corresponding TMQ analogs (I and II). 5. These chemically novel lipophilic bicyclic compounds provide a new lead to the development of agents useful for the treatment of asthma and thrombotic disorders.

  2. Non-Destructive Assessment of Aroma Volatiles from a Climacteric Near-Isogenic Line of Melon Obtained by Headspace Stir-Bar Sorptive Extraction

    Science.gov (United States)

    Fernández-Trujillo, Juan Pablo; Dos-Santos, Noelia; Martínez-Alcaraz, Rocío; Le Bleis, Inés

    2013-01-01

    A climacteric aromatic near-isogenic line (NIL) of melon (Cucumis melo L.) SC3-5-1 contained an introgression of the non-climacteric Korean cultivar “Shongwan Charmi” accession PI 161375 (SC) in the genetic background of the non-climacteric cultivar “Piel de Sapo” (PS). The aroma production was monitored during ripening at 21 °C in intact fruit using headspace sorptive bar extraction (HSSE). Bars were composed of polydimethylsiloxane (PDMS) and aromas were desorbed and analyzed by gas-chromatography mass-spectrometry. The aromatic profile was composed of 70 aromatic compounds plus 21 alkanes with a predominance of esters, particularly acetate (2-methylbutyl acetate, 2-methylpropyl acetate, hexyl acetate, and phenylmethyl acetate). Some compounds were severely affected by postharvest time. The acetate esters (3-methylbutyl acetate, butan-2-yl acetate and phenylmethyl acetate) decreased with ripening and sulfur-derived compounds (S-methyl butanethioate and S-methyl 3-methylbutanethioate) increased gradually with ripening. A few compounds increased at the senescence phase (propyl ethanoate). Other compounds such as hexadecanoic acid showed a marked decrease after harvest, some decreasing from a relative maximum at harvest (2-methylpropyl hexanoate; n-hexanoic acid; nonanoic acid).

  3. Bio-electrochemical synthesis of commodity chemicals by autotrophic acetogens utilizing CO2 for environmental remediation.

    Science.gov (United States)

    Jabeen, Gugan; Farooq, Robina

    2016-09-01

    Bio-electrochemical synthesis (BES) is a technique in which electro-autotrophic bacteria such as Clostridium ljungdahlii utilize electric currents as an electron source from the cathode to reduce CO2 to extracellular, multicarbon, exquisite products through autotrophic conversion. The BES of volatile fatty acids and alcohols directly from CO2 is a sustainable alternative for non-renewable, petroleum-based polymer production. This conversion of CO2 implies reduction of greenhouse gas emissions. The synthesis of heptanoic acid, heptanol, hexanoic acid and hexanol, for the first time, by Clostridium ljungdahlii was a remarkable achievement of BES. In our study, these microorganisms were cultivated on the cathode of a bio-electrochemical cell at -400 mV by a DC power supply at 37 degree Centrigrade, pH 6.8, and was studied for both batch and continuous systems. Pre-enrichment of bio-cathode enhanced the electroactivity of cells and resulted in maximizing extracellular products in less time. The main aim of the research was to investigate the impact of low-cost substrate CO2, and the longer cathode recovery range was due to bacterial reduction of CO2 to multicarbon chemical commodities with electrons driven from the cathode. Reactor design was simplified for cost-effectiveness and to enhance energy efficiencies. The Columbic recovery of ethanoic acid, ethanol, ethyl butyrate, hexanoic acid, heptanoic acid and hexanol being in excess of 80 percent proved that BES was a remarkable technology.

  4. Alkyl CH Stretch Vibrations as a Probe of Conformational Preferences

    Science.gov (United States)

    Sibert, Edwin L. Sibert, Iii; Buchanan, Evan G.; Zwier, Timothy S.

    2013-06-01

    Theoretical IR spectra of 1,2-diphenoxyethane (C_6H_5-O-CH_2-CH_2-O-C_6H_5 DPOE) and 1,2-diphenylethane (C_6H_5-CH_2-CH_2-C_6H_5 DPE) are presented and compared to results of single-conformation spectroscopy of jet cooled molecules. The theoretical transition energies and intensites are obtained from a model based on a local mode Hamiltonian that includes all local cubic stretch-bend couplings that are then projected onto the normal modes. The model parameters are obtained from density functional theory methods. Full dimensional calculations are compared to those of reduced dimensions that include anharmonic CH streches Fermi coupled to scissor modes. Excellent agreement is found. Scale factors of select terms in the reduced dimensional Hamiltonian are determined by fitting the theoretical Hamiltonian to the anti DPE spectrum. Using the same scaling, Hamiltonians for other conformers of the above molecules are generated and used to predict structures by comparing to experimentally determined spectra in the alkyl CH stretch region. The level patterns in the resulting spectra are elucidated in terms of the model parameters. The model results are extended to interpret the spectra of more complicated macrocycles containing multiple -CH_2CH_2- ethano bridges such as the dibenzo-15-crown-5 ether and 2,2,2-paracyclophane.

  5. Inhibitory effects of Zingiber officinale Roscoe derived components on aldose reductase activity in vitro and in vivo.

    Science.gov (United States)

    Kato, Atsushi; Higuchi, Yasuko; Goto, Hirozo; Kizu, Haruhisa; Okamoto, Tadashi; Asano, Naoki; Hollinshead, Jackie; Nash, Robert J; Adachi, Isao

    2006-09-06

    Ginger (Zingiber officinale Roscoe) continues to be used as an important cooking spice and herbal medicine around the world. Scientific research has gradually verified the antidiabetic effects of ginger. Especially gingerols, which are the major components of ginger, are known to improve diabetes including the effect of enhancement against insulin-sensitivity. Aldose reductase inhibitors have considerable potential for the treatment of diabetes, without increased risk of hypoglycemia. The assay for aldose reductase inhibitors in ginger led to the isolation of five active compounds including 2-(4-hydroxy-3-methoxyphenyl)ethanol (2) and 2-(4-hydroxy-3-methoxyphenyl)ethanoic acid (3). Compounds 2 and 3 were good inhibitors of recombinant human aldose reductase, with IC50 values of 19.2 +/- 1.9 and 18.5 +/- 1.1 microM, respectively. Furthermore, these compounds significantly suppressed not only sorbitol accumulation in human erythrocytes but also lens galactitol accumulation in 30% of galactose-fed cataract rat model. A structure-activity relationship study revealed that the applicable side alkyl chain length and the presence of a C3 OCH3 group in the aromatic ring are essential features for enzyme recognition and binding. These results suggested that it would contribute to the protection against or improvement of diabetic complications for a dietary supplement of ginger or its extract containing aldose reductase inhibitors.

  6. First-principles molecular dynamics simulations of NH4(+) and CH3COO(-) adsorption at the aqueous quartz interface.

    Science.gov (United States)

    Wright, Louise B; Walsh, Tiffany R

    2012-12-14

    The ability to exert molecular-level control at the aqueous interface between biomolecules and inorganic substrates is pivotal to advancing applications ranging from sustainable manufacturing to targeted therapeutics. Progress is hindered by a lack of structural information of these interfaces with atomic resolution. Molecular simulation is one approach to obtain such data, but can be limited by the reliability of the force-field used. First-principles simulations, in principle, can provide insights into such aqueous interfaces, but are resource-intensive, limiting previous first-principles studies to approximate the environment of liquid water. Here, we use Car-Parrinello simulations to investigate adsorption of two charged adsorbates that are functional groups common to all amino-acids--ethanoate and ammonium--at the interface between hydroxylated quartz and liquid water, directly incorporating full solvation effects at the interface. Our findings reveal the stable character of carboxylate-quartz binding, as well as the surprisingly indifferent nature of ammonium-quartz interactions, in liquid water.

  7. QUERCETIN CONTENT AND ANTIOXIDANT ACTIVITY OF ARMENIAN CRATAEGUS LAEVIGATA, PLANTAGO MAJOR AND ARTEMISIA ABSINTHIUM PLANTS EXTRACTS

    Directory of Open Access Journals (Sweden)

    Vardapetyan H

    2014-05-01

    Full Text Available In present study in vitro antioxidant properties of ethanolic extracts of Armenian plants Crataegus laevigata, Plantago major and Artemisia absinthium was investigated by DPPH stable radical chemical model with simultaneous monitoring of the total flavonoids and selected polyphenolic compounds content. Experimental results indicates that ethanolic extract of Crataegus laevigata exhibit the highest radical scavenging activity in neutralization of DPPH with an IC50 value of 12.5 ± 0.08 µl, while the lowest activity was reported in Plantago major extract (IC50 = 45 ± 0.1 µl and IC50 of Artemisia absinthium extract was 35 ± 0.1 µl. Present study also demonstrates a possible relationship between quercetin content and antioxidant activity of extracts. Crataegus laevigata ethanoic extract showed highest antiradical potential as well as the highest concentration of quercetin (7.47 ± 0.2 µg/ml and it can be proposed as a potential sources of natural antioxidants and bioactive phytopharmaceuticals.

  8. Lift-off of mesoporous layers by electrochemical etching on Si (100) substrates with miscut of 6{sup o} off towards (111)

    Energy Technology Data Exchange (ETDEWEB)

    Garralaga Rojas, E., E-mail: garralaga@isfh.de [Institut fuer Solarenergieforschung Hameln, Am Ohrberg 1, 31860 Emmerthal (Germany); Terheiden, B.; Plagwitz, H.; Hensen, J. [Institut fuer Solarenergieforschung Hameln, Am Ohrberg 1, 31860 Emmerthal (Germany); Wiedemeier, V.; Berth, G.; Zrenner, A. [Centre for Optoelectronics and Photonics Paderborn, University of Paderborn, Warburger Str. 100, 33098 Paderborn (Germany); Brendel, R. [Institut fuer Solarenergieforschung Hameln, Am Ohrberg 1, 31860 Emmerthal (Germany)

    2011-10-31

    Uniform mesoporous Si double layers are formed on 4 inch p-type < 100> wafers with an off orientation of 6{sup o} towards < 111> by means of electrochemical etching in ethanoic-based HF electrolytes. These substrates are of interest for the epitaxial growth of III-V compound semiconductor stacks on their top for the production of multi-junction solar cells and very thin electronic devices. We demonstrate transfer of porous layers after an annealing process in hydrogen atmosphere. Electron Back-Scatter Diffraction analysis confirms that the substrate orientation is conserved during the etching and annealing steps. Confocal {mu}-Raman spectroscopy analysis shows a decrease in the Raman signal intensity after etching and a subsequent increase after annealing while no shift is observed. By means of Atomic Force Microscopy, analysis the surface appearance after the etching and annealing steps can be visualized. The mean surface roughness varies during the process from 0.55 nm for the unprocessed wafers to 0.27 nm after etching and 0.78 nm after annealing. The decrease of average roughness after etching is caused by an electropolishing step prior to porous formation. Despite of slight increase of mean surface roughness after annealing the samples are still appropriate for high quality epitaxial growth and subsequent lift-off.

  9. Olfactory sensitivity and odor structure-activity relationships for aliphatic carboxylic acids in CD-1 mice.

    Science.gov (United States)

    Can Güven, Selçuk; Laska, Matthias

    2012-01-01

    Using a conditioning paradigm, the olfactory sensitivity of CD-1 mice for a homologous series of aliphatic n-carboxylic acids (ethanoic acid to n-octanoic acid) and several of their isomeric forms was investigated. With all 14 odorants, the animals significantly discriminated concentrations as low as 0.03 ppm (parts per million) from the solvent, and with four odorants the best-scoring animals even detected concentrations as low as 3 ppt (parts per trillion). Analysis of odor structure-activity relationships showed that the correlation between olfactory detection thresholds of the mice for the unbranched carboxylic acids and carbon chain length can best be described as a U-shaped function with the lowest threshold values at n-butanoic acid. A significant positive correlation between olfactory detection thresholds and carbon chain length of the carboxylic acids with their branching next to the functional carboxyl group was found. In contrast, no such correlation was found for carboxylic acids with their branching at the distal end of the carbon chain relative to the functional carboxyl group. Finally, a significant correlation was found between olfactory detection thresholds and the position of the branching of the carboxylic acids. Across-species comparisons suggest that mice are more sensitive for short-chained (C(2) to C(4)) aliphatic n-carboxylic acids than other mammalian species, but not for longer-chained ones (C(5) to C(8)). Further comparisons suggest that odor structure-activity relationships are both substance class- and species-specific.

  10. Integrated basic treatment of activated carbon for enhanced CO{sub 2} selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Adelodun, Adedeji Adebukola; Jo, Young-Min, E-mail: ymjo@khu.ac.kr

    2013-12-01

    We attempted the use of three chemical agents viz nitric acid (HN), calcium nitrate (CaN) and calcium ethanoate (CaEt) to achieve enhanced CO{sub 2} selective adsorption by activated carbon (AC). In dry phase treatment, microporous coconut shell-based carbon (CS) exhibits higher CO{sub 2} capacity than coal-based. However, upon wet-phase pre-treatment, modified CS samples showed lesser CO{sub 2} adsorption efficiency. Surface characterization with X-ray photoelectron spectroscopy confirms the presence of calcium and amine species on the samples with integrated treatment (A-CaN). These samples recorded the highest low-level CO{sub 2} capture despite calcinated CaEt-doped samples (C-CaEt) showing the highest value for pure and high level CO{sub 2} adsorption capacities. The slope and linearity values of isobaric desorption were used to estimate the proportion of CO{sub 2} chemisorbed and heterogeneity of the adsorbents’ surfaces respectively. Consequently, integrated basic impregnation provides the most efficient adsorbents for selective adsorption of both indoor and outdoor CO{sub 2} levels.

  11. Co-existence of Distinct Supramolecular Assemblies in Solution and in the Solid State.

    Science.gov (United States)

    Reddy, G N Manjunatha; Huqi, Aida; Iuga, Dinu; Sakurai, Satoshi; Marsh, Andrew; Davis, Jeffery T; Masiero, Stefano; Brown, Steven P

    2017-02-16

    The formation of distinct supramolecular assemblies, including a metastable species, is revealed for a lipophilic guanosine (G) derivative in solution and in the solid state. Structurally different G-quartet-based assemblies are formed in chloroform depending on the nature of the cation, anion and the salt concentration, as characterized by circular dichroism and time course diffusion-ordered NMR spectroscopy data. Intriguingly, even the presence of potassium ions that stabilize G-quartets in chloroform was insufficient to exclusively retain such assemblies in the solid state, leading to the formation of mixed quartet and ribbon-like assemblies as revealed by fast magic-angle spinning (MAS) NMR spectroscopy. Distinct N-H⋅⋅⋅N and N-H⋅⋅⋅O intermolecular hydrogen bonding interactions drive quartet and ribbon-like self-assembly resulting in markedly different 2D (1) H solid-state NMR spectra, thus facilitating a direct identification of mixed assemblies. A dissolution NMR experiment confirmed that the quartet and ribbon interconversion is reversible-further demonstrating the changes that occur in the self-assembly process of a lipophilic nucleoside upon a solid-state to solution-state transition and vice versa. A systematic study for complexation with different cations (K(+) , Sr(2+) ) and anions (picrate, ethanoate and iodide) emphasizes that the existence of a stable solution or solid-state structure may not reflect the stability of the same supramolecular entity in another phase.

  12. Determination of SCFAs in water using GC-FID. Selection of the separation system.

    Science.gov (United States)

    Banel, Anna; Jakimska, Anna; Wasielewska, Marta; Wolska, Lidia; Zygmunt, Bogdan

    2012-02-24

    In the present study, an analytical procedure was developed for the determination of short-chain fatty acids (SCFAs) in landfill leachate and municipal wastewater employing injection of aqueous samples to gas chromatograph with flame ionization detector (GC-FID). Chromatographic conditions such as a separation system, injection volume, oven temperature program were investigated and selected. With two columns, one with a polar (polyethylene glycol) and one with a non-polar (dimethylpolisiloxane) stationary phase, good separation of SCFAs, containing from 2 to 8 carbon atoms, was achieved. The sample volume was 2 μL and the temperature program 80°C (30 s) then 7 °C min(-1) to 220 °C (2 min). LOQs values were below 0.25 mg L(-1). The concentrations of the acids in the landfill leachate studied ranged from 0.45±0,059 (average ± extended uncertainty) mg L(-1) for pentanoic acid to 15.2±0.73 mg L(-1) for ethanoic acid. Concentrations of SCFAs in the municipal wastewater were lower than LOQs.

  13. Bio-electrochemical synthesis of commodity chemicals by autotrophic acetogens utilizing CO_{2} for environmental remediation

    Indian Academy of Sciences (India)

    GUGAN JABEEN; ROBINA FAROOQ

    2016-09-01

    Bio-electrochemical synthesis (BES) is a technique in which electro-autotrophic bacteria such as Clostridiumljungdahlii utilize electric currents as an electron source from the cathode to reduce CO_{2} to extracellular, multicarbon,exquisite products through autotrophic conversion. The BES of volatile fatty acids and alcohols directly fromCO_{2} is a sustainable alternative for non-renewable, petroleum-based polymer production. This conversion ofCO_{2} implies reduction of greenhouse gas emissions. The synthesis of heptanoic acid, heptanol, hexanoic acidand hexanol, for the first time, by Clostridium ljungdahlii was a remarkable achievement of BES. In ourstudy, these microorganisms were cultivated on the cathode of a bio-electrochemical cell at −400 mV by aDC power supply at 37°C, pH 6.8, and was studied for both batch and continuous systems. Pre-enrichment ofbio-cathode enhanced the electroactivity of cells and resulted in maximizing extracellular products in lesstime. The main aim of the research was to investigate the impact of low-cost substrate CO_{2}, and the longercathode recovery range was due to bacterial reduction of CO_{2} to multicarbon chemical commodities withelectrons driven from the cathode. Reactor design was simplified for cost-effectiveness and to enhance energyefficiencies. The Columbic recovery of ethanoic acid, ethanol, ethyl butyrate, hexanoic acid, heptanoic acidand hexanol being in excess of 80% proved that BES was a remarkable technology.

  14. Crystal structure of poly[N,N-diethyl-2-hy-droxy-ethan-1-aminium [μ3-cyanido-κ(3) C:C:N-di-μ-cyanido-κ(4) C:N-dicuprate(I)

    Science.gov (United States)

    Corfield, Peter W R; Cleary, Emma; Michalski, Joseph F

    2016-07-01

    In the title compound, {(C6H16NO)[Cu2(CN)3]} n , the cyanide groups link the Cu(I) atoms into an open three-dimensional anionic network, with the mol-ecular formula Cu2(CN)3 (-). One Cu(I) atom is tetra-hedrally bound to four CN groups, and the other Cu(I) atom is bonded to three CN groups in an approximate trigonal-planar coordination. The tetra-hedrally coordinated Cu(I) atoms are linked into centrosymmetric dimers by the C atoms of two end-on bridging CN groups which bring the Cu(I) atoms into close contact at 2.5171 (7) Å. Two of the cyanide groups bonded to the Cu(I) atoms with trigonal-planar surrounding link the dimeric units into columns along the a axis, and the third links the columns together to form the network. The N,N-di-ethyl-ethano-lamine mol-ecules used in the synthesis have become protonated at the N atoms and are situated in cavities in the network, providing charge neutrality, with no covalent inter-actions between the cations and the anionic network.

  15. Changes of phosphorylation of cAMP response element binding protein in rat nucleus accumbens after chronic ethanol intake: naloxone reversal

    Institute of Scientific and Technical Information of China (English)

    LIJing; LIYue-Hua; YUANXiao-Ru

    2003-01-01

    AIM: To study the changes in the expression and phosphorylation of cAMP response element binding protein(CREB) in the rat nucleus accumbens after chronic ethanol intake and its withdrawal. METHODS: Ethanol wasgiven in drinking water at the concentration of 6 % (v/v), for one month. Changes in the levels of CREB andphospho-CREB (p-CREB) protein in the nucleus accumbens were measured by immunohistochemistry methods.RESULTS: Ethanol given to rats in drinking water decreased the level of p-CREB protein in the nucleus accumbens(-75 %) at the time of exposure to ethanol. The decrement of p-CREB protein in the nucleus accumbens remainedat 24 h (-35 %) and 72 h (-28 %) of ethanol withdrawal, which recovered toward control level after 7 d of ethanolwithdrawal. However, chronic ethanol, as well as ethanol withdrawal failed to produce any significant alteration inthe level of CREB protein in the nucleus accumbens. Naloxone (alone) treatment of rats had no effect on the levelsof CREB and p-CREB protein in the nucleus accumbens. However, when naloxone was administered concurrentlywith ethanol treatment, it antagonized the down-regulation of p-CREB protein in the nucleus accumbens (142 %) ofrats exposed to ethanol. CONCLUSION: A long-term intake of ethanol solution down-regulates the phosphoryla-tion of CREB in the nucleus accumbens, and those changes can be reversed by naloxone, which may be one kindof the molecular mechanisms associated with ethano1 dependence.

  16. Effect of methylene spacers on the spectral, electrochemical, and structural properties of bis(4,4'-disubstituted-2,2'-bipyridyl) ruthenium(II) dye analogues.

    Science.gov (United States)

    Lense, Sheri; Hardcastle, Kenneth I; MacBeth, Cora E

    2009-09-28

    Two new ruthenium complexes, [Ru(L1OMe)2(NCS)2] and [Ru(L2OMe)2(NCS)2] (where L1OMe = 2,2'-bipyridine-4,4'-di(methyl ethanoate) and L2OMe = 2,2'-bipyridine-4,4'-di(methyl propionate)), have been synthesized and characterized using spectroscopic and electrochemical techniques. The [Ru(L2OMe)2(NCS)2] complex has also been characterized by X-ray diffraction studies and reveals a distorted octahedral coordination geometry about the ruthenium center. Cyclic voltammetry studies of both complexes exhibit quasi-reversible Ru(II/III) couples and a number of ligand reduction events. The complex with one methylene spacer between the bipyridyl ligand and the methyl ester functional group, [Ru(L1OMe)2(NCS)2], was particularly unstable under reducing conditions. The properties of these complexes are compared with the ethyl ester analogue of the N3 photosensitizer [Ru(L0OEt)2(NCS)2].

  17. Meteorites and the RNA World: A Thermodynamic Model of Nucleobase Synthesis within Planetesimals

    CERN Document Server

    Pearce, Ben K D

    2016-01-01

    The possible meteorite parent body origin of Earth's pregenetic nucleobases is substantiated by the guanine (G), adenine (A) and uracil (U) measured in various meteorites. Cytosine (C) and thymine (T) however are absent in meteorites, making the emergence of a RNA and later RNA/DNA/protein world problematic. We investigate the meteorite parent body (planetesimal) origin of all nucleobases by computationally modeling 18 reactions that potentially contribute to nucleobase formation in such environments. Out of this list, we identify the two most important reactions for each nucleobase and find that these involve small molecules such as HCN, CO, NH3, and water that ultimately arise from the protoplanetary disks in which planetesimals are built. The primary result of this study is that cytosine is unlikely to persist within meteorite parent bodies due to aqueous deamination. Thymine has a thermodynamically favourable reaction pathway from uracil, formaldehyde and formic acid, but likely did not persist within pla...

  18. Effect of base pairing on the electrochemical oxidation of guanine.

    Science.gov (United States)

    Costentin, Cyrille; Hajj, Viviane; Robert, Marc; Savéant, Jean-Michel; Tard, Cédric

    2010-07-28

    The effect of base pairing by cytosine on the electrochemical oxidation of guanine is examined by means of cyclic voltammetry on carefully purified reactants in a solvent, CHCl(3), which strongly favors the formation of an H-bonded pair. The thermodynamics and kinetics of the oxidation reaction are not strongly influenced by the formation of the pair. They are actually similar to those of the reaction in which 2,6-lutidine, an encumbered base that cannot form a pair with guanine, replaces cytosine. The reaction does not entail a concerted proton-electron mechanism, as attested by the absence of H/D isotope effect. It rather involves the rate-determining formation of the cation radical, followed by its deprotonation and dimerization of the resulting neutral radical in competition with its further oxidation.

  19. IRE1α nucleotide sequence cleavage specificity in the unfolded protein response.

    Science.gov (United States)

    Poothong, Juthakorn; Sopha, Pattarawut; Kaufman, Randal J; Tirasophon, Witoon

    2017-01-01

    Inositol-requiring enzyme 1 (IRE1) is a conserved sensor of the unfolded protein response that has protein kinase and endoribonuclease (RNase) enzymatic activities and thereby initiates HAC1/XBP1 splicing. Previous studies demonstrated that human IRE1α (hIRE1α) does not cleave Saccharomyces cerevisiae HAC1 mRNA. Using an in vitro cleavage assay, we show that adenine to cytosine nucleotide substitution at the +1 position in the 3' splice site of HAC1 RNA is required for specific cleavage by hIRE1α. A similar restricted nucleotide specificity in the RNA substrate was observed for XBP1 splicing in vivo. Together these findings underscore the essential role of cytosine nucleotide at +1 in the 3' splice site for determining cleavage specificity of hIRE1α.

  20. Direct Isolation of Purines and Pyrimidines from Nucleic Acids Using Sublimation

    Science.gov (United States)

    Glavin, Daniel P.; Schubert, Michael; Bada, Jeffrey L.

    2003-01-01

    A sublimation technique was developed to isolate purines and pyrimidines directly from lambda-deoxyribonucleic acid (lambda-DNA) and Escherichia coli cells. The sublimation of adenine, cytosine, guanine, and thymine from lambda-DNA was tested under reduced pressure (approx. 0.5 Torr) at temperatures of >150 C. With the exception of guanine, approximately 60 -75% of each base was sublimed directly from the lambda-DNA and recovered on a coldfinger of the sublimation apparatus after heating to 450 C. Several nucleobases including adenine, cytosine, thymine, and uracil were also recovered from E. coli bacteria after heating the cells to the same temperature, although some thermal decomposition of the bases also occurred. These results demonstrate the feasibility of using sublimation to isolate purines and pyrimidines from native E. coli DNA and RNA without any chemical treatment of the cells.

  1. Cryptococcus socialis sp. nov. and Cryptococcus consortionis sp. nov., Antarctic basidioblastomycetes

    Science.gov (United States)

    Vishniac, H. S.

    1985-01-01

    New yeasts from the Ross Desert (dry valley area) of Antarctica include Cryptococcus socialis sp. nov. and Cryptococcus consortionis sp. nov. Cryptococcus socialis MYSW A801-3aY1 (= ATCC 56685) requires no vitamins, assimilates L-arabinose, cellobiose, D-glucuronate, maltose, melezitose, raffinose, soluble starch, sucrose, and trehalose, and may be distinguished from all other basidioblastomycetes by the combination of amylose production, cellobiose assimilation, and failure to utilize nitrate, D-galactose, myo-inositol, and mannitol. Its guanine-plus-cytosine content is 56 mol%. Cryptococcus consortionis MYSW A801-3aY92 (= ATCC 56686) requires thiamine, assimilates L-arabinose, D-glucuronate, 2-ketogluconate, salicin, succinate, sucrose, trehalose, and D-xylose, and may be distinguished from all other basidioblastomycetes by the combination of amylose production and failure to utilize nitrate, cellobiose, D-galactose, myo-inositol, and mannitol. Its guanine-plus-cytosine content is 56 mol%.

  2. [Induction and maintenance treatment of acute myelogenous leukemia in adults by sequential use of combination chemotherapy (author's transl)].

    Science.gov (United States)

    Fülle, H H

    1977-04-15

    The therapeutic regimens for acute myelogenous leukemia in 2 different periods of time will be described with comparison of their results. A. 28 adults were treated with cytosine arabinoside and 6-thioguanine only. Thereby, 28% complete and 16% partial remissions were achieved. The mean duration of the complete remissions was 23 weeks. The mean survival time of the patients with complete remission amounted to 53 weeks B. 46% complete and 12% partial remissions were obtained in 37 patients treated with cytosine arabinoside and 6-thioguanine doubling the dosage of the above mentioned regimen followed by 3 cycles of TRAP (and COAP). Using a maintenance therapy with modified TRAP, COAP, and POMP cycles the complete remissions lasted 47 weeks at an average. The mean survival time of patients with complete remission was 87 weeks after start of treatment.

  3. Modulation of DNA methylation and gene expression in cultured sycamore cells treated by hypomethylating base analog.

    Science.gov (United States)

    Ngernprasirtsiri, J; Akazawa, T

    1990-12-12

    The selective suppression of photosynthetic genes in both the nuclear and plastid genomes of the nonphotosynthetic white wild-type cell line of sycamore (Acer pseudoplatanus) has been found to be inversely related to the presence of a variety of methylated bases, especially 5-methylcytosine (5-MeCyt) and N6-methyladenine (N6-MeAde), localized in regions of the plastid genome containing silent genes. We used hypomethylating base analogs to manipulate the level of cytosine and adenine methylation in the white cells of sycamore, and examined the effects of changes in methylation on gene expression. Treatment with 5-azacytidine (5-AzaCyd) and N6-benzyladenine (N6-BzlAde) decreased cytosine and adenine methylation. This was accompanied by restoration of transcriptional activity in photosynthetic genes which are usually suppressed. Both 5-MeCyt and N6-MeAde suppressed nuclear gene expression, but only 5-MeCyt suppressed plastid gene expression.

  4. Deoxyribonucleic acid (DNA methylation and its impact in generation of Cancer

    Directory of Open Access Journals (Sweden)

    Rajeswari J

    2014-07-01

    Full Text Available The arrangement of genes in the chromosome is dependent on histone modifications, deoxyribonucleic acid (DNA binding proteins and methylation of cytosines within 51–cytosine-phosphate-Guanine–31 (CpG dinucleotides. DNA methylation can modify the gene activity without changing the gene sequence. Aberrant hypomethylation and hypermethylations, causal or heritable gene expressions play an important role in tumour initiation and progression. Global hypomethylation at some part of genome and hypermethylation at the promoter regions of the tumour suppressor genes could generate mutations in several types of cancers. Reversal or inhibition of DNA methylation mechanism provides a promising improvement in the treatment of cancer along with chemotherapy. A combined approach utilising epigenetic treatment along with standard chemotherapy appears to hold promise as a future therapy.

  5. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation

    DEFF Research Database (Denmark)

    Shaknovich, Rita; Cerchietti, Leandro; Tsikitas, Lucas;

    2011-01-01

    The phenotype of germinal center (GC) B cells includes the unique ability to tolerate rapid proliferation and the mutagenic actions of activation induced cytosine deaminase (AICDA). Given the importance of epigenetic patterning in determining cellular phenotypes, we examined DNA methylation and t......, the GC B cells of Dnmt1 hypomorphic animals showed evidence of increased DNA damage, suggesting dual roles for DNMT1 in DNA methylation and double strand DNA break repair.......The phenotype of germinal center (GC) B cells includes the unique ability to tolerate rapid proliferation and the mutagenic actions of activation induced cytosine deaminase (AICDA). Given the importance of epigenetic patterning in determining cellular phenotypes, we examined DNA methylation...... and the role of DNA methyltransferases in the formation of GCs. DNA methylation profiling revealed a marked shift in DNA methylation patterning in GC B cells versus resting/naive B cells. This shift included significant differential methylation of 235 genes, with concordant inverse changes in gene expression...

  6. Photochemistry. Chemiexcitation of melanin derivatives induces DNA photoproducts long after UV exposure.

    Science.gov (United States)

    Premi, Sanjay; Wallisch, Silvia; Mano, Camila M; Weiner, Adam B; Bacchiocchi, Antonella; Wakamatsu, Kazumasa; Bechara, Etelvino J H; Halaban, Ruth; Douki, Thierry; Brash, Douglas E

    2015-02-20

    Mutations in sunlight-induced melanoma arise from cyclobutane pyrimidine dimers (CPDs), DNA photoproducts that are typically created picoseconds after an ultraviolet (UV) photon is absorbed at thymine or cytosine. We found that in melanocytes, CPDs are generated for >3 hours after exposure to UVA, a major component of the radiation in sunlight and in tanning beds. These "dark CPDs" constitute the majority of CPDs and include the cytosine-containing CPDs that initiate UV-signature C→T mutations. Dark CPDs arise when UV-induced reactive oxygen and nitrogen species combine to excite an electron in fragments of the pigment melanin. This creates a quantum triplet state that has the energy of a UV photon but induces CPDs by energy transfer to DNA in a radiation-independent manner. Melanin may thus be carcinogenic as well as protective against cancer. These findings also validate the long-standing suggestion that chemically generated excited electronic states are relevant to mammalian biology.

  7. Síntesis y actividad antimicrobiana de derivados de 4,6-diaminopirimidinas análogos de citosina

    Directory of Open Access Journals (Sweden)

    Gricela Lobo

    2012-09-01

    Full Text Available A new synthesis of novel 4,6-diaminopyrimidines 2a-j, cytosine analogous, is described. This involves the base-assisted cyclization reaction of benzylidenemalononitriles 1a-j (BMNs with urea. Compounds 1a-j were prepared by a Knoevenagel condensation reaction from benzaldehyde and malononitrile using EtOH as solvent at room temperature conditions. The antimicrobial activity against Gram-positive microorganisms: Staphylococcus aureus (ATCC 25923 and Bacillus cereus (ATCC 14579 and Gram-negative: Escherichia coli (ATCC 35218 and Pseudomonas aeruginosa (ATCC 27853 and th yeast Candida tropicalis (MLDM 372 is also reported. The compounds 2c, 2e, 2f, 2g, 2i and 2j are considered wide spectrum. Antimicrobial activity, Benzylidenemalononitriles (BMNs, Cytosine, Diaminopyrimidine, Urea,

  8. An Integrated Workflow for DNA Methylation Analysis

    Institute of Scientific and Technical Information of China (English)

    Pingchuan Li; Feray Demirci; Gayathri Mahalingam; Caghan Demirci; Mayumi Nakano; Blake C.Meyers

    2013-01-01

    The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes.DNA methylation has a demonstrated role in the genome stability and protection,regulation of gene expression and many other aspects of genome function and maintenance.BS-seq is a relatively unbiased method for profiling the DNA methylation,with a resolution capable of measuring methylation at individual cytosines.Here we describe,as an example,a workflow to handle DNA methylation analysis,from BS-seq library preparation to the data visualization.We describe some applications for the analysis and interpretation of these data.Our laboratory provides public access to plant DNA methylation data via visualization tools available at our "Next-Gen Sequence" websites (http://mpss.udel.edu),along with small RNA,RNA-seq and other data types.

  9. Detection and monitoring of hypermethylated RASSF1A in serum from patients with metastatic breast cancer

    DEFF Research Database (Denmark)

    Kristiansen, Søren; Nielsen, Dorte; Söletormos, Georg

    2016-01-01

    BACKGROUND: Circulating hypermethylated RASSF1A could be a novel and potential useful marker for monitoring patients with metastatic breast cancer. Technical obstacles include fragmentation of the circulating DNA, fluctuations in the concentration, low concentrations of circulating tumor DNA......, and different locations of methylation in the RASSF1A gene among patients. One common method for detection of hypermethylated genes is sodium bisulfite conversion of non-methylated cytosine to uracil, followed by detection with PCR. However, the method relies on full conversion of all non-methylated cytosines...... of the rare circulating tumor DNA was initially optimized. By analysis of production of PCR amplicons from HpaII- or BstUI-treated DNA isolated from 24 patients with metastatic breast cancer, we located four regions resulting in sensitivities from 63 to 83 %. When examining samples from 24 control subjects...

  10. Linkage of proton binding to the thermal dissociation of triple helix complex.

    Science.gov (United States)

    Petraccone, Luigi; Erra, Eva; Mattia, Carlo Andrea; Fedullo, Vito; Barone, Guido; Giancola, Concetta

    2004-07-01

    The effects of cytosine protonation on the thermodynamic properties of parallel pyrimidine motif DNA triplex were investigated and characterized by different techniques, such as circular dichroism (CD), ultraviolet spectroscopy (UV) and differential scanning calorimetry (DSC). A thermodynamic model was developed which, by linking the cytosine ionization equilibrium to the dissociation process of the triplex, is able to rationalize the experimental data and to reproduce the pH dependence of the free energy, enthalpy and entropy changes associated with the triplex formation. The results are useful to systematically introduce the effect of pH in a more general model able to predict the stability of DNA triplexes on the basis of the sequence alone.

  11. Hypermethylated SUPERMAN epigenetic alleles in arabidopsis.

    Science.gov (United States)

    Jacobsen, S E; Meyerowitz, E M

    1997-08-22

    Mutations in the SUPERMAN gene affect flower development in Arabidopsis. Seven heritable but unstable sup epi-alleles (the clark kent alleles) are associated with nearly identical patterns of excess cytosine methylation within the SUP gene and a decreased level of SUP RNA. Revertants of these alleles are largely demethylated at the SUP locus and have restored levels of SUP RNA. A transgenic Arabidopsis line carrying an antisense methyltransferase gene, which shows an overall decrease in genomic cytosine methylation, also contains a hypermethylated sup allele. Thus, disruption of methylation systems may yield more complex outcomes than expected and can result in methylation defects at known genes. The clark kent alleles differ from the antisense line because they do not show a general decrease in genomic methylation.

  12. Synthesis of Novel Metal Ion Sensors Based on DNA-Metal Interactions

    Institute of Scientific and Technical Information of China (English)

    Akira Ono; Shiqi Cao; Humika Togashi; Yoko Miyake

    2005-01-01

    @@ 1Introduction The interactions of metal ions with nucleic acids, nucleosides, and nucleo-bases have been extensively investigated[1,2]. We have reported that thymine-thymine (T-T) and cytosine-cytosine (C- C) miss base pairs in DNA duplexes highly selectively capture HgⅡ ion and Ag Ⅰ ion, which result in formations of metal-mediated base pairs, T-HgⅡ -T and C-AgⅠ -C, in duplexes[3]. The phenomenon is expected to be useful for a variety of studies such as synthesis of nano-wires containing metal ions, developing metal-ion sensing methods, etc.Here, we report novel oligodeoxyribonucleotide (ODN)-based sensors that detect HgⅡ ions and AgⅠ ions in aqueous solutions.

  13. Cell and molecular biology of DNA methyltransferase 1.

    Science.gov (United States)

    Mohan, K Naga; Chaillet, J Richard

    2013-01-01

    The DNA cytosine methyltransferase 1 (DNMT1) is a ubiquitous nuclear enzyme that catalyzes the well-established reaction of placing methyl groups on the unmethylated cytosines in methyl-CpG:CpG base pairs in the hemimethylated DNA formed by methylated parent and unmethylated daughter strands. This activity regenerates fully methylated methyl-CpG:methyl-CpG pairs. Despite the straightforward nature of its catalytic activity, detailed biochemical, genetic, and developmental studies revealed intricate details of the central regulatory role of DNMT1 in governing the epigenetic makeup of the nuclear genome. DNMT1 mediates demethylation and also participates in seemingly wide cellular functions unrelated to maintenance DNA methylation. This review brings together mechanistic details of maintenance methylation by DNMT1, its regulation at transcriptional and posttranscriptional levels, and the seemingly unexpected functions of DNMT1 in the context of DNA methylation which is central to epigenetic changes that occur during development and the process of cell differentiation.

  14. Methyl-CpG binding proteins in the nervous system

    Institute of Scientific and Technical Information of China (English)

    Guoping FAN; Leah HUTNICK

    2005-01-01

    Classical methyl-CpG binding proteins contain the conserved DNA binding motif methyl-cytosine binding domain (MBD), which preferentially binds to methylated CpG dinucleotides. These proteins serve as transcriptional repressors,mediating gene silencing via DNA cytosine methylation. Mutations in methyl-CpG binding protein 2 (MeCP2) have been linked to the human mental retardation disorder Rett syndrome, suggesting an important role for methyl-CpG binding proteins in brain development and function. This mini-review summarizes the recent advances in studying the diverse functions of MeCP2 as a prototype for other methyl-CpG binding proteins in the development and function of the vertebrate nervous system.

  15. Pt(Ⅱ), Pd(Ⅱ) and Ni(Ⅱ) Complexes Binding to the N(7) Position of Guanine: Influence on the Guanine and Watson-crick GC Base Pair

    Institute of Scientific and Technical Information of China (English)

    章志强; 周立新; 和芹; 赵亚英

    2005-01-01

    Comprehensive ab initio calculations were performed on the coordination of Pt(II), Pd(II) and Ni(II) adducts to the N(7) of guanine and guanine-cytosine (GC) base pair at the DFT level. The fully optimized geometries of the metal complexes were obtained and the stabilization energies of the interaction between metal adducts and nucleobase were calculated with B3LYP method by using 6-31* basis set for the light atom. While the effective core potential (ECP) is used for metal cation. The results show that both cispalladium and cisnickel cause similar geometric changes of the base pair as cisplatin. For the coordination of metal adducts to guanine, platinum adduct possesses the highest stabilization energy; but the interaction between metal-guanine and cytosine for nickel is larger than that for platinum and palladium. It is worthy to note that hydrolysis effect can also cause significant changes in H-bonds.

  16. Kennedy's disease and partial androgen insensitivity syndrome. Report of 4 cases and literature review.

    Science.gov (United States)

    Valera Yepes, Rocío; Virgili Casas, Maria; Povedano Panades, Monica; Guerrero Gual, Mireia; Villabona Artero, Carles

    2015-05-01

    Kennedy's disease, also known as bulbospinal muscular atrophy, is a rare, X-linked recessive neurodegenerative disorder affecting adult males. It is caused by expansion of an unstable cytosine-adenine-guanine tandem-repeat in exon 1 of the androgen-receptor gene on chromosome Xq11-12, and is characterized by spinal motor neuron progressive degeneration. Endocrinologically, these patients often have the features of hypogonadism associated to the androgen insensitivity syndrome, particularly its partial forms. We report 4 cases with the typical neurological presentation, consisting of slowly progressing generalized muscle weakness with atrophy and bulbar muscle involvement; these patients also had several endocrine manifestations; the most common non-neurological manifestation was gynecomastia. In all cases reported, molecular analysis showed an abnormal cytosine-adenine-guanine triplet repeat expansion in the androgen receptor gene.

  17. Electron Attachment to DNA and RNA Nucleobases: An EOMCC Investigation

    CERN Document Server

    Dutta, Chintya Kumar; Vaval, Nayana; Pal, Sourav

    2014-01-01

    We report a benchmark theoretical investigation of both adiabatic and vertical electron affinities of five DNA and RNA nucleobases: adenine, guanine, cytosine, thymine and uracil using state-of-the-art equation of motion coupled cluster (EOMCC) method. We have calculated the vertical electron affinity values of first five electron attached states of the DNA and RNA nucleobases and only the first electron attached state is found to be energetically accessible in gas phase. An analysis of the natural orbitals shows that the first electron attached states of uracil and thymine are valence-bound type and undergo significant structural changes on attachment of excess electron, which is reflected in the deviation of the adiabatic electron affinity from the vertical one. On the other hand, the first electron attached state of cytosine, adenine and guanine are dipole-bound type and their structure remain unaffected on attachment of an extra electron, which results in small deviation of adiabatic electron affinity fro...

  18. Pyrosequencing Analysis for Breast Cancer DNA Methylome.

    Science.gov (United States)

    Kuscu, Cem; Kuscu, Canan

    2016-01-01

    Unraveling DNA methylation profile of tumor is important for the diagnosis and treatment of cancer patients. Because of the heterogeneity of clinical samples, it is very difficult to get methylation profile of only tumor cells. Laser capture Microdissection (LCM) is giving us a chance to isolate the DNA only from the tumor cells without any stroma cell's DNA contamination. Once we capture the breast tumor cells, we can isolate the genomic DNA which is followed by the bisulfite treatment in which unmethylated cytosines of the CG pairs are converted into uracil; however, methylated cytosine does not go into any chemical change during this reaction. Next, bisulfite treated DNA is used in the regular PCR reaction to get a single band PCR amplicon which will be used as a template for the pyrosequencing. Pyrosequencing is a powerful method to make a quantitative methylation analysis for each specific CG pair.

  19. Optoelectronic studies on heterocyclic bases of deoxyribonucleic acid for DNA photonics.

    Science.gov (United States)

    El-Diasty, Fouad; Abdel-Wahab, Fathy

    2015-10-01

    The optoelectronics study of large molecules, particularly π-stacking molecules, such as DNA is really an extremely difficult task. We perform first electronic structure calculations on the heterocyclic bases of 2'-deoxyribonucleic acid based on Lorentz-Fresnel dispersion theory. In the UV-VIS range of spectrum, many of the optoelectronic parameters for DNA four bases namely adenine, guanine, cytosine and thymine are calculated and discussed. The results demonstrate that adenine has the highest hyperpolarizability, whereas thymine has the lowest hyperpolarizability. Cytosine has the lower average oscillator energy and the higher lattice energy. Thymine infers the most stable nucleic base with the lower phonon energy. Thymine also has the highest average oscillator energy and the lower lattice energy. Moreover, the four nucleic acid bases have large band gap energies less than 5 eV with a semiconducting behavior. Guanine shows the smallest band gap and the highest Fermi level energy, whereas adenine elucidates the highest band gap energy.

  20. Noncovalent interactions of a benzo[a]pyrene diol epoxide with DNA base pairs: insight into the formation of adducts of (+)-BaP DE-2 with DNA.

    Science.gov (United States)

    Hargis, Jacqueline C; Schaefer, Henry F; Houk, K N; Wheeler, Steven E

    2010-02-01

    Noncovalent complexes of a tumorigenic benzo[a]pyrene diol epoxide with the guanine-cytosine (GC) and adenine-thymine (AT) base pairs have been examined computationally. (+)-BaP DE-2 forms covalent adducts with DNA via nucleophilic attack on the (+)-BaP DE-2 epoxide. Computational results predict five thermodynamically accessible complexes of AT with (+)-BaP DE-2 that are compatible with intact DNA. Among these, two are expected to lead to adenine adducts. In the lowest energy AT...(+)-BaP DE-2 complex, which has a gas-phase interaction energy of -20.9 kcal mol(-1), the exocyclic NH(2) of adenine is positioned for backside epoxide attack and formation of a trans adduct. The most energetically favorable complex leading to formation of a cis ring-opened adduct lies only 0.6 kcal mol(-1) higher in energy. For GC...(+)-BaP DE-2, there are only two thermodynamically accessible complexes. The higher-lying complex, bound in the gas phase by 24.4 kcal mol(-1) relative to separated GC and (+)-BaP DE-2, would lead to a trans ring-opened N(2)-guanine adduct. In the global minimum energy GC...(+)-BaP DE-2 complex, bound by 27.3 kcal mol(-1), the exocyclic NH(2) group of cytosine is positioned for cis epoxide addition. However, adducts of (+)-BaP DE-2 with cytosine are rarely observed experimentally. The paucity of cytosine adducts, despite the predicted thermodynamic stability of this GC...(+)-BaP DE-2 complex, is attributed to the electrostatic destabilization of the benzylic cation intermediate thought to precede cis addition.

  1. Minireview: Epigenetic Programming of Diabetes and Obesity: Animal Models

    OpenAIRE

    2012-01-01

    A growing body of evidence suggests that the intrauterine (IU) environment has a significant and lasting effect on the long-term health of the growing fetus and the development of metabolic disease in later life as put forth in the fetal origins of disease hypothesis. Metabolic diseases have been associated with alterations in the epigenome that occur without changes in the DNA sequence, such as cytosine methylation of DNA, histone posttranslational modifications, and micro-RNA. Animal models...

  2. Synthesis of triazole-nucleoside phosphoramidites and their use in solid-phase oligonucleotide synthesis.

    Science.gov (United States)

    Peel, Brandon J; Efthymiou, Tim C; Desaulniers, Jean-Paul

    2014-12-19

    Triazole-backbone oligonucleotides are macromolecules that have one or more triazole units that are acting as a backbone mimic. Triazoles within the backbone have been used within oligonucleotides for a variety of applications. This unit describes the preparation and synthesis of two triazole-nucleoside phosphoramidites [uracil-triazole-uracil (UtU) and cytosine-triazole-uracil (CtU)] based on a PNA-like scaffold, and their incorporation within oligonucleotides.

  3. B3LYP, BLYP and PBE DFT band structures of the nucleotide base stacks

    Science.gov (United States)

    Szekeres, Zs; Bogár, F.; Ladik, J.

    DFT crystal orbital (band structure) calculations have been performed for the nucleotide base stacks of cytosine, thymine, adenine, and guanine arranged in DNA B geometry. The band structures obtained with PBE, BLYP, and B3LYP functionals are presented and compared to other related experimental and theoretical results. The influence of the quality of the basis set on the fundamental gap values was also investigated using Clementi's double ζ, 6-31G and 6-31G* basis sets.

  4. Cleavage of oligodeoxyribonucleotides from controlled-pore glass supports and their rapid deprotection by gaseous amines.

    Science.gov (United States)

    Boal, J H; Wilk, A; Harindranath, N; Max, E E; Kempe, T; Beaucage, S L

    1996-08-01

    A novel method for the deprotection of oligodeoxyribonucleotides has been developed. Gaseous amines such as ammonia or methylamine were employed under pressure to achieve mild and rapid deprotection conditions. For example, oligodeoxyribonucleotides having a (tert-butyl)phenoxyacetyl group for the protection of the exocyclic amino function of cytosine, adenine and guanine were released from controlled-pore glass supports and fully deprotected by ammonia or methylamine under gas phase conditions, at room temperature, within 35 or 2 min respectively.

  5. AN OVERVIEW ON ANTIFUNGAL THERAPY

    OpenAIRE

    Karki, Nirmal K.; Ahmed, Azhar; Charde, Rita; Charde, Manoj; Gandhare, Bhushan

    2011-01-01

    The number of fungi causing systemic disease is growing and the number of systemic diseases caused by fungi is increasing. The currently available antifungal agents for the treatment of systemic mycoses include polyene antibiotics (Amphotericin B), fluoropyrimidine (Flu cytosine), and Nystatin andazole group of drugs (Ketoconazole, Fluconazole, and Itraconazole). Novel drug delivery systems for antifungal therapy, based on the type of formulation are classified as Liposomes Nanocochleates, Na...

  6. Capillary Electrophoresis in the Presence of Fosfomycin

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Fosfomyein, a sodim salt of cis-(3-methyloxiranyl) phosphonic acid, was used as electrolyte in binary methanol-water media for capillary electrophoresis. The variety of electroosmotic flow with pH*,methanol concentration and ionic strength was investigated. The migration behavior of nine bases was examined under various conditions, and the separation of thymine, cytosine, 5-flurouracil, 4,6-diamino-pyrimidine, purine was accomplished.

  7. Physical mapping of the restriction fragments obtained from bacteriophage T4 dC-DNA with the restriction endonucleases SmaI, KpnI and BglII.

    Science.gov (United States)

    Kiko, H; Niggemann, E; Rüger, W

    1979-01-01

    The cytosine-containing DNA of a mutant of bacteriophage T4 was digested with restriction endonucleases SmaI, KpnI and BglII producing 5, 7 and 13 fragments respectively. Complete physical maps of the T4 genome were constructed with the enzymes SmaI and KpnI and an almost complete map with the enzyme BglII.

  8. Hydroxyl-radical-induced oxidation of 5-methylcytosine in isolated and cellular DNA.

    Science.gov (United States)

    Madugundu, Guru S; Cadet, Jean; Wagner, J Richard

    2014-06-01

    The methylation and oxidative demethylation of cytosine in CpG dinucleotides plays a critical role in the regulation of genes during cell differentiation, embryogenesis and carcinogenesis. Despite its low abundance, 5-methylcytosine (5mC) is a hotspot for mutations in mammalian cells. Here, we measured five oxidation products of 5mC together with the analogous products of cytosine and thymine in DNA exposed to ionizing radiation in oxygenated aqueous solution. The products can be divided into those that arise from hydroxyl radical (•OH) addition at the 5,6-double bond of 5mC (glycol, hydantoin and imidazolidine products) and those that arise from H-atom abstraction from the methyl group of 5mC including 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC). Based on the analysis of these products, we show that the total damage at 5mC is about 2-fold greater than that at C in identical sequences. The formation of hydantoin products of 5mC is favored, compared to analogous reactions of thymine and cytosine, which favor the formation of glycol products. The distribution of oxidation products is sequence dependent in specific ODN duplexes. In the case of 5mC, the formation of 5hmC and 5fC represents about half of the total of •OH-induced oxidation products of 5mC. Several products of thymine, cytosine, 5mC, as well as 8-oxo-7,8-dihydroguanine (8oxoG), were also estimated in irradiated cells.

  9. Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases

    DEFF Research Database (Denmark)

    Harris, R Alan; Nagy-Szakal, Dorottya; Pedersen, Natalia;

    2012-01-01

    Crohn's disease (CD) and ulcerative colitis (UC) are common forms of inflammatory bowel disease (IBD). Monozygotic (MZ) twin discordance rates and epidemiologic data implicate that environmental changes and epigenetic factors may play a pathogenic role in IBD. DNA methylation (the methylation...... of cytosines within CpG dinucleotides) is an epigenetic modification, which can respond to environmental influences. We investigated whether DNA methylation might be connected with IBD in peripheral blood leukocyte (PBL) DNA by utilizing genome-wide microarrays....

  10. Implementation of Quantum Logic Gates by Nuclear Magnetic Resonance Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    DU Jiang-Feng; WU Ji-Hui; SHI Ming-Jun; HAN Liang; ZHOU Xian-Yi; YE Bang-Jiao; WENG Hui-Ming; HAN Rong-Dian

    2000-01-01

    Using nuclear magnetic resonance techniques with a solution of cytosine molecules, we show an implementation of certain quantum logic gates (including NOT gate, square-root of NOT gate and controlled-NOT gate), which have central importance in quantum computing. In addition, experimental results show that nuclear magnetic resonance spectroscopy can efficiently measure the result of quantum computing without attendant wave-function collapse.

  11. A strategy for developing a hammerhead ribozyme for selective RNA cleavage depending on substitutional RNA editing

    OpenAIRE

    Fukuda, Masatora; Kurihara, Kei; Tanaka, Yasuyoshi; Deshimaru, Masanobu

    2012-01-01

    Engineered site-specific RNA cleavage is widely used for gene regulation, RNA mapping, and synthetic RNA production. Here the authors extend the range of engineered recognition selectivity to include cleavage of sequence motifs containing naturally occurring base modifications. They describe and implement a designer hammerhead ribozyme that cleaves a target sequence 1 nt from a site of adenosine to inosine (A-to-I) or cytosine to uracil (C-to-U) editing in synthetic or physiological mRNA cont...

  12. Distinctive Klf4 mutants determine preference for DNA methylation status

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-09-04

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

  13. Transgenerational Radiation Epigenetics

    Science.gov (United States)

    2014-11-01

    showed altered expression in normal lung from F3 mice. Thus, traces of the effects of a single dose of radiation during development persist into...radiation showed a loss of global cytosine methylation in DNA from thymus , implicating profound epigenetic dysregulation (Tawa et al., 1998; Pogribny...for the carcinogenic and transgenerational effects of radiation. It is also anticipated that these epigenetic signatures will be developed as

  14. DNA Methylation

    OpenAIRE

    Alokail, Majed S.; Alenad, Amal M.

    2015-01-01

    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication e...

  15. Chromatin Memory in the Development of Human Cancers

    OpenAIRE

    Yao, Yixin; Des Marais, Thomas L; Costa, Max

    2014-01-01

    Cancer is a complex disease with acquired genomic and epigenomic alterations that affect cell proliferation, viability and invasiveness. Almost all the epigenetic mechanisms including cytosine methylation and hydroxymethylation, chromatin remodeling and non-coding RNAs have been found associate with carcinogenesis and cancer specific expression profile. Altered histone modification as an epigenetic hallmark is frequently found in tumors. Understanding the epigenetic alterations induced by car...

  16. Hyperchromicity and strand separation in bacterial DNA.

    Science.gov (United States)

    FREIFELDER, D; DAVISON, P F

    1962-05-01

    Studies of the per cent of strand separation of N(14)-N(15) hybrid coli DNA heated to various temperatures in formaldehyde have shown that the process of strand separation is a function of temperature and formaldehyde concentration and is directly related to the measured hyperchromicity. No strands separate until about 75 per cent of full hyperchromicity is obtained, and even at apparently full hyperchromicity a large fraction of the strands may be held together, possibly by guanine-cytosine-rich regions.

  17. PCR bias in amplification of androgen receptor alleles, a trinucleotide repeat marker used in clonality studies.

    OpenAIRE

    Mutter, G L; Boynton, K A

    1995-01-01

    Trinucleotide CAG repeats in the X-linked human androgen receptor gene (HUMARA) have proved a useful means of determining X chromosome haplotypes, and when combined with methylation analysis of nearby cytosine residues permits identification of non-random X inactivation in tumors of women. Co-amplification of two alleles in a heterozygote generates PCR products which differ in the number of CAG units, and thus their melting and secondary structure characteristics. We have shown that under opt...

  18. Detection of DNA methylation changes during seed germination in rapeseed (Brassica napus)

    Institute of Scientific and Technical Information of China (English)

    LU Guangyuan; WU Xiaoming; CHEN Biyun; GAO Guizhen; XU Kun; LI Xiangzhi

    2006-01-01

    DNA methylation is known to play a crucial role in regulating plant development and organ or tissue differentiation. In this study, we assessed the extent and pattern of cytosine methylation during rapeseed (Brassica napus L.) seed germination, and compared the methylation level of various tissues in seedling, using the techniques of methylation-sensitive amplified polymorphism (MSAP) and HPLC separation and quantification of nucleosides. In all, 484 bands, each representing a recognition site cleaved by either or both of the isoschizomers, were amplified by 12 pairs of selective primers in DNA obtained from dry seeds. A total of 76 sites were found to be differentially digested by the isoschizomers, indicating that approximately 15.7% of 5(-CCGG-3( sites in the genome were cytosine methylated. Four classes of patterns were observed in a comparative assay of cytosine methylation in the dry and germinating seeds; a small number of hypermethylation events occurred at 5(-CCGG-3( sites in germinating seeds compared with dry seeds, while many more hypomethylation events were detected after seed germination. Differences in DNA methylation level in various tissues were also detected; radicel was less methylated than hypocotyl and cotyledon. These observations were further confirmed by HPLC analysis. In addition, sequencing of eleven differentially methylated fragments and the subsequent blast search revealed that cytosine methylated 5(-CCGG- 3( sequences were equally distributed between coding and non-coding regions. These results clearly demonstrate the power of MSAP technique for large-scale DNA methylation detection in rapeseed genome, and the complexity of DNA methylation change during seed germination. DNA Hypomethylation going with seed germination appears to be a necessary step toward transcriptional activation in gene expression, and 5 well contribute to the developmental gene regulation.

  19. Molecular data for a biochemical model of DNA damage: Electron impact ionization and dissociative ionization cross sections of DNA bases and sugar-phosphate backbone

    Energy Technology Data Exchange (ETDEWEB)

    Huo, Winifred M. [NASA Ames Research Center, Mail Stop T27B-1, Moffett Field, CA 94035-1000 (United States)]. E-mail: whuo@mail.arc.nasa.gov; Dateo, Christopher E. [ELORET Corporation, Sunnyvale, CA (United States); Fletcher, Graham D. [ELORET Corporation, Sunnyvale, CA (United States)

    2006-10-15

    As part of the database for building up a biochemical model of DNA radiation damage, electron impact ionization cross sections of sugar-phosphate backbone and DNA bases have been calculated using the improved binary-encounter dipole (iBED) model. It is found that the total ionization cross sections of C{sub 3}{sup '}- and C{sub 5}{sup '}-deoxyribose-phosphate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C{sub 3}{sup '}- and C{sub 5}{sup '}-deoxyribose-phosphate cross sections, differing by less than 10%, an indication that a building-up principle may be applicable. Of the four DNA bases, the ionization cross section of guanine is the largest, then in decreasing order, adenine, thymine, and cytosine. The order is in accordance with the known propensity of oxidation of the bases by ionizing radiation. Dissociative ionization (DI), a process that both ionizes and dissociates a molecule, is investigated for cytosine. The DI cross section for the formation of H and (cytosine-H1){sup +}, with the cytosine ion losing H at the 1 position, is also reported. The threshold of this process is calculated to be 16.9eV. Detailed analysis of ionization products such as in DI is important to trace the sequential steps in the biochemical process of DNA damage.

  20. DNA Methylation: Bisulphite Modification and Analysis

    OpenAIRE

    Patterson, Kate; Molloy, Laura; Qu, Wenjia; Clark, Susan

    2011-01-01

    Epigenetics describes the heritable changes in gene function that occur independently to the DNA sequence. The molecular basis of epigenetic gene regulation is complex, but essentially involves modifications to the DNA itself or the proteins with which DNA associates. The predominant epigenetic modification of DNA in mammalian genomes is methylation of cytosine nucleotides (5-MeC). DNA methylation provides instruction to gene expression machinery as to where and when the gene should be expres...

  1. Characterization of in vitro haploid and doubled haploid Chrysanthemum morifolium plants via unfertilized ovule culture for phenotypical traits and DNA methylation pattern.

    Directory of Open Access Journals (Sweden)

    Haibin eWang

    2014-12-01

    Full Text Available Chrysanthemum is one of important ornamental species in the world. Its highly heterozygous state complicates molecular analysis, so it is of interest to derive haploid forms. A total of 2,579 non-fertilized chrysanthemum ovules pollinated by Argyranthemum frutescens were cultured in vitro to isolate haploid progeny. One single regenerant emerged from each of three of the 105 calli produced. Chromosome counts and microsatellite fingerprinting showed that only one of the regenerants was a true haploid. Nine doubled haploid derivatives were subsequently generated by colchicine treatment of 80 in vitro cultured haploid nodal segments. Morphological screening showed that the haploid plant was shorter than the doubled haploids, and developed smaller leaves, flowers and stomata. An in vitro pollen germination test showed that few of the haploid's pollen were able to germinate and those which did so were abnormal. Both the haploid and the doubled haploids produced yellow flowers, whereas those of the maternal parental cultivar were mauve. Methylation-sensitive amplification polymorphism (MSAP profiling was further used to detect alterations in cytosine methylation caused by the haploidization and/or the chromosome doubling processes. While 52.2% of the resulting amplified fragments were cytosine methylated in the maternal parent's genome, the corresponding proportions for the haploid's and doubled haploids' genomes were, respectively, 47.0% and 51.7%, demonstrating a reduction in global cytosine methylation caused by haploidization and a partial recovery following chromosome doubling.

  2. DNA abasic site-directed formation of fluorescent silver nanoclusters for selective nucleobase recognition

    Energy Technology Data Exchange (ETDEWEB)

    Ma Kun; Cui Qinghua; Liu Guiying; Wu Fei; Xu Shujuan; Shao Yong, E-mail: yshao@zjnu.cn [Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang (China)

    2011-07-29

    DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation related diseases. Various methods for SNP detection have been proposed and many are already in use. Here, we find that the abasic site (AP site) in the DNA duplex can be developed as a capping scaffold for the generation of fluorescent silver nanoclusters (Ag NCs). As a proof of concept, the DNA sequences from fragments near codon 177 of cancer supression gene p53 were used as a model for SNP detection by in situ formed Ag NCs. The formation of fluorescent Ag NCs in the AP site-containing DNA duplex is highly selective for cytosine facing the AP site and guanines flanking the site and can be employed in situ as readout for SNP detection. The fluorescent signal-on sensing for SNP based on this inorganic fluorophore is substantially advantageous over the previously reported signal-off responses using low-molecular-weight organic ligands. The strong dependence of fluorescent Ag NC formation on the sequences surrounding the AP site was successfully used to identify mutations in codon 177 of cancer supression gene p53. We anticipate that this approach will be employed to develop a practical SNP detection method by locating an AP site toward the midway cytosine in a target strand containing more than three consecutive cytosines.

  3. Electrochemical DNA probe for Hg(2+) detection based on a triple-helix DNA and Multistage Signal Amplification Strategy.

    Science.gov (United States)

    Wang, Huan; Zhang, Yihe; Ma, Hongmin; Ren, Xiang; Wang, Yaoguang; Zhang, Yong; Wei, Qin

    2016-12-15

    In this work, an ultrasensitive electrochemical sensor was developed for detection of Hg(2+). Gold nanoparticles decorated bovine serum albumin reduction of graphene oxide (AuNP-BSA-rGO) were used as subsurface material for the immobilization of triple-helix DNA. The triple-helix DNA containing a thiol labelled single-stranded DNA (sDNA) and a thymine-rich DNA (T-rich DNA), which could be unwinded in the present of Hg(2+) to form more stable thymine-Hg(2+)-thymine (T-Hg(2+)-T) complex. T-Hg(2+)-T complex was then removed and the sDNA was left on the electrode. At this time, gold nanoparticle carrying thiol labelled cytosine-rich complementary DNA (cDNA-AuNP) could bind with the free sDNA. Meanwhile, the other free cDNA on AuNP could bind with each other in the present of Ag(+) to form the stable cytosine-Ag(+)-cytosine (C-Ag(+)-C) complex and circle amplification. Plenty of C-Ag(+)-C could form silver nanoclusters by electrochemical reduction and the striping signal of Ag could be measured for purpose of the final electrochemical detection of Hg(2+). This sensor could detect Hg(2+) over a wide concentration range from 0.1 to 130nM with a detection limit of 0.03nM.

  4. Molecular mechanisms of primary resistance to flucytosine in Candida albicans.

    Science.gov (United States)

    Hope, William W; Tabernero, Lydia; Denning, David W; Anderson, Michael J

    2004-11-01

    Primary resistance in Candida albicans to flucytosine (5-FC) was investigated in 25 strains by identifying and sequencing the genes FCA1, FUR1, FCY21, and FCY22, which code for cytosine deaminase, uracil phosphoribosyltransferase (UPRT), and two purine-cytosine permeases, respectively. These proteins are involved in pyrimidine salvage and 5-FC metabolism. An association between a polymorphic nucleotide and resistance to 5-FC was found within FUR1 where the substitution of cytidylate for thymidylate at nucleotide position 301 results in the replacement of arginine with cysteine at amino acid position 101 in UPRT. Isolates that are homozygous for this mutation display increased levels of resistance to 5-FC, whereas heterozygous isolates have reduced susceptibility. Three-dimensional protein modeling of UPRT suggests that the Arg101Cys mutation disturbs the quaternary structure of the enzyme, which is postulated to compromise optimal enzyme activity. A single resistant isolate, lacking the above polymorphism in FUR1, has a homozygous polymorphism in FCA1 that results in a glycine-to-aspartate substitution at position 28 in cytosine deaminase.

  5. Iron Supplementation Reverses the Reduction of Hydroxymethylcytosine in Hepatic DNA Associated With Chronic Alcohol Consumption in Rats

    Science.gov (United States)

    Tammen, Stephanie A.; Park, Jung Eun; Shin, Phil Kyung; Friso, Simonetta; Chung, Jayong; Choi, Sang-Woon

    2016-01-01

    Background Alcohol is known to affect two epigenetic phenomena, DNA methylation and DNA hydroxymethylation, and iron is a cofactor of ten-eleven translocation (TET) enzymes that catalyze the conversion from methylcytosine to hydroxymethylcytosine. In the present study we aimed to determine the effects of alcohol on DNA hydroxymethylation and further effects of iron on alcohol associated epigenetic changes. Methods Twenty-four male Sprague-Dawley rats were fed either Lieber-DeCarli alcohol diet (36% calories from ethanol) or Lieber-DeCarli control diet along with or without iron supplementation (0.6% carbonyl iron) for 8 weeks. Hepatic non-heme iron concentrations were measured by colorimetric assays. Protein levels of hepatic ferritin and transferrin receptor were determined by Western blotting. Methylcytosine, hydroxymethylcytosine and unmodified cytosine in DNA were simultaneously measured by liquid chromatography/mass spectrometry method. Results Iron supplementation significantly increased hepatic non-heme iron contents (P iron significantly increased hepatic ferritin levels and decreased hepatic transferrin receptor levels (P iron supplementation to alcohol diet did not change DNA hydroxymethylation. There was no significant difference in methylcytosine levels, while unmodified cytosine levels were significantly increased in alcohol-fed groups compared to control (95.61% ± 0.08% vs. 95.26% ± 0.12%, P = 0.03), suggesting that alcohol further increases the conversion from hydroxymethylcytosine to unmodified cytosine. Conclusions Chronic alcohol consumption alters global DNA hydroxymethylation in the liver but iron supplementation reverses the epigenetic effect of alcohol. PMID:28053961

  6. Nitric oxide as a carcinogen. Analysis by yeast functional assay of inactivating p53 mutations induced by nitric oxide

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    Murata, Jun-Ichi; Tada, Mitsuhiro; Sawamura, Yutaka; Shinohe, Yumiko; Abe, Hiroshi [Laboratory for Molecular Brain Research, Department of Neurosurgery, Hokkaido University School of Medicine, Sapporo (Japan); Iggo, Richard D. [Oncogene group, Swiss Institute for Experimental Cancer Research ISREC, Epalinges (Switzerland)

    1997-10-06

    We have used a yeast p53 functional assay to study induction of mutations in the p53 tumor suppressor gene by nitric oxide and cytosine methylation. The yeast assay identifies only biologically important p53 mutations. p53 cDNA was treated with the nitric oxide donor sydnonimine, PCR-amplified and transfected into yeast. Sydnonimine produced a significant, dose-dependent increase in C:G->A:T transversions. Many important p53 mutational hotspots are postulated to arise by deamination of methylCpG in tumors. We therefore examined nitric oxide induction of mutations in p53 cDNA methylated by PCR-mediated substitution of 5-methylcytosine for cytosine or by treatment with the SssI CpG methylase. Both methylation procedures increased the baseline mutation rate, and nitric oxide treatment produced a further increase in mutation yield. Sequence analysis showed that methylation alone led to C:G->T:A transitions, whereas nitric oxide treatment simply produced more C:G->A:T transversions. Thus the most important factor in C:G->T:A transition at CpG sites identified in this experimental system is cytosine methylation, consistent with spontaneous conversion of 5-methylcytosine to thymine by deamination

  7. Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes.

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    Irene Keller

    2007-02-01

    Full Text Available Comparisons of the DNA sequences of metazoa show an excess of transitional over transversional substitutions. Part of this bias is due to the relatively high rate of mutation of methylated cytosines to thymine. Postmutation processes also introduce a bias, particularly selection for codon-usage bias in coding regions. It is generally assumed, however, that there is a universal bias in favour of transitions over transversions, possibly as a result of the underlying chemistry of mutation. Surprisingly, this underlying trend has been evaluated only in two types of metazoan, namely Drosophila and the Mammalia. Here, we investigate a third group, and find no such bias. We characterize the point substitution spectrum in Podisma pedestris, a grasshopper species with a very large genome. The accumulation of mutations was surveyed in two pseudogene families, nuclear mitochondrial and ribosomal DNA sequences. The cytosine-guanine (CpG dinucleotides exhibit the high transition frequencies expected of methylated sites. The transition rate at other cytosine residues is significantly lower. After accounting for this methylation effect, there is no significant difference between transition and transversion rates. These results contrast with reports from other taxa and lead us to reject the hypothesis of a universal transition/transversion bias. Instead we suggest fundamental interspecific differences in point substitution processes.

  8. B-Myb Induces APOBEC3B Expression Leading to Somatic Mutation in Multiple Cancers

    Science.gov (United States)

    Chou, Wen-Cheng; Chen, Wei-Ting; Hsiung, Chia-Ni; Hu, Ling-Yueh; Yu, Jyh-Cherng; Hsu, Huan-Ming; Shen, Chen-Yang

    2017-01-01

    The key signature of cancer genomes is the accumulation of DNA mutations, the most abundant of which is the cytosine-to-thymine (C-to-T) transition that results from cytosine deamination. Analysis of The Cancer Genome Atlas (TCGA) database has demonstrated that this transition is caused mainly by upregulation of the cytosine deaminase APOBEC3B (A3B), but the mechanism has not been completely characterized. We found that B-Myb (encoded by MYBL2) binds the A3B promoter, causing transactivation, and this is responsible for the C-to-T transitions and DNA hypermutation in breast cancer cells. Analysis of TCGA database yielded similar results, supporting that MYBL2 and A3B are upregulated and putatively promote C-to-T transitions in multiple cancer types. Moreover, blockade of EGF receptor with afatinib attenuated B-Myb–A3B signaling, suggesting a clinically relevant means of suppressing mutagenesis. Our results suggest that B-Myb–A3B contributes to DNA damage and could be targeted by inhibiting EGF receptor. PMID:28276478

  9. Site-Selective Monitoring of the Interaction of the SRA Domain of UHRF1 with Target DNA Sequences Labeled with 2-Aminopurine.

    Science.gov (United States)

    Greiner, Vanille J; Kovalenko, Lesia; Humbert, Nicolas; Richert, Ludovic; Birck, Catherine; Ruff, Marc; Zaporozhets, Olga A; Dhe-Paganon, Sirano; Bronner, Christian; Mély, Yves

    2015-10-06

    UHRF1 plays a central role in the maintenance and transmission of epigenetic modifications by recruiting DNMT1 to hemimethylated CpG sites via its SET and RING-associated (SRA) domain, ensuring error-free duplication of methylation profiles. To characterize SRA-induced changes in the conformation and dynamics of a target 12 bp DNA duplex as a function of the methylation status, we labeled duplexes by the environment-sensitive probe 2-aminopurine (2-Ap) at various positions near or far from the central CpG recognition site containing either a nonmodified cytosine (NM duplex), a methylated cytosine (HM duplex), or methylated cytosines on both strands (BM duplex). Steady-state and time-resolved fluorescence indicated that binding of SRA induced modest conformational and dynamical changes in NM, HM, and BM duplexes, with only slight destabilization of base pairs, restriction of global duplex flexibility, and diminution of local nucleobase mobility. Moreover, significant restriction of the local motion of residues flanking the methylcytosine in the HM duplex suggested that these residues are more rigidly bound to SRA, in line with a slightly higher affinity of the HM duplex as compared to that of the NM or BM duplex. Our results are consistent with a "reader" role, in which the SRA domain scans DNA sequences for hemimethylated CpG sites without perturbation of the structure of contacted nucleotides.

  10. Anhydrous crystals of DNA bases are wide gap semiconductors.

    Science.gov (United States)

    Maia, F F; Freire, V N; Caetano, E W S; Azevedo, D L; Sales, F A M; Albuquerque, E L

    2011-05-07

    We present the structural, electronic, and optical properties of anhydrous crystals of DNA nucleobases (guanine, adenine, cytosine, and thymine) found after DFT (Density Functional Theory) calculations within the local density approximation, as well as experimental measurements of optical absorption for powders of these crystals. Guanine and cytosine (adenine and thymine) anhydrous crystals are predicted from the DFT simulations to be direct (indirect) band gap semiconductors, with values 2.68 eV and 3.30 eV (2.83 eV and 3.22 eV), respectively, while the experimentally estimated band gaps we have measured are 3.83 eV and 3.84 eV (3.89 eV and 4.07 eV), in the same order. The electronic effective masses we have obtained at band extremes show that, at low temperatures, these crystals behave like wide gap semiconductors for electrons moving along the nucleobases stacking direction, while the hole transport are somewhat limited. Lastly, the calculated electronic dielectric functions of DNA nucleobases crystals in the parallel and perpendicular directions to the stacking planes exhibit a high degree of anisotropy (except cytosine), in agreement with published experimental results.

  11. High-resolution photoelectron spectra of the pyrimidine-type nucleobases.

    Science.gov (United States)

    Fulfer, K D; Hardy, D; Aguilar, A A; Poliakoff, E D

    2015-06-14

    High-resolution photoelectron spectra of the gas phase pyrimidine-type nucleobases, thymine, uracil, and cytosine, were collected using synchrotron radiation over the photon energy range 17 ≤ hν ≤ 150 eV. These data provide the highest resolution photoelectron spectra of thymine, uracil, and cytosine published to date. By comparing integrated regions of the energy dependent photoelectron spectra of thymine, the ionization potentials of the first four ionic states of thymine were estimated to be 8.8, 9.8, 10.3, and 10.8 eV. The thymine data also show evidence for low energy shape resonances in three of the outermost valence electronic states. Comparing the uracil spectrum with the thymine spectrum, the four outermost valence electronic states of uracil likely begin at binding energies 9.3, 9.9, 10.5, and 11.0 eV. High-resolution spectra indicate only one tautomeric form of cytosine contributes significantly to the spectrum with the four outermost valence electronic states beginning at binding energies 8.9, 9.9, 10.4, and 10.85 eV.

  12. High-resolution photoelectron spectra of the pyrimidine-type nucleobases

    Energy Technology Data Exchange (ETDEWEB)

    Fulfer, K. D.; Hardy, D.; Poliakoff, E. D., E-mail: epoliak@lsu.edu [Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Aguilar, A. A. [Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2015-06-14

    High-resolution photoelectron spectra of the gas phase pyrimidine-type nucleobases, thymine, uracil, and cytosine, were collected using synchrotron radiation over the photon energy range 17 ≤ hν ≤ 150 eV. These data provide the highest resolution photoelectron spectra of thymine, uracil, and cytosine published to date. By comparing integrated regions of the energy dependent photoelectron spectra of thymine, the ionization potentials of the first four ionic states of thymine were estimated to be 8.8, 9.8, 10.3, and 10.8 eV. The thymine data also show evidence for low energy shape resonances in three of the outermost valence electronic states. Comparing the uracil spectrum with the thymine spectrum, the four outermost valence electronic states of uracil likely begin at binding energies 9.3, 9.9, 10.5, and 11.0 eV. High-resolution spectra indicate only one tautomeric form of cytosine contributes significantly to the spectrum with the four outermost valence electronic states beginning at binding energies 8.9, 9.9, 10.4, and 10.85 eV.

  13. GPU-BSM: a GPU-based tool to map bisulfite-treated reads.

    Science.gov (United States)

    Manconi, Andrea; Orro, Alessandro; Manca, Emanuele; Armano, Giuliano; Milanesi, Luciano

    2014-01-01

    Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads.

  14. Formation of Nucleobases from the UV Irradiation of Pyrimidine in Astrophysical Ice Analogs

    Science.gov (United States)

    Sandford, Scott A.; Nuevo, Michel; Materese, Christopher K.

    2014-01-01

    Nucleobases are the informational subunits of DNA and RNA. They consist of Nheterocycles that belong to either the pyrimidine-base group (uracil, cytosine, and thymine) or the purinebase group (adenine and guanine). Several nucleobases, mostly purine bases, have been detected in meteorites [1-3], with isotopic signatures consistent with an extraterrestrial origin [4]. Uracil is the only pyrimidine-base compound formally reported in meteorites [2], though the presence of cytosine cannot be ruled out [5,6]. However, the actual process by which the uracil was made and the reasons for the non-detection of thymine in meteorites have yet to be fully explained. Although no N-heterocycles have ever been observed in the ISM [7,8], the positions of the 6.2-µm interstellar emission features suggest a population of such molecules is likely to be present [9]. In this work we study the formation of pyrimidine-based molecules, including the three nucleobases uracil, cytosine, and thymine from the ultraviolet (UV) irradiation of pyrimidine in ices consisting of several combinations of H(sub2)O, NH(sub3), CH(sub3)OH, and CH(sub4) at low temperature, in order to simulate the astrophysical conditions under which prebiotic species may be formed in the interstellar medium, in the protosolar nebula, and on icy bodies of the Solar System.

  15. FadE: whole genome methylation analysis for multiple sequencing platforms.

    Science.gov (United States)

    Souaiaia, Tade; Zhang, Zheng; Chen, Ting

    2013-01-01

    DNA methylation plays a central role in genomic regulation and disease. Sodium bisulfite treatment (SBT) causes unmethylated cytosines to be sequenced as thymine, which allows methylation levels to reflected in the number of 'C'-'C' alignments covering reference cytosines. Di-base color reads produced by lifetech's SOLiD sequencer provide unreliable results when translated to bases because single sequencing errors effect the downstream sequence. We describe FadE, an algorithm to accurately determine genome-wide methylation rates directly in color or nucleotide space. FadE uses SBT unmethylated and untreated data to determine background error rates and incorporate them into a model which uses Newton-Raphson optimization to estimate the methylation rate and provide a credible interval describing its distribution at every reference cytosine. We sequenced two slides of human fibroblast cell-line bisulfite-converted fragment library with the SOLiD sequencer to investigate genome-wide methylation levels. FadE reported widespread differences in methylation levels across CpG islands and a large number of differentially methylated regions adjacent to genes which compares favorably to the results of an investigation on the same cell-line using nucleotide-space reads at higher coverage levels, suggesting that FadE is an accurate method to estimate genome-wide methylation with color or nucleotide reads. http://code.google.com/p/fade/.

  16. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA.

    Science.gov (United States)

    Squires, Jeffrey E; Patel, Hardip R; Nousch, Marco; Sibbritt, Tennille; Humphreys, David T; Parker, Brian J; Suter, Catherine M; Preiss, Thomas

    2012-06-01

    The modified base 5-methylcytosine (m(5)C) is well studied in DNA, but investigations of its prevalence in cellular RNA have been largely confined to tRNA and rRNA. In animals, the two m(5)C methyltransferases NSUN2 and TRDMT1 are known to modify specific tRNAs and have roles in the control of cell growth and differentiation. To map modified cytosine sites across a human transcriptome, we coupled bisulfite conversion of cellular RNA with next-generation sequencing. We confirmed 21 of the 28 previously known m(5)C sites in human tRNAs and identified 234 novel tRNA candidate sites, mostly in anticipated structural positions. Surprisingly, we discovered 10,275 sites in mRNAs and other non-coding RNAs. We observed that distribution of modified cytosines between RNA types was not random; within mRNAs they were enriched in the untranslated regions and near Argonaute binding regions. We also identified five new sites modified by NSUN2, broadening its known substrate range to another tRNA, the RPPH1 subunit of RNase P and two mRNAs. Our data demonstrates the widespread presence of modified cytosines throughout coding and non-coding sequences in a transcriptome, suggesting a broader role of this modification in the post-transcriptional control of cellular RNA function.

  17. Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Huy Q Dinh

    Full Text Available Deep sequencing after bisulfite conversion (BS-Seq is the method of choice to generate whole genome maps of cytosine methylation at single base-pair resolution. Its application to genomic DNA of Arabidopsis flower bud tissue resulted in the first complete methylome, determining a methylation rate of 6.7% in this tissue. BS-Seq reads were mapped onto an in silico converted reference genome, applying the so-called 3-letter genome method. Here, we present BiSS (Bisufite Sequencing Scorer, a new method applying Smith-Waterman alignment to map bisulfite-converted reads to a reference genome. In addition, we introduce a comprehensive adaptive error estimate that accounts for sequencing errors, erroneous bisulfite conversion and also wrongly mapped reads. The re-analysis of the Arabidopsis methylome data with BiSS mapped substantially more reads to the genome. As a result, it determines the methylation status of an extra 10% of cytosines and estimates the methylation rate to be 7.7%. We validated the results by individual traditional bisulfite sequencing for selected genomic regions. In addition to predicting the methylation status of each cytosine, BiSS also provides an estimate of the methylation degree at each genomic site. Thus, BiSS explores BS-Seq data more extensively and provides more information for downstream analysis.

  18. DNA abasic site-directed formation of fluorescent silver nanoclusters for selective nucleobase recognition

    Science.gov (United States)

    Ma, Kun; Cui, Qinghua; Liu, Guiying; Wu, Fei; Xu, Shujuan; Shao, Yong

    2011-07-01

    DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation related diseases. Various methods for SNP detection have been proposed and many are already in use. Here, we find that the abasic site (AP site) in the DNA duplex can be developed as a capping scaffold for the generation of fluorescent silver nanoclusters (Ag NCs). As a proof of concept, the DNA sequences from fragments near codon 177 of cancer supression gene p53 were used as a model for SNP detection by in situ formed Ag NCs. The formation of fluorescent Ag NCs in the AP site-containing DNA duplex is highly selective for cytosine facing the AP site and guanines flanking the site and can be employed in situ as readout for SNP detection. The fluorescent signal-on sensing for SNP based on this inorganic fluorophore is substantially advantageous over the previously reported signal-off responses using low-molecular-weight organic ligands. The strong dependence of fluorescent Ag NC formation on the sequences surrounding the AP site was successfully used to identify mutations in codon 177 of cancer supression gene p53. We anticipate that this approach will be employed to develop a practical SNP detection method by locating an AP site toward the midway cytosine in a target strand containing more than three consecutive cytosines.

  19. High-molecular-weight DNA and the sedimentation coefficient: a new perspective based on DNA from T7 bacteriophage and two novel forms of T4 bacteriophage.

    Science.gov (United States)

    Clark, R W; Wever, G H; Wiberg, J S

    1980-01-01

    The DNA molecules from T7 bacteriophage and a recently obtained mutant form of T4D were studied. The DNA of this T4 mutant contains cytosine in place of all of the glucosylated hydroxymethylcytosines normally present in T4. Molecular weights were measured with an electron microscope technique, and sedimentation coefficients were determined in isokinetic sucrose gradients. T7 DNA was found to have an Mr of 26.5 x 10(6). The T4 mutant, which we have termed T4c, produces two distinct phage head and DNA size clases. DNA from the standard heads (T4c DNA) has an Mr of 114.9 x 10(6), and DNA from the petite heads (T4cp DNA) has an Mr of 82.9 x 10(6). This enabled the derivation of an equation of sedimentation coefficient at zero concentration corrected to water at 20 degrees C versus Mr for the molecular weight range of 25 x 10(6) to 115 x 10(6) that is based solely on cytosine-containing DNA standards, thereby avoiding possible anomalies introduced by the glucosylation and hydroxymethylation of cytosine. The theory of Gray et al. provided the best description of the sedimentation coefficient versus Mr relationship, based on the sedimentation coefficients and the molecular weights of the three DNA standards and other evidence.

  20. Label-Free Detection of Ag+ Based on Gold Nanoparticles and Ag+-Specific DNA.

    Science.gov (United States)

    Pu, Wendan; Zhao, Zhao; Wu, Liping; Liu, Yue; Zhao, Huawen

    2015-08-01

    A sensitive label-free method was presented for the determination of silver ion (Ag+) in this paper. Cytosine-rich DNA (C-DNA) was used as Ag+ specific DNA. Without Ag+ in the solution, fluorescence of fluorescein (FAM) is quenched by C-DNA stabilized gold nanoparticles (AuNPs) in high salt environment. When Ag+ is present in the solution, however, Ag+-mediated cytosine-Ag+-cytosine (C-Ag+-C) base pairs induced the C-DNA folding into a hairpin structure, which can not stabilize AuNPs in high salt environment, thus causing AuNPs aggregation. After centrifugation to remove the aggregated AuNPs, the quenching ability of the supernatant for FAM is decreased and the fluorescence intensity of solution increases with increasing the Ag+ concentration. Due to the highly specific interaction of the C-DNA towards Ag+ and the strong fluorescent quenching ability of AuNPs for FAM, the method has high selectivity and sensitivity for Ag+. Under the optimal conditions, the fluorescence intensity at 515 nm increased linearly with the concentration of Ag+ ranging from 15 nM to 700 nM, and the detection limit was determined as 6 nM based on 3 σ/slope. This method is simple, sensitive, and may be applied to other detection systems by selecting the appropriate DNA sequences.

  1. GPU-BSM: a GPU-based tool to map bisulfite-treated reads.

    Directory of Open Access Journals (Sweden)

    Andrea Manconi

    Full Text Available Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads.

  2. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.

    Directory of Open Access Journals (Sweden)

    Vardhman K Rakyan

    2004-12-01

    Full Text Available The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine-guanine dinucleotides, DNA methylation is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of such methylation variable positions will significantly improve our understanding of genome biology and our ability to diagnose disease. Here, we report the results of the pilot study for the Human Epigenome Project entailing the methylation analysis of the human major histocompatibility complex. This study involved the development of an integrated pipeline for high-throughput methylation analysis using bisulphite DNA sequencing, discovery of methylation variable positions, epigenotyping by matrix-assisted laser desorption/ionisation mass spectrometry, and development of an integrated public database available at http://www.epigenome.org. Our analysis of DNA methylation levels within the major histocompatibility complex, including regulatory exonic and intronic regions associated with 90 genes in multiple tissues and individuals, reveals a bimodal distribution of methylation profiles (i.e., the vast majority of the analysed regions were either hypo- or hypermethylated, tissue specificity, inter-individual variation, and correlation with independent gene expression data.

  3. Genetic analysis of the cardiac methylome at single nucleotide resolution in a model of human cardiovascular disease.

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    Michelle D Johnson

    2014-12-01

    Full Text Available Epigenetic marks such as cytosine methylation are important determinants of cellular and whole-body phenotypes. However, the extent of, and reasons for inter-individual differences in cytosine methylation, and their association with phenotypic variation are poorly characterised. Here we present the first genome-wide study of cytosine methylation at single-nucleotide resolution in an animal model of human disease. We used whole-genome bisulfite sequencing in the spontaneously hypertensive rat (SHR, a model of cardiovascular disease, and the Brown Norway (BN control strain, to define the genetic architecture of cytosine methylation in the mammalian heart and to test for association between methylation and pathophysiological phenotypes. Analysis of 10.6 million CpG dinucleotides identified 77,088 CpGs that were differentially methylated between the strains. In F1 hybrids we found 38,152 CpGs showing allele-specific methylation and 145 regions with parent-of-origin effects on methylation. Cis-linkage explained almost 60% of inter-strain variation in methylation at a subset of loci tested for linkage in a panel of recombinant inbred (RI strains. Methylation analysis in isolated cardiomyocytes showed that in the majority of cases methylation differences in cardiomyocytes and non-cardiomyocytes were strain-dependent, confirming a strong genetic component for cytosine methylation. We observed preferential nucleotide usage associated with increased and decreased methylation that is remarkably conserved across species, suggesting a common mechanism for germline control of inter-individual variation in CpG methylation. In the RI strain panel, we found significant correlation of CpG methylation and levels of serum chromogranin B (CgB, a proposed biomarker of heart failure, which is evidence for a link between germline DNA sequence variation, CpG methylation differences and pathophysiological phenotypes in the SHR strain. Together, these results will

  4. Association of ATRX with pericentric heterochromatin and the Y chromosome of neonatal mouse spermatogonia

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    De La Fuente Rabindranath

    2008-03-01

    Full Text Available Abstract Background Establishment of chromosomal cytosine methylation and histone methylation patterns are critical epigenetic modifications required for heterochromatin formation in the mammalian genome. However, the nature of the primary signal(s targeting DNA methylation at specific genomic regions is not clear. Notably, whether histone methylation and/or chromatin remodeling proteins play a role in the establishment of DNA methylation during gametogenesis is not known. The chromosomes of mouse neonatal spermatogonia display a unique pattern of 5-methyl cytosine staining whereby centromeric heterochromatin is hypo-methylated whereas chromatids are strongly methylated. Thus, in order to gain some insight into the relationship between global DNA and histone methylation in the germ line we have used neonatal spermatogonia as a model to determine whether these unique chromosomal DNA methylation patterns are also reflected by concomitant changes in histone methylation. Results Our results demonstrate that histone H3 tri-methylated at lysine 9 (H3K9me3, a hallmark of constitutive heterochromatin, as well as the chromatin remodeling protein ATRX remained associated with pericentric heterochromatin regions in spite of their extensive hypo-methylation. This suggests that in neonatal spermatogonia, chromosomal 5-methyl cytosine patterns are regulated independently of changes in histone methylation, potentially reflecting a crucial mechanism to maintain pericentric heterochromatin silencing. Furthermore, chromatin immunoprecipitation and fluorescence in situ hybridization, revealed that ATRX as well as H3K9me3 associate with Y chromosome-specific DNA sequences and decorate both arms of the Y chromosome, suggesting a possible role in heterochromatinization and the predominant transcriptional quiescence of this chromosome during spermatogenesis. Conclusion These results are consistent with a role for histone modifications and chromatin remodeling proteins

  5. Production of non-proteinogenic amino acids from α-keto acid precursors with recombinant Corynebacterium glutamicum.

    Science.gov (United States)

    Kim, Ju-Yeon; Lee, Young-A; Wittmann, Christoph; Park, Jin-Byung

    2013-11-01

    In the present work, Corynebacterium glutamicum was metabolically engineered for the enantioselective synthesis of non-proteinogenic amino acids as valuable building blocks for pharmaceuticals and agrochemicals. The novel bio-catalytic activity of C. glutamicum was obtained by heterologous expression of the branched chain aminotransferase IlvE from Escherichia coli. Upon this modification, the recombinant cells converted the α-keto acid precursor 2-(3-hydroxy-1-adamantyl)-2-oxoethanoic acid (HOAE) into the corresponding amino acid 2-(3-hydroxy-1-adamantyl)-(2S)-amino ethanoic acid (HAAE). Similarly, also L-tert-leucine could be obtained from trimethyl pyruvate indicating a broader applicability of the novel strategy. In both cases, the amino group donor glutamate was supplied from the endogenous metabolism of the recombinant producer. Hereby, the uptake of the precursor and secretion of the product was supported by an enhanced cell permeability through treatment of ethambutol, which inhibits arabinosyl transferases involved in cell wall biosynthesis. The excretion of HAAE into the reaction medium was linked to the secretion of glutamate, indicating a similar mechanism for the export of both compounds. On the other hand, the efflux of L-tert-leucine appeared to be driven by active transport. Subsequent bioprocess engineering enabled HAAE and L-tert-leucine to be produced at a rate of 0.21 and 0.42 mmol (g dry cells)⁻¹  h⁻¹, respectively up to a final product titer of 40 mM. Beyond the given examples, integrated metabolic and cell envelop engineering might extend the production of a variety of other non-proteinogenic amino acids as well as chiral amines by C. glutamicum.

  6. Alkaloids with Activity against the Zika Virus Vector Aedes aegypti (L.—Crinsarnine and Sarniensinol, Two New Crinine and Mesembrine Type Alkaloids Isolated from the South African Plant Nerine sarniensis

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    Marco Masi

    2016-10-01

    Full Text Available Two new Amaryllidaceae alkaloids, belonging to the mesembrine- and crinine-types, named crinsarnine (1 and sarniensinol (2, were isolated from the dried bulbs of Nerine sarniensis together with bowdensine (3, sarniensine (4, hippadine (5 and 1-O-acetyl-lycorine (6. Crinsarnine (1 and sarniensinol (2 were characterized using spectroscopic and chiroptical methods as (1S,2S,4aR,10bS-2,7-dimethoxy-1,2,3,4,4a,6-hexahydro-5,11b-ethano[1,3]dioxolo-[4,5-j]phenanthridin-1-yl acetate and (6-(3aR,4Z,6S,7aS-6-methoxy-1-methyl-2,3,3a,6,7,7a-hexa-hydro-1H-indol-3a-ylbenzo[d][1,3]dioxol-5-ylmethanol, respectively. Furthermore, the complete spectroscopic characterization of bowdensine (3 is reported for the first time. Compounds 1–6 were evaluated against the Orlando reference strain of Aedes aegypti. None of compounds showed mortality against 1st instar Ae. aegypti larvae at the concentrations tested. In adult topical bioassays, only 1 displayed adulticidal activity with an LD50 = 2.29 ± 0.049 μg/mosquito. As regards the structure-activity relationship, the pretazettine and crinine scaffold in 2 and 4 and in 1 and 3 respectively, proved to be important for their activity, while the pyrrole[de]phenanthridine scaffold present in 5 and 6 was important for their reactivity. Among the pretazettine group compounds, opening of the B ring or the presence of a B ring lactone as well as the trans-stereochemistry of the A/B ring junction, appears to be important for activity, while in crinine-type alkaloids, the substituent at C-2 seems to play a role in their activity.

  7. Towards a first-principles model of Fermi resonance in the alkyl CH stretch region: Application to 1,2-diphenylethane and 2,2,2-paracyclophane

    Science.gov (United States)

    Buchanan, Evan G.; Dean, Jacob C.; Zwier, Timothy S.; Sibert, Edwin L.

    2013-02-01

    The spectroscopy of two flexible hydrocarbons, 1,2-diphenylethane (DPE) and 2,2,2-paracyclophane (TCP) is presented, and a predictive theoretical model for describing the alkyl CH stretch region of these hydrocarbons is developed. Ultraviolet hole-burning spectroscopy identified two isomers of DPE and a single conformation of TCP present in the supersonic jet expansion. Through the analysis of the ground state low-frequency vibronic spectroscopy obtained by dispersed fluorescence, conformational assignments were made for both DPE and TCP. The two isomers of DPE were found to retain the low energy structures of butane, being present in both the gauche and anti structures. TCP forms a C2 symmetric structure, differing from the predicted lower energy C3 conformation by the symmetry of the ethano bridges (-CH2CH2-) linking the phenyl substituents. Resonant ion-dip infrared spectroscopy is used to record single-conformation IR spectra of the two conformers of DPE and the single conformer of TCP in the alkyl CH stretch region and in the mid-IR that covers the CH bend fundamentals. A local mode Hamiltonian that incorporates cubic stretch-bend coupling is developed. Its parameters are obtained from density functional theory methods. Full dimensional calculations are compared to those that use reduced dimensional Hamiltonians in which anharmonic CH stretches and scissor modes are Fermi coupled. Excellent agreement is found. Scale factors of select terms in the reduced dimensional Hamiltonian are determined by fitting the theoretical Hamiltonian to the anti-DPE spectrum. The scaled Hamiltonian is then used to predict successfully structures for the remaining lower symmetry experimentally determined spectra in the alkyl CH stretch region.

  8. Use of Novel Light Sources and Melatonin Delivery Systems in the Maintenance of Temporal Organization of Physiological and Behavioral Circadian Rhythms

    Science.gov (United States)

    Winget, C. M.; Singh, M. S.; Syrkin, N. C.; Holley, D. C.

    1998-01-01

    The synchronization of physiological and behavioral rhythms are controlled by an endogenous biological clock. It is generally accepted that environmental lighting is the strongest entrainer of this clock. The pineal gland is an important physiological transducer of environmental lighting via systemic melatonin secretion. We have used a novel light source using light emitting diode (LED) technology to entrain circadian rhythms in rats, and propose a novel percutaneous exogenous melatonin delivery system to entrain rat rhythms. We used 5 groups of Sprague-Dawley rats (175-350 g; N = 8/group) and showed normal entrainment of gross locomotor activity, feeding, and drinking circadian rhythms at light intensities varying from 80 lux to 0.1 lux (22.4 to 0.03 sq cm). To improve the delivery of melatonin across the skin stratum corneum it was formulated in a suitable vehicle in a transdermal drug delivery system. Various saturated and unsaturated fatty acids were used E, akin penetration enhancers. Our best vehicle formulation was achieved with a combination-of ethano1:water (60:40) along with 5% oleic acid as the enhancer. This formulation mixture was studied using Franz diffusion cell (0.636 sq cm diffusional area) and 1 cu cm dorsal skin isolated from Sprague Dawley rats. Our results showed that oleic acid in combination with the water ethanol mixture improved the flux of melatonin by more than 18 fold. The lag time for melatonin permeation was 2-3 hrs and the peak concentrations were achieved in 8-10 hrs. Our approaches in the future will involve the use of our transdermal melatonin delivery system and under the influence of LED light and microgravity.

  9. Prevention of Catheter-related Bloodstream Infection in ICU%ICU患者中心静脉导管相关性血流感染的预防

    Institute of Scientific and Technical Information of China (English)

    徐文

    2011-01-01

    Central venous catheter( CVC )is one of the most common technique for monitoring and treatment in ICU. But There is a risk of catheter-related bloodstream infection causing prolonged hospital stay and increased mortality. Positioning the CVC through the subclavian vein and using a antibiotic catheter can help to reduce the incidence of CRBSI. A bundle stratige is of a crucial role in CRBSI provention.It should include strict hand hygiene, sterilizing with mixture of 70% ethano and 2% chlorhexidine, maximal sterile barrier and regular dressing change. The efficiency of regular CVC replacement and of antibiotic based catheter lock solution are not clear, and are not recommended as a routine.%留置中心静脉导管是ICU中最常用的监测和治疗措施,但其同时存在发生导管相关性血流感染(CRBSI)的风险,从而导致患者住院时间延长和病死率升高.选择锁骨下穿刺径路、使用抗生素导管可减少CRBSI的发生.应用集束化预防措施进行置管及日常护理是预防CRBSI发生的重要措施,包括严格的手卫生、应用2%氯己定和70%乙醇混合液消毒皮肤、最大消毒屏障以及定期更换辅料.定期更换导管及使用抗生素封管对预防CRBSI效果不明确,不作为常规推荐.

  10. Production of Cellulosic Polymers from Agricultural Wastes

    Directory of Open Access Journals (Sweden)

    A. U. Israel

    2008-01-01

    Full Text Available Cellulosic polymers namely cellulose, di-and triacetate were produced from fourteen agricultural wastes; Branch and fiber after oil extraction from oil palm (Elais guineensis, raffia, piassava, bamboo pulp, bamboo bark from raphia palm (Raphia hookeri, stem and cob of maize plant (Zea mays, fruit fiber from coconut fruit (Cocos nucifera, sawdusts from cotton tree (Cossypium hirsutum, pear wood (Manilkara obovata, stem of Southern gamba green (Andropogon tectorus, sugarcane baggase (Saccharium officinarum and plantain stem (Musa paradisiaca. They were subjected to soda pulping and hypochlorite bleaching system. Results obtained show that pulp yield from these materials were: 70.00, 39.59, 55.40, 86.00, 84.60, 80.00, 40.84, 81.67, 35.70, 69.11, 4.54, 47.19, 31.70 and 52.44% respectively. The pulps were acetylated with acetic anhydride in ethanoic acid catalyzed by conc. H2SO4 to obtain cellulose derivatives (Cellulose diacetate and triacetate. The cellulose diacetate yields were 41.20, 17.85, 23.13, 20.80, 20.23, 20.00, 39.00, 44.00, 18.80, 20.75, 20.03, 41.20, 44.00, and 39.00% respectively while the results obtained as average of four determinations for cellulose triacetate yields were: 52.00, 51.00, 43.10, 46.60, 49.00, 35.00, 40.60, 54.00, 57.50, 62.52, 35.70. 52.00, 53.00 and 38.70% respectively for all the agricultural wastes utilized. The presence of these cellulose derivatives was confirmed by a solubility test in acetone and chloroform.

  11. Acetylsalicylic acid regulates overexpressed small GTPase RhoA in vascular smooth muscle cells through prevention of new synthesis and enhancement of protein degradation.

    Science.gov (United States)

    Li, Dong-Bo; Fu, Zhi-Xuan; Ruan, Shu-Qin; Hu, Shen-Jiang; Li, Xia

    2012-04-01

    RhoA has been shown to play a major role in vascular processes and acetylsalicylic acid (aspirin) is known to exert a cytoprotective effect via multiple mechanisms. In the present study, we aimed at investigating the effect of aspirin on RhoA expression under a stress state in rat VSMCs (vascular smooth muscle cells) and the underlying mechanisms. The expression of iNOS (inducible nitric oxide synthase) and iNOS activity as well as NO concentration was significantly promoted by LPS (lipopolysaccharide) accompanying the elevation of RhoA expression, which was blocked by the addition of the iNOS inhibitor L-NIL [L-N6-(1-iminoethyl)lysine dihydrochloride]. Aspirin (30 μM) significantly attenuated the elevation of RhoA, while indomethacin and salicylate had no similar effect. The sGC (soluble guanylate cyclase) inhibitor ODQ (1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one) showed the same effect as aspirin in down-regulating RhoA but was reversed by the addition of the cGMP analogue 8-Br-PET-cGMP (β-phenyl-1,N2-ethano-8-bromoguanosine 3',5'-cyclic monophosphorothioate). 8-Br-PET-cGMP solely enhanced the RhoA expression that was abrogated by preincubation with aspirin. Degradation analysis indicated that aspirin enhanced the protein degradation rate of RhoA and GDP-bound RhoA seemed to be more susceptible to aspirin-enhanced degradation compared with the GTP-bound form. Our results indicate that aspirin attenuates the LPS-induced overexpression of RhoA both by inhibiting new synthesis and accelerating protein degradation, which may help elucidate the multiple beneficial effects of aspirin.

  12. Beta-Phosphinoethylboranes as Ambiphilic Ligands in Nickel-Methyl Complexes

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-10-28

    The ambiphilic {beta}-phosphinoethylboranes Ph{sub 2}PCH{sub 2}CH{sub 2}BR{sub 2} (BR{sub 2} = BCy{sub 2} (1a), BBN (1b)), which feature a ethano spacer CH{sub 2}CH{sub 2} between the Lewis acidic boryl and Lewis basic phosphino groups, were synthesized in nearly quantitative yields via the hydroboration of vinyldiphenylphosphine. Compounds 1a and 1b were fully characterized by elemental analysis, and by NMR and IR spectroscopy. X-ray crystallographic studies of compound 1b revealed infinite helical chains of the molecules connected through P{hor_ellipsis}B donor-acceptor interactions. The ability of these ambiphilic ligands to concurrently act as donors and acceptors was highlighted by their reactions with (dmpe)NiMe{sub 2}. Zwitterionic complexes (dmpe)NiMe(Ph{sub 2}PCH{sub 2}CH{sub 2}BCy{sub 2}Me) (2a) and (dmpe)NiMe(Ph{sub 2}PCH{sub 2}CH{sub 2}[BBN]Me) (2b) were generated via the abstraction of one of the methyl groups, forming a borate, and intramolecular coordination of the phosphine moiety to the resulting cationic metal center. Compound 2b was characterized by X-ray crystallography. Furthermore, B(C{sub 6}F{sub 5}){sub 3} abstracts the methyl group of a coordinated borate ligand to generate a free, 3-coordinate borane center in [(dmpe)NiMe(1a)]{sup +}[MeB(C{sub 6}F{sub 5}){sub 3}]{sup -} (3).

  13. 嘧霉胺有机酸盐衍生物的合成研究%Synthesis and Biological Activity of Pyrimethanil Salts of Organic Acid Derivatives

    Institute of Scientific and Technical Information of China (English)

    徐韶康; 于康平; 朱卫华; 罗志会; 张海军

    2016-01-01

    开发了新的杀菌剂,利用有机碱与有机酸易结合成鎓盐的原理,分别以萘乙酸、萘氧乙酸、醋酸与嘧霉胺反应,合成了3个嘧霉胺有机酸盐衍生物。经紫外光谱、红外光谱、核磁共振波谱及元素分析测试等结构鉴定分析,论证了合成产物为目的产物。本方法简捷、环保,易落实工业化。合成分离的母液,循环套用五到六次,产率分别为99%、98.5%和99%,接近理论收率。新化合物研究均未见文献报道。%A new sterilization agent was developed .With the principle that organic alkali and organic acids can easily combined into onium salt , respectively with naphthylacetic acid and naphthalene oxygen ethanoic acid , acetic acid and pyrimethanil reaction , three pyrimethanil organic acid salt derivatives were synthetized , after structure identification and analysis by ultraviolet spectrum , infrared spectrum , nuclear magnetic resonance ( NMR) and elemental analysis , the synthetic product was conformed as the purpose product .This method is simple , with environmental protection , easy to implement industrialization .Synthesis and separation of mother liquor recycling applied five to six times respectively , the yield was 99%, 98.5%and 99%, close to the theoretical yield , new compounds were not reported in the literature .

  14. Development and validation of a gas chromatography/mass spectrometry method for the assessment of genomic DNA methylation.

    Science.gov (United States)

    Rossella, Federica; Polledri, Elisa; Bollati, Valentina; Baccarelli, Andrea; Fustinoni, Silvia

    2009-09-01

    A method for the determination of DNA global methylation, taken as the ratio (%) of 5-methylcytosine (5mCyt) versus the sum of cytosine (Cyt) and 5mCyt, via gas chromatography/mass spectrometry (GC/MS), was developed and validated. DNA (2.5 microg) was hydrolyzed with aqueous formic acid 88%, spiked with cytosine-2,4-(13)C(2),(15)N(3) and 5-methyl-(2)H(3)-cytosine-6-(2)H(1) as internal standards, and derivatized with N-methyl-N-(tert-butyldimethylsilyl)trifluoroacetamide and 1% tert-butyldimethylchlorosilane, in the presence of acetonitrile and pyridine. GC/MS, operating in single ion monitoring mode, separated and specifically detected all nucleobases as tert-butyldimethylsilyl derivatives, without interferences, with the exception of guanosine. The method was linear throughout the range of clinical interest and had good sensitivity, with a limit of quantification of 3.2 pmol for Cyt and 0.056 pmol for 5mCyt, the latter corresponding to a methylation level of 0.41%. Intra- and inter-day precision and accuracy were below 4.0% for both analytes and methylation. The matrix absolute effect, process efficiency and coefficient of variation ranged from 96.5 to 101.2%. The matrix relative effect was below 1%. The method was applied to the analysis of different human DNAs, including: nonmethylated DNA from PCR (methylation 0.00%), hypermethylated DNA prepared using M.SssI CpG methyltransferase (methylation 18.05%), DNA from peripheral blood leukocytes of healthy subjects (N = 6, median methylation 5.45%), DNA from bone marrow of leukemia patients (N = 5, 3.58%) and DNA from myeloma cell lines (N = 4, 2.74%).

  15. Heavy-ion radiation induces both activation of multiple endogenous transposable elements and alterations in DNA methylation in rice

    Science.gov (United States)

    Zhang, Meng; Sun, Yeqing; Li, Xishan; Xiaolin, Cui; Li, Xiang

    2012-07-01

    Space radiation represents a complex environmental condition in which several interacting factors such as electron, neutron, proton, heavy-ion are involved, which may provoke stress responses and jeopardize genome integrity. Given the inherent property of epigenetic modifications to respond to intrinsic aswell as external perturbations, it is conceivable that epigenetic markers like DNA methylation and transposition may undergo alterations in response to space radiation. Cytosine DNA methylation plays important roles in maintaining genome stability and controlling gene expression. A predominant means for Transposable elements (TEs) to cause genetic instability is via their transpositional activation. To find the detailed molecular characterization of the nature of genomic changes induced by space radiation, the seeds of rice were exposed to 0.02, 0.2, 1, 2 and 20 Gy dose of ^{12}C heavy-ion radiation, respectively. We found that extensive alteration in both DNA methylation and gene expression occurred in rice plants after different dose of heavy-ion radiation. Here we shown that heavy-ion radiation has induced transposition of mPing and Tos17 in rice, which belong to distinct classes including the miniature inverted terminal repeat TEs (MITEs) and long-terminal repeat (LTR) retrotransposons, respectively. mPing and Tos17 mobility were found to correlate with cytosine methylation alteration detected by MSAP and genetic variation detected by AFLP. The result showed that at least in some cases transposition of TEs was associated with cytosine demethylation within the elements. Our results implicate that the heavy-ion radiation represents a potent mutagenic agent that can cause genomic instabilities by eliciting transposition of endogenous TEs in rice. Keywords: Heavy-ion radiation, DNA methylation, Transposable elements, mPing, Tos17

  16. A Phytase-Based Reporter System for Identification of Functional Secretion Signals in Bifidobacteria.

    Directory of Open Access Journals (Sweden)

    Annika Osswald

    Full Text Available Health-promoting effects have been attributed to a number of Bifidobacterium sp. strains. These effects as well as the ability to colonise the host depend on secreted proteins. Moreover, rational design of protein secretion systems bears the potential for the generation of novel probiotic bifidobacteria with improved health-promoting or therapeutic properties. To date, there is only very limited data on secretion signals of bifidobacteria available. Using in silico analysis, we demonstrate that all bifidobacteria encode the major components of Sec-dependent secretion machineries but only B. longum strains harbour Tat protein translocation systems. A reporter plasmid for secretion signals in bifidobacteria was established by fusing the coding sequence of the signal peptide of a sialidase of Bifidobacterium bifidum S17 to the phytase gene appA of E. coli. The recombinant strain showed increased phytase activity in spent culture supernatants and reduced phytase levels in crude extracts compared to the control indicating efficient phytase secretion. The reporter plasmid was used to screen seven predicted signal peptides in B. bifidum S17 and B. longum E18. The tested signal peptides differed substantially in their efficacy to mediate protein secretion in different host strains. An efficient signal peptide was used for expression and secretion of a therapeutically relevant protein in B. bifidum S17. Expression of a secreted cytosine deaminase led to a 100-fold reduced sensitivity of B. bifidum S17 to 5-fluorocytosine compared to the non-secreted cytosine deaminase suggesting efficient conversion of 5-fluorocytosine to the cytotoxic cancer drug 5-fluorouracil by cytosine deaminase occurred outside the bacterial cell. Selection of appropriate signal peptides for defined protein secretion might improve therapeutic efficacy as well as probiotic properties of bifidobacteria.

  17. Silver- and gold-mediated nucleobase bonding.

    Science.gov (United States)

    Acioli, Paulo H; Srinivas, Sudha

    2014-08-01

    We report the results of a density functional theory investigation of the bonding of nucleobases mediated by silver and gold atoms in the gas phase. Our calculations use the Becke exchange and Perdew-Wang correlation functional (BPW91) combined with the Stuttgart effective core potentials to represent the valence electrons of gold, silver, and platinum, and the all-electron DGTZVP basis set for C, H, N, and O. This combination was chosen based on tests on the metal atoms and tautomers of adenine, cytosine, and guanine. To establish a benchmark to understand the metal-mediated bonding, we calculated the binding energy of each of the base pairs in their canonical forms. Our calculations show rather strong bonds between the Watson-Crick base pairs when compared with typical values for N-H-N and N-H-O hydrogen bonds. The neutral metal atoms tend to bond near the nitrogen atoms. The effect of the metal atoms on the bonding of nucleobases differs depending on whether or not the metal atoms bond to one of the hydrogen-bonding sites. When the silver or gold atoms bond to a non-hydrogen-bonding site, the effect is a slight enhancement of the cytosine-guanine bonding, but there is almost no effect on the adenine-thymine pairing. The metal atoms can block one of the hydrogen-bonding sites, thus preventing the normal cytosine-guanine and adenine-thymine pairings. We also find that both silver and gold can bond to consecutive guanines in a similar fashion to platinum, albeit with a significantly lower binding energy.

  18. Theoretical predictions for ionization cross sections of DNA nucleobases impacted by light ions

    Energy Technology Data Exchange (ETDEWEB)

    Champion, C; Lekadir, H; Hanssen, J [Laboratoire de Physique Moleculaire et des Collisions, ICPMB (FR CNRS 2843), Institut de Physique, Universite Paul Verlaine-Metz, 1 bd Arago, 57078 Metz Cedex 3 (France); Galassi, M E; Fojon, O; Rivarola, R D, E-mail: champion@univ-metz.f [Instituto de Fisica Rosario, CONICET and Universidad Nacional de Rosario, Avenida Pellegrini 250, 2000 Rosario (Argentina)

    2010-10-21

    Induction of DNA double strand breaks after irradiation is considered of prime importance for producing radio-induced cellular death or injury. However, up to now ion-induced collisions on DNA bases remain essentially experimentally approached and a theoretical model for cross section calculation is still lacking. Under these conditions, we here propose a quantum mechanical description of the ionization process induced by light bare ions on DNA bases. Theoretical predictions in terms of differential and total cross sections for proton, {alpha}-particle and bare ion carbon beams impacting on adenine, cytosine, thymine and guanine bases are then reported in the 10 keV amu{sup -1}-10 MeV amu{sup -1} energy range. The calculations are performed within the first-order Born approximation (FBA) with biological targets described at the restricted Hartree-Fock level with geometry optimization. Comparisons to recent theoretical data for collisions between protons and cytosine point out huge discrepancies in terms of differential as well as total cross sections whereas very good agreement is shown with our previous classical predictions, especially at high impact energies (E{sub i} {>=} 100 keV amu{sup -1}). Finally, in comparison to the rare existing experimental data a systematic underestimation is observed in particular for adenine and thymine whereas a good agreement is reported for cytosine. Thus, further improvements appear as necessary, in particular by using higher order theories like the continuum-distorted-wave one in order to obtain a better understanding of the underlying physics involved in such ion-DNA reactions.

  19. [Uracil-DNA glycosylases].

    Science.gov (United States)

    Pytel, Dariusz; Słupianek, Artur; Ksiazek, Dominika; Skórski, Tomasz; Błasiak, Janusz

    2008-01-01

    Uracil is one of four nitrogen bases, most frequently found in normal RNA. Uracyl can be found also in DNA as a result of enzymatic or non-enzymatic deamination of cytosine as well as misincorporation of dUMP instead of dTMP during DNA replication. Uracil from DNA can be removed by DNA repair enzymes with apirymidine site as an intermediate. However, if uracil is not removed from DNA a pair C:G in parental DNA can be changed into a T:A pair in the daughter DNA molecule. Therefore, uracil in DNA may lead to a mutation. Uracil in DNA, similarly to thymine, forms energetically most favorable hydrogen bonds with adenine, therefore uracil does not change the coding properties of DNA. Uracil in DNA is recognized by uracil DNA glycosylase (UDGs), which initiates DNA base excision repair, leading to removing of uracil from DNA and replacing it by thymine or cytosine, when arose as a result of cytosine deamination. Eukaryotes have at least four nuclear UDGs: UNG2, SMUG1, TDG i MBD4, while UNG1 operates in the mitochondrium. UNG2 is involved in DNA repair associated with DNA replication and interacts with PCNA and RPA proteins. Uracil can also be an intermediate product in the process of antigen-dependent antibody diversification in B lymphocytes. Enzymatic deamination of viral DNA by host cells can be a defense mechanism against viral infection, including HIV-1. UNG2, MBD4 and TDG glycosylases may cooperate with mismatch repair proteins and TDG can be involved in nucleotide excision repair system.

  20. Integration of Cytological Features with Molecular and Epigenetic Properties of Rice Chromosome 4

    Institute of Scientific and Technical Information of China (English)

    Ben-Liang Yin; Lan Guo; Dong-Fen Zhang; William Terzaghi; Xiang-Feng Wang; Ting-Ting Liu; Hang He; Zhu-Kuan Cheng; Xing Wang Deng

    2008-01-01

    It has been reported that rice chromosome 4 has eight major heterochromatic knobs within the heterochromatic half and that this organization correlates with chromosomal-leveI transcriptiOnaI activity.To better understand this chromosomaI organization,we created a modeI based on the statisticaI distribution of various types of gene models to divide chromosome 4 into 17 euchromatic and heterochromatic regions that correspond with the cytological staining.Fluorescence in.situ hvbridization(FISH)experiments using a set of bacteriaI artificiaI chromosome(BAC)clones from chromosome 4 placed all 18 clones in the region predicted by the model.Elevated levels of H3K4 di-and tri-methylation detected by chromatin-immunoprecipitation(CHIP)on chip were correlated with euchromatic regions whereas lower levels of these two modifications were detected in heterochromatic regions.Small RNAs were more abundant in the het erochromatic regions.To validate these findings,H3K4 trimethylation,H3K9 acetylation,H4K12 acetylation,and H3K9 di-and tri-methylation of 19 Individual genes were measured by Chlp-PCR.Genes in heterochromatic regions had elevated H3K9 di-and tri-methylation while genes in euchromatic regions had elevated levels of the other three modIfications.We also assayed cytosine methylation of these genes using the restriction enzymes McrBC,Hapll.and Msp I.This analysis indicated that cytosines of transposable elements and some genes located in heterochromatic regions were methylated while cytosines of the other genes were unmethylated.These results suggest that IocaI transcriptional activity may retiect the organization of the corresponding part of the chromosome.They also indicate that epigenetic regulation plays an important role in correlating chromosomal organization with transcriptionaI activity.

  1. A Nucleolar PUF RNA-binding Protein with Specificity for a Unique RNA Sequence.

    Science.gov (United States)

    Zhang, Chi; Muench, Douglas G

    2015-12-11

    PUF proteins are a conserved group of sequence specific RNA-binding proteins that bind to RNA in a modular fashion. The RNA-binding domain of PUF proteins typically consists of eight clustered Puf repeats. Plant genomes code for large families of PUF proteins that show significant variability in their predicted Puf repeat number, organization, and amino acid sequence. Here we sought to determine whether the observed variability in the RNA-binding domains of four plant PUFs results in a preference for nonclassical PUF RNA target sequences. We report the identification of a novel RNA binding sequence for a nucleolar Arabidopsis PUF protein that contains an atypical RNA-binding domain. The Arabidopsis PUM23 (APUM23) binding sequence was 10 nucleotides in length, contained a centrally located UUGA core element, and had a preferred cytosine at nucleotide position 8. These RNA sequence characteristics differ from those of other PUF proteins, because all natural PUFs studied to date bind to RNAs that contain a conserved UGU sequence at their 5' end and lack specificity for cytosine. Gel mobility shift assays validated the identity of the APUM23 binding sequence and supported the location of 3 of the 10 predicted Puf repeats in APUM23, including the cytosine-binding repeat. The preferred 10-nucleotide sequence bound by APUM23 is present within the 18S rRNA sequence, supporting the known role of APUM23 in 18S rRNA maturation. This work also reveals that APUM23, an ortholog of yeast Nop9, could provide an advanced structural backbone for Puf repeat engineering and target-specific regulation of cellular RNAs.

  2. Use of MSAP markers to analyse the effects of salt stress on DNA methylation in rapeseed (Brassica napus var. oleifera.

    Directory of Open Access Journals (Sweden)

    Gianpiero Marconi

    Full Text Available Excessive soil salinity is a major ecological and agronomical problem, the adverse effects of which are becoming a serious issue in regions where saline water is used for irrigation. Plants can employ regulatory strategies, such as DNA methylation, to enable relatively rapid adaptation to new conditions. In this regard, cytosine methylation might play an integral role in the regulation of gene expression at both the transcriptional and post-transcriptional levels. Rapeseed, which is the most important oilseed crop in Europe, is classified as being tolerant of salinity, although cultivars can vary substantially in their levels of tolerance. In this study, the Methylation Sensitive Amplified Polymorphism (MSAP approach was used to assess the extent of cytosine methylation under salinity stress in salinity-tolerant (Exagone and salinity-sensitive (Toccata rapeseed cultivars. Our data show that salinity affected the level of DNA methylation. In particular methylation decreased in Exagone and increased in Toccata. Nineteen DNA fragments showing polymorphisms related to differences in methylation were sequenced. In particular, two of these were highly similar to genes involved in stress responses (Lacerata and trehalose-6-phosphatase synthase S4 and were chosen to further characterization. Bisulfite sequencing and quantitative RT-PCR analysis of selected MSAP loci showed that cytosine methylation changes under salinity as well as gene expression varied. In particular, our data show that salinity stress influences the expression of the two stress-related genes. Moreover, we quantified the level of trehalose in Exagone shoots and found that it was correlated to TPS4 expression and, therefore, to DNA methylation. In conclusion, we found that salinity could induce genome-wide changes in DNA methylation status, and that these changes, when averaged across different genotypes and developmental stages, accounted for 16.8% of the total site

  3. Use of MSAP markers to analyse the effects of salt stress on DNA methylation in rapeseed (Brassica napus var. oleifera).

    Science.gov (United States)

    Marconi, Gianpiero; Pace, Roberta; Traini, Alessandra; Raggi, Lorenzo; Lutts, Stanley; Chiusano, Marialuisa; Guiducci, Marcello; Falcinelli, Mario; Benincasa, Paolo; Albertini, Emidio

    2013-01-01

    Excessive soil salinity is a major ecological and agronomical problem, the adverse effects of which are becoming a serious issue in regions where saline water is used for irrigation. Plants can employ regulatory strategies, such as DNA methylation, to enable relatively rapid adaptation to new conditions. In this regard, cytosine methylation might play an integral role in the regulation of gene expression at both the transcriptional and post-transcriptional levels. Rapeseed, which is the most important oilseed crop in Europe, is classified as being tolerant of salinity, although cultivars can vary substantially in their levels of tolerance. In this study, the Methylation Sensitive Amplified Polymorphism (MSAP) approach was used to assess the extent of cytosine methylation under salinity stress in salinity-tolerant (Exagone) and salinity-sensitive (Toccata) rapeseed cultivars. Our data show that salinity affected the level of DNA methylation. In particular methylation decreased in Exagone and increased in Toccata. Nineteen DNA fragments showing polymorphisms related to differences in methylation were sequenced. In particular, two of these were highly similar to genes involved in stress responses (Lacerata and trehalose-6-phosphatase synthase S4) and were chosen to further characterization. Bisulfite sequencing and quantitative RT-PCR analysis of selected MSAP loci showed that cytosine methylation changes under salinity as well as gene expression varied. In particular, our data show that salinity stress influences the expression of the two stress-related genes. Moreover, we quantified the level of trehalose in Exagone shoots and found that it was correlated to TPS4 expression and, therefore, to DNA methylation. In conclusion, we found that salinity could induce genome-wide changes in DNA methylation status, and that these changes, when averaged across different genotypes and developmental stages, accounted for 16.8% of the total site-specific methylation differences

  4. Chemical display of pyrimidine bases flipped out by modification-dependent restriction endonucleases of MspJI and PvuRts1I families.

    Directory of Open Access Journals (Sweden)

    Evelina Zagorskaitė

    Full Text Available The epigenetic DNA modifications 5-methylcytosine (5mC and 5-hydroxymethylcytosine (5hmC in eukaryotes are recognized either in the context of double-stranded DNA (e.g., by the methyl-CpG binding domain of MeCP2, or in the flipped-out state (e.g., by the SRA domain of UHRF1. The SRA-like domains and the base-flipping mechanism for 5(hmC recognition are also shared by the recently discovered prokaryotic modification-dependent endonucleases of the MspJI and PvuRts1I families. Since the mechanism of modified cytosine recognition by many potential eukaryotic and prokaryotic 5(hmC "readers" is still unknown, a fast solution based method for the detection of extrahelical 5(hmC would be very useful. In the present study we tested base-flipping by MspJI- and PvuRts1I-like restriction enzymes using several solution-based methods, including fluorescence measurements of the cytosine analog pyrrolocytosine and chemical modification of extrahelical pyrimidines with chloroacetaldehyde and KMnO4. We find that only KMnO4 proved an efficient probe for the positive display of flipped out pyrimidines, albeit the method required either non-physiological pH (4.3 or a substitution of the target cytosine with thymine. Our results imply that DNA recognition mechanism of 5(hmC binding proteins should be tested using a combination of all available methods, as the lack of a positive signal in some assays does not exclude the base flipping mechanism.

  5. N2-fixing vibrios isolated from the gastrointestinal tract of sea urchins.

    Science.gov (United States)

    Guerinot, M L; Patriquin, D G

    1981-03-01

    Facultatively anaerobic bacteria, capable of fixing N2 anaerobically or at low O2 concentrations, were isolated from the gastrointestinal tracts of temperate (Strongylocentrotus droebachiensis) and tropical (Tripneustes ventricosus) sea urchins. Morphological and biochemical characteristics, as well as the guanine plus cytosine content of their DNA (45.9 and 48.4 mol%), place these isolates in the genus Vibrio Pacini 1865 in the family Vibrionaceae. Members of this family have not previously been shown to fix N2. These isolates are not identical to any described species in the Vibrio genus and can be distinguished by a combination of biochemical and physiological traits.

  6. Active DNA demethylation by oxidation and repair

    Institute of Scientific and Technical Information of China (English)

    Zhizhong Gong; Jian-Kang Zhu

    2011-01-01

    DNA methylation and demethylation are increasingly recognized as important epigenetic factors in both plants and animals.DNA methylation,which is catalyzed by DNA methyltransferases (DNMTs),is a relatively stable and heritable modification that controls gene expression,cellular differentiation,genomic imprinting,paramutation,transposon movement,X-inactivation,and embryogenesis [1].The methylation of cytosine to 5-methylcytosine (5mC) is an important example of DNA modification in animals and plants.This highlight concerns DNA demethylation mechanisms in mammals and whether they are similar to that in plants.

  7. Spongiozna encefalopatija (1920.–2010.)

    OpenAIRE

    Jung, Mirko

    2010-01-01

    U radu se istražuju prve prionske bolesti od kojih je većina genetskog podrijetla. Uključuju točkaste mutacije (promjena jedno baznog para, change in a single base pair Adenine/Guanine, Thymin/Cytosine) DNA, insercija oktapeptida u N-ti dio prionskog proteina (3 do 216 oktapeptida), delecije (samo dva ili tri su poznata do sada). Tri ili više insercija potrebna za ovu bolest. To je 35 točkastih mutacija (najčešće su na kodonima 102, 178 i 200). Najnovija varijanta CJB, koja nastaje konzumacij...

  8. Catalytic activity of APOBEC3F is required for efficient restriction of Vif-deficient human immunodeficiency virus.

    Science.gov (United States)

    Albin, John S; Brown, William L; Harris, Reuben S

    2014-02-01

    APOBEC3 proteins are DNA cytosine deaminases that restrict the replication of human immunodeficiency virus deficient in the counterdefense protein Vif. Here, we address the capacity of APOBEC3F to restrict via deaminase-dependent and -independent mechanisms by monitoring spreading infections in diverse T cell lines. Our data indicate that only a deaminase-proficient protein is capable of long-term restriction of Vif-deficient HIV in T cells, analogous to prior reports for APOBEC3G. This indicates that the principal mechanism of APOBEC3F restriction is deaminase-dependent.

  9. A Case of Juvenile Huntington Disease in a 6-Year-Old Boy

    Directory of Open Access Journals (Sweden)

    Jun-Sang Sunwoo

    2010-10-01

    Full Text Available Huntington disease is a neurodegenerative disorder distinguished by the triad of dominant inheritance, choreoathetosis and dementia, usually with onset in the fourth and fifth decades. It is caused by an unstable cytosine-adenine-guanine (CAG trinucleotide repeat expansion in the gene IT15 in locus 4p16.3. Juvenile HD that constitutes about 3% to 10% of all patients is clinically different from adult-onset form and characterized by a larger number of CAG repeats typically exceeding 60. We report a case of a 6-year-old boy with myoclonic seizure and 140 CAG repeats confirmed by molecular genetic analysis.

  10. Effect of copper ions on voltammetric signals of aminopurines at a carbon electrode

    Directory of Open Access Journals (Sweden)

    Frantisek Jelen

    2010-12-01

    Full Text Available Electrochemical oxidations of aminopurines (adenine–Ade, 2–aminopurine, 2AP, 2,6–diaminopurine, 2,6–DAP and theircomplexes with Cu(I on carbon electrodes (pencil–PeGE wereinvestigated by means of linear sweep voltammetry (LSV andelimination voltammetry with linear scan (EVLS. We found thatthe Cu(I–purine complex was formed not only by aminopurines butalso by purine. On the other hand the complex is not formed in thecase of imidazol or cytosine. The results showed that carbonelectrodes in connection with EVLS can be an excellent prototypefor cheap and fast working sensor for aminopurines in the presenceof copper.

  11. Activation of Innate Immunity in Healthy Macaca mulatta Macaques by a Single Subcutaneous Dose of GMP CpG 7909: Safety Data and Interferon-Inducible Protein-10 Kinetics for Humans and Macaques▿

    OpenAIRE

    Stewart, V. Ann; McGrath, Shannon; Krieg, Arthur M.; Larson, Noelle S.; Angov, Evelina; Smith, Christopher L.; Brewer, Thomas G; Heppner, D. Gray

    2007-01-01

    Following a demonstration that mouse-optimized cytosine-guanosine dinucleotide (CpG) oligodeoxynucleotides stimulated innate immune protection against intracellular pathogens, we tested the ability of CpG 7909, a primate-optimized Toll-like receptor 9 (TLR9) agonist, to stimulate rhesus macaques to produce interferon-inducible protein-10 (IP-10), a biomarker of immune activation. This study was performed prior to a similar trial with humans in order to facilitate the development of CpG 7909 a...

  12. Spinocerebellar ataxia type-7: Report of a family in Northwest Nigeria.

    Science.gov (United States)

    Alkali, Nura Hamidu; Bwala, Sunday A; Alimi, Saeed A; Oyakhire, Shyngle I

    2016-01-01

    Spinocerebellar ataxia type-7 (SCA7) is a cytosine-adenine-guanine (CAG) repeat polyglutamine disorder characterized by progressive degeneration of the cerebellum, brainstem, spinal cord, and retina. Clinical features include progressive ataxia, visual loss, pyramidal weakness, sensory impairment, and dementia. Among the autosomal dominant cerebellar ataxias, SCA7 is relatively common in Scandinavia and South Africa but rare worldwide and is not previously reported in Nigeria. In this study, we describe a family in Katsina State, Northwest Nigeria, with nine individuals across three generations affected by the SCA7 phenotype. Analysis of DNA from proband and two affected relatives revealed 39 CAG repeat expansions in one allele of ataxin-7 in each.

  13. Alterations of pyrimidine and nucleic acid synthesis during adaptive growth of liver induced by nafenopin, a peroxisome proliferator. An in vivo study.

    Science.gov (United States)

    Seifert, J; Mostecká, H

    1989-08-01

    The de novo synthesis of pyrimidine nucleotides in the rat liver after administration of nafenopin (NFP) was studied with the aid of [14C]orotic acid; the utilization of preformed nucleosides (salvage pathways) was followed using the [14C]cytidine and [14C]thymidine. A single dose (400 mg/kg) as well as repeated doses (100 mg/kg/day) of NFP increased the concentration of the cytidine and uridine components of the acid-soluble extract (ASE) of rat liver. Increase in the concentration of the cytidine components preceded the increase in the uridine components. The uptake of [14C]cytidine by the liver of rats that had been given a single dose of NFP was observed 24 h after the administration of the drug and a decrease followed after this period. The specific activity of RNA and DNA cytosine paralleled the changes of the specific activity of ASE. A single dose of NFP had no marked effect on the uptake of [14C]orotic acid. The specific activity of the uridine components of ASE remained unaltered for 2 days. After this period it decreased because of an increase in the amount of the soluble uridine components. A mild drop of the specific activity of cytidine components of ASE occurred on the second day, the total radioactivity of cytidine components increased 24 h after the administration of NFP. The specific activity of DNA pyrimidines was markedly increased 24 h after administration of the drug. On the fourth day the specific activity of DNA cytosine in the experimental group was the same as in the control group, whereas the activity of DNA thymine was lower. Following repeated administration of NFP (100 mg/kg/day) a decreased uptake of [14C]orotic acid was observed; its utilization for the synthesis of the uridine components of ASE, expressed as total radioactivity of soluble uridine components, was continuously suppressed. No changes in the specific activity of cytidine components were observed. The specific activity of DNA cytosine and thymine was distributed unevenly

  14. A new image of plantain diversity assessed by SSR, AFLP and MSAP markers.

    Science.gov (United States)

    Noyer, J L; Causse, S; Tomekpe, K; Bouet, A; Baurens, F C

    2005-05-01

    Using both SSR and AFLP markers, the genetic diversity of 30 plantains constituting a representative sample of the phenotypic diversity was assessed. The results confirmed a very narrow genetic base of this cultivar group. SSR and AFLP data support the hypothesis that these cultivars may have arisen from vegetative multiplication of a single seed. MSAP were used to survey cytosine methylation status at CCGG sites in order to obtain an alternative source of diversity data. A higher degree of polymorphism was revealed allowing the classification of the samples into three clusters. No correlation was observed between the phenotypic classification and methylation diversity. Implications for breeding programs are discussed.

  15. Keeping Uracil Out of DNA: Physiological Role, Structure and Catalytic Mechanism of dUTPases

    OpenAIRE

    2009-01-01

    The thymine-uracil exchange constitutes one of the major chemical differences between DNA and RNA. Although these two bases form the same Watson-Crick base pairs with adenine and are equivalent for both information storage and transmission, uracil incorporation in DNA is usually a mistake that needs to be excised. There are two ways for uracil to appear in DNA: thymine replacement and cytosine deamination. Most DNA polymerases readily incorporate dUMP as well as dTMP depending solely on the a...

  16. Indoleamine 2,3-dioxygenase specific, cytotoxic T cells as immune regulators

    DEFF Research Database (Denmark)

    Sørensen, Rikke Bæk; Hadrup, Sine Reker; Svane, Inge Marie;

    2011-01-01

    , this caused an increase in the production of the proinflammatory cytokines IL-6 and tumor necrosis factor-alpha while decreasing the IL-10 production. Finally, the addition of IDO-inducing agents (ie, the TLR9 ligand cytosine-phosphate- guanosine, soluble cytotoxic T lymphocyte-associated antigen 4...... show that the presence of such IDO-specific CD8(+) T cells boosted T-cell immunity against viral or tumor-associated antigens by eliminating IDO+ suppressive cells. This had profound effects on the balance between interleukin-17 (IL-17)-producing CD4(+) T cells and regulatory T cells. Furthermore...

  17. Enantiomeric Synthesis of Novel Apiosyl Nucleosides as Potential Antiviral Agents

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ai Hong; Hong, Joon Hee [Chosun University, Gwangju (Korea, Republic of)

    2004-02-15

    A series of 2',3'-dideoxy-3'-fluoro-D-apiosyl nucleosides 15, 16, 17 and 18 were synthesized enantiomerically with L-Gulonic-{gamma}-lactone as the starting material. The reduction of butenolide 1 with DIBAL-H followed by the Luche procedure afforded the allylic alcohol 2. Ozonolysis and the reduction of compound 4 induced the cyclized lactol, which was acetylated to give the acetate 7. Condensation of the acetate 7 with silylated pyrimidine (N{sup 4}-benzoyl cytosine) and a purine base (6-chloropurine) under Vorbruggen conditions and deblocking afforded a series of fluorinated apiosyl nucleosides

  18. Nucleic Acid i-Motif Structures in Analytical Chemistry.

    Science.gov (United States)

    Alba, Joan Josep; Sadurní, Anna; Gargallo, Raimundo

    2016-09-02

    Under the appropriate experimental conditions of pH and temperature, cytosine-rich segments in DNA or RNA sequences may produce a characteristic folded structure known as an i-motif. Besides its potential role in vivo, which is still under investigation, this structure has attracted increasing interest in other fields due to its sharp, fast and reversible pH-driven conformational changes. This "on/off" switch at molecular level is being used in nanotechnology and analytical chemistry to develop nanomachines and sensors, respectively. This paper presents a review of the latest applications of this structure in the field of chemical analysis.

  19. Heat stable cell growth inhibiting factor isolated from rat liver microsomes.

    Directory of Open Access Journals (Sweden)

    Inaba,Kozo

    1979-08-01

    Full Text Available A heat stable cell growth inhibiting factor was isolated from rat liver microsomes by hot salt extraction, ethanol fractionation and the hot phenol method. The factor was contained in the RNA fraction (designated as mhRNA. mhRNA inhibited the growth of mouse fibroblast (L-929 cells at a relatively low concentration (55 microgram/ml of culture medium. The molecular weight of mhRNA was about 27,000 and the base composition was guanine and cytosine rich.

  20. Alterations of 5-Hydroxymethylcytosine in Human Cancers

    Directory of Open Access Journals (Sweden)

    Ali Yesilkanal

    2013-06-01

    Full Text Available Prior to 2009, 5-methylcytosine (5-mC was thought to be the only biologically significant cytosine modification in mammalian DNA. With the discovery of the TET enzymes, which convert 5-methylcytosine (5-mC to 5-hydroxymethylcytosine (5-hmC, however, intense interest has emerged in determining the biological function of 5-hmC. Here, we review the techniques used to study 5-hmC and evidence that alterations to 5-hmC physiology play a functional role in the molecular pathogenesis of human cancers.

  1. Remission induction and remission maintenance in adult acute nonlymphocytic leukemia employing a modified cytostatic (COAP) regimen.

    Science.gov (United States)

    Gerecke, D; Hirschmann, W D; Voigtmann, R; Gross, R

    1979-07-01

    Thirty adult patients suffering from acute nonlymphocytic leukemia (ANLL) were treated according to a modified COAP regimen. Vincristine, cyclophosphamide, and prednisone were given by push injection, while cytosine arabinoside was infused over periods of 8 h. Nineteen patients (63%) achieved complete remission. Remission maintenance therapy consisted of 6-mercaptopurine daily and methotrexate twice weekly. Later in the study, COAP consolidation and reinduction was added, which improved the median duration of complete remission from 7 to 24 months. Comparison of the results with the literature shows that the modified COAP regimen is one of the most effective treatment schedules for adult ANLL.

  2. [Treatment of acute leukemias].

    Science.gov (United States)

    Gross, R; Gerecke, D

    1982-11-12

    The effective treatment of acute (myeloblastic and lymphoblastic) leukaemias depends on the induction of remissions as well as on the maintenance of these remissions. Whereas the use of anthracyclines and of cytosine arabinoside in different combinations notably increased the rate of induction of remissions, their maintenance was less successful until now. We present a scheme using, beside MTX and 6-MP, modified COAP regimes periodically every 3 months. The follow-up of 26 patients treated in this way is encouraging since nearly one third remained in full haematological remission after 3 years of observation.

  3. DNA-Templated Silver Nanoclusters Formation at Gold Electrode Surface and Its Application to Hydrogen Peroxide Detection

    Institute of Scientific and Technical Information of China (English)

    许媛媛; 陈阳阳; 杨娜娜; 孙丽洲; 李根喜

    2012-01-01

    In this work, we have prepared Ag nanoclusters (Ag NCs) at gold electrode surface by using thiol-modified oligodeoxynucleotide consisting of eighteen cytosine deoxyribonucleotides (polyC18) as template and NaBH4 as reducing agent. Experimental results show that Ag nanoclusters (Ag NCs) can be formed around the template polyC18, while the formation can be characterized with electrochemical method. Further studies reveal that the fab- ricated Ag NCs may display high catalytic activity for the reduction of hydrogen peroxide (H2O2), which can be further used for the detection of H20〉

  4. Hair root FMRP expression for screening of fragile X full mutation females

    OpenAIRE

    Lantip Rujito; Dwi Kustiani; Lies Anne Severijnen; Peter Hanzon; Sultana MH Faradz; Rob Willemsen

    2016-01-01

    The fragile X syndrome is the most common form of inherited mental retardation in humans, caused by an expansion of the cytosine-guanine-guanine (CGG) repeat in the fragile X mental retardation 1 (FMR1) gene located on the X chromosome. Antibody tests have been developed to identify fragile X patients, based on the presence or absence of fragile mental retardation protein (FMRP) in both lymphocytes and hair roots. The objective of this study was to compare correlations of hair root and lympho...

  5. Evolving DNA motifs to predict GeneChip probe performance

    Directory of Open Access Journals (Sweden)

    Harrison AP

    2009-03-01

    Full Text Available Abstract Background Affymetrix High Density Oligonuclotide Arrays (HDONA simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 human tissue samples from NCBI's GEO database to indicated the quality of individual HG-U133A probes. Low correlation indicates a poor probe. Results Regular expressions can be automatically created from a Backus-Naur form (BNF context-free grammar using strongly typed genetic programming. Conclusion The automatically produced motif is better at predicting poor DNA sequences than an existing human generated RE, suggesting runs of Cytosine and Guanine and mixtures should all be avoided.

  6. Signatures of molecular recognition from the topography of electrostatic potential

    Indian Academy of Sciences (India)

    Dhimoy K Roy; P Balanarayan; Shridhar R Gadre

    2009-09-01

    The recognition of interaction between two molecules is analysed via the topography of their molecular electrostatic potentials (MESP). The point of recognition between two species is proposed to be the geometry at which there is a change in the nature of the set of MESP critical points of one of the molecules vis-a-vis with its MESP topography at infinite separation. These results are presented for certain model systems such as pyridine and benzene dimers, cytosine-guanine and adenine-thymine base pairs in various orientations of approach of the two species.

  7. Improved negative selection protocol for Plasmodium berghei in the rodent malarial model

    Directory of Open Access Journals (Sweden)

    Orr Rachael Y

    2012-03-01

    Full Text Available Abstract An improved methodology is presented here for transgenic Plasmodium berghei lines that express the negative selectable marker yFCU (a bifunctional protein that combines yeast cytosine deaminase and uridyl phosphoribosyl transferase (UPRT and substitutes delivery of selection drug 5-fluorocytosine (5FC by intraperitoneal injection for administration via the drinking water of the mice. The improved methodology is shown to be as effective, less labour-intensive, reduces animal handling and animal numbers required for successful selection thereby contributing to two of the "three Rs" of animal experimentation, namely refinement and reduction.

  8. Structure of 2,4-Diaminopyrimidine - Theobromine Alternate Base Pairs

    Science.gov (United States)

    Gengeliczki, Zsolt; Callahan, Michael P.; Kabelac, Martin; Rijs, Anouk M.; deVries, Mattanjah S.

    2011-01-01

    We report the structure of clusters of 2,4-diaminopyrimidine with 3,7-dimethylxanthine (theobromine) in the gas phase determined by IR-UV double resonance spectroscopy in both the near-IR and mid-IR regions in combination with ab initio computations. These clusters represent potential alternate nucleobase pairs, geometrically equivalent to guanine-cytosine. We have found the four lowest energy structures, which include the Watson-Crick base pairing motif. This Watson-Crick structure has not been observed by resonant two-photon ionization (R2PI) in the gas phase for the canonical DNA base pairs.

  9. Hyperchromicity and Strand Separation in Bacterial DNA

    Science.gov (United States)

    Freifelder, David; Davison, Peter F.

    1962-01-01

    Studies of the per cent of strand separation of N14-N15 hybrid coli DNA heated to various temperatures in formaldehyde have shown that the process of strand separation is a function of temperature and formaldehyde concentration and is directly related to the measured hyperchromicity. No strands separate until about 75 per cent of full hyperchromicity is obtained, and even at apparently full hyperchromicity a large fraction of the strands may be held together, possibly by guanine-cytosine-rich regions. PMID:13894962

  10. Isolation and characterization of a bacteriophage specific for Sphaerotilus natans which contain an unusual base in its deoxyribonucleic acid.

    Science.gov (United States)

    Winston, V; Thompson, T L

    1979-05-01

    A bacteriophage was isolated specific for Sphaerotilus natans, an organism for which bacteriophages have not been previously described. This phage (designated SN1) was found to infect both the single-cell (S-type) and filamentous (R-type) forms of the host, although the sheath appeared to provide R-type cells with a degree of physical protection from infection. SN1 had a hexagonal head and a long flexible tail resembling most closely the phages in Bradley's group B. The nucleic acid was found to be deoxyribonucleic acid and contained an unusual base which substituted for 35% of the guanine. Deoxyribonucleic acid base composition was 56% cytosine plus guanine.

  11. Optical Characterization of Oligonucleotide DNA Influenced by Magnetic Fields

    Directory of Open Access Journals (Sweden)

    Seyedeh Maryam Banihashemian

    2013-09-01

    Full Text Available UV-VIS spectroscopic analysis of oligonucleotide DNA exposed to different magnetic fields was performed in order to investigate the relationship between DNA extinction coefficients and optical parameters according to magnetic-field strength. The results with the oligonucleotides adenine-thymine 100 mer (AT-100 DNA and cytosine-guanine 100 mer (CG-100 DNA indicate that the magnetic field influences DNA molar extinction coefficients and refractive indexes. The imaginary parts of the refractive index and molar extinction coefficients of the AT-100 and CG-100 DNA decreased after exposure to a magnetic field of 750 mT due to cleavage of the DNA oligonucleotides into smaller segments.

  12. A smart DNA tetrahedron that isothermally assembles or dissociates in response to the solution pH value changes.

    Science.gov (United States)

    Liu, Zhiyu; Li, Yingmei; Tian, Cheng; Mao, Chengde

    2013-06-10

    This communication reports a DNA tetrahedron whose self-assembly is triggered by an acidic environment. The key element is the formation/dissociation of a short, cytosine (C)-containing, DNA triplex. As the solution pH value oscillates between 5.0 and 8.0, the DNA triplex will form and dissociate that, in turn, leads to assembly or disassembly of the DNA tetrahedron, which has been demonstrated by native polyacrylamide gel electrophoresis (PAGE). We believe that such environment-responsive behavior will be important for potential applications of DNA nanocages such as on-demand drug release.

  13. Divergent mechanisms for enzymatic excision of 5-formylcytosine and 5-carboxylcytosine from DNA

    OpenAIRE

    Maiti, Atanu; Michelson, Anna Zhachkina; Armwood, Cherece J; Lee, Jeehiun K.; Drohat, Alexander C.

    2013-01-01

    5-methylcytosine (mC) is an epigenetic mark that impacts transcription, development, and genome stability, and aberrant DNA methylation contributes to aging and cancer. Active DNA demethylation involves stepwise oxidation of mC to 5-hydroxymethylcytosine, 5-formylcytosine (fC), and potentially 5-carboxylcytosine (caC), excision of fC or caC by thymine DNA glycosylase (TDG), and restoration of cytosine via follow-on base excision repair. Here, we investigate the mechanism for TDG excision of f...

  14. Would Dissociative Recombination of DNA+ be a Possible Pathway of DNA Damage?

    Science.gov (United States)

    Kwon, H. C.; Chen, Z. P.; Strom, R. A.; Andrianarijaona, V. M.

    2015-05-01

    It is known that dissociative recombination (DR) is one of the very efficient processes of destruction of molecular cations into neutral particles. During the past few years, the focus of DR has been expanded from small inorganic molecules to macromolecular cation. We are probing the possibility of the DR of DNA+ after ionization of DNA, for example due to ionizing radiation. Therefore we are investigating the existence of autoionization states within nucleotide bases (Guanine, Adenine, Cytosine, and Thymine). Our results from computational analysis using the modern electronic structure program ORCA will be presented. Authors wish to give special thanks to Pacific Union College Student Senate for their financial support.

  15. Epigenetic integration of environmental and genomic signals in honey bees: the critical interplay of nutritional, brain and reproductive networks.

    Science.gov (United States)

    Maleszka, Ryszard

    2008-01-01

    The discovery of a family of highly conserved DNA cytosine methylases in honey bees and other insects suggests that, like mammals, invertebrates possess a mechanism for storing epigenetic information that controls heritable states of gene expression. Recent data also show that silencing DNA methylation in young larvae mimics the effects of nutrition on early developmental processes that determine the reproductive fate of honey bee females. We evaluate the impact of these findings on future studies of environmentally-driven phenotypic plasticity in social insects, and discuss how they may help in understanding the nutritional basis of epigenetic reprogramming in humans.

  16. Case of Herpes encephalitis followed-up by CT

    Energy Technology Data Exchange (ETDEWEB)

    Fukui, Y.; Nagai, S.; Nishibayashi, Y.; Okamoto, H.; Goishi, J. (Matsuyama Red Cross Hospital, Ehime (Japan))

    1982-03-01

    A 9-month-old girl was admitted with lethargy, fever and convulsion. EGG showed localized slow waves in the right temporal region. CT showed a localized low density area accompanied by a hemorrhagic focus in the right frontal lobe. Herpes encephalitis was suspected, and cytosine arabinoside was administered. The antibody titers of the serum and cerebrospinal fluid against herpes simplex virus type I significantly rose. Clinically the patient recovered without serious sequelae. CT revealed marked cerebral atrophy and subdural hematoma which were surgically treated. The importance of CT in the diagnosis and prognosis of herpes encephalitis was argued, and CT findings of herpes encephalitis were discussed.

  17. True single-molecule DNA sequencing of a pleistocene horse bone

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Ginolhac, Aurélien; Raghavan, Maanasa

    2011-01-01

    -preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing...... to the standard Helicos DNA template preparation protocol further increase the proportion of horse DNA for this sample by 3-fold. Comparison of Helicos-specific biases and sequence errors in modern DNA with those in ancient DNA also reveals extensive cytosine deamination damage at the 3' ends of ancient templates...

  18. Bifunctional chimeric SuperCD suicide gene -YCD: YUPRT fusion is highly effective in a rat hepatoma model

    Institute of Scientific and Technical Information of China (English)

    Florian Graepler; Ulrike A Lauer; Reinhard Vonthein; Michael Gregor; Sorin Armeanu; Michael Bitzer; Ulrich M. Lauer; Marie-Luise Lemken; Wolfgang A Wybranietz; Ulrike Schmidt; Irina Smirnow; Christine D Groβ; Martin Spiegel; Andrea Schenk; Hansj(o)rg Graf

    2005-01-01

    AIM: To investigate the effects of catalytically superior gene-directed enzyme prodrug therapy systems on a rat hepatoma model.METHODS: To increase hepatoma cell chemosensitivity for the prodrug 5-fluorocytosine (5-FC), we generated a chimeric bifunctional SuperCD suicide gene, a fusion of the yeast cytosine deaminase (YCD) and the yeast uracil phosphoribosyltransferase (YUPRT) gene.RESULTS: In vitro stably transduced Morris rat hepatoma cells (MH) expressing the bifunctional SuperCD suicide gene (MH SuperCD) showed a clearly marked enhancement in cell killing when incubated with 5-FC as compared with MH ceils stably expressing YCD solely (MH YCD) or the cytosine deaminase gene of bacterial origin(MH BCD), respectively. In vivo, MH SuperCD tumors implanted both subcutaneously as well as orthotopically into the livers of syngeneic ACI rats demonstrated significant tumor regressions (P<0.01) under both high dose as well as low dose systemic 5-FC application,whereas MH tumors without transgene expression (MH naive) showed rapid progression. For the first time, an order of in vivo suicide gene effectiveness (SuperCD>>YCD > > BCD > > > negative control) was defi ned as a result of a directin vivo comparison of all three suicide genes.CONCLUSION: Bifunctional SuperCD suicide gene expression is highly effective in a rat hepatoma model,thereby significantly improving both the therapeutic index and the efficacy of hepatocellular carcinoma killing by fluorocytosine.

  19. DNA methylation detection based on difference of base content

    Science.gov (United States)

    Sato, Shinobu; Ohtsuka, Keiichi; Honda, Satoshi; Sato, Yusuke; Takenaka, Shigeori

    2016-04-01

    Methylation frequently occurs in cytosines of CpG sites to regulate gene expression. The identification of aberrant methylation of certain genes is important for cancer marker analysis. The aim of this study was to determine the methylation frequency in DNA samples of unknown length and/or concentration. Unmethylated cytosine is known to be converted to thymine following bisulfite treatment and subsequent PCR. For this reason, the AT content in DNA increases with an increasing number of methylation sites. In this study, the fluorescein-carrying bis-acridinyl peptide (FKA) molecule was used for the detection of methylation frequency. FKA contains fluorescein and two acridine moieties, which together allow for the determination of the AT content of double-stranded DNA fragments. Methylated and unmethylated human genomes were subjected to bisulfide treatment and subsequent PCR using primers specific for the CFTR, CDH4, DBC1, and NPY genes. The AT content in the resulting PCR products was estimated by FKA, and AT content estimations were found to be in good agreement with those determined by DNA sequencing. This newly developed method may be useful for determining methylation frequencies of many PCR products by measuring the fluorescence in samples excited at two different wavelengths.

  20. Determination of 5-methylcytosine from plant DNA by high-performance liquid chromatography.

    Science.gov (United States)

    Wagner, I; Capesius, I

    1981-06-26

    The relative amounts of the five nucleosides (deoxycytidine, 5-methyldeoxycytidine, deoxyadenosine, deoxyguanosine and thymidine) in the DNA of nine plant species, one plant satellite DNA, and one animal species were determined by high performance liquid chromatography. The method allows the clean separation of the nucleosides from 10 microgram samples with 15 min. The following values for the proportion of methylated cytosines among all cytosines were obtained: Lobularia maritima 18.5%, Nicotiana tabacum 32.6%, Pisum sativum 23.2%, Rhinanthus minor 29.2%, Sinapsis alba 12.2%, Vicia faba 30.5%, Viscum album 23.2%, Cymbidium pumilum 18.8%, Cymbidium pumilum AT-rich satellite DNA 15.8%, Triticum aestivum 22.4%. DNA of an animal, the gerbil, Meriones unguiculatus, had a methylation percentage of 3.1%. An estimate of the GC content based on the buoyant density of DNA tends to be lower than the actual value, an estimate based on the melting temperature tends to be higher. This supports the finding by other authors that DNA methylation decreases the buoyant density and may increase the melting temperature at high m5C concentration.

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

    Science.gov (United States)

    Fang, Jing Yuan; Xiao, Shu Dong

    2003-01-01

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

  2. Shotgun Bisulfite Sequencing of the Betula platyphylla Genome Reveals the Tree’s DNA Methylation Patterning

    Directory of Open Access Journals (Sweden)

    Chang Su

    2014-12-01

    Full Text Available DNA methylation plays a critical role in the regulation of gene expression. Most studies of DNA methylation have been performed in herbaceous plants, and little is known about the methylation patterns in tree genomes. In the present study, we generated a map of methylated cytosines at single base pair resolution for Betula platyphylla (white birch by bisulfite sequencing combined with transcriptomics to analyze DNA methylation and its effects on gene expression. We obtained a detailed view of the function of DNA methylation sequence composition and distribution in the genome of B. platyphylla. There are 34,460 genes in the whole genome of birch, and 31,297 genes are methylated. Conservatively, we estimated that 14.29% of genomic cytosines are methylcytosines in birch. Among the methylation sites, the CHH context accounts for 48.86%, and is the largest proportion. Combined transcriptome and methylation analysis showed that the genes with moderate methylation levels had higher expression levels than genes with high and low methylation. In addition, methylated genes are highly enriched for the GO subcategories of binding activities, catalytic activities, cellular processes, response to stimulus and cell death, suggesting that methylation mediates these pathways in birch trees.

  3. DNA Methylation Alterations at 5'-CCGG Sites in the Interspecific and Intraspecific Hybridizations Derived from Brassica rapa and B. napus.

    Directory of Open Access Journals (Sweden)

    Wanshan Xiong

    Full Text Available DNA methylation is an important regulatory mechanism for gene expression that involved in the biological processes of development and differentiation in plants. To investigate the association of DNA methylation with heterosis in Brassica, a set of intraspecific hybrids in Brassica rapa and B. napus and interspecific hybrids between B. rapa and B. napus, together with parental lines, were used to monitor alterations in cytosine methylation at 5'-CCGG sites in seedlings and buds by methylation-sensitive amplification polymorphism analysis. The methylation status of approximately a quarter of the methylation sites changed between seedlings and buds. These alterations were related closely to the genomic structure and heterozygous status among accessions. The methylation status in the majority of DNA methylation sites detected in hybrids was the same as that in at least one of the parental lines in both seedlings and buds. However, the association between patterns of cytosine methylation and heterosis varied among different traits and between tissues in hybrids of Brassica, although a few methylation loci were associated with heterosis. Our data suggest that changes in DNA methylation at 5'-CCGG sites are not associated simply with heterosis in the interspecific and intraspecific hybridizations derived from B. rapa and B. napus.

  4. Insights into ligand binding to PreQ1 Riboswitch Aptamer from molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Zhou Gong

    Full Text Available Riboswitches play roles in transcriptional or translational regulation through specific ligand binding of their aptamer domains. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, preQ1 riboswitch aptamer domain from Bacillus subtilis is studied by overall 1.5 μs all-atom molecular dynamics simulations We found that the ligand-free aptamer has a stable state with a folded P1-L3 and open binding pocket. The latter forms a cytosine-rich pool in which the nucleotide C19 oscillates between close and open positions, making it a potential conformation for preQ1 entrance. The dynamic picture further suggests that the specific recognition of preQ1 by the aptamer domain is not only facilitated by the key nucleotide C19 but also aided and enhanced by other cytosines around the binding pocket. These results should help to understand the details of preQ1 binding.

  5. Reassessing APOBEC3G Inhibition by HIV-1 Vif-Derived Peptides.

    Science.gov (United States)

    Richards, Christopher M; Li, Ming; Perkins, Angela L; Rathore, Anurag; Harki, Daniel A; Harris, Reuben S

    2017-01-06

    The human APOBEC3G (A3G) enzyme restricts HIV-1 in the absence of the viral accessory protein viral infectivity factor (Vif) by deaminating viral cDNA cytosines to uracils. These uracil lesions base-pair with adenines during the completion of reverse transcription and result in A3G signature G-to-A mutations in the viral genome. Vif protects HIV-1 from A3G-mediated restriction by forming an E3-ubiquitin ligase complex to polyubiquitinate A3G and trigger its degradation. Prior studies indicated that Vif may also directly block the enzymatic activity of A3G and, provocatively, that Vif-derived peptides, Vif 25-39 and Vif 105-119, are similarly inhibitory. Here, we show that Vif 25-39 does not inhibit A3G enzymatic activity and that the inhibitory effect of Vif 105-119 and that of a shorter derivative Vif 107-115, although recapitulated, are non-specific. We also elaborate a simple method for assaying DNA cytosine deaminase activity that eliminates potential polymerase chain reaction-induced biases. Our results show that these Vif-derived peptides are unlikely to be useful as tools to study A3G function or as leads for the development of future therapeutics.

  6. Coupled-cluster and density functional theory studies of the electronic 0-0 transitions of the DNA bases.

    Science.gov (United States)

    Ovchinnikov, Vasily A; Sundholm, Dage

    2014-04-21

    The 0-0 transitions of the electronic excitation spectra of the lowest tautomers of the four nucleotide (DNA) bases have been studied using linear-response approximate coupled-cluster singles and doubles (CC2) calculations. Excitation energies have also been calculated at the linear-response time-dependent density functional theory (TDDFT) level using the B3LYP functional. Large basis sets have been employed for ensuring that the obtained excitation energies are close to the basis-set limit. Zero-point vibrational energy corrections have been calculated at the B3LYP and CC2 levels for the ground and excited states rendering direct comparisons with high-precision spectroscopy measurements feasible. The obtained excitation energies for the 0-0 transitions of the first excited states of guanine tautomers are in good agreement with experimental values confirming the experimental assignment of the energetic order of the tautomers of the DNA bases. For the experimentally detected guanine tautomers, the first excited state corresponds to a π→π* transition, whereas for the tautomers of adenine, thymine, and the lowest tautomer of cytosine the transition to the first excited state has n →π* character. The calculations suggest that the 0-0 transitions of adenine, thymine, and cytosine are not observed in the absorption spectrum due to the weak oscillator strength of the formally symmetry-forbidden transitions, while 0-0 transitions of thymine have been detected in fluorescence excitation spectra.

  7. Tris(1,3-dichloro-2-propyl)phosphate Induces Genome-Wide Hypomethylation within Early Zebrafish Embryos

    Science.gov (United States)

    2016-01-01

    Tris(1,3-dichloro-2-propyl)phosphate (TDCIPP) is a high-production volume organophosphate-based plasticizer and flame retardant widely used within the United States. Using zebrafish as a model, the objectives of this study were to determine whether (1) TDCIPP inhibits DNA methyltransferase (DNMT) within embryonic nuclear extracts; (2) uptake of TDCIPP from 0.75 h postfertilization (hpf, 2-cell) to 2 hpf (64-cell) or 6 hpf (shield stage) leads to impacts on the early embryonic DNA methylome; and (3) TDCIPP-induced impacts on cytosine methylation are localized to CpG islands within intergenic regions. Within this study, 5-azacytidine (5-azaC, a DNMT inhibitor) was used as a positive control. Although 5-azaC significantly inhibited zebrafish DNMT, TDCIPP did not affect DNMT activity in vitro at concentrations as high as 500 μM. However, rapid embryonic uptake of 5-azaC and TDCIPP from 0.75 to 2 hpf resulted in chemical- and chromosome-specific alterations in cytosine methylation at 2 hpf. Moreover, TDCIPP exposure predominantly resulted in hypomethylation of positions outside of CpG islands and within intragenic (exon) regions of the zebrafish genome. Overall, these findings provide the foundation for monitoring DNA methylation dynamics within zebrafish as well as identifying potential associations among TDCIPP exposure, adverse health outcomes, and DNA methylation status within human populations. PMID:27574916

  8. Microarray-based method for detecting methylation changes of p16Ink4a gene 5'-CpG islands in gastric carcinomas

    Institute of Scientific and Technical Information of China (English)

    Peng Hou; Jia-Yao Shen; Mei-Ju Ji; Nong-Yue He; Zu-Hong Lu

    2004-01-01

    AIM: Aberrant DNA methylation of CpG site is among the earliest and most frequent alterations in cancer. Several studies suggest that aberrant methylation of the CpG sites of the tumor suppressor gene is closely associated with carcinogenesis. However, large-scale analysis of candidate genes has so far been hampered by the lack of highthroughput approach for analyzing DNA methylation. The aim of this study was to describe a microarray-based method for detecting changes of DNA methylation in cancer.METHODS: This method used bisulfite-modified DNA as a template for PCR amplification, resulting in conversion of unmethylated cytosine, but not methylated cytosine, into thymine within CpG islands of interest. Therefore, the amplified product might contain a pool of DNA fragments with altered nucleotide sequences due to differential methylation status.Nine sets of oligonucleotide probes were designed to fabricate a DNA microarray to detect the methylation changes of p16 gene CpG islands in gastric carcinomas. The results were further validated by methylation-specific PCR (MSP).RESULTS: The experimental results showed that the microarray assay could successfully detect methylation changes of p16 gene in 18 gastric tumor samples. Moreover,it could also potentially increase the frequency of detecting p16 methylation from tumor samples than MSP.CONCLUSION: Microarray assay could be applied as a useful tool for mapping methylation changes in multiple CpG loci and for generating epigenetic profiles in cancer.

  9. Functional heterologous expression and purification of a mammalian methyl-CpG binding domain in suitable yield for DNA methylation profiling assays.

    Science.gov (United States)

    Boyd, Mary E; Heimer, Brandon W; Sikes, Hadley D

    2012-04-01

    DNA methylation is a major epigenetic modification in mammalian cells, and patterns involving methylation of cytosine bases, known as CpG methylation, have been implicated in the development of many types of cancer. Methyl binding domains (MBDs) excised from larger mammalian methyl-CpG-binding proteins specifically recognize methyl-cytosine bases of CpG dinucleotides in duplex DNA. Previous molecular diagnostic studies involving MBDs have employed Escherichia coli for protein expression with either low soluble yields or the use of time-consuming denaturation-renaturation purification procedures to improve yields. Efficient MBD-based diagnostics require expression and purification methods that maximize protein yield and minimize time and resource expenditure. This study is a systematic optimization analysis of MBD expression using both SDS-PAGE and microscopy and it provides a comparison of protein yield from published procedures to that from the conditions found to be optimal in these experiments. Protein binding activity and specificity were verified using a DNA electrophoretic mobility shift assay, and final protein yield was improved from the starting conditions by a factor of 65 with a simple, single-step purification.

  10. miRNAting control of DNA methylation

    Indian Academy of Sciences (India)

    Ashwani Jha; Ravi Shankar

    2014-06-01

    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 homologous proteins with siRNAs recruits the enzyme DRM2, which adds a methyl group at certain cytosine residues within the DNA sequence. In this study, it was found that de novo DNA methylation might be regulated by miRNAs through systematic targeting of the genes involved in DNA methylation. A comprehensive genome-wide and system-level study of miRNA targeting, transcription factors, DNA-methylation-causing genes and their target genes has provided a clear picture of an interconnected relationship of all these factors which regulate DNA methylation in Arabidopsis. The study has identified a DNA methylation system that is controlled by four different genes: IDN2, IDNl1, IDNl2 and DRM2. These four genes along with various critical transcription factors appear to be controlled by five different miRNAs. Altogether, DNA methylation appears to be a finely tuned process of opposite control systems of DNA-methylation-causing genes and certain miRNAs pitted against each other.

  11. N(4)-Acyl derivatives as lipophilic prodrugs of cidofovir and its 5-azacytosine analogue, (S)-HPMP-5-azaC: chemistry and antiviral activity.

    Science.gov (United States)

    Krečmerová, Marcela; Pohl, Radek; Masojídková, Milena; Balzarini, Jan; Snoeck, Robert; Andrei, Graciela

    2014-05-15

    Even number fatty acid residues-docosanoyl (behenoyl) and stearoyl were selected for introduction to the N(4)-position of (S)-1-[3-hydroxy-2-(phosphonomethoxy)propyl]cytosine) (HPMPC, cidofovir), and its 5-azacytosine counterpart, (S)-1-[3-hydroxy-2-(phosphonomethoxy)propyl]cytosine) (HPMP-5-azaC) with the aim to prepare a new type of lipophilic prodrugs. The study on the influence of these modifications to the stability and biological activity of both antivirals was performed. Different reactivity of both systems towards acylation reactions was also found: the 4-NH2 group of cidofovir was more reactive compared to that of HPMP-5-azaC. In 5-azacytosine derivatives, we found mostly a destabilizing effect of the N(4)-acylation but this could be compensated by a positive influence of the esterification of the phosphonate group. Chemical stability of the 5-azacytosine moiety in the HPMP series is increasing in the following order: HPMP-5-azaC

  12. Down-regulation of CXCR4 expression by tamoxifen is associated with DNA methyltransferase 3B up-regulation in MCF-7 breast cancer cells.

    Science.gov (United States)

    Kubarek, Ł; Kozłowska, A; Przybylski, M; Lianeri, M; Jagodzinski, P P

    2009-09-01

    The CXCR4 chemokine receptor is a seven transmembrane G protein-coupled receptor present on the surface of various cells including cancer cells. The CXCR4 receptor contributes to the induction of several intracellular signalling pathways that enhance survival, proliferation, and migration of malignant cells. We observed that tamoxifen (Tam) reduced the CXCR4 transcript and protein levels in MCF-7 breast cancer cells. However, we did not see a Tam effect on CXCR4 transcript and protein levels in MCF-7(LVMT3B) cells with RNA interference-mediated knockdown of DNMT3B. We also observed that Tam significantly increased, for several hours, the expression of enzymatically active DNMT3B splice variants in MCF-7 cells. However, there was no Tam effect on these DNMT3B splice variants' expression in MCF-7(LVMT3B) cells. Bisulfite sequencing suggests that Tam may reduce CXCR4 expression via increased methylation of cytosine in the cytosine-guanosine (CpG) dinucleotide island of the CXCR4 promoter of MCF-7 breast cancer cells. Our findings suggest that Tam induces an increase in DNMT3B expression that is associated with the increase of CpG dinucleotide methylation in the CXCR4 promoter and significant reduction of CXCR4 gene expression in MCF-7 cells.

  13. The solute specificity profiles of nucleobase cation symporter 1 (NCS1) from Zea mays and Setaria viridis illustrate functional flexibility.

    Science.gov (United States)

    Rapp, Micah; Schein, Jessica; Hunt, Kevin A; Nalam, Vamsi; Mourad, George S; Schultes, Neil P

    2016-03-01

    The solute specificity profiles (transport and binding) for the nucleobase cation symporter 1 (NCS1) proteins, from the closely related C4 grasses Zea mays and Setaria viridis, differ from that of Arabidopsis thaliana and Chlamydomonas reinhardtii NCS1. Solute specificity profiles for NCS1 from Z. mays (ZmNCS1) and S. viridis (SvNCS1) were determined through heterologous complementation studies in NCS1-deficient Saccharomyces cerevisiae strains. The four Viridiplantae NCS1 proteins transport the purines adenine and guanine, but unlike the dicot and algal NCS1, grass NCS1 proteins fail to transport the pyrimidine uracil. Despite the high level of amino acid sequence similarity, ZmNCS1 and SvNCS1 display distinct solute transport and recognition profiles. SvNCS1 transports adenine, guanine, hypoxanthine, cytosine, and allantoin and competitively binds xanthine and uric acid. ZmNCS1 transports adenine, guanine, and cytosine and competitively binds, 5-fluorocytosine, hypoxanthine, xanthine, and uric acid. The differences in grass NCS1 profiles are due to a limited number of amino acid alterations. These amino acid residues do not correspond to amino acids essential for overall solute and cation binding or solute transport, as previously identified in bacterial and fungal NCS1, but rather may represent residues involved in subtle solute discrimination. The data presented here reveal that within Viridiplantae, NCS1 proteins transport a broad range of nucleobase compounds and that the solute specificity profile varies with species.

  14. Mutational Pressure in Zika Virus: Local ADAR-Editing Areas Associated with Pauses in Translation and Replication

    Science.gov (United States)

    Khrustalev, Vladislav V.; Khrustaleva, Tatyana A.; Sharma, Nitin; Giri, Rajanish

    2017-01-01

    Zika virus (ZIKV) spread led to the recent medical health emergency of international concern. Understanding the variations in virus system is of utmost need. Using available complete sequences of ZIKV we estimated directions of mutational pressure along the length of consensus sequences of three lineages of the virus. Results showed that guanine usage is growing in ZIKV RNA plus strand due to adenine to guanine transitions, while adenine usage is growing due to cytosine to adenine transversions. Especially high levels of guanine have been found in two-fold degenerated sites of certain areas of RNA plus strand with high amount of secondary structure. The usage of cytosine in two-fold degenerated sites shows direct dependence on the amount of secondary structure in 52% (consensus sequence of East African ZIKV lineage)—32% (consensus sequence of epidemic strains) of the length of RNA minus strand. These facts are the evidences of ADAR-editing of both strands of ZIKV genome during pauses in replication. RNA plus strand can also be edited by ADAR during pauses in translation caused by the appearance of groups of rare codons. According to our results, RNA minus strand of epidemic ZIKV strain has lower number of points in which polymerase can be stalled (allowing ADAR-editing) compared to other strains. The data on preferable directions of mutational pressure in epidemic ZIKV strain is useful for future vaccine development and understanding the evolution of new strains. PMID:28275585

  15. Methylation specific targeting of a chromatin remodeling complex from sponges to humans

    Science.gov (United States)

    Cramer, Jason M.; Pohlmann, Deborah; Gomez, Fernando; Mark, Leslie; Kornegay, Benjamin; Hall, Chelsea; Siraliev-Perez, Edhriz; Walavalkar, Ninad M.; Sperlazza, M. Jeannette; Bilinovich, Stephanie; Prokop, Jeremy W.; Hill, April L.; Williams Jr., David C.

    2017-01-01

    DNA cytosine methylation and methyl-cytosine binding domain (MBD) containing proteins are found throughout all vertebrate species studied to date. However, both the presence of DNA methylation and pattern of methylation varies among invertebrate species. Invertebrates generally have only a single MBD protein, MBD2/3, that does not always contain appropriate residues for selectively binding methylated DNA. Therefore, we sought to determine whether sponges, one of the most ancient extant metazoan lineages, possess an MBD2/3 capable of recognizing methylated DNA and recruiting the associated nucleosome remodeling and deacetylase (NuRD) complex. We find that Ephydatia muelleri has genes for each of the NuRD core components including an EmMBD2/3 that selectively binds methylated DNA. NMR analyses reveal a remarkably conserved binding mode, showing almost identical chemical shift changes between binding to methylated and unmethylated CpG dinucleotides. In addition, we find that EmMBD2/3 and EmGATAD2A/B proteins form a coiled-coil interaction known to be critical for the formation of NuRD. Finally, we show that knockdown of EmMBD2/3 expression disrupts normal cellular architecture and development of E. muelleri. These data support a model in which the MBD2/3 methylation-dependent functional role emerged with the earliest multicellular organisms and has been maintained to varying degrees across animal evolution. PMID:28094816

  16. Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.

    Science.gov (United States)

    Serre, Laurence; Pereira de Jésus, Karine; Boiteux, Serge; Zelwer, Charles; Castaing, Bertrand

    2002-06-17

    The formamidopyrimidine-DNA glycosylase (Fpg, MutM) is a bifunctional base excision repair enzyme (DNA glycosylase/AP lyase) that removes a wide range of oxidized purines, such as 8-oxoguanine and imidazole ring-opened purines, from oxidatively damaged DNA. The structure of a non-covalent complex between the Lactoccocus lactis Fpg and a 1,3-propanediol (Pr) abasic site analogue-containing DNA has been solved. Through an asymmetric interaction along the damaged strand and the intercalation of the triad (M75/R109/F111), Fpg pushes out the Pr site from the DNA double helix, recognizing the cytosine opposite the lesion and inducing a 60 degrees bend of the DNA. The specific recognition of this cytosine provides some structural basis for understanding the divergence between Fpg and its structural homologue endo nuclease VIII towards their substrate specificities. In addition, the modelling of the 8-oxoguanine residue allows us to define an enzyme pocket that may accommodate the extrahelical oxidized base.

  17. Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data.

    Science.gov (United States)

    Tsuji, Junko; Weng, Zhiping

    2016-11-01

    Cytosine methylation regulates many biological processes such as gene expression, chromatin structure and chromosome stability. The whole genome bisulfite sequencing (WGBS) technique measures the methylation level at each cytosine throughout the genome. There are an increasing number of publicly available pipelines for analyzing WGBS data, reflecting many choices of read mapping algorithms as well as preprocessing and postprocessing methods. We simulated single-end and paired-end reads based on three experimental data sets, and comprehensively evaluated 192 combinations of three preprocessing, five postprocessing and five widely used read mapping algorithms. We also compared paired-end data with single-end data at the same sequencing depth for performance of read mapping and methylation level estimation. Bismark and LAST were the most robust mapping algorithms. We found that Mott trimming and quality filtering individually improved the performance of both read mapping and methylation level estimation, but combining them did not lead to further improvement. Furthermore, we confirmed that paired-end sequencing reduced error rate and enhanced sensitivity for both read mapping and methylation level estimation, especially for short reads and in repetitive regions of the human genome.

  18. Hairpin DNA probe with 5'-TCC/CCC-3' overhangs for the creation of silver nanoclusters and miRNA assay.

    Science.gov (United States)

    Xia, Xiaodong; Hao, Yuanqiang; Hu, Shengqiang; Wang, Jianxiu

    2014-01-15

    A facile strategy for the assay of target miRNA using fluorescent silver nanoclusters (AgNCs) has been described. Due to the preferable interaction between cytosine residues and Ag(+), a short cytosine-rich oligonucleotide (ODN) with only six bases 5'-TCCCCC-3' served as an efficient scaffold for the creation of the AgNCs. The AgNCs displayed a bright red emission when excited at 545nm. Such ODN base-stabilized AgNCs have been exploited for miRNA sensing. Overhangs of TCC at the 5' end (5'-TCC) and CCC at the 3' end (CCC-3') (denoted as 5'-TCC/CCC-3') appended to the hairpin ODN probe which also contains recognition sequences for target miRNA were included. Interestingly, the AgNCs/hairpin ODN probe showed similar spectral properties as that templated by 5'-TCCCCC-3'. The formation of the hairpin ODN probe/miRNA duplex separated the 5'-TCC/CCC-3' overhangs, thus disturbing the optical property or structure of the AgNCs. As a result, fluorescence quenching of the AgNCs/hairpin ODN probe was obtained, which allows for facile determination of target miRNA. The proposed method is simple and cost-effective, holding great promise for clinical applications.

  19. Methylation of chloroplast DNA does not affect viability and maternal inheritance in tobacco and may provide a strategy towards transgene containment

    Science.gov (United States)

    Jaffé, Benjamin; Kovács, Katalin; Andras, Calin; Bódi, Zsuzsanna; Liu, Zheng

    2008-01-01

    We report the integration of a type II restriction-methylase, mFokI, into the tobacco chloroplast genome and we demonstrate that the introduced enzyme effectively directs the methylation of its target sequence in vivo and does not affect maternal inheritance. We further report the transformation of tobacco with an E. coli dcm methylase targeted to plastids and we demonstrate efficient cytosine methylation of the plastid genome. Both adenosine methylation of FokI sites and cytosine methylation of dcm sites appeared phenotypically neutral. The ability to tolerate such plastid genome methylation is a pre-requisite for a proposed plant transgene containment system. In such a system, a chloroplast located, maternally inherited restriction methylase would provide protection from a nuclear-encoded, plastid targeted restriction endonuclease. As plastids are not paternally inherited in most crop species, pollen from such plants would carry the endonuclease transgene but not the corresponding methylase; the consequence of this should be containment of all nuclear transgenes, as pollination will only be viable in crosses to the appropriate transplastomic maternal background. PMID:18536921

  20. The Photochemistry of Pyrimidine in Pure H2O Ice Subjected to Different Radiation Environments and the Formation of Uracil

    Science.gov (United States)

    Nuevo, M.; Chen, Y.-J.; Materese. C. K..; Hu, W.-J.; Qiu, J.-M.; Wu, S.-R.; Fung, H.-S.; Sandford, S. A.; Chu, C.-C.; Yih, T.-S.; Wu, R.; Ip, W.-H.

    2013-01-01

    Nucleobases are N-heterocycles which are the informational subunits of DNA and RNA. They include pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in several meteorites, although no Nheterocycles have been observed in space to data. Laboratory experiments showed that the ultraviolet (UV) irradiation of pyrimidine in pure H2O ice at low temperature (<=20 K) leads to the formation of pyrimidine derivatives including the nucleobase uracil and its precursor 4(3H)-pyrimidone. These results were confirmed by quantum chemical calculations. When pyrimidine is mixed with combinations of H2O, NH3, CH3OH, and CH4 ices under similar conditions, uracil and cytosine are formed. In the present work we study the formation of 4(3H)-pyrimidone and uracil from the irradiation of pyrimidine in H2O ice with high-energy UV photons (Lyman , He I, and He II lines) provided by a synchrotron source. The photo-destruction of pyrimidine in these H2O ices as well as the formation yields for 4(3H)-pyrimidone and uracil are compared with our previous results in order to study the photo-stability of pyrimidine and the production efficiency of uracil as a function of the photon energy.