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Hydroxymethylation

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https://www.readbyqxmd.com/read/28441516/epoxynemanione-a-nemanifuranones-a-f-and-nemanilactones-a-c-from-nemania-serpens-an-endophytic-fungus-isolated-from-riesling-grapevines
#1
Ashraf Ibrahim, Dan Sørensen, Hilary A Jenkins, Linda Ejim, Alfredo Capretta, Mark W Sumarah
Ten polyketide specialized metabolites, epoxynemanione A, nemanifuranones A-F, and nemanilactones A-C, were isolated from the culture filtrate of Nemania serpens (Pers.) Grey (1821), an endophytic fungus from a Riesling grapevine (Vitis vinifera) found in Canada's Niagara region. Additionally, four known metabolites 2-(hydroxymethyl)-3-methoxy-benzoic acid, phyllostine, 5-methylmellein and a nordammarane triterpenoid were isolated. A related known metabolite 2,3-dihydro-2-hydroxy-2,4-dimethyl-5-trans-propenylfuran-3-one has also been included for structural and biological comparison to the nemanifuranones...
April 22, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28437360/dna-hydroxymethylation-by-ten-eleven-translocation-methylcytosine-dioxygenase-1-and-3-regulates-nociceptive-sensitization-in-a-chronic-inflammatory-pain-model
#2
Zhiqiang Pan, Zhou-Ya Xue, Guo-Fang Li, Meng-Lan Sun, Ming Zhang, Ling-Yun Hao, Qian-Qian Tang, Li-Jiao Zhu, Jun-Li Cao
BACKGROUND: Ten-eleven translocation methylcytosine dioxygenase converts 5-methylcytosine in DNA to 5-hydroxymethylcytosine, which plays an important role in gene transcription. Although 5-hydroxymethylcytosine is enriched in mammalian neurons, its regulatory function in nociceptive information processing is unknown. METHODS: The global levels of 5-hydroxymethylcytosine and ten-eleven translocation methylcytosine dioxygenase were measured in spinal cords in mice treated with complete Freund's adjuvant...
April 24, 2017: Anesthesiology
https://www.readbyqxmd.com/read/28428825/comprehensive-evaluation-of-genome-wide-5-hydroxymethylcytosine-profiling-approaches-in-human-dna
#3
Ksenia Skvortsova, Elena Zotenko, Phuc-Loi Luu, Cathryn M Gould, Shalima S Nair, Susan J Clark, Clare Stirzaker
BACKGROUND: The discovery that 5-methylcytosine (5mC) can be oxidized to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation (TET) proteins has prompted wide interest in the potential role of 5hmC in reshaping the mammalian DNA methylation landscape. The gold-standard bisulphite conversion technologies to study DNA methylation do not distinguish between 5mC and 5hmC. However, new approaches to mapping 5hmC genome-wide have advanced rapidly, although it is unclear how the different methods compare in accurately calling 5hmC...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28422379/increased-5-hydroxymethylation-levels-in-the-hippocampus-of-rat-extinguished-from-cocaine-self-administration
#4
Anna Sadakierska-Chudy, Małgorzata Frankowska, Karolina Wydra, Joanna Jastrzębska, Joanna Miszkiel, Małgorzata Filip
Drug craving and relapse risk during abstinence from cocaine are thought to be caused by persistent changes in transcription and chromatin regulation. Although several brain regions are involved in these processes, the hippocampus seems to play an important role in context-evoked craving and drug-seeking behavior. Only a few studies have examined epigenetic alterations during a period of cocaine abstinence. To investigate the effects of cocaine abstinence on DNA methylation and gene expression, rats that self-administered the drug underwent cocaine abstinence in two time points with extinction training...
April 19, 2017: Hippocampus
https://www.readbyqxmd.com/read/28418776/7-glutathione-pyrrole-and-7-cysteine-pyrrole-are-potential-carcinogenic-metabolites-of-pyrrolizidine-alkaloids
#5
Xiaobo He, Qingsu Xia, Peter P Fu
Many pyrrolizidine alkaloids (PAs) are hepatotoxic, genotoxic, and carcinogenic phytochemicals. Metabolism of PAs in vivo generates four (±)-6,7-dihydro-7-hydroxy-1-hydroxymethyl-5H-pyrrolizine (DHP)-DNA adducts that have been proposed to be responsible for PA-induced liver tumor formation in rats. In this present study, we determined that the same set of DHP-DNA adducts was formed upon the incubation of 7-glutathione-DHP and 7-cysteine-DHP with cultured human hepatocarcinoma HepG2 cells. These results suggest that 7-glutathione-DHP and 7-cysteine-DHP are reactive metabolites of PAs that can bind to cellular DNA to form DHP-DNA adducts in HepG2 cells, and can potentially initiate liver tumor formation...
March 1, 2017: Journal of Environmental Science and Health. Part C, Environmental Carcinogenesis & Ecotoxicology Reviews
https://www.readbyqxmd.com/read/28415401/a-new-2-amino-3-pynanopyrane-3-carbonitrile-derivative-for-electrocatalytic-oxidation-and-determination-of-hydrazine
#6
Leili Shahidi, Masoumeh Taei, Seyed Hossein Banitaba, Nahid Tavakkoli
A noble glassy carbon electrode modified with Au nanoparticles and 2-amino-4-(3,4-dihydroxyphenyl)-6-(hydroxymethyl)-8-oxo-4,8-dihydropyrano[3,2-b]pyran-3-carbonitrile, was fabricated for electrocatalytic determination of hydrazine (AuNPs/APP/GCE). Large over-potential and interference of some species are two limitation factors for the determination of hydrazine at bare electrode. This modified electrode is able to shift a signal to the negative potential, and can amplify the oxidation current of hydrazine by 28...
June 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28411610/benchmark-study-of-the-structural-and-spectroscopic-parameters-of-the-hydroxymethyl-peroxy-hoch2oo-radical-and-its-decomposition-reaction-to-ho2-and-h2co
#7
Roberto Linguerri, Cristina Puzzarini, Muneerah Mogren Al Mogren, Joseph S Francisco, Majdi Hochlaf
The hydroxymethyl peroxy (HMOO) radical is a product of the oxidation of non-methane hydrocarbons. The present study provides the first accurate computational determination of critical spectroscopic features of the title radical that should aid in its experimental characterization. Structure, energetics, vibrational frequencies, and rotational parameters are reported for the three stable isomers on the ground electronic state of HMOO. While preliminary computations have been carried out using density functional theory as well as second-order Møller-Plesset perturbation theory, for the accurate structural and spectroscopic characterization we made use of coupled-cluster techniques, herewith considering both standard and explicitly correlated methods...
April 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28411382/interaction-between-maternal-and-paternal-shmt1-c1420t-predisposes-to-neural-tube-defects-in-the-fetus-evidence-from-case-control-and-family-based-triad-approaches
#8
Prasoona K Rebekah, Sunitha Tella, Srinadh Buragadda, Muni Kumari Tiruvatturu, Jyothy Akka
BACKGROUND: Neural tube defects (NTDs) are caused by the failure of neural tube formation which occurs during early embryonic development. NTDs are the most severe and leading cause of fetal mortality. Serine hydroxymethyl transferase (SHMT1) provides one-carbon units necessary for embryogenesis and defects in one-carbon production result in specific pathological conditions during pregnancy. The present study is aimed to evaluate the association of SHMT1 C1420T with NTD risk in the fetus using fetal, maternal and paternal groups by applying both case-control and family-based triad approaches...
April 14, 2017: Birth Defects Res
https://www.readbyqxmd.com/read/28395827/inhibitory-mechanism-of-quercetin-against-the-formation-of-5-hydroxymethyl-2-furaldehyde-in-buckwheat-flour-bread-by-ultra-performance-liquid-chromatography-coupled-with-high-resolution-tandem-mass-spectrometry
#9
Yinan Zhang, Xiaoning An
Ultra-performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UPLC-HRMS/MS) was employed to investigate the inhibitory mechanism of quercetin against the formation of 5-(hydroxymethyl)-2-furaldehyde (HMF) in buckwheat flour bread. The HMF and HMF precursors (3,4-dideoxyglucosone-3-ene (3,4-DGE), 3-deoxyglucosone (3-DG), or fructofuranosyl cation dehydration products (FCDPs)) adducts of quercetin were detected in buckwheat flour bread, with the trapping of these compounds by quercetin to form corresponding adducts with HMF or its precursors in 1:1, 1:2, 1:3, and 1:4 ratios (where "1" refers to quercetin in all cases)...
May 2017: Food Research International
https://www.readbyqxmd.com/read/28395199/design-synthesis-and-biological-evaluation-of-nad-p-h-quinone-oxidoreductase-nqo1-targeted-oridonin-prodrugs-possessing-indolequinone-moiety-for-hypoxia-selective-activation
#10
Shengtao Xu, Hong Yao, Lingling Pei, Mei Hu, Dahong Li, Yangyi Qiu, Guangyu Wang, Liang Wu, Hequan Yao, Zheying Zhu, Jinyi Xu
The enzyme NQO1 is a potential target for selective cancer therapy due to its overexpression in certain hypoxic tumors. A series of prodrugs possessing a variety of cytotoxic diterpenoids (oridonin and its analogues) as the leaving groups activated by NQO1 were synthesized by functionalization of 3-(hydroxymethyl)indolequinone, which is a good substrate of NQO1. The target compounds (29a-m) exhibited relatively higher antiproliferative activities against NQO1-rich human colon carcinoma cells (HT-29) and human lung carcinoma (A549) cells (IC50 = 0...
March 25, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28393957/photo-cleavable-analog-of-bapta-for-the-fast-and-efficient-release-of-ca-2
#11
Mariia V Sutton, Matthew McKinley, Revathy Kulasekharan, Vladimir V Popik
A new photocleavable analog of BAPTA chelating ligand has a high affinity towards Ca(2+) ions (K = 2.5 × 10(6) M(-1)). The use of photolabile 3-(hydroxymethyl)-2-naphthol core in the design of photo-BAPTA allows for the efficient (Φ = 0. 63) and very fast (τ < 12 μs) release of Ca(2+) ions upon 300 or 350 nm irradiation.
April 10, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28393907/involvement-of-a-velvet-protein-clvelb-in-the-regulation-of-vegetative-differentiation-oxidative-stress-response-secondary-metabolism-and-virulence-in-curvularia-lunata
#12
Jin-Xin Gao, Chuan-Jin Yu, Meng Wang, Jia-Nan Sun, Ya-Qian Li, Jie Chen
The ortholog of Aspergillus nidulans VelB, which is known as ClVelB, was studied to gain a broader insight into the functions of a velvet protein in Curvularia lunata. With the expected common and specific functions of ClVelB, the deletion of clvelB results in similar though not identical phenotypes. The pathogenicity assays revealed that ΔClVelB was impaired in colonizing the host tissue, which corresponds to the finding that ClVelB controls the production of conidia and the methyl 5-(hydroxymethyl) furan-2-carboxylate toxin in C...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28393704/epigenetic-regulation-of-memory-therapeutic-potential-for-disorders
#13
Padmanabh Singh, Sweta Srivas, M K Thakur
Memory is a vital function which declines in different physiological and pathological conditions such as aging and neurodegenerative diseases. Research in the past has reported that memory formation and consolidation require the precise expression of synaptic plasticity genes. However, little is known about the regulation of these genes. Epigenetic modification is now a well established mechanism that regulates synaptic plasticity genes and neuronal functions including memory. Such modification includes mainly DNA methylation and hydroxymethylation, histone acetylation and methylation which involve chromatin modifying enzymes...
April 4, 2017: Current Neuropharmacology
https://www.readbyqxmd.com/read/28388873/changes-in-the-dna-methylation-and-hydroxymethylation-status-of-the-intercellular-adhesion-molecule-1-gene-promoter-in-thyrocytes-from-autoimmune-thyroiditis-patients
#14
Tingting Liu, Jie Sun, Zhaojun Wang, Wenqing Yang, Hao Zhang, Chenling Fan, Zhongyan Shan, Weiping Teng
BACKGROUND: The intercellular adhesion molecule 1 (ICAM1) gene is not expressed in normal thyroid tissue but was shown to be expressed in the thyroid tissue of autoimmune thyroiditis (AIT) patients. METHODS: This study aimed to explore whether the DNA methylation and hydroxymethylation status of the ICAM1 promoter are aberrantly altered in the thyroid cells of AIT patients and whether this change is associated with dysfunctional expression of ICAM1. A total of 35 AIT patients and 35 sex- and age-matched controls were studied...
April 7, 2017: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/28387726/rethinking-the-epigenetic-framework-to-unravel-the-molecular-pathology-of-schizophrenia
#15
REVIEW
Ariel Cariaga-Martinez, Raúl Alelú-Paz
Schizophrenia is a complex mental disorder whose causes are still far from being known. Although researchers have focused on genetic or environmental contributions to the disease, we still lack a scientific framework that joins molecular and clinical findings. Epigenetic can explain how environmental variables may affect gene expression without modifying the DNA sequence. In fact, neuroepigenomics represents an effort to unify the research available on the molecular pathology of mental diseases, which has been carried out through several approaches ranging from interrogating single DNA methylation events and hydroxymethylation patterns, to epigenome-wide association studies, as well as studying post-translational modifications of histones, or nucleosomal positioning...
April 7, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28375005/expanding-the-chemical-repertoire-of-the-endophyte-streptomyces-albospinus-rle7-reveals-amphotericin-b-as-an-inducer-of-a-fungal-phenotype
#16
Fernanda Oliveira Chagas, Andrés Mauricio Caraballo-Rodríguez, Pieter C Dorrestein, Mônica Tallarico Pupo
During an investigation of the chemistry of the endophytic actinobacterium Streptomyces albospinus RLe7, which was isolated from the roots of the Brazilian medicinal plant Lychnophora ericoides, three new natural products, (2R*,4S*)-2-((1'S*)-hydroxy-4'-methylpentyl)-4-(hydroxymethyl)butanolide (1), (3R*,4S*,5R*,6S*)-tetrahydro-4-hydroxy-3,5,6-trimethyl-2-pyranone (2), and 1-O-(phenylacetyl)glycerol (3), together with known secondary metabolites (S)-4-benzyl-3-oxo-3,4-dihydro-1H-pyrrolo[2,1-c][1,4]oxazine-6-carbaldehyde (4), (S)-4-isobutyl-3-oxo-3,4-dihydro-1H-pyrrolo[2,1-c][1,4]oxazine-6-carbaldehyde (5), and the diketopiperazines cyclo(l-Tyr-l-Pro) (6) and cyclo(l-Val-l-Pro) (7), were isolated...
April 4, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28371147/quantitative-lc-ms-provides-no-evidence-for-m-6-da-or-m-4-dc-in-the-genome-of-mouse-embryonic-stem-cells-and-tissues
#17
Sarah Schiffers, Charlotte Ebert, René Rahimoff, Olesea Kosmatchev, Jessica Steinbacher, Alexandra-Viola Bohne, Fabio Spada, Stylianos Michalakis, Jörg Nickelsen, Markus Müller, Thomas Carell
Until recently, it was believed that the genomes of higher organisms contain, in addition to the four canonical DNA bases, only 5-methyl-dC (m(5) dC) as a modified base to control epigenetic processes. In recent years, this view has changed dramatically with the discovery of 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5-carboxy-dC (cadC) in DNA from stem cells and brain tissue. N(6) -methyldeoxyadenosine (m(6) dA) is the most recent base reported to be present in the genome of various eukaryotic organisms...
March 30, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28370485/19f-nmr-spectroscopic-analysis-of-the-binding-modes-in-triple-helical-pna-microrna-complexes
#18
Pasi Markus Virta, Ville Tähtinen, Lotta Granqvist, Merita Murtola, Roger Strömberg
Triplex-forming peptide nucleic acids (TFPNAs) were targeted to double helical regions of 19F-labelled RNA hairpin models (a UA-rich duplex with a hexaethylene glycol (heg) loop and a miR-215 model). In addition to the conventional UV- and CD-based detection, the binding was monitored by 19F NMR spectroscopy. Detailed information considering the stoichiometry and transition between the triple helical PNA/RNA- and (PNA)2/RNA-binding modes could be obtained. γ-(R)-hydroxymethyl-modified (thymine-1-yl- and 2-aminopyridin-3-yl-acetyl derivatives) TFPNAs were additionally synthesized, targeted to the same RNA models and the effect of the γ-(R)-hydroxymethyl group on the binding was studied...
March 28, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28369586/uracil-dna-glycosylase-udg-activities-in-bradyrhizobium-diazoefficiens-characterization-of-a-new-class-of-udg-with-broad-substrate-specificity
#19
Ullas Valiya Chembazhi, Vinod Vikas Patil, Shivjee Sah, Wayne Reeve, Ravi P Tiwari, Euijeon Woo, Umesh Varshney
Repair of uracils in DNA is initiated by racil NA lycosylases (UDGs). Family 1 UDGs (Ung) are the most efficient and ubiquitous proteins having an exquisite specificity for uracils in DNA. Ung are characterized by motifs A (GQDPY) and B (HPSPLS) sequences. We report a novel dimeric UDG, Blr0248 ( Bdi Ung) from Bradyrhizobium diazoefficiens . Although Bdi Ung contains the motif A (GQDPA), it has low sequence identity to known UDGs. Bdi Ung prefers single stranded DNA and excises uracil, 5-hydroxymethyl-uracil or xanthine from it...
March 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28368586/bioactive-pentacyclic-triterpene-ester-derivatives-from-alnus-viridis-ssp-viridis-bark
#20
Miroslav Novakovic, Jasmina Nikodinovic-Runic, Jovana Veselinovic, Tatjana Ilic-Tomic, Vera Vidakovic, Vele Tesevic, Slobodan Milosavljevic
Seven derivatives of pentacyclic triterpene acids (1-7) were isolated from the bark of Alnus viridis ssp. viridis using a combination of column chromatography and semipreparative HPLC. Compounds 1-3, 6, and 7 were determined to be new after spectroscopic data interpretation and were assigned as 27-hydroxyalphitolic acid derivatives (1-3), a 27-hydroxybetulinic acid derivative (6), and a 3-epi-maslinic acid derivative (7), respectively. Pentacyclic triterpenoids with a C-27 hydroxymethyl group have been found in species of the genus Alnus for the first time...
April 3, 2017: Journal of Natural Products
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