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John P Thomson, Richard R Meehan
Since its initial characterization in 2009 there has been a great degree of interest in comparative profiling of 5-hydroxymethylcytosine (5hmC) nucleotides in vertebrate DNA. Through a host of genome-wide studies the distribution of 5hmC has been mapped in a range of cell lines, tissue types and organisms; the majority of which have been generated through affinity-based methods for 5hmC enrichment. Although recent advances in the field have resulted in the ability to investigate the levels of both methylated and hydroxymethylated cytosines at single base resolution, such studies are still relatively cost-prohibitive as well as technically challenging...
2018: Methods in Molecular Biology
Maria Jung, Glen Kristiansen, Dimo Dietrich
Circulating cell-free DNA in body fluids is an analyte of great interest in basic and clinical research. The analyses of DNA methylation and hydroxymethylation patterns in body fluids might allow one to determine the certain state of a disease, in particular of cancer. DNA methylation biomarkers in liquid biopsies, i.e. blood plasma samples, may help optimizing personalized therapy for individual patients. DNA methylation analyses of specific loci usually require a bisulfite conversion of the DNA, which requires a sufficiently high amount of DNA at the appropriate concentration...
2018: Methods in Molecular Biology
John M Greally
Restriction enzymes have been valuable tools for representing the genome for DNA methylation assays, whether by using methylation-dependent enzymes or by sampling a reduced representation of the genome using a methylation-insensitive enzyme. These survey assays have remained mainstays of genome-wide approaches even with the development of more comprehensive shotgun genome-wide bisulphite sequencing-based assays, as they are significantly more affordable. DNA methylation survey assays are numerous and include reduced representation bisulphite sequencing (RRBS), the Illumina HumanMethylation450K and EPIC microarray system, and our evolving series of HELP-based assays...
2018: Methods in Molecular Biology
Agustin F Fernandez, Luis Valledor, Fernando Vallejo, Maria Jesús Cañal, Mario F Fraga
Global DNA methylation was classically considered the relative percentage of 5-methylcysine (5mC) with respect to total cytosine (C). Early approaches were based on the use of high-performance separation technologies and UV detection. However, the recent development of protocols using mass spectrometry for the detection has increased sensibility and permitted the precise identification of peak compounds based on their molecular masses. This allows work to be conducted with much less genomic DNA starting material and also to quantify 5-hydroxymethyl-cytosine (5hmC), a recently identified form of methylated cytosine that could play an important role in active DNA demethylation...
2018: Methods in Molecular Biology
Michael Murray, Tina B Gillani, Sussan Ghassabian, Robert J Edwards, Tristan Rawling
The tyrosine kinase inhibitors sorafenib and imatinib are important in the treatment of a range of cancers but adverse effects in some patients necessitate dosage modifications. CYP3A4 has a major role in the oxidation of sorafenib to its N-oxide and N-hydroxymethyl metabolites and also acts in concert with CYP2C8 to mediate imatinib N-demethylation. CYP3A4 expression and function are impaired in patients with advanced liver disease, whereas the functions of CYP2C enzymes are relatively preserved. We evaluated the biotransformation of sorafenib and imatinib in well-characterized microsomal fractions from 17 control subjects and 19 individuals with hepatic cirrhosis of varying severity...
December 6, 2017: European Journal of Pharmaceutical Sciences
P Horký, M Voráčová, K Konečná, D Sedlák, P Bartůněk, J Vacek, J Kuneš, M Pour
A library of thirty two 3,4-diphenylfuranones related to both combretastatin A-4 and antifungal 5-(acyloxymethyl)-3-(halophenyl)-2,5-dihydrofuran-2-ones was prepared. Cytotoxic effects on a panel of cancer and normal cell lines and antiinfective activity were evaluated, and the data were complemented with tests for the activation of caspase 3 and 7. High cytotoxicity was observed in some of the halogenated analogues, eg. 3-(3,4-dichlorophenyl)-4-(4-methylphenyl)-2,5-dihydrofuran-2-one with IC50 0.12-0.23 μM, but the compounds were also highly toxic against non-malignant control cells...
November 29, 2017: European Journal of Medicinal Chemistry
Siemon De Nys, Radu-Corneliu Duca, Tim Nawrot, Peter Hoet, Bart Van Meerbeek, Kirsten L Van Landuyt, Lode Godderis
BACKGROUND: Epigenetic changes, such as DNA methylation, are observed in response to environmental exposure and in the development of several chronic diseases. Consequently, DNA methylation alterations might serve as indicators of early effects. In this context, the aim of this study was to assess the temporal variability of global DNA methylation and hydroxymethylation levels in buccal cells from healthy adult volunteers. METHODS: Global DNA methylation (%5mdC) and hydroxymethylation (%5hmdC) levels in human buccal cells, collected from 26 healthy adults at different time points, were quantified by UPLC-MS/MS...
December 4, 2017: Environment International
Feng-An Liu, Xiuping Lin, Xuefeng Zhou, Minghao Chen, Xiuling Huang, Bin Yang, Huaming Tao
Chemical investigation of the fungus Penicillium sp. SCSIO Ind16F01 derived from deep-sea sediment sample afforded a new xanthone, 3,8-dihydroxy-2-methyl-9-oxoxanthene-4-carboxylic acid methyl ester (1) and a new chromone, coniochaetone J (2), together with three known xanthones, 8-hydroxy-6-methyl-9-oxo-9H-xanthene-1-carboxylic acid methyl ester (3), 7,8-dihydroxy-6-methyl-9-oxo-9H-xanthene-1-carboxylic acid methyl ester (4), 1,6,8-trihydroxy-3-(hydroxymethyl)anthraquinone (5), three known chromones, coniochaetone B (6), citrinolactones B (7), epiremisporine B (8), and four reported rare class of N-methyl quinolone lactams: quinolactacins B (9), C1 (10), and C2 (11), and quinolonimide (12)...
December 7, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Shinobu Yamamoto, Akiko Matsumoto, Yuko Yui, Shota Miyazaki, Shinji Kumagai, Hajime Hori, Masayoshi Ichiba
OBJECTIVES: N,N-Dimethylacetamide (DMAC) is widely used in industry as a solvent. It can be absorbed through human skin. Therefore, it is necessary to determine exposure to DMAC via biological monitoring. However, the precision of traditional gas chromatography (GC) is low due to the thermal decomposition of metabolites in the high-temperature GC injection port. To overcome this problem, we have developed a new method for the simultaneous separation and quantification of urinary DMAC metabolites using liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
December 6, 2017: Journal of Occupational Health
Osvaldo Graña, Hugo López-Fernández, Florentino Fdez-Riverola, David González Pisano, Daniel Glez-Peña
Summary: High-throughput sequencing of bisulfite-converted DNA is a technique used to measure DNA methylation levels. Although a considerable number of computational pipelines have been developed to analyze such data, none of them tackles all the peculiarities of the analysis together, revealing limitations that can force the user to manually perform additional steps needed for a complete processing of the data. This article presents bicycle, an integrated, flexible analysis pipeline for bisulfite sequencing data...
December 1, 2017: Bioinformatics
Aleksandar Cvetkovski, Valeria Ferretti, Valerio Bertolasi
Two mixed crystals were obtained by crystallizing the active pharmaceutical ingredient pyridoxine [systematic name: 4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol, PN] with (E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoic acid (ferulic acid) and 4-hydroxy-3,5-dimethoxybenzoic acid (syringic acid). PN and the coformers crystallize in the form of pharmaceutical salts in a 1:1 stoichiometric ratio, namely 3-hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridin-1-ium (E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate, C8H12NO3+·C9H9O5-, and 3-hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridin-1-ium 4-hydroxy-3,5-dimethoxybenzoate monohydrate, C8H12NO3+·C10H11O5-·H2O, the proton exchange between PN and the acidic partner being supported by the differences of the pKa values of the two components and by the C-O bond lengths of the carboxylate groups...
December 1, 2017: Acta Crystallographica. Section C, Structural Chemistry
Szymon Malinowski, Justyna Jaroszyńska-Wolińska, Tony Herbert
We present quantum chemical theoretical estimations of the anti-corrosive properties of THAM (tris(hydroxymethyl)aminomethane) and three derivatives that differ in the number of benzene rings: THAM-1 (2-amino-3-hydroxy-2-(hydroxymethyl) propylobenzoate), THAM-2 (2-amino-2-(hydroxymetyl)prapan-1,3-diyldibenzoate) and THAM-3 (2-amino-propan-1,2,3-triyltribenzoate). Fourteen exchange-correlation functionals based on the density functional theory (DFT) were chosen for quantum chemical study of THAM derivatives...
December 4, 2017: Journal of Molecular Modeling
Michael Almond, Mustapha G Suleiman, Matthew Hawkins, Daniel Winder, Thomas Robshaw, Megan Waddoups, Paul N Humphreys, Andrew P Laws
Alpha and beta-glucoisosaccharinic acids ((2S,4S)-2,4,5-trihydroxy-2-(hydroxymethyl)pentanoic acid and (2R,4S)-2,4,5-trihydroxy-2-(hydroxymethyl)pentanoic acid) which are produced when cellulosic materials are treated with aqueous alkali are potentially valuable platform chemicals. Their highly functionalised carbon skeleton, with fixed chirality at C-2 and C-4, makes them ideal starting materials for use in synthesis. In order to assess the potential of these saccharinic acids as platform chemicals we have explored the protecting group chemistry of the lactone form of alpha-glucoisosaccharinic acid (α-GISAL)...
November 26, 2017: Carbohydrate Research
Deepa Hammaker, Gary S Firestein
PURPOSE OF REVIEW: Aberrant epigenetic changes in DNA methylation, histone marks, and noncoding RNA expression regulate the pathogenesis of many rheumatic diseases. The present article will review the recent advances in the epigenetic profile of inflammatory arthritis and discuss diagnostic biomarkers and potential therapeutic targets. RECENT FINDINGS: Methylation signatures of fibroblast-like synoviocytes not only distinguish rheumatoid arthritis (RA) and osteoarthritis (OA), but also early RAs from late RAs or juvenile idiopathic arthritis...
November 30, 2017: Current Opinion in Rheumatology
Yitao Pan, Xiaoyang Wang, Leo W Y Yeung, Nan Sheng, Qianqian Cui, Ruina Cui, Hongxia Zhang, Jiayin Dai
Phthalates are a large family of ubiquitous environmental pollutants suspected of being endocrine disruptors. Epidemiological studies have associated phthalate metabolites with decreased reproductive parameters and linked phthalate exposure with the level of urinary 5-methyl-2'-deoxycytidine (5mdC, a product of methylated DNA). In this study, adult male mice were exposed to 450mg di-isobutyl phthalate (DiBP)/(kg·day) via dietary exposure for 28days. Mono-isobutyl phthalate (MiBP, the urinary metabolite) and reproductive function parameters were determined...
November 2017: Journal of Environmental Sciences (China)
Manosij Ghosh, Deniz Öner, Katrien Poels, Ali M Tabish, Jelle Vlaanderen, Anjoeka Pronk, Eelco Kuijpers, Qing Lan, Roel Vermeulen, Bram Bekaert, Peter Hm Hoet, Lode Godderis
This study was designed to assess the epigenetic alterations in blood cells, induced by occupational exposure to multi-wall carbon nanotubes (MWCNT). The study population comprised of MWCNT-exposed workers (n=24) and unexposed controls (n=43) from the same workplace. We measured global DNA methylation/hydroxymethylation levels on the 5th cytosine residues using a validated liquid chromatography tandem-mass spectrometry (LC-MS/MS) method. Sequence-specific methylation of LINE1 retrotransposable element 1 (L1RE1) elements, and promoter regions of functionally important genes associated with epigenetic regulation [DNA methyltransferase-1 (DNMT1) and histone deacetylase 4 (HDAC4)], DNA damage/repair and cell cycle pathways [nuclear protein, coactivator of histone transcription/ATM serine/threonine kinase (NPAT/ATM)], and a potential transforming growth factor beta (TGF-β) repressor [SKI proto-oncogene (SKI)] were studied using bisulfite pyrosequencing...
November 30, 2017: Nanotoxicology
Marek Foksinski, Ewelina Zarakowska, Daniel Gackowski, Magdalena Skonieczna, Karolina Gajda, Dorota Hudy, Anna Szpila, Karol Bialkowski, Marta Starczak, Anna Labejszo, Jaroslaw Czyz, Joanna Rzeszowska-Wolny, Ryszard Olinski
Active demethylation of 5-methylcytosine moiety in DNA occurs by its sequential oxidation to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, catalysed by enzymes of the Ten-Eleven Translocation family proteins (TETs 1, 2 and 3). Here we analyzed for the first time all the intermediate products of DNA demethylation pathway in the form of deoxynucleosides (5-methyl-2'-deoxycytidine, 5-(hydroxymethyl)-2'-deoxycytidine, 5-formyl-2'-deoxycytidine and 5-carboxy-2'-deoxycytidine as well as 5-(hydroxymethyl)-2'-deoxyuridine) using automated isotope-dilution online two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry...
2017: PloS One
Veronica Esposito, Annapina Russo, Teresa Amato, Valentina Vellecco, Mariarosaria Bucci, Luciano Mayol, Giulia Russo, Antonella Virgilio, Aldo Galeone
BACKGROUND: The thrombin binding aptamer (TBA) is endowed with both anticoagulant and antiproliferative activities. Its chemico-physical and/or biological properties can be tuned by the site-specific replacement of selected residues. METHODS: Four oligodeoxynucleotides (ODNs) based on the TBA sequence (5'-GGTTGGTGTGGTTGG-3') and containing 2'-deoxyuridine (U) or 5-bromo-2'-deoxyuridine (B) residues at positions 4 or 13 have been investigated by NMR and CD techniques...
November 15, 2017: Bioorganic Chemistry
Li-Cheng Song, Liang Zhu, Fu-Qiang Hu, Yong-Xiang Wang
On the basis of preparation and characterization of [Fe]-H2ase models (2-COCH2-6-HOCH2C5H3N)Fe(CO)2L (A, L = η1-SCOMe; B, L = η1-2-SC5H4N), the chemical reactivities of A and B with various electrophilic and nucleophilic reagents have been investigated, systematically. Thus, when A reacted with 1 equiv of MeCOCl in the presence of Et3N in MeCN to give the η2-SCOMe-coordinated acylation product (2-COCH2-6-MeCO2CH2C5H3N)Fe(CO)2(η2-SCOMe) (1), treatment of A with excess HBF4·Et2O in MeCN gave the cationic MeCN-coordinated complex [(2-COCH2-6-HOCH2C5H3N)Fe(CO)2(MeCN)](BF4) (2)...
November 30, 2017: Inorganic Chemistry
Pei-Song Yang, Shi-Yun Tang, Chun-Bo Liu, Ling Ye, Feng-Mei Zhang, Pei He, Zhi-Hua Liu, Yong-Kuan Chen, Ming-Ming Miao, Qin-Peng Shen, Jia-Qiang Wang
Three new sesquiterpenes, methyl 4-isopropyl-7-methoxy-6-methylnaphthalene-1-carboxylate (1), methyl 2-hydroxy-4-isopropyl-7-methoxy-6-methylnaphthalene-1-carboxylate (2), and methyl 2-hydroxy-6-(hydroxymethyl)-4-isopropyl-7-methoxynaphthalene-1-carboxylate (3), together with three known sesquiterpenes (4-6), were isolated from the stems of Nicotiana tabacum. Their structures were determined by means of HRESIMS and extensive 1D and 2D NMR spectroscopic studies. The results showed that compounds 2, 3, and 5 exhibited high anti-TMV activity with inhibition rates of 33...
November 30, 2017: Journal of Asian Natural Products Research
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