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Hydroxymethylation

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https://www.readbyqxmd.com/read/27924045/a-novel-method-for-the-simultaneous-identification-of-methylcytosine-and-hydroxymethylcytosine-at-a-single-base-resolution
#1
Yuki Kawasaki, Yukiko Kuroda, Isao Suetake, Shoji Tajima, Fumitoshi Ishino, Takashi Kohda
Since the discovery of oxidative demethylation of methylcytosine (mC) by Tet enzymes, an analytical method has been urgently needed that would enable the identification of mC and hydroxymethylcytosine (hmC) at the single base resolution level, because their roles in gene regulation are quite different from each other. However, the bisulfite sequencing method, the gold standard for DNA methylation analysis at present, does not distinguish them. Recently reported alternative methods, such as oxBS-seq and TAB-seq, are not even capable of determining mC and hmC simultaneously...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913181/squarate-based-carbocyclic-nucleosides-syntheses-computational-analyses-and-anticancer-antiviral-evaluation
#2
Meijun Lu, Qing-Bin Lu, John F Honek
Squaric acid and its derivatives are versatile synthons and have demonstrated applications in medicinal chemistry, notably as non-classical bioisosteric replacements for functional groups such as carboxylic acids, alpha-amino acids, urea, guanidine, peptide bonds and phosphate/pyrophosphate linkages. Surprisingly, no reports have appeared concerning its possible application as a nucleobase substitute in nucleosides. A preliminary investigation of such an application is reported herein. 3-Amino-4-((1R,4S)-4-(hydroxymethyl)cyclopent-2-en-1-yl)amino-cyclobut-3-ene-1,2-dione, 3-((1R,4S)-4-(hydroxymethyl)cyclopent-2-en-1-yl)amino-4-methoxycyclobut-3-ene-1,2-dione, and 3-hydroxy-4-((1R,4S)-4-(hydroxymethyl)cyclopent-2-en-1-yl)amino-cyclobut-3-ene-1,2-dione sodium salt were synthesized...
November 23, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27911668/association-of-5-hydroxymethylation-and-5-methylation-of-dna-cytosine-with-tissue-specific-gene-expression
#3
V K Chaithanya Ponnaluri, Kenneth C Ehrlich, Guoqiang Zhang, Michelle Lacey, Douglas Johnston, Sriharsa Pradhan, Melanie Ehrlich
Differentially methylated or hydroxymethylated regions (DMRs) in mammalian DNA are often associated with tissue-specific gene expression but the functional relationships are still being unraveled. To elucidate these relationships, we studied 16 human genes containing myogenic DMRs by analyzing profiles of their epigenetics and transcription and quantitatively assaying 5-hydroxymethylcytosine (5 hmC) and 5-methylcytosine (5 mC) at specific sites in these genes in skeletal muscle (SkM), myoblasts, heart, brain, and diverse other samples...
December 2, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27911399/tools-to-study-the-role-of-architectural-protein-hmgb1-in-the-processing-of-helix-distorting-site-specific-dna-interstrand-crosslinks
#4
Anirban Mukherjee, Karen M Vasquez
High mobility group box 1 (HMGB1) protein is a non-histone architectural protein that is involved in regulating many important functions in the genome, such as transcription, DNA replication, and DNA repair. HMGB1 binds to structurally distorted DNA with higher affinity than to canonical B-DNA. For example, we found that HMGB1 binds to DNA interstrand crosslinks (ICLs), which covalently link the two strands of the DNA, cause distortion of the helix, and if left unrepaired can cause cell death. Due to their cytotoxic potential, several ICL-inducing agents are currently used as chemotherapeutic agents in the clinic...
November 10, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27910223/synthesis-and-preliminary-evaluation-of-a-99m-tc-labeled-folate-pamam-dendrimer-for-fr-imaging
#5
Manli Song, Zhide Guo, Mengna Gao, Changrong Shi, Duo Xu, Linyi You, Xiaowei Wu, Xinhui Su, Rongqiang Zhuang, Weimin Pan, Ting Liu, Xianzhong Zhang
Folate receptor is an ideal target for tumor-specific diagnostic and therapeutic. The aim of this study was to synthesize (99m) Tc-labeled folate-polyamidoamine dendrimer modified with 2-hydrazinonicotinic acid ((99m) Tc-HP3 FA) for FR imaging. The (99m) Tc-HP3 FA conjugate was prepared using N-tris-(hydroxymethyl)-methylglycine and trisodium triphenylphosphine-3,3',3″-trisulfonate as coligands. Physicochemical properties, in vitro cell uptake study, and in vivo micro-single-photon emission computed tomography/CT imaging were performed...
November 7, 2016: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/27905619/highly-fluorescent-nitrogen-doped-carbon-dots-with-excellent-thermal-and-photo-stability-applied-as-invisible-ink-for-loading-important-information-and-anti-counterfeiting
#6
Yingbo Liu, Liang Zhou, Yanan Li, Ruiping Deng, Hongjie Zhang
High quantum yields (QY) and stable performances are prerequisites for implementing carbon dots in practical applications. In this study, we demonstrate that nitrogen-doped carbon dots (N-CDs), which were prepared via the hydrothermal treatment of citric acid (CA) and tris(hydroxymethyl)methyl aminomethane (Tris), have a high QY of 75%, together with excellent thermal and photo stability. These N-CDs deliver an excellent thermal stability performance over the temperature range of 25 °C to 95 °C, and even at a heating temperature of 90 °C for 360 min...
December 1, 2016: Nanoscale
https://www.readbyqxmd.com/read/27905578/2-r-fluorinated-mc-hmc-fc-and-cac-triphosphates-are-substrates-for-dna-polymerases-and-tet-enzymes
#7
A S Schröder, E Parsa, K Iwan, F R Traube, M Wallner, S Serdjukow, T Carell
A deeper investigation of the chemistry that occurs on the newly discovered epigenetic DNA bases 5-hydroxymethyl-(hmdC), 5-formyl-(fdC), and 5-carboxy-deoxycytidine (cadC) requires chemical tool compounds, which are able to dissect the different potential reaction pathways in cells. Here we report that the 2'-(R)-fluorinated derivatives F-hmdC, F-fdC, and F-cadC, which are resistant to removal by base excision repair, are good substrates for DNA polymerases and TET enzymes. This result shows that the fluorinated compounds are ideal tool substances to investigate potential C-C-bond cleaving reactions in the context of active demethylation...
December 1, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27903986/adult-t-cell-leukemia-aggressivenness-correlates-with-loss-of-both-5-hydroxymethylcytosine-and-tet2-expression
#8
Ambroise Marçais, Laetitia Waast, Julie Bruneau, Katia Hanssens, Vahid Asnafi, Philippe Gaulard, Felipe Suarez, Patrice Dubreuil, Antoine Gessain, Olivier Hermine, Claudine Pique
Mutations in TET2, encoding one of the TET members responsible for the conversion of DNA cytosine methylation to hydroxymethylation (5-hmc), have been recently described in Human T-lymphotropic virus type 1-associated adult T-cell leukemia/lymphoma (ATLL). However, neither the amount of genomic 5-hmc in ATLL tumor cells nor TET2 expression has been studied yet. In this study, we analyzed these two parameters as well as the mutational status of TET2 in ATLL patients. By employing a direct in situ approach, we documented that tumor T cells infiltrating lymph nodes exhibit low level of 5-hmc compared to residual normal T cells...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27903915/max-is-an-epigenetic-sensor-of-5-carboxylcytosine-and-is-altered-in-multiple-myeloma
#9
Dongxue Wang, Hideharu Hashimoto, Xing Zhang, Benjamin G Barwick, Sagar Lonial, Lawrence H Boise, Paula M Vertino, Xiaodong Cheng
The oncogenic transcription factor MYC and its binding partner MAX regulate gene expression by binding to DNA at enhancer-box (E-box) elements 5'-CACGTG-3'. In mammalian genomes, the central E-box CpG has the potential to be methylated at the 5-position of cytosine (5mC), or to undergo further oxidation to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), or 5-carboxyl (5caC) forms. We find that MAX exhibits the greatest affinity for a 5caC or unmodified C-containing E-box, and much reduced affinities for the corresponding 5mC, 5hmC or 5fC forms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899849/statin-therapy-review-of-safety-and-potential-side-effects
#10
REVIEW
Satish Ramkumar, Ajay Raghunath, Sudhakshini Raghunath
BACKGROUND: Hydroxymethyl glutaryl coenzyme A reductase inhibitors, commonly called statins, are some of the most commonly prescribed medications worldwide. Evidence suggests that statin therapy has significant mortality and morbidity benefit for both primary and secondary prevention from cardiovascular disease. Nonetheless, concern has been expressed regarding the adverse effects of long term statin use. The purpose of this article was to review the current medical literature regarding the safety of statins...
November 2016: Acta Cardiologica Sinica
https://www.readbyqxmd.com/read/27895708/continuous-production-of-biohythane-from-hydrothermal-liquefied-cornstalk-biomass-via-two-stage-high-rate-anaerobic-reactors
#11
Bu-Chun Si, Jia-Ming Li, Zhang-Bing Zhu, Yuan-Hui Zhang, Jian-Wen Lu, Rui-Xia Shen, Chong Zhang, Xin-Hui Xing, Zhidan Liu
BACKGROUND: Biohythane production via two-stage fermentation is a promising direction for sustainable energy recovery from lignocellulosic biomass. However, the utilization of lignocellulosic biomass suffers from specific natural recalcitrance. Hydrothermal liquefaction (HTL) is an emerging technology for the liquefaction of biomass, but there are still several challenges for the coupling of HTL and two-stage fermentation. One particular challenge is the limited efficiency of fermentation reactors at a high solid content of the treated feedstock...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/27894968/crystallographic-structure-intermolecular-packing-energetics-crystal-morphology-and-surface-chemistry-of-salmeterol-xinafoate-form-i
#12
Alexandru A Moldovan, Ian Rosbottom, Vasuki Ramachandran, Christopher M Pask, Oboroghene Olomukhoro, Kevin J Roberts
Single crystals of salmeterol xinafoate (form I), prepared from slow cooled supersaturated propan-2-ol solutions, crystallise in a triclinic P‾1 symmetry with two closely related independent salt pairs within the asymmetric unit, with an approximately double unit cell volume compared to the previously published crystal structure(1). Synthonic analysis of the bulk intermolecular packing confirms the similarity in packing energetics between the two salt pairs. The strongest synthons, as expected, are dominated by coulombic interactions...
November 25, 2016: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27894515/glycine-buffered-synthesis-of-layered-iron-ii-iron-iii-hydroxides-green-rusts
#13
Weizhao Yin, Lizhi Huang, Emil Bjerglund Pedersen, Cathrine Frandsen, Hans Christian B Hansen
Layered Fe(II)-Fe(III) hydroxides (green rusts, GRs) are efficient reducing agents against oxidizing contaminants such as chromate, nitrate, selenite, and nitroaromatic compounds and chlorinated solvents. In this study, we adopted a buffered precipitation approach where glycine (GLY) was used in the synthesis of sulfate-interlayered GR (GRSO4) by aerial oxidation of Fe(II) or co-precipitation by adding Fe(III) salt to an aqueous solution of Fe(II) at constant pH. In both the oxidation and the co-precipitation methods pure crystalline GRSO4 was precipitated in the presence of 70mM GLY (pH 8...
November 22, 2016: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/27886677/differences-in-global-dna-methylation-of-testicular-seminoma-are-not-associated-with-changes-in-histone-modifications-clinical-prognosis-braf-mutations-or-gene-expression
#14
Louise Holm Pedersen, John E Nielsen, Gedske Daugaard, Thomas V O Hansen, Ewa Rajpert-De Meyts, Kristian Almstrup
Testicular germ cell tumours of young adults are comprised of a heterogeneous group of non-seminomas and a homogeneous group of seminomas. While the majority of seminomas retain a hypo-methylated genome, a small fraction displays a highly methylated genome, resembling hyper-methylated non-seminomas. It is well established from e.g. melanoma, colorectal and thyroid cancer that a methylated phenotype can be correlated to prognosis and can be related to BRAF mutations. In the present study we investigated the global methylation level in 67 seminomas and classified them as hypo-methylated, intermediate, patchy and hyper-methylated, respectively...
November 2016: Cancer Genetics
https://www.readbyqxmd.com/read/27884512/design-synthesis-and-antithrombotic-evaluation-of-novel-non-peptide-thrombin-inhibitors
#15
Dongxing Chen, Jinyu Shi, Jing Liu, Xueying Zhang, Xiaoying Deng, Yanyan Yang, Shuang Cui, Qihua Zhu, Guoqing Gong, Yungen Xu
Ten derivatives of 4-((1,2,3,4-tetrahydrobenzo[4,5]imidazo[1,2-a]pyrazin-1-yl)methyl)benzimida-mide (I-1∼I-2, II-1∼II-8) were designed, synthesized and evaluated for their inhibitory effect on human thrombin. Compound II-7 (IC50=82.8nM), which showed the strongest thrombin inhibitory activity among the tested compounds, was chosen as the lead compound, and ten carbamate derivatives (II-9a∼II-13a, II-9b∼II-12b, II-14) were prepared and evaluated for their anticoagulant activity. The results indicate that most of the tested compounds exhibit a certain degree of inhibitory effect on thrombin-induced platelet aggregation, among which compounds II-11a (IC50=8...
November 9, 2016: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/27879253/the-yin-yang-dynamics-of-dna-methylation-is-the-key-regulator-for-smooth-muscle-cell-phenotype-switch-and-vascular-remodeling
#16
Jianhui Zhuang, Peipei Luan, Hailing Li, Kai Wang, Pei Zhang, Yawei Xu, Wenhui Peng
OBJECTIVE: DNA methylation plays an important role in chronic diseases such as atherosclerosis, yet the mechanisms are poorly understood. The objective of our study is to indicate the regulatory mechanisms of DNA methylation in vascular smooth muscle cells (VSMCs) and its roles in atherosclerosis. APPROACH AND RESULTS: In ApoE(-/-) mice fed a Western diet, DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine, significantly attenuated atherosclerotic lesions (20...
November 22, 2016: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/27878282/the-importance-of-mitochondrial-folate-enzymes-in-human-colorectal-cancer
#17
Masaaki Miyo, Masamitsu Konno, Hugh Colvin, Naohiro Nishida, Jun Koseki, Koichi Kawamoto, Kenta Tsunekuni, Junichi Nishimura, Taishi Hata, Ichiro Takemasa, Tsunekazu Mizushima, Yuichiro Doki, Masaki Mori, Hideshi Ishii
Folate plays a pivotal role in the one-carbon metabolism needed for methylation reactions, nucleotide synthesis, and DNA repair. Although folate metabolism was recently shown to be associated with carcinogenesis in some solid tumors, the importance of folate metabolism in colorectal cancer remains unclear. In the present investigation we found that expression of three mitochondrial folate metabolic enzymes, serine hydroxymethyl transferase (SHMT2), methylenetetrahydrofolate dehydrogenase (MTHFD2) and aldehyde dehydrogenase 1 family member L2 (ALDH1L2), were upregulated in human colorectal tumor tissues compared to normal tissues...
November 22, 2016: Oncology Reports
https://www.readbyqxmd.com/read/27877088/aloe-emodin-suppresses-hypoxia-induced-retinal-angiogenesis-via-inhibition-of-hif-1%C3%AE-vegf-pathway
#18
Jianming Wu, Xiao Ke, Wei Wang, Hongcheng Zhang, Na Ma, Wei Fu, Manxi Zhao, Xiaoping Gao, Xiaofeng Hao, Zhirong Zhang
Background: Aloe-emodin (AE) has been reported to possess the antiangiogenic effect on laser induced choroidal neovascularization. AE inhibits the vessel formation in the zebrafish embryos. However, it is still unclear whether AE can alleviate neovascularization. Here, we investigated the inhibitory effect of AE on the hypoxia-induced retinal neovascularization and the possible mechanisms. Methods: We established a vascular endothelial growth factor (VEGF) secretion model under chemical induced hypoxia by exposure of 150 µM CoCl2 to the ARPE-19 cells, then treated the cells with different concentrations of AE (0...
2016: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/27869536/comparative-analysis-of-nonvolatile-and-volatile-metabolites-in-lichtheimia-ramosa-cultivated-in-different-growth-media
#19
Hyun Chung, NaKyeom Lee, Jeong-Ah Seo, Young-Suk Kim
Lichtheimia ramosa is one of the predominant filamentous fungi in Korean traditional nuruk. The nonvolatile and volatile metabolites of L. ramosa cultivated in three growth media: complete medium (CM), potato dextrose broth (PDB), and sabouraud dextrose broth (SDB), were investigated and compared. Among nonvolatile metabolites, serine, lysine, and ornithine increased in CM and PDB cultivated with L. ramosa during the exponential phase. In addition, glucose level increased in CM whereas decreased in PDB and SDB...
November 21, 2016: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/27866463/pharmacokinetics-distribution-and-disposition-of-esaxerenone-a-novel-highly-potent-and-selective-non-steroidal-mineralocorticoid-receptor-antagonist-in-rats-and-monkeys
#20
Makiko Yamada, Makoto Takei, Eiko Suzuki, Hideo Takakusa, Masakatsu Kotsuma, Takuo Washio, Nobuyuki Murayama, Shin-Ichi Inoue, Takashi Izumi
1. Esaxerenone (CS-3150) is a novel non-steroidal mineralocorticoid receptor antagonist. The pharmacokinetics, tissue distribution, excretion, and metabolism of esaxerenone were evaluated in rats and monkeys. 2. Following intravenous dosing of esaxerenone at 0.1 to 3 mg/kg, the total body clearance and the volume of distribution were 3.53 to 6.69 mL/min/kg and 1.47 to 2.49 L/kg, respectively in rats, and 2.79 to 3.69 mL/min/kg and 1.34 to 1.54 L/kg, respectively in monkeys. The absolute oral bioavailability was 61...
November 21, 2016: Xenobiotica; the Fate of Foreign Compounds in Biological Systems
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