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Hydroxymethylation

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https://www.readbyqxmd.com/read/29474406/the-role-of-the-folate-pathway-in-pancreatic-cancer-risk
#1
Shirisha Chittiboyina, Zhongxue Chen, E Gabriela Chiorean, Lisa M Kamendulis, Barbara A Hocevar
BACKGROUND: Pancreatic cancer is the third leading cause of cancer related deaths in the United States. Several dietary factors have been identified that modify pancreatic cancer risk, including low folate levels. In addition to nutrition and lifestyle determinants, folate status may be influenced by genetic factors such as single nucleotide polymorphisms (SNPs). In the present study, we investigated the association between folate levels, genetic polymorphisms in genes of the folate pathway, and pancreatic cancer...
2018: PloS One
https://www.readbyqxmd.com/read/29469975/biological-activities-of-3-4-5-trihydroxypiperidines-and-their-n-and-o-derivatives
#2
REVIEW
Kate Prichard, David Campkin, Nicholas O'Brien, Atsushi Kato, George W J Fleet, Michela I Simone
3,4,5-Trihydroxypiperidines belong to the family of 1,5-dideoxy-1,5-iminosugar natural products and are structural analogues of pentose monosaccharides in the pyranose form. The biological activities of these apparently structurally simple molecules and their N- and O-alkylated and -arylated derivatives are no less remarkable than their C-6 hydroxymethyl counterparts of the hexoses (such as 1-deoxynojirimycin, DNJ). Their biological profiles indicate that the hydroxymethyl branch is crucial to neither potency nor selectivity, with O-alkylation demonstrated to produce exquisite selectivity extending beyond glycosidase inhibition, to immunosuppressant and antibacterial activities...
February 22, 2018: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29468129/conversion-and-assimilation-of-furfural-and-5-hydroxymethyl-furfural-by-pseudomonas-putida-kt2440
#3
Michael T Guarnieri, Mary Ann Franden, Christopher W Johnson, Gregg T Beckham
The sugar dehydration products, furfural and 5-(hydroxymethyl)furfural (HMF), are commonly formed during high-temperature processing of lignocellulose, most often in thermochemical pretreatment, liquefaction, or pyrolysis. Typically, these two aldehydes are considered major inhibitors in microbial conversion processes. Many microbes can convert these compounds to their less toxic, dead-end alcohol counterparts, furfuryl alcohol and 5-(hydroxymethyl)furfuryl alcohol. Recently, the genes responsible for aerobic catabolism of furfural and HMF were discovered in Cupriavidus basilensis HMF14 to enable complete conversion of these compounds to the TCA cycle intermediate, 2-oxo-glutarate...
June 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29458854/5-hydroxymethyl-2-furaldehyde-from-marine-bacterium-bacillus-subtilis-inhibits-biofilm-and-virulence-of-candida-albicans
#4
Ganapathy Ashwinkumar Subramenium, Thirukannamangai Krishnan Swetha, Prasanth Mani Iyer, Krishnaswamy Balamurugan, Shunmugiah Karutha Pandian
Candida albicans is considered as the primary etiologic agent of candidiasis, a very common fungal infection in human. The yeast to hyphal transition and ability to form hypoxic biofilm on medical devices is well allied with virulence and antifungal resistance of C. albicans. Antagonistic agents that inhibit biofilm formation and alter susceptibility of C. albicans to conventional antifungals is of profound need. The present study explores the antibiofilm efficacy of Bacillus subtilis, a marine bacterial isolate from Palk Bay against C...
March 2018: Microbiological Research
https://www.readbyqxmd.com/read/29458163/dna-adduct-profiling-of-in-vitro-colonic-meat-digests-to-map-red-vs-white-meat-genotoxicity
#5
Lieselot Y Hemeryck, Caroline Rombouts, Ellen De Paepe, Lynn Vanhaecke
The consumption of red meat has been linked to an increased colorectal cancer (CRC) risk. One of the major hypotheses states that heme iron (present in red meat) stimulates the formation of genotoxic N-nitroso compounds (NOCs) and lipid peroxidation products (LPOs). By means of DNA adductomics, chemically induced DNA adduct formation can be mapped in relation to e.g. dietary exposures. In this study, this state-of-the-art methodology was used to investigate alkylation and (lipid per)oxidation induced DNA adduct formation in in vitro red vs...
February 16, 2018: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/29457136/unexpected-evolutionary-benefit-to-phages-imparted-by-bacterial-crispr-cas9
#6
Pan Tao, Xiaorong Wu, Venigalla Rao
Bacteria and bacteriophages arm themselves with various defensive and counterdefensive mechanisms to protect their own genome and degrade the other's. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated) is an adaptive bacterial defense mechanism that recognizes short stretches of invading phage genome and destroys it by nuclease attack. Unexpectedly, we discovered that the CRISPR-Cas system might also accelerate phage evolution. When Escherichia coli bacteria containing CRISPR-Cas9 were infected with phage T4, its cytosine hydroxymethylated and glucosylated genome was cleaved poorly by Cas9 nuclease, but the continuing CRISPR-Cas9 pressure led to rapid evolution of mutants that accumulated even by the time a single plaque was formed...
February 2018: Science Advances
https://www.readbyqxmd.com/read/29456240/novel-synthetic-bisindolylmaleimide-alkaloids-inhibit-stat3-activation-by-binding-to-the-sh2-domain-and-suppress-breast-xenograft-tumor-growth
#7
Xia Li, Hongguang Ma, Lin Li, Yifan Chen, Xiao Sun, Zizheng Dong, Jing-Yuan Liu, Weiming Zhu, Jian-Ting Zhang
Signal transducer and activator of transcription 3 (STAT3) is constitutively activated in malignant tumors and plays important roles in multiple aspects of cancer aggressiveness. Thus, targeting STAT3 promises to be an attractive strategy for the treatment of advanced metastatic tumors. Bisindolylmaleimide alkaloid (BMA) has been shown to have anti-cancer activities and was thought to suppress tumor cell growth by inhibiting protein kinase C. In this study, we show that a newly synthesized BMA analog, BMA097, is effective in suppressing tumor cell and xenograft growth and in inducing spontaneous apoptosis...
February 19, 2018: Oncogene
https://www.readbyqxmd.com/read/29445804/one-dimensional-hydrogen-bonding-networks-of-bis-hydroxylated-diamantane-formed-inside-double-walled-carbon-nanotubes
#8
Yusuke Nakanishi, Haruka Omachi, Natalie A Fokina, Peter R Schreiner, Jonathan Becker, Jeremy E P Dahl, Robert M K Carlson, Hisanori Shinohara
1,6-Bis(hydroxymethyl)diamantane spontaneously aligns inside double-walled carbon nanotubes. The encapsulated molecules form a one-dimensional network within the double-walled carbon nanotubes through hydrogen bonding that leads to a highly dense filling as compared to unfunctionalized diamantane. Improving the encapsulation yields of precursors via functionalization is crucial to prepare novel one-dimensional materials.
February 15, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29433907/in%C3%A2-vitro-nuclear-receptor-inhibition-and-cytotoxicity-of-hydraulic-fracturing-chemicals-and-their-binary-mixtures
#9
Peter A Bain, Anu Kumar
The widespread use of hydraulic fracturing (HF) in oil and gas extraction operations has led to concern over environmental risks posed by chemicals used in HF fluids. Here we employed a suite of stable luciferase reporter gene assays to investigate the potential for selected HF chemicals or geogenics to activate or antagonise nuclear receptor signalling. We screened three biocides (bronopol [BP], glutaraldehyde [GA], and tetrakis(hydroxymethyl)phosphonium sulfate [THPS]), a surfactant (2-butoxyethanol), a friction reducer (polyacrylamide), and a coal seam geogenic (o-cresol) for their potential to act as agonists or antagonists of the estrogen receptor, androgen receptor, progesterone receptor (PR), glucocorticoid receptor or peroxisome proliferator-activated receptor gamma (PPARγ)...
January 9, 2018: Chemosphere
https://www.readbyqxmd.com/read/29431832/protected-5-hydroxymethyl-uracil-nucleotides-bearing-visible-light-photocleavable-groups-as-building-blocks-for-polymerase-synthesis-of-photocaged-dna
#10
Soňa Boháčová, Lucie Ludvíková, Lenka Poštová Slavětínská, Zuzana Vaníková, Petr Klán, Michal Hocek
Nucleosides, nucleotides and 2'-deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)uracil protected with photocleavable groups (2-nitrobenzyl-, 6-nitropiperonyl or 9-anthrylmethyl) were prepared and tested as building blocks for the polymerase synthesis of photocaged oligonucleotides and DNA. Photodeprotection (photorelease) reactions were studied in detail on model nucleoside monophosphates and their photoreaction quantum yields were determined. Photocaged dNTPs were then tested and used as substrates for DNA polymerases in primer extension or PCR...
February 12, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29431791/the-disclosure-of-mesoscale-behaviour-of-a-3d-smm-monolayer-on-au-111-through-a-multilevel-approach
#11
Guglielmo Fernandez Garcia, Alessandro Lunghi, Federico Totti, Roberta Sessoli
Here we present a computational study of a full- and a half-monolayer of a Fe4 single molecule magnet ([Fe4(L)2(dpm)6], where H3L = 2-hydroxymethyl-2-phenylpropane-1,3-diol and Hdpm = dipivaloylmethane, Fe4Ph) on an unreconstructed surface of Au(111). This has been possible through the application of an integrated approach, which allows the explicit inclusion of the packing effects in the classical dynamics to be used in a second step in periodic and non-periodic high level DFT calculations. In this way we can obtain access to mesoscale geometrical data and verify how they can influence the magnetic properties of interest of the single Fe4 molecule...
February 12, 2018: Nanoscale
https://www.readbyqxmd.com/read/29430663/dna-hydroxymethylation-rate-in-the-ache-and-hoxc4-promoter-associated-with-human-sperm-quality
#12
Y Li, Y H Li, X Zhou, B Wu, J P Chen, Z K Wang, X Wang, H J Shi, R S Li
The relationship of altered DNA 5'-hydroxymethylation in human spermatozoa with seminal parameters remains unclear. The aim of the study was to investigate the association between the 5'-hydroxymethylcytosine (5hmC) rate in the promoters of acetylcholinesterase (AChE) and homeobox C4 (HoxC4) genes and human sperm concentration/motility. The study population consisted of three groups: asthenozoospermia (AZ), oligoasthenozoospermia (OAZ) and normozoospermia (NZ). The 5hmC rate in the promoter was measured by CCGG loci-dependent MspI/HpaII restriction mapping of glycosylation-modified sperm DNA combined with a hydroxymethylation-specific real-time polymerase chain reaction assay...
February 11, 2018: Andrologia
https://www.readbyqxmd.com/read/29429347/hyperbranched-multiarm-copolymer-with-a-ucst-phase-transition-topological-effect-and-mechanism
#13
Meiwei Qi, Ke Li, Yongli Zheng, Tahir Rasheed, Yongfeng Zhou
A Novel thermoresponsive hyperbranched multiarm copolymer with a hydrophobic hyperbranched poly[3-ethyl-3-(hydroxymethyl)oxetane] (HBPO) core and many poly(acrylamide-co-acrylonitrile) (P(AAm-co-AN)) arms was for the first time synthesized through a reversible addition-fragmentation chain-transfer (RAFT) polymerization. These copolymers show reversible, sharp and controlled temperature-responsive phase transitions at the upper critical solution temperature (UCST) in water and electrolyte solution. It is the first report on the hyperbranched copolymers with a UCST transition...
February 11, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29428975/5-hydroxymethylcytosine-preferentially-targets-genes-upregulated-in-isocitrate-dehydrogenase-1-mutant-high-grade-glioma
#14
Wioletta K Glowacka, Harshika Jain, Makiko Okura, Abulizi Maimaitiming, Yasin Mamatjan, Romina Nejad, Hamza Farooq, Michael D Taylor, Kenneth Aldape, Paul Kongkham
Gliomas demonstrate epigenetic dysregulation exemplified by the Glioma CpG Island Methylator Phenotype (G-CIMP) seen in IDH1 mutant tumors. 5-Hydroxymethylcytosine (5hmC) is implicated in glioma pathogenesis; however, its role in IDH1 mutant gliomas is incompletely understood. To characterize 5hmC in IDH1 mutant gliomas further, we examine 5hmC in a cohort of IDH1 mutant and wild-type high-grade gliomas (HGG) using a quantitative locus-specific approach. Regions demonstrating high 5hmC abundance and differentially hydroxymethylated regions (DHMR) enrich for enhancers implicated in glioma pathogenesis...
February 10, 2018: Acta Neuropathologica
https://www.readbyqxmd.com/read/29425851/mechanistic-aspects-of-epigenetic-dysregulation-in-sle
#15
Christian Michael Hedrich
Epigenetic events have been linked with disease expression in individuals genetically predisposed to the development of systemic lupus erythematosus (SLE), a severe systemic autoimmune/inflammatory disease. Altered DNA methylation and hydroxymethylation as well as histone modifications mediate changes in chromatin accessibility and gene expression in immune cells from SLE patients. Defective epigenetic control contributes to uncontrolled expression of inflammatory mediators, including cytokines and co-receptors, resulting in systemic inflammation and tissue damage...
February 6, 2018: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/29422991/preeclampsia-is-associated-with-hypermethylation-of-igf-1-promoter-mediated-by-dnmt1
#16
Min Ma, Qiong-Jie Zhou, Yu Xiong, Bin Li, Xiao-Tian Li
Previous studies have demonstrated a dynamic epigenetic regulation of genes expression in placenta trophoblasts and a dynamic imbalance of DNA methylation and hydroxymethylation. Reduced IGF-1 has been observed in preeclampsia. This study was to investigate the interactive roles between IGF-1 and the global DNA methylation/hydroxymethylation, and the status of DNA methylation/hydroxymethylation and associated enzymes such as DNMTs and TETs in peeeclamptic placentas and hypoxic trophoblasts. It was found that IGF-1 was decreased in preeclamptic placentas and hypoxic trophoblasts when compared to the control group using immunohistochemisty, western blot, qRT-PCR and ELISA...
2018: American Journal of Translational Research
https://www.readbyqxmd.com/read/29421047/a-molecular-dynamics-study-of-cellulose-inclusion-complexes-in-naoh-urea-aqueous-solution
#17
Gang Liu, Heng Sun, Guokui Liu, Heng Zhang, Shiling Yuan, Qingzeng Zhu
We investigated the dissolution state of cellulose in NaOH/urea aqueous solution using molecular dynamics simulations. All the components, including cellulose, NaOH, urea and H2O were combined into one simulation. A clear and detailed description for the formation of cellulose inclusion complexes has been stated. The simulation results showed that the cellulose inclusion complexes exhibited anisotropic properties. In this system, the sodium ions and hydroxide ions located at the regions of hydroxyl and hydroxymethyl groups in cellulose molecules...
April 1, 2018: Carbohydrate Polymers
https://www.readbyqxmd.com/read/29415265/oxidation-products-of-5-methyl-cytosine-are-decreased-in-senescent-cells-and-tissues-of-progeroid-mice
#18
Ewelina Zarakowska, Jolanta Czerwinska, Agnieszka Tupalska, Matt J Yousefzadeh, Siobhán Q Gregg, Claudette M St Croix, Laura J Niedernhofer, Marek Foksinski, Daniel Gackowski, Anna Szpila, Marta Starczak, Barbara Tudek, Ryszard Olinski
5-Hydroxymethylcytosine and 5-formylcytosine are stable DNA base modifications generated from 5-methylcytosine by the ten-eleven translocation protein family that function as epigenetic markers. 5-Hydroxymethyluracil may also be generated from thymine by ten-eleven translocation enzymes. Here, we asked if these epigenetic changes accumulate in senescent cells, since they are thought to be inversely correlated with proliferation. Testing this in ERCC1-XPF-deficient cells and mice also enabled discovery if these DNA base changes are repaired by nucleotide excision repair...
February 3, 2018: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/29414037/dft-investigation-on-the-selective-complexation-of-fe3-and-al3-with-hydroxypyridinones-used-for-treatment-of-the-aluminium-and-iron-overload-diseases
#19
Sadegh Kaviani, Mohammad Izadyar, Mohammad Reza Housaindokht
The chelating agents for Al3+ and Fe3+ metal cations with therapeutic applications have been considered in the recent years. In designing of the hydroxypyridinones (HPOs) as the therapeutic chelating agents for iron and aluminium overload pathologies, quantum mechanical (QM) calculations are necessary for predicting the binding energies and thermodynamic parameters of the metal-HPO complexes. Three derivatives of the HPOs called 3-hydroxy-1,2-dimethylpyridin-4(1H)-one (DFP), 3-hydroxy-4(1H)-pyridinone (HOPO) and 5-hydroxy-2-(hydroxymethyl)pyridin-4(1H)-one (P1) were investigated for complexation with Fe3+ and Al3+ metal ions...
January 29, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29413354/fluorometric-detection-of-nitroaromatics-by-fluorescent-lead-complexes-a-spectroscopic-assessment-of-detection-mechanism
#20
Tanmay Chattopadhyay, Sourav Chatterjee, Ishani Majumder, Soumen Ghosh, Sangee Yoon, Eunji Sim
Three Schiff base ligands such as 2‑[(2‑Hydroxy‑3‑methoxy‑benzylidene)‑amino]‑2‑hydroxymethyl‑propane‑1,3‑diol (HL1), 2‑[(2‑Hydroxy‑benzylidene)‑amino]‑2‑hydroxymethyl‑propane‑1,3‑diol (HL2), 2‑[(3,5‑Dichloro‑2‑hydroxy‑benzylidene)‑amino]‑2‑hydroxymethyl‑propane‑1,3‑diol (HL3) have been synthesized by condensation of aldehydes (such as 3,5‑Dichloro‑2‑hydroxy benzaldehyde, 2‑Hydroxy‑benzaldehyde, and 2‑Hydroxy‑3‑methoxy‑benzaldehyde) with Tris‑(hydroxymethyl)amino methane and characterized by IR, UV-vis and 1H NMR spectroscopy...
April 5, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
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