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Natalie M McAdams, Rachel M Simpson, Runpu Chen, Yijun Sun, Laurie Read
The trypanosome RNA Editing Substrate Binding Complex (RESC) acts as the platform for mitochondrial uridine insertion/deletion RNA editing and facilitates the protein-protein and protein-RNA interactions required for the editing process. RESC is broadly comprised of two subcomplexes: GRBC (Guide RNA Binding Complex) and REMC (RNA Editing Mediator Complex). Here, we characterize the function and position in RESC organization of a previously unstudied RESC protein, MRB7260. We show that MRB7260 forms numerous RESC-related complexes, including a novel, small complex with the guide RNA binding protein, GAP1, which is a canonical GRBC component, and REMC components MRB8170 and TbRGG2...
January 12, 2018: RNA
Shufang Wang, Yongxin Gao, Shigang Shen, Hui Wen, Huaqing Cui
C5-modified uridines are a valuable class of nucleoside analogues, both as potent chemotherapy agents and through their use as the conjunction site in DNA labeling strategies. As an important C5-modified uridine, BrdU has been used in cell proliferation assays since the 1980s. Currently, the detection of BrdU relies on traditional immunostaining; however, this approach has its limitations. Thus, it is desirable, albeit difficult, to develop chemistry methods to fluorescently label BrdU in a cellular context...
January 12, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Dnyaneshwar B Gophane, Burkhard Endeward, Thomas F Prisner, Snorri Th Sigurdsson
A new isoindoline-derived benzimidazole nitroxide spin label, ImUm, was synthesized and incorporated into RNA oligoribonucleotides. ImUm is the first example of a conformationally unambiguous spin label for RNA, in which the nitroxide N-O bond lies on the same axis as the single bond used to attach the rigid isoindoline-based spin label to a uridine base. This results in minimal displacement of the nitroxide upon rotation of this single bond, which is a useful property for a label to be used for distance measurements...
January 12, 2018: Organic & Biomolecular Chemistry
Liqun Lei, Hongquan Chen, Wei Xue, Bei Yang, Bian Hu, Jia Wei, Lijie Wang, Yiqiang Cui, Wei Li, Jianying Wang, Lei Yan, Wanjing Shang, Jimin Gao, Jiahao Sha, Min Zhuang, Xingxu Huang, Bin Shen, Li Yang, Jia Chen
The APOBEC-AID family of cytidine deaminase prefers single-stranded nucleic acids for cytidine-to-uridine deamination. Single-stranded nucleic acids are commonly involved in the DNA repair system for breaks generated by CRISPR-Cas9. Here, we show in human cells that APOBEC3 can trigger cytidine deamination of single-stranded oligodeoxynucleotides, which ultimately results in base substitution mutations in genomic DNA through homology-directed repair (HDR) of Cas9-generated double-strand breaks. In addition, the APOBEC3-catalyzed deamination in genomic single-stranded DNA formed during the repair of Cas9 nickase-generated single-strand breaks in human cells can be further processed to yield mutations mainly involving insertions or deletions (indels)...
January 2018: Nature Structural & Molecular Biology
Steffen G Oeser, Jon-Paul Bingham, Abby C Collier
The hepatic uridine 5'-diphosphate-glucuronosyl transferases (UGTs) are critical for detoxifying endo- and xenobiotics. Since UGTs are also dynamically responsive to endogenous and exogenous stimuli, we examined whether epigenetic DNA methylation can regulate hepatic UGT expression and differential effects of ethnicity, obesity, and sex. The methylation status of UGT isoforms was determined with Illumina Methylation 450 BeadChip arrays, with genotyping confirmed by sequencing and gene expression confirmed with quantitative reverse transcriptase polymerase chain reaction (q-RT-PCR)...
January 7, 2018: Pharmaceutics
Claudia S Sepúlveda, Cybele C García, Elsa B Damonte
The aim of this study was to investigate the effect of A771726, the active metabolite of leflunomide, against the infection with Junín virus (JUNV), agent of Argentine hemorrhagic fever (AHF). The treatment with non-cytotoxic concentrations of A771726 of Vero and A549 cells infected with JUNV inhibited virus replication in a dose-dependent manner, as determined by virus yield reduction assay. The antiviral effectiveness of A771726 was not importantly affected by the multiplicity of infection and the virus strain...
January 5, 2018: Journal of Medical Virology
Yufeng Gong, Haijun Zhang, Ningbo Geng, Liguo Xing, Jingfeng Fan, Yun Luo, Xiaoyao Song, Xiaoqian Ren, Feidi Wang, Jiping Chen
Short-chain chlorinated paraffins (SCCPs) are known to disturb thyroid hormone (TH) homeostasis in rodents. However, the mechanism remains to be fully characterized. In this study, male Sprague Dawley rats received SCCPs (0, 1, 10, or 100mg/kg/day) via gavage once a day for consecutive 28days. Plasma and hepatic TH concentrations, thyrocyte structure, as well as thyroid and hepatic mRNA and protein levels of genes associated with TH homeostasis were examined. Moreover, we performed molecular docking to predict interactions between constitutive androstane receptor (CAR), a key regulator in xenobiotic-induced TH metabolism, with different SCCP molecules...
January 2, 2018: Science of the Total Environment
Upendra A Argikar
Over the past two decades, saccharolactone has been routinely used in in vitro microsomal incubations, and sometimes in incubations with recombinant Uridine diphosphoglucuronosyl transferases (UGT) while investigating glucuronidation reactions. The addition of saccharolactone is aimed at completely inhibiting β-glucuronidases that may be present in the microsomes, in the anticipation of accurate identification and quantification of the formed glucuronide metabolites. Recent research has demonstrated that saccharolatone may not serve the intended objective, and may even lead to inhibition of certain UGTs...
December 29, 2017: Current Drug Metabolism
Katrin S Hoydal, Bjørn M Jenssen, Robert J Letcher, Maria Dam, Augustine Arukwe
Faroe Island pilot whales have been documented to have high body burdens of organohalogen contaminants (OHCs), including polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), but low burdens of their respective hydroxylated metabolites (OH-PCBs and OH-PBDEs). The present study investigated the hepatic expression and/or catalytic activities of phase I and II biotransformation enzymes in relation to hepatic concentrations of target OHCs, including OH-PCBs and OH-PBDEs, in long-finned pilot whales (Globicephala melas) from the Northeastern Atlantic...
December 19, 2017: Marine Environmental Research
Małgorzata Sierant, Katarzyna Kulik, Elzbieta Sochacka, Rafal Szewczyk, Milena Sobczak, Barbara Nawrot
The 5-substituted 2-thiouridines (R5S2U) present in the first (wobble) position of the anticodons of transfer RNAs (tRNAs) contribute to accuracy in reading mRNA codons and tune protein synthesis. Previously, we have shown that, under oxidative stress conditions in vitro, R5S2Us are sensitive to hydrogen peroxide (H2O2), and their oxidative desulfuration produces 5-substituted uridines (R5Us) and 4-pyrimidinone nucleosides (R5H2Us) at a ratio that depends on pH and an R5 substituent. Here, we demonstrate that the desulfuration of 2-thiouridines, either alone or within an RNA/tRNA chain, is catalyzed by cytochrome C (cyt C)...
December 29, 2017: Chembiochem: a European Journal of Chemical Biology
Fangfang Fan, Nan-Hao Chen, Yong-Heng Wang, Ruibo Wu, Zexing Cao
The pyrimidine-specific nucleoside hydrolase Yeik (CU-NH) from Escherichia coli cleaves the N-glycosidic bond of uridine and cytidine with a 102~104-fold faster than that of purine nucleoside substrates such as inosine. Such remarkable substrate specificity and the plausible hydrolytic mechanisms of uridine have been explored by using QM/MM and MM MD simulations. The present calculations show that the relatively stronger hydrogen bond interactions between uridine and the active-site residues Gln227 and Tyr231 in CU-NH play an important role in enhancing the substrate binding and thus promoting the N-glycosidic bond cleavage, in comparison with inosine...
December 29, 2017: Journal of Physical Chemistry. B
Miao Guo, Zi-Jie Wang, Hai-Wei Yang, Ling Meng, Ruo-Yun Tan, Min Gu, Ji-Fu Wei
Mycophenolic acid (MPA) is an immunosuppressive drug widely used in the treatment of organ transplantation and autoimmune diseases. Pharmacokinetics and pharmacodynamics of MPA varies between individuals, the potential reasons being the genetic polymorphisms in key enzymes, drug transporters and target proteins of MPA, involving uridine diphosphate glucuronosyltransferase enzymes, organic anion transport polypeptides, multidrug resistance-associated protein 2, inosine monophosphate dehydrogenase and others...
December 27, 2017: Current Drug Metabolism
Ying Huang, Jian Su, Xiaosui Huang, Danxia Lu, Zhi Xie, Suqing Yang, Weibang Guo, Zhiyi Lv, Hongsui Wu, Xuchao Zhang
BACKGROUND: Uridine-diphosphoglucuronosyl transferase 1A1 (UGT1A1), UGT1A1*28 polymorphism can reduce UGT1A1 enzymatic activity, which may lead to severe toxicities in patients who receive irinotecan. This study tries to build a fragment analysis method to detect UGT1A1*28 polymorphism. METHODS: A total of 286 blood specimens from the lung cancer patients who were hospitalized in Guangdong General Hospital between April 2014 to May 2015 were detected UGT1A1*28 polymorphism by fragment analysis method...
December 20, 2017: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
Muthian Shanmugasundaram, Annamalai Senthilvelan, Anilkumar R Kore
This unit describes a simple, reliable, and efficient chemical method for the synthesis of 5-(3-aminoallyl)-2'-deoxyuridine-5'-O-triphosphate (AA-dUTP) and 5-(3-aminoallyl)-uridine-5'-O-triphosphate (AA-UTP), starting from the corresponding nucleoside triphosphate. The presented strategy involves regioselective iodination of nucleoside triphosphate using N-iodosuccinimide followed by the palladium-catalyzed Heck coupling with allylamine to provide the corresponding (E)-5-aminoallyl-uridine-5'-O-triphosphate in good yields...
December 24, 2017: Current Protocols in Nucleic Acid Chemistry
Dipali Bhoye, Sarah S Cherian
An F35L mutation in the N-terminal domain of the polymerase acidic protein (PA-Nter), which contains the active site of the endonuclease, has been reported to result in higher polymerase activity in mouse-adapted strains of the 2009 pandemic influenza A H1N1 virus. We modeled wild and mutant complexes of uridine 5'-monophosphate (UMP) as the endonuclease substrate and performed molecular dynamics simulations. The results demonstrated that the F35L mutation could result in a changed orientation of a helix containing active site residues and improve the ligand affinity in the mutant strain...
December 22, 2017: Archives of Virology
Marzia Pasquali, Chunli Yu, Bradford Coffee
Disclaimer: These ACMG Standards and Guidelines are developed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these Standards and Guidelines is voluntary and does not necessarily assure a successful medical outcome. These Standards and Guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results...
October 26, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Yonghai Fan, Mengna Yu, Miao Liu, Rui Zhang, Wei Sun, Mingchao Qian, Huichun Duan, Wei Chang, Jinqi Ma, Cunmin Qu, Kai Zhang, Bo Lei, Kun Lu
Galactinol synthase (GolS) is a key enzyme in raffinose family oligosaccharide (RFO) biosynthesis. The finding that GolS accumulates in plants exposed to abiotic stresses indicates RFOs function in environmental adaptation. However, the evolutionary relationships and biological functions of GolS family in rapeseed (Brassica napus) and tobacco (Nicotiana tabacum) remain unclear. In this study, we identified 20 BnGolS and 9 NtGolS genes. Subcellular localization predictions showed that most of the proteins are localized to the cytoplasm...
December 20, 2017: International Journal of Molecular Sciences
G R Nalin Rathnayake, N Savitri Kumar, Lalith Jayasinghe, Hiroshi Araya, Yoshinori Fujimoto
Phialemonium curvatum, an endophytic fungus isolated from the leaves of Passiflora edulis was cultured in potato dextrose broth (PDB) media and chromatographic separation of the EtOAc extract of the broth and mycelium led to the isolation of 4-hydroxybenzoic acid (1), 3-indole acetic acid (2), solaniol (3), uracil (4), uridine (5) and glycerol (6). Compound 2 showed a weak antifungal activity against Cladosporium cladosporioides. This is the first report of the isolation of the endophytic fungus P. curvatum from P...
December 20, 2017: Natural Product Research
Vijay Gayakhe, Anant Ramakant Kapdi, Yulia Borozdina, Carola Schulzke
The mol-ecule of the title compound, C21H18N2O6, has a bent rather than a linear conformation supported by three intra-molecular C-H⋯O hydrogen bonds. The packing in the crystal lattice is largely determined by inter-actions between hydrogen atoms with oxygen atom lone pairs with one mol-ecule inter-acting with neigbouring mol-ecules via O-H⋯O, N-H⋯O and C-H⋯O hydrogen bonds. The title compound crystallizes in the chiral ortho-rhom-bic space group P212121. Its absolute structure could not be determined crystallographically and was assumed with reference to that of the reactant 5-iodo-2'-de-oxy-uridine...
October 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
Thalia Salinas-Giegé, Marina Cavaiuolo, Valérie Cognat, Elodie Ubrig, Claire Remacle, Anne-Marie Duchêne, Olivier Vallon, Laurence Maréchal-Drouard
The unicellular photosynthetic organism, Chlamydomonas reinhardtii, represents a powerful model to study mitochondrial gene expression. Here, we show that the 5'- and 3'-extremities of the eight Chlamydomonas mitochondrial mRNAs present two unusual characteristics. First, all mRNAs start primarily at the AUG initiation codon of the coding sequence which is often marked by a cluster of small RNAs. Second, unusual tails are added post-transcriptionally at the 3'-extremity of all mRNAs. The nucleotide composition of the tails is distinct from that described in any other systems and can be partitioned between A/U-rich tails, predominantly composed of Adenosine and Uridine, and C-rich tails composed mostly of Cytidine...
December 15, 2017: Nucleic Acids Research
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