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https://www.readbyqxmd.com/read/28820319/a-to-i-rna-editing-thinking-beyond-the-single-nucleotide
#1
Nabeel S Ganem, Ayelet T Lamm
Adenosine-to-inosine RNA editing is a conserved process, which is performed by ADAR enzymes. By changing nucleotides in coding regions of genes and altering codons, ADARs expand the cell's protein repertoire. This function of the ADAR enzymes is essential for human brain development. However, most of the known editing sites are in non-coding repetitive regions in the transcriptome and the purpose of editing in these regions is unclear. Recent studies, which have shown that editing levels of transcripts vary between tissues and developmental stages in many organisms, suggest that the targeted RNA and ADAR editing are both regulated...
August 18, 2017: RNA Biology
https://www.readbyqxmd.com/read/28820109/pseudomonas-wadenswilerensis-sp-nov-and-pseudomonas-reidholzensis-sp-nov-two-novel-species-within-the-pseudomonas-putida-group-isolated-from-forest-soil
#2
David Frasson, Michael Opoku, Tara Picozzi, Tanja Torossi, Stefanie Balada, Theo H M Smits, Urs Hilber
Within the frame of a biotechnological screening, we isolated two Pseudomonas strains from forest soil. 16S rRNA gene sequence analysis indicated that strain CCOS 864T shared 99.8 % similarity with Pseudomonas donghuensis HYST, while strain CCOS 865T shared 99.0 % similarity with Pseudomonas putida DSM 291T and lower similarity with other P. putida group type strains. Based on multilocus sequence analysis, the two strains were genotypically distinct from each other, each forming a separate clade. Strains CCOS 864T and CCOS 865T were Gram-stain-negative, motile and rod-shaped, growing at a temperature range of 4-37 °C...
August 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28819113/insights-into-the-role-of-endonuclease-v-in-rna-metabolism-in-trypanosoma-brucei
#3
Daniel García-Caballero, Guiomar Pérez-Moreno, Antonio M Estévez, Luis Miguel Ruíz-Pérez, Antonio E Vidal, Dolores González-Pacanowska
Inosine may arise in DNA as a result of oxidative deamination of adenine or misincorporation of deoxyinosine triphosphate during replication. On the other hand, the occurrence of inosine in RNA is considered a normal and essential modification induced by specific adenosine deaminases acting on mRNA and tRNA. In prokaryotes, endonuclease V (EndoV) can recognize and cleave inosine-containing DNA. In contrast, mammalian EndoVs preferentially cleave inosine-containing RNA, suggesting a role in RNA metabolism for the eukaryotic members of this protein family...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818035/comparative-analysis-of-inosine-substituted-duplex-dna-by-circular-dichroism-and-x-ray-crystallography
#4
Justin P Peters, Ewa A Kowal, Pradeep S Pallan, Martin Egli, L James Maher
Leveraging structural biology tools, we report the results of experimentsseeking to determine if the different mechanical properties of DNA polymers with base analog substitutions can be attributed, at least in part, to induced changes from classical B-form DNA. The underlying hypothesis is that different inherent bending and twisting flexibilities may characterize non-canonical B-DNA, so that it is inappropriate to interpret mechanical changes caused by base analog substitution as resulting simply from 'electrostatic' or 'base stacking' influences without considering the larger context of altered helical geometry...
August 18, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28815296/autoantibodies-against-rods-and-rings-related-impdh2-in-hepatitis-c-genotype-1-and-daa-therapy-in-a-real-life-cohort
#5
Werner Dammermann, Susanne Polywka, Inga Dettmann, Swantje Mindorf, Lars Komorowski, Malte Wehmeyer, Julian Schulze Zur Wiesch, Winfried Stöcker, Stefan Lüth
Autoantibodies against inosine-5'-monophosphate-dehydrogenase-2 (IMPDH2; "rods and rings" pattern) develop in chronic hepatitis C (CHC) patients under treatment with peg-interferon (IFN) and ribavirin (RBV), an inhibitor of IMPDH2. We investigated the influence of the alternative therapy with direct-acting antivirals (DAA)/ribavirin on anti-IMPDH2 autoantibody generation and the use of anti-IMPDH2 development as a marker for therapy outcome (sustained virologic response, SVR). We analyzed a "real life" cohort of 104 unselected CHC genotype 1 (GT1) patients treated with IFN/first-generation DAA/RBV prospectively compared to a historic cohort of 59 IFN/RBV-treated CHC GT1 patients...
August 16, 2017: Medical Microbiology and Immunology
https://www.readbyqxmd.com/read/28812932/celebrating-wobble-decoding-half-a-century-and-still-much-is-new
#6
Paul F Agris, Emily R Eruysal, Amithi Narendran, Ville Y P Väre, Sweta Vangaveti, Srivathsan V Ranganathan
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons...
August 16, 2017: RNA Biology
https://www.readbyqxmd.com/read/28807916/inhibition-of-calcineurin-or-impdh-exerts-moderate-to-potent-antiviral-activity-against-norovirus-replication
#7
Wen Dang, Yuebang Yin, Yijin Wang, Wenshi Wang, Junhong Su, Dave Sprengers, Luc J W van der Laan, Krzysztof Felczak, Krzysztof W Pankiewicz, Kyeong-Ok Chang, Marion P G Koopmans, Herold J Metselaar, Maikel P Peppelenbosch, Qiuwei Pan
Norovirus is a major cause of acute gastroenteritis worldwide and has emerged as an important issue of chronic infection in transplantation patients. Since no approved antiviral is available, we evaluated the effects of different immunosuppressants and ribavirin on norovirus and explored their mechanism-of-actions by using a human norovirus (HuNV) replicon-harboring model and a surrogate murine norovirus (MNV) infectious model. Roles of corresponding drug targets were investigated by gain- or loss-of-function approaches...
August 14, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28803399/blood-purine-measurements-as-a-rapid-real-time-indicator-of-reversible-brain-ischaemia
#8
Faming Tian, Fakhra Bibi, Nicholas Dale, Christopher H E Imray
To preserve the disequilibrium between ATP and ADP necessary to drive cellular metabolism, enzymatic pathways rapidly convert ADP to adenosine and the downstream purines inosine and hypoxanthine. During ischaemia, these same pathways result in the production of purines. We performed a prospective observational study to test whether purine levels in arterial blood might correlate with brain ischaemia. We made real-time perioperative measurements, via microelectrode biosensors, of the purine levels in untreated arterial blood from 18 patients undergoing regional anaesthetic carotid endarterectomy...
August 12, 2017: Purinergic Signalling
https://www.readbyqxmd.com/read/28794265/reconstituted-impdh-polymers-accommodate-both-catalytically-active-and-inactive-conformations
#9
Sajitha A Anthony, Anika L Burrell, Matthew C Johnson, Krisna C Duong-Ly, Yin-Ming Kuo, Jacqueline C Simonet, Peter Michener, Andrew Andrews, Justin M Kollman, Jeffrey R Peterson
Several metabolic enzymes undergo reversible polymerization into macromolecular assemblies. The function of these assemblies is often unclear but in some cases they regulate enzyme activity and metabolic homeostasis. The guanine nucleotide biosynthetic enzyme inosine monophosphate dehydrogenase (IMPDH) forms octamers that polymerize into helical chains. In mammalian cells, IMPDH filaments can associate into micron-length assemblies. Polymerization and enzyme activity are regulated in part by binding of purine nucleotides to an allosteric regulatory domain...
August 9, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28780317/enzymatic-synthesis-of-ribo-and-2-deoxyribonucleosides-from-glycofuranosyl-phosphates-an-approach-to-facilitate-isotopic-labeling
#10
Wenhui Zhang, Toby Turney, Ivana Surjancev, Anthony S Serianni
Milligram quantities of α-D-ribofuranosyl 1-phosphate (sodium salt) (αR1P) were prepared by the phosphorolysis of inosine, catalyzed by purine nucleoside phosphorylase (PNPase). The αR1P was isolated by chromatography in >95% purity and characterized by (1)H and (13)C NMR spectroscopy. Aqueous solutions of αR1P were stable at pH 6.4 and 4 °C for several months. The isolated αR1P was N-glycosylated with different nitrogen bases (adenine, guanine and uracil) using PNPase or uridine phosphorylase (UPase) to give the corresponding ribonucleosides in high yield based on the glycosyl phosphate...
July 20, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/28766293/methods-for-the-detection-of-adenosine-to-inosine-editing-events-in-cellular-rna
#11
Eimile Oakes, Pranathi Vadlamani, Heather A Hundley
Modification of RNA is essential for properly expressing the repertoire of RNA transcripts necessary for both cell type and developmental specific functions. RNA modifications serve to dynamically re-wire and fine-tune the genetic information carried by an invariable genome. One important type of RNA modification is RNA editing and the most common and well-studied type of RNA editing is the hydrolytic deamination of adenosine to inosine. Inosine is a biological mimic of guanosine; therefore, when RNA is reverse transcribed, inosine is recognized as guanosine by the reverse transcriptase and a cytidine is incorporated into the complementary DNA (cDNA) strand...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28762759/adenosine-to-inosine-rna-editing-in-health-and-disease
#12
Aikaterini Gatsiou, Nikolaos Vlachogiannis, Federica Francesca Lunella, Marco Sachse, Konstantinos Stellos
SIGNIFICANCE: Adenosine deaminase in transcriptome results in formation of inosine, a process that is called A-to-I RNA editing. Adenosine deaminase is one of the more than 140 described RNA modifications. A-to-I RNA editing is catalysed by the adenosine deaminases acting on RNA (ADAR) enzymes and is essential for life. Recent Advances: Accumulating evidence supports a critical role of RNA editing in all aspects of RNA metabolism including mRNA stability, splicing, nuclear export and localisation, as well as in recoding of proteins...
August 1, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28758223/metabonomics-profiling-of-marinated-meat-in-soy-sauce-during-processing
#13
Yang Yang, Yangfang Ye, Daodong Pan, Yangying Sun, Ying Wang, Jinxuan Cao
BACKGROUND: Marinated meat in soy sauce is one of the most popular traditional cured meat products in China. Its taste quality is directly related to primary and secondary metabolites. Herein, the change of metabolite composition of marinated meat in soy sauce during processing was systematically characterized using (1) H NMR and multivariate data analysis. RESULTS: The marinated meat in soy sauce metabonome was dominated by 26 metabolites, including amino acids, sugars, organic acids, nucleic aides and their derivatives...
July 31, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28754146/population-and-allelic-variation-of-a-to-i-rna-editing-in-human-transcriptomes
#14
Eddie Park, Jiguang Guo, Shihao Shen, Levon Demirdjian, Ying Nian Wu, Lan Lin, Yi Xing
BACKGROUND: A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism for generating transcriptome diversity. However, there remain significant knowledge gaps about the variation and function of RNA editing. RESULTS: In order to determine the influence of genetic variation on A-to-I RNA editing, we integrate genomic and transcriptomic data from 445 human lymphoblastoid cell lines by combining an RNA editing QTL (edQTL) analysis with an allele-specific RNA editing (ASED) analysis...
July 28, 2017: Genome Biology
https://www.readbyqxmd.com/read/28752025/biased-activity-of-soluble-guanylyl-cyclase-the-janus-face-of-thymoquinone
#15
REVIEW
Charlotte Detremmerie, Paul M Vanhoutte, Susan Leung
The natural compound thymoquinone, extracted from Nigella sativa (black cumin), is widely used in humans for its anti-oxidative properties. Thymoquinone is known for its acute endothelium-independent vasodilator effects in isolated rat aortae and pulmonary arteries, depending in part on activation of adenosine triphosphate-sensitive potassium channels and inhibition of voltage-dependent calcium channels. The compound also improves endothelial dysfunction in mesenteric arteries of ageing rodents and in aortae of rabbits treated with pyrogallol, by inhibiting oxidative stress...
July 2017: Acta Pharmaceutica Sinica. B
https://www.readbyqxmd.com/read/28747868/protective-effect-of-momordica-charantia-water-extract-against-liver-injury-in-restraint-stressed-mice-and-the-underlying-mechanism
#16
Yuanyuan Deng, Qin Tang, Yan Zhang, Ruifen Zhang, Zhencheng Wei, Xiaojun Tang, Mingwei Zhang
Background: Momordica charantia is used in China for its jianghuo (heat-clearing and detoxifying) effects. The concept of shanghuo (the antonym of jianghuo, excessive internal heat) in traditional Chinese medicine is considered a type of stress response of the body. The stress process involves internal organs, especially the liver. Objective: We hypothesized that Momordica charantia water extract (MWE) has a hepatoprotective effect and can protect the body from stress. The aim of this study was to investigate the possible effects of MWE against liver injury in restraint-stressed mice...
2017: Food & Nutrition Research
https://www.readbyqxmd.com/read/28739786/benzoxazoles-phthalazinones-and-arylurea-based-compounds-with-impdh-independent-antibacterial-activity-against-francisella-tularensis
#17
Suresh Kumar Gorla, Yan Zhang, Meaghan M Rabideau, Aiping Qin, Shibin Chacko, Amanda L House, Corey R Johnson, Kavitha Mandapati, Hannah M Bernstein, Elizabeth S McKenney, Helena Boshoff, Minjia Zhang, Ian J Glomski, Joanna B Goldberg, Gregory D Cuny, Barbara J Mann, Lizbeth Hedstrom
Francisella tularensis is the causative agent of tularemia and a potential biowarfare agent. The virulence of F. tularensis is decreased by deletion of guaB, the gene encoding inosine monophosphate dehydrogenase (IMPDH), suggesting that this enzyme is a target for antibacterial design. Here we report that F. tularensis growth is blocked by inhibitors of bacterial IMPDHs. Seventeen compounds from two different frameworks, designated D and Q, display antibacterial activity with minimum inhibitory concentrations less than 1 μM...
July 24, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28732107/characteristic-flavor-of-traditional-soup-made-by-stewing-chinese-yellow-feather-chickens
#18
Jun Qi, Deng-Yong Liu, Guang-Hong Zhou, Xing-Lian Xu
The traditional recipe for Chinese chicken soup creates a popular taste of particular umami and aroma. The present study investigated the effects of stewing time (1, 2, and 3 h) on the principal taste-active and volatile compounds and the overall flavor profile of traditional Chinese chicken soup by measuring the contents of free amino acids (FAAs), 5'-nucleotides, minerals and volatile compounds and by evaluating the taste and aroma profiles using an electronic nose, an electronic tongue and a human panel...
July 21, 2017: Journal of Food Science
https://www.readbyqxmd.com/read/28730859/molecular-targeting-of-inosine-5-monophosphate-dehydrogenase-by-ff-10501-promotes-erythropoiesis-via-ros-mapk-pathway
#19
Michiko Ichii, Kenji Oritani, Motohiko Murase, Kensuke Komatsu, Mao Yamazaki, Rie Kyoden, Nobuko Kito, Yusuke Nozaki, Motoki Saito, Hiroyuki Iwamura, Yuzuru Kanakura
One of the major symptoms of myelodysplastic syndromes (MDS) is severe cytopenia. Despite cytokine therapies, such as erythropoiesis-stimulating agents, many patients still require blood transfusions, and the development of new therapeutic approaches is needed. In this work, we studied the effects of the inosine-5'-monophosphate (IMP) dehydrogenase (IMPDH) inhibitor FF-10501 on erythropoiesis of human hematopoietic cells. Differentiation of K562 chronic myeloid leukemia cells to an erythroid lineage was promoted by FF-10501 in a dose-dependent manner...
July 21, 2017: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/28729763/serum-and-plasma-metabolomic-biomarkers-for-lung-cancer
#20
Nishith Kumar, Md Shahjaman, Md Nurul Haque Mollah, S M Shahinul Islam, Md Aminul Hoque
In drug invention and early disease prediction of lung cancer, metabolomic biomarker detection is very important. Mortality rate can be decreased, if cancer is predicted at the earlier stage. Recent diagnostic techniques for lung cancer are not prognosis diagnostic techniques. However, if we know the name of the metabolites, whose intensity levels are considerably changing between cancer subject and control subject, then it will be easy to early diagnosis the disease as well as to discover the drug. Therefore, in this paper we have identified the influential plasma and serum blood sample metabolites for lung cancer and also identified the biomarkers that will be helpful for early disease prediction as well as for drug invention...
2017: Bioinformation
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