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https://www.readbyqxmd.com/read/28208661/differential-binding-of-three-major-human-adar-isoforms-to-coding-and-long-non-coding-transcripts
#1
Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Masaru Tomita, Kumiko Ui-Tei
RNA editing by deamination of adenosine to inosine is an evolutionarily conserved process involved in many cellular pathways, from alternative splicing to miRNA targeting. In humans, it is carried out by no less than three major adenosine deaminases acting on RNA (ADARs): ADAR1-p150, ADAR1-p110, and ADAR2. However, the first two derive from alternative splicing, so that it is currently impossible to delete ADAR1-p110 without also knocking out ADAR1-p150 expression. Furthermore, the expression levels of ADARs varies wildly among cell types, and no study has systematically explored the effect of each of these isoforms on the cell transcriptome...
February 11, 2017: Genes
https://www.readbyqxmd.com/read/28202999/-changes-of-productions-of-energy-metabolism-in-masseter-of-rats-induced-by-occlusal-interference
#2
X X Xu, Y Cao, K Y Fu, Q F Xie
OBJECTIVE: To investigate the effect of occlusal interference on the energy metabolism of masticatory muscle by studying the changes of adenosine triphosphate (ATP), adenosine diphosphate (ADP), inosine monophosphate (IMP), phosphocreatine, creatine, lactate and pH level in masseter muscles of rats after occlusal interference. METHODS: Fifty male Sprague-Dawley rats were randomly assigned into experimental group (n=40) and control group (n=10). In experimental group, 0...
February 18, 2017: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
https://www.readbyqxmd.com/read/28199767/alkaliphilic-bacillus-species-show-potential-application-in-concrete-crack-repair-by-virtue-of-rapid-spore-production-and-germination-then-extracellular-calcite-formation
#3
T K Sharma, M Alazhari, A Heath, K Paine, R M Cooper
AIMS: Characterisation of alkaliphilic Bacillus species for spore production and germination and calcite formation as a prelude to investigate their potential in micro-crack remediation in concrete. METHODS AND RESULTS: Conditions, extent and timing of endospore production was determined by dark field light microscopy; germination induction and kinetics was assessed by combining reduction in optical density with formation of refractile bodies by phase contrast microscopy...
February 15, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28199207/assessing-the-potential-function-of-adar1-in-virus-associated-sepsis
#4
Yugang Zhuang, Hu Peng, Yuanzhuo Chen, Shuqin Zhou, Yanqing Chen
Sepsis syndrome is a common and frequently fatal clinical condition. It is defined by the presence of both infection and an uncontrolled systemic inflammatory response. It represents a major, although largely unappreciated, healthcare problem worldwide. It is especially problematic in infants and toddlers who show markedly increased susceptibility to severe infections caused by various pathogens, including viruses. Viruses are important causative agents of sepsis. Host adenosine deaminase acting on RNA 1 (ADAR1) catalyzes adenosine to inosine (A-to-I) editing of RNA transcripts, thus changing viral RNAs and exerting antiviral and proviral effects...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28198766/the-differential-effect-of-apyrase-treatment-and-hcd39-overexpression-on-chronic-renal-fibrosis-following-ischemia-reperfusion-injury
#5
Veena Roberts, Duncan J Campbell, Bo Lu, Joanne Chia, Peter J Cowan, Karen M Dwyer
BACKGROUND: Renal ischemia reperfusion injury (IRI) leads to acute kidney injury and renal fibrosis. CD39 is a key purinergic enzyme in the hydrolysis of ATP and increased CD39 enzymatic activity protects from acute IRI but its effect on renal fibrosis is not known. METHODS: Using a mouse model of unilateral renal IRI, the effects of increased CD39 activity (using soluble apyrase and mice expressing human CD39 transgene) on acute and chronic renal outcomes were examined...
February 14, 2017: Transplantation
https://www.readbyqxmd.com/read/28189056/metabolic-responses-to-intestine-regeneration-in-sea-cucumbers-apostichopus-japonicus
#6
Lina Sun, Jingchun Sun, Qinzeng Xu, Xiaoni Li, Libin Zhang, Hongsheng Yang
Sea cucumbers are excellent models for studying organ regeneration due to their striking capacity to regenerate most of their viscera after evisceration. In this study, we applied NMR-based metabolomics to determine the metabolite changes that occur during the process of intestine regeneration in sea cucumbers. Partial least-squares discriminant analysis showed that there was significant differences in metabolism between regenerative intestines at 3, 7, and 14days post evisceration (dpe) and normal intestines...
February 4, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28188894/emerging-rna-editing-biomarkers-will-foster-drug-development
#7
REVIEW
Siem van der Laan, Nicolas Salvetat, Dinah Weissmann, Franck Molina
Unanticipated adverse drug reactions (ADRs) on the central nervous system are a major cause of clinical attrition and market withdrawal. Current practices for their prospective assessment still lean on extensive analysis of rodent behaviour despite their highly controversial predictive value. Human-derived in vitro models that objectively quantify mechanism-related biomarkers can greatly contribute to better ADR prediction at early developmental stages. Adenosine-to-inosine RNA editing constitutes a physiological cellular process that translates environmental cues by regulating protein function at the synaptic level in health and disease...
February 7, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/28188804/metabolite-profiling-of-infection-associated-metabolic-markers-of-onchocerciasis
#8
Sasisekhar Bennuru, Sara Lustigman, David Abraham, Thomas B Nutman
The global efforts for onchocerciasis elimination may require additional tools (safe micro and macrofilaricidal drugs, vaccines and biomarkers) as elimination efforts move toward the "end game". Efforts toward the identification of suitable biomarkers have focused on specific protein(s) and/or nucleic acids, but metabolites present an alternative option as they have limited half-lives and are the result of combinatorial effects. In comparison to previously used methodology of LC-MS for metabolomic approaches, we used a non-targeted capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS) to analyze the serum metabolic profiles of Ov-infected and -uninfected individuals (n=20)...
February 8, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28188287/a-to-i-rna-editing-up-regulates-human-dihydrofolate-reductase-in-breast-cancer
#9
Masataka Nakano, Tatsuki Fukami, Saki Gotoh, Miki Nakajima
Dihydrofolate reductase (DHFR) plays a key role in folate metabolism and is a target molecule of methotrexate. An increase in the cellular expression level of DHFR is one of the mechanisms of tumor resistance to methotrexate. The present study investigated the possibility that adenosine-to-inosine RNA editing, which causes nucleotide conversion by adenosine deaminase acting on RNA (ADAR) enzymes, might modulate DHFR expression. In human breast adenocarcinoma-derived MCF-7 cells, 26 RNA editing sites were identified in the 3'-UTR of DHFR...
February 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28167531/adenosine-deaminase-that-acts-on-rna-3-adar3-binding-to-glutamate-receptor-subunit-b-pre-mrna-inhibits-rna-editing-in-glioblastoma
#10
Eimile Oakes, Ashley Anderson, Aaron Cohen-Gadol, Heather A Hundley
RNA editing is a cellular process that precisely alters nucleotide sequences, thus regulating gene expression and generating protein diversity. Over 60% of human transcripts undergo adenosine to inosine RNA editing and editing is required for normal development and proper neuronal function of animals. Editing of one adenosine in the transcript encoding the glutamate receptor subunit B, GRIA2, modifies a codon replacing the genomically encoded glutamine (Q) with arginine (R); thus this editing site is referred to as the Q/R site...
February 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28166241/evolutionary-analysis-reveals-regulatory-and-functional-landscape-of-coding-and-non-coding-rna-editing
#11
Rui Zhang, Patricia Deng, Dionna Jacobson, Jin Billy Li
Adenosine-to-inosine RNA editing diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. Here we show the cis-regulation and stepwise selection of RNA editing during Drosophila evolution and pinpoint a large number of functional editing sites. We found that the establishment of editing and variation in editing levels across Drosophila species are largely explained and predicted by cis-regulatory elements...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28165327/itpase-activity-modulates-the-severity-of-anaemia-in-hcv-related-cirrhosis-treated-with-ribavirin-containing-interferon-free-regimens
#12
Nicola Coppola, Stefania De Pascalis, Vincenzo Messina, Giovanni Di Caprio, Salvatore Martini, Giorgio de Stefano, Mario Starace, Gianfranca Stornaiuolo, Maria Stanzione, Tiziana Ascione, Carmine Minichini, Vincenzo Sangiovanni, Rosa Zampino, Federica Calò, Luca Rinaldi, Marcello Persico, Alessandro Federico, Antonio Riccardo Buonomo, Guglielmo Borgia, Giovanni Battista Gaeta, Pietro Filippini, Ivan Gentile
BACKGROUND: To investigate the association between inosine triphosphatase (ITPase) activity and the degree of anemia occurring during directly acting antiviral (DAA)/ribavirin (RBV)-based therapy in patients with cirrhosis. METHODS: In a multicenter, prospective study 227 patients with HCV-related cirrhosis treated with DAA and RBV were enrolled. All patients were screened for the rs1127354 and rs7270101 ITPA single nucleotide polymorphisms using direct sequencing...
February 6, 2017: Antiviral Therapy
https://www.readbyqxmd.com/read/28161934/identification-of-diverse-adenosine-to-inosine-rna-editing-subtypes-in-colorectal-cancer
#13
Si-Hyun Lee, Hwang-Phill Kim, Jun-Kyu Kang, Sang-Hyun Song, Sae-Won Han, Tae-You Kim
Purpose: RNA editing generates protein diversity by altering RNA sequences in coding regions without changing the overall DNA sequence. Adenosine-to-Inosine (A-to-I) RNA editing events have recently been reported in some types of cancer, but they are rare in human colorectal cancer. Therefore, this study was conducted to identify diverse RNA editing in colorectal cancer. Materials and Methods: We compared transcriptome data of 39 colorectal cancer (CRC) samples and paired adjacent tissues from The Cancer Genome Atlas database to identify RNA editing patterns in CRC, focusing on canonical A-to-I RNA edits in coding sequence regions...
January 25, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28160163/nucleotide-selectivity-in-abiotic-rna-polymerization-reactions
#14
Kristin M Coari, Rebecca C Martin, Kopal Jain, Linda B McGown
In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products...
February 3, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28153317/optimizing-2d-gas-chromatography-mass-spectrometry-for-robust-tissue-serum-and-urine-metabolite-profiling
#15
Zhanru Yu, Honglei Huang, Alexander Reim, Philip D Charles, Alan Northage, Dianne Jackson, Ian Parry, Benedikt M Kessler
Two-dimensional gas chromatography mass spectrometry (GCxGC-MS) is utilized to an increasing extent in biomedical metabolomics. Here, we established and adapted metabolite extraction and derivatization protocols for cell/tissue biopsy, serum and urine samples according to their individual properties. GCxGC-MS analysis revealed detection of ~600 molecular features from which 165 were characterized representing different classes such as amino acids, fatty acids, lipids, carbohydrates, nucleotides and small polar components of glycolysis and the Krebs cycle using electron impact (EI) spectrum matching and validation using external standard compounds...
April 1, 2017: Talanta
https://www.readbyqxmd.com/read/28148949/construction-of-a-guide-rna-for-site-directed-rna-mutagenesis-utilising-intracellular-a-to-i-rna-editing
#16
Masatora Fukuda, Hiromitsu Umeno, Kanako Nose, Azusa Nishitarumizu, Ryoma Noguchi, Hiroyuki Nakagawa
As an alternative to DNA mutagenesis, RNA mutagenesis can potentially become a powerful gene-regulation method for fundamental research and applied life sciences. Adenosine-to-inosine (A-to-I) RNA editing alters genetic information at the transcript level and is an important biological process that is commonly conserved in metazoans. Therefore, a versatile RNA-mutagenesis method can be achieved by utilising the intracellular RNA-editing mechanism. Here, we report novel guide RNAs capable of inducing A-to-I mutations by guiding the editing enzyme, human adenosine deaminase acting on RNA (ADAR)...
February 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28146558/genome-wide-exonic-small-interference-rna-mediated-gene-silencing-regulates-sexual-reproduction-in-the-homothallic-fungus-fusarium-graminearum
#17
Hokyoung Son, Ae Ran Park, Jae Yun Lim, Chanseok Shin, Yin-Won Lee
Various ascomycete fungi possess sex-specific molecular mechanisms, such as repeat-induced point mutations, meiotic silencing by unpaired DNA, and unusual adenosine-to-inosine RNA editing, for genome defense or gene regulation. Using a combined analysis of functional genetics and deep sequencing of small noncoding RNA (sRNA), mRNA, and the degradome, we found that the sex-specifically induced exonic small interference RNA (ex-siRNA)-mediated RNA interference (RNAi) mechanism has an important role in fine-tuning the transcriptome during ascospore formation in the head blight fungus Fusarium graminearum...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28144740/hibernation-reduces-cellular-damage-caused-by-warm-hepatic-ischemia-reperfusion-in-ground-squirrels
#18
Jessica P Otis, Amanda C Pike, Jose R Torrealba, Hannah V Carey
During the hibernation season, livers from 13-lined ground squirrels (Ictidomys tridecemlineatus) are resistant to damage induced by ex vivo, cold ischemia-warm reperfusion (IR) compared with livers from summer squirrels or rats. Here, we tested the hypothesis that hibernation also reduces damage to ground squirrel livers in an in vivo, warm IR model, which more closely resembles complications associated with traumatic injury or surgical interventions. We also examined whether protection is mediated by two metabolites, inosine and biliverdin, that are elevated in ground squirrel liver during interbout arousals...
January 31, 2017: Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology
https://www.readbyqxmd.com/read/28132026/dna-editing-in-dna-rna-hybrids-by-adenosine-deaminases-that-act-on-rna
#19
Yuxuan Zheng, Claire Lorenzo, Peter A Beal
Adenosine deaminases that act on RNA (ADARs) carry out adenosine (A) to inosine (I) editing reactions with a known requirement for duplex RNA. Here, we show that ADARs also react with DNA/RNA hybrid duplexes. Hybrid substrates are deaminated efficiently by ADAR deaminase domains at dA-C mismatches and with E to Q mutations in the base flipping loop of the enzyme. For a long, perfectly matched hybrid, deamination is more efficient with full length ADAR2 than its isolated deaminase domain. Guide RNA strands for directed DNA editing by ADAR were used to target six different 2'-deoxyadenosines in the M13 bacteriophage ssDNA genome...
January 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28128521/itpa-gene-variation-and-ribavirin-induced-anemia-in-patients-with-genotype-2-chronic-hepatitis-c-treated-with-sofosbuvir-plus-ribavirin
#20
Miyako Murakawa, Yasuhiro Asahina, Hiroko Nagata, Mina Nakagawa, Sei Kakinuma, Sayuri Nitta, Fukiko Kawai-Kitahata, Satoshi Otani, Shun Kaneko, Masato Miyoshi, Tomoyuki Tsunoda, Yu Asano, Ayako Sato, Yasuhiro Itsui, Seishin Azuma, Toshihiko Nouchi, Yohei Furumoto, Tooru Asano, Yoshimichi Chuganji, Shuji Tohda, Mamoru Watanabe
AIM: Sofosbuvir (SOF) and ribavirin (RBV) combination therapy produces a sustained response in many patients with genotype 2 chronic hepatitis C. However, RBV-induced anemia is a troublesome side effect that may limit this treatment. Genetic variation leading to inosine triphosphatase (ITPA) deficiency is known to protect against RBV-induced hemolytic anemia. This study aimed to evaluate the relationships between the efficacy and safety of SOF/RBV treatment and ITPA gene variants. METHODS: Ninety patients with genotype 2 chronic hepatitis C treated with SOF/RBV were studied...
January 27, 2017: Hepatology Research: the Official Journal of the Japan Society of Hepatology
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