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https://www.readbyqxmd.com/read/28641402/ec-tagging-allows-cell-type-specific-rna-analysis
#1
Naoki Hida, Mohamed Y Aboukilila, Dana A Burow, Rakesh Paul, Marc M Greenberg, Michael Fazio, Samantha Beasley, Robert C Spitale, Michael D Cleary
Purification of cell type-specific RNAs remains a significant challenge. One solution involves biosynthetic tagging of target RNAs. RNA tagging via incorporation of 4-thiouracil (TU) in cells expressing transgenic uracil phosphoribosyltransferase (UPRT), a method known as TU-tagging, has been used in multiple systems but can have limited specificity due to endogenous pathways of TU incorporation. Here, we describe an alternative method that requires the activity of two enzymes: cytosine deaminase (CD) and UPRT...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28640668/absence-of-the-fragile-x-mental-retardation-protein-results-in-defects-of-rna-editing-of-neuronal-mrnas-in-mouse
#2
Alice Filippini, Daniela Bonini, Caroline Lacoux, Laura Pacini, Maria Zingariello, Laura Sancillo, Daniela Bosisio, Valentina Salvi, Jessica Mingardi, Luca La Via, Francesca Zalfa, Claudia Bagni, Alessandro Barbon
The fragile X syndrome (FXS), the most common form of inherited intellectual disability, is due to the absence of FMRP, a protein regulating RNA metabolism. Recently, an unexpected function of FMRP in modulating the activity of Adenosine Deaminase Acting on RNA (ADAR) enzymes has been reported both in Drosophila and Zebrafish. ADARs are RNA-binding proteins that increase transcriptional complexity through a post-transcriptional mechanism called RNA editing. In order to evaluate the ADAR2-FMRP interaction in mammals we analysed several RNA editing re-coding sites in the fmr1 knockout (KO) mice...
June 22, 2017: RNA Biology
https://www.readbyqxmd.com/read/28640667/restricting-retrotransposons-adar1-is-another-guardian-of-the-human-genome
#3
Elisa Orecchini, Loredana Frassinelli, Alessandro Michienzi
ADAR1 is an enzyme that belongs to the Adenosine Deaminases Acting on RNA (ADARs) family. These enzymes deaminate adenosines to inosines (RNA editing A-to-I) within double-stranded RNA regions in transcripts. Since inosines are recognized as guanosines by the cellular machinery, RNA editing mediated by ADARs can either lead to the formation of an altered protein (recoding) or affect different aspects of RNA metabolism. Recently, a proteomic analysis led to the identification of novel ADAR1-associated factors and found that a good fraction of them is shared with the Long Interspersed Element 1 (LINE-1 or L1) ribonucleoparticles (RNPs)...
June 22, 2017: RNA Biology
https://www.readbyqxmd.com/read/28639414/brachiaria-grasses-brachiaria-spp-harbor-a-diverse-bacterial-community-with-multiple-attributes-beneficial-to-plant-growth-and-development
#4
Collins Mutai, Joyce Njuguna, Sita Ghimire
Endophytic and plant-associated bacteria were isolated from plants and rhizoplane soil of naturally grown Brachiaria grasses at International Livestock Research Institute in Nairobi, Kenya. Eighty-four bacterial strains were isolated from leaf tissues, root tissues, and rhizoplane soil on nutrient agar and 869 media. All bacterial strains were identified to the lowest possible taxonomic unit using 16S rDNA primers and were characterized for the production of Indole-3-acetic acid, hydrogen cyanide, and ACC deaminase; phosphate solubilization; siderophore production; antifungal properties; and plant biomass production...
June 21, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28638573/acute-intermittent-porphyria-a-test-of-clinical-acumen
#5
Rashmi Dhital, Sijan Basnet, Dilli Ram Poudel, Khema Raj Bhusal
Acute intermittent porphyria (AIP) is a rare autosomal dominant hepatic porphyria due to deficiency of hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase leading to accumulation of porphyrin precursors. However, gene defect alone is usually not sufficient to cause an acute attack, and many extrinsic factors play a role. Diagnostic tests are defined, but clinical suspicion is often delayed as symptoms mimic other common conditions. We report a case of a 18-year-old male with severe, persistent, and generalized abdominal pain along with marked hyponatremia, with subsequent development of altered mentation needing intensive care...
March 2017: Journal of Community Hospital Internal Medicine Perspectives
https://www.readbyqxmd.com/read/28638227/relationship-between-serum-adenosine-deaminase-levels-and-liver-histology-in-autoimmune-hepatitis
#6
Murat Torgutalp, Cumali Efe, Hakan Babaoglu, Taylan Kav
AIM: To evaluate the relationship between serum adenosine deaminase (ADA) levels and histological features in patients with autoimmune hepatitis (AIH). METHODS: A total of 80 subjects (52 AIH cases and 28 healthy controls) were included in the study. Patients were diagnosed according to the simplified criteria suggested by the International Autoimmune Hepatitis Group. All of the cases had been diagnosed with AIH between 2010-2015 at Hacettepe University, Department of Gastroenterology...
June 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28637869/heat-shock-proteins-stimulate-apobec-3-mediated-cytidine-deamination-in-the-hepatitis-b-virus
#7
Zhigang Chen, Thomas L Eggerman, Alexander V Bocharov, Irina N Baranova, Tatyana G Vishnyakova, Roger Kurlander, Amy P Patterson
Apolipoprotein B mRNA-editing enzyme catalytic subunit 3 (APOBEC-3) enzymes are cytidine deaminases that are broadly and constitutively expressed. They are often upregulated during carcinogenesis and candidate genes for causing the major single-base substitution in cancer-associated DNA mutations. Moreover, APOBEC-3s are involved in host innate immunity against many viruses. However, how APOBEC-3 mutational activity is regulated in normal and pathological conditions remains largely unknown. Heat shock protein levels are often elevated in both carcinogenesis and viral infection and are associated with DNA mutations...
June 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28634398/mutations-in-human-aid-differentially-affect-its-ability-to-deaminate-cytidine-and-5-methylcytidine-in-ssdna-substrates-in-vitro
#8
Lucyna Budzko, Paulina Jackowiak, Karol Kamel, Joanna Sarzynska, Janusz M Bujnicki, Marek Figlerowicz
Activation-induced cytidine deaminase (AID) is known for its established role in antibody production. AID induces the diversification of antibodies by deaminating deoxycytidine (C) within immunoglobulin genes. The capacity of AID to deaminate 5-methyldeoxycytidine (5 mC) and/or 5-hydroxymethyldeoxycytidine (5 hmC), and consequently AID involvement in active DNA demethylation, is not fully resolved. For instance, structural determinants of AID activity on different substrates remain to be identified. To better understand the latter issue, we tested how mutations in human AID (hAID) influence its ability to deaminate C, 5 mC, and 5 hmC in vitro...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634232/the-phosphocarrier-protein-hpr-of-the-bacterial-phosphotransferase-system-globally-regulates-energy-metabolism-by-directly-interacting-with-multiple-enzymes-in-escherichia-coli
#9
Irina A Rodionova, Zhongge Zhang, Jitender Mehla, Norman Goodacre, Mohan Babu, Andrew Emili, Peter Uetz, Milton H Saier
The histidine-phosphorylatable phosphocarrier protein HPr, is an essential component of the sugar-transporting phosphotransferase system (PTS) in many bacteria. Recent interactome findings suggested that HPr interacts with several carbohydrate-metabolizing enzymes, but whether HPr plays a regulatory role was unclear. Here, we provide evidence that HPr interacts with a large number of proteins in Escherichia coli. We demonstrate HPr-dependent allosteric regulation of the activities of pyruvate kinase (PykF, but not PykA), phosphofructokinase (PfkB, but not PfkA), glucosamine 6-phosphate deaminase (NagB) and adenylate kinase (Adk)...
June 20, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28630076/what-are-the-primary-limitations-in-b-cell-affinity-maturation-and-how-much-affinity-maturation-can-we-drive-with-vaccination-is-affinity-maturation-a-self-defeating-process-for-eliciting-broad-protection
#10
Christopher T Stamper, Patrick C Wilson
Vaccinations are one of the greatest success stories of modern medicine, saving millions of lives since their widespread adoption. However, several diseases continue to elude highly effective vaccination strategies. Chief among these are human immunodeficiency virus (HIV) and influenza (flu), both of which will require vaccines that can guide the creation of highly mutated, broadly neutralizing antibodies (bnAbs). The generation of bnAbs is hindered by our inability to effectively drive the high levels of affinity maturation required to achieve them in a large number of cells...
June 19, 2017: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/28626219/base-excision-repair-proteins-couple-activation-induced-cytidine-deaminase-and-endonuclease-g-during-replication-stress-induced-mll-destabilization
#11
B Gole, E Mian, M Rall, L Wiesmüller
The breakpoint cluster region of the MLL gene (MLLbcr) is frequently rearranged in therapy-related and infant acute leukaemia, but the destabilizing mechanism is poorly understood. We recently proposed that DNA replication stress results in MLLbcr cleavage via Endonuclease G (EndoG) and represents the common denominator of genotoxic therapy-induced MLL destabilization. Here we performed a siRNA screen for new factors involved in replication stress-induced MLL rearrangements employing an EGFP-based reporter system...
June 19, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28622881/discovery-of-%C3%AE-d-2-deoxy-2-dichlorouridine-nucleotide-prodrugs-as-potent-inhibitors-of-hepatitis-c-virus-replication
#12
Pedro Pinho, Genadiy Kalayanov, Hans Westerlind, Åsa Rosenquist, Horst Wähling, Christian Sund, Maria Almeida, Susana Ayesa, Jan Tejbrant, Paul Targett-Adams, Anders Eneroth, Annelie Lindqvist
Discovery of sofosbuvir has radically changed hepatitis C treatment and nucleoside/tide NS5B inhibitors are now viewed as one of the key components in combination therapies with other direct-acting antiviral agents. As part of our program to identify new nucleoside inhibitors of HCV replication, we now wish to report on the discovery of β-d-2'-deoxy-2'-dichlorouridine nucleotide prodrugs as potent inhibitors of HCV replication. Although, cytidine analogues have long been recognized to be metabolized to both cytidine and uridine triphosphates through the action of cytidine deaminase, uridine analogues are generally believed to produce exclusively uridine triphosphate...
May 26, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28622646/enhanced-degradation-of-chlorpyrifos-in-rice-oryzasativa-l-by-five-strains-of-endophytic-bacteria-and-their-plant-growth-promotional-ability
#13
Fayun Feng, Jing Ge, Yisong Li, Shuang He, Jianfeng Zhong, Xianjing Liu, Xiangyang Yu
Endophytic bacteria reside in plant tissues, such as roots, stems, leaves and seeds. Most of them can stimulate plant growth or alleviate phytotoxicity of pollutants. There are handful species with dual functions stimulating plant growth and degrading pollutants have been reported. Five endophytic bacteria were isolated from chlorpyrifos (CP) treated rice plants and identified as Pseudomonas aeruginosa strain RRA, Bacillus megaterium strain RRB, Sphingobacterium siyangensis strain RSA, Stenotrophomonas pavanii strain RSB and Curtobacterium plantarum strain RSC according to morphological characteristics, physiological and biochemical tests, and 16S rDNA phylogeny...
June 3, 2017: Chemosphere
https://www.readbyqxmd.com/read/28621910/allospecific-memory-b-cell-responses-are-dependent-on-autophagy
#14
Miguel Fribourg, Jie Ni, F Nina Papavasiliou, Zhenyu Yue, Peter S Heeger, Jeremy S Leventhal
Long-lived, donor-reactive memory B cells (Bmem) can produce alloantibodies that mediate transplant injury. Autophagy, an intrinsic mechanism of cell organelle/component recycling, is required for Bmem survival in infectious and model antigen systems but whether autophagy impacts alloreactive Bmem is unknown. We studied mice with an inducible yellow fluorescent protein (YFP) reporter expressed under the Activation-Induced Cytidine Deaminase (AID) promoter active in B cells undergoing germinal center reactions...
June 16, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28620460/a-putative-antiviral-role-of-plant-cytidine-deaminases
#15
Susana Martín, José M Cuevas, Ana Grande-Pérez, Santiago F Elena
BACKGROUND: A mechanism of innate antiviral immunity operating against viruses infecting mammalian cells has been described during the last decade.  Host cytidine deaminases ( e.g., APOBEC3 proteins) edit viral genomes, giving rise to hypermutated nonfunctional viruses; consequently, viral fitness is reduced through lethal mutagenesis.  By contrast, sub-lethal hypermutagenesis may contribute to virus evolvability by increasing population diversity.  To prevent genome editing, some viruses have evolved proteins that mediate APOBEC3 degradation...
2017: F1000Research
https://www.readbyqxmd.com/read/28620107/cicalese-mp-ferrua-f-castagnaro-l-et-al-update-on-the-safety-and-efficacy-of-retroviral-gene-therapy-for-immunodeficiency-due-to-adenosine-deaminase-deficiency-blood-2016-128-1-45-54
#16
https://www.readbyqxmd.com/read/28612840/toll-like-receptor-3-in-nasal-cd103-dendritic-cells-is-involved-in-immunoglobulin-a-production
#17
H Takaki, S Kure, H Oshiumi, Y Sakoda, T Suzuki, A Ainai, H Hasegawa, M Matsumoto, T Seya
Intranasal inoculation with influenza hemagglutinin subunit with polyinosine-polycytidylic (polyI:C), a synthetic analog for double-stranded RNA, enhances production of vaccine-specific immunoglobulin (Ig) A, which is superior to IgG in prophylactic immunity. The mechanism whereby polyI:C skews to IgA production in the nasal-associated lymph tissue (NALT) was investigated in mouse models. Nasally instilled polyI:C was endocytosed into CD103(+) dendritic cells (DCs) and induced T-cell activation, including interferon (IFN)-γ production...
June 14, 2017: Mucosal Immunology
https://www.readbyqxmd.com/read/28611548/hippocampal-characteristics-and-invariant-sequence-elements-distribution-of-glra2-and-glra3-c-to-u-editing
#18
Philipp Schaefermeier, Sarah Heinze
Glycine receptor α2 and α3 subunit (GLRA2/GLRA3) high-affinity variants, of which the subjacent amino acid substitutions issue from C-to-U RNA editing, are thought to influence tonic inhibition and pathophysiology. In light of the detection of GLRA3 NM_006529:r.1157C>U and GLRA2 NM_002063:r.1416C>U exchanges in hippocampus explants of temporal lobe epilepsy patients, we now examine the healthy situation and relate it to the epileptic situation by ascertaining controls in a legitimate reanalysis. The GLRA2 and GLRA3 editing events that would ultimately result in a glycine receptor with increased affinity occur in the postmortem nonepileptic hippocampus...
March 2017: Molecular Syndromology
https://www.readbyqxmd.com/read/28611497/stress-tolerant-viridibacillus-arenosi-strain-ihb-b-7171-from-tea-rhizosphere-as-a-potential-broad-spectrum-microbial-inoculant
#19
Rishu Thakur, K C Sharma, Ashu Gulati, R K Sud, Arvind Gulati
Viridibacillus arenosi strain IHB B 7171 identified based on 16S rRNA gene sequence produced colony forming units (cfu/ml) ranging from 3.3 × 10(4) to 1.2 × 10(10) under pH 5-11, 2.2 × 10(2) to 1.4 × 10(10) for temperature 5-40 °C, 2.4 × 10(2) to 1.1 × 10(10) for PEG 6000 10-30%, 2.2 × 10(2) to 1.4 × 10(10) for 2.5-10% NaCl, 3.1 × 10(3) to 1.7 × 10(9) for 2.5-7.5 mM CaCl2, 2.2 × 10(2) to 1.4 × 10(7) for 2.5-7.5 mM AlCl3, and 3.2 × 10(2) to 1.2 × 10(7) for 2.5-7...
June 2017: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/28604942/micrornas-regulate-apobec-gene-expression
#20
REVIEW
Wei Cao, Wei Wu
Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) is a family of evolutionarily conserved cytidine deaminases, encoded by eleven genes located in the human genome. APOBECs play key roles in innate immunity through their ability to mutagenize viral DNA and restrict rival replication. Recent cancer genomics revealed APOBEC3 subtype-mediated APOBEC-signature mutations are common in a broad spectrum of human cancers. The pervasive APOBEC3 activation in the host genome which converts cytosine to uracile during RNA editing has been suggested to depend on ATR/chk1 pathways...
June 12, 2017: Histology and Histopathology
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