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https://www.readbyqxmd.com/read/27911725/the-multiple-roles-of-the-nucleocapsid-in-retroviral-rna-conversion-into-proviral-dna-by-reverse-transcriptase
#1
REVIEW
Jean-Luc Darlix, Hugues de Rocquigny, Yves Mély
Retroviruses are enveloped plus-strand RNA viruses that can cause cancer, immunodeficiency and neurological disorder in human and animals. Retroviruses have several unique properties, such as a genomic RNA in a dimeric form found in the virus, and a replication strategy called 'copy-and-paste' during which the plus-strand genomic RNA is converted into a double-stranded DNA, subsequently integrated into the cellular genome. Two essential viral enzymes, reverse transcriptase (RT) and integrase (IN), direct this 'copy-and-paste' replication...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27878264/silencing-of-anxa3-expression-by-rna-interference-inhibits-the-proliferation-and-invasion-of-breast-cancer-cells
#2
Tao Zhou, Yong Li, Li Yang, Liang Liu, Yingchao Ju, Chunxiao Li
The present study aimed to explore the expression of Annexin A3 (ANXA3) in breast cancer cells and the mechanisms involved in the regulatory effects of ANXA3 on proliferation, invasion and migration of breast cancer cells. Fluorescence quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and western blotting were used to measure the expression of ANXA3 mRNA and protein in two breast cancer cell lines (MDA-MB-231 and MCF-7). Three ANXA3 silencing shRNA plasmids (ANXA3-sh1-3) and one negative control plasmid were constructed, and the Lipofectamine transfection method was used for transfecting human breast cancer cell line MDA-MB-231...
November 16, 2016: Oncology Reports
https://www.readbyqxmd.com/read/27827540/meteorites-and-the-rna-world-a-thermodynamic-model-of-nucleobase-synthesis-within-planetesimals
#3
Ben K D Pearce, Ralph E Pudritz
The possible meteorite parent body origin of Earth's pregenetic nucleobases is substantiated by the guanine (G), adenine (A), and uracil (U) measured in various meteorites. Cytosine (C) and thymine (T), however, are absent in meteorites, making the emergence of an RNA and later RNA/DNA/protein world problematic. We investigated the meteorite parent body (planetesimal) origin of all nucleobases by computationally modeling 18 reactions that potentially contribute to nucleobase formation in such environments. Out of this list, we identified the two most important reactions for each nucleobase and found that these involve small molecules such as HCN, CO, NH3, and water that ultimately arise from the protoplanetary disks in which planetesimals are built...
November 2016: Astrobiology
https://www.readbyqxmd.com/read/27825925/molecular-mechanism-of-dna-topoisomerase-i-dependent-rdna-silencing-sir2p-recruitment-at-ribosomal-genes
#4
Anna D'Alfonso, Francesca Di Felice, Valentina Carlini, Christine M Wright, Marla I Hertz, Mary-Ann Bjornsti, Giorgio Camilloni
Saccharomyces cerevisiae sir2Δ or top1Δ mutants exhibit similar phenotypes involving ribosomal DNA, including (i) loss of transcriptional silencing, resulting in non-coding RNA hyperproduction from cryptic RNA polymerase II promoters; (ii) alterations in recombination; and (iii) a general increase in histone acetylation. Given the distinct enzymatic activities of Sir2 and Top1 proteins, a histone deacetylase and a DNA topoisomerase, respectively, we investigated whether genetic and/or physical interactions between the two proteins could explain the shared ribosomal RNA genes (rDNA) phenotypes...
November 5, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27795362/novel-mirna-involved-in-host-response-to-avian-pathogenic-escherichia-coli-identified-by-deep-sequencing-and-integration-analysis
#5
Xinzheng Jia, Qinghua Nie, Xiquan Zhang, Lisa K Nolan, Susan J Lamont
Avian pathogenic Escherichia coli (APEC) causes one of the most common bacterial diseases of poultry worldwide. Effective control methods are, therefore, desirable and will be facilitated by a better understanding of the host response to the pathogen. Currently, miRNAs involved in host resistance to APEC are unknown. Here, we applied RNA sequencing to explore the changed miRNAs and deregulated genes in the spleen of broilers from non-challenged (NC), APEC challenged-mild pathology (CM), and APEC challenged-severe pathology (CS) groups...
October 17, 2016: Infection and Immunity
https://www.readbyqxmd.com/read/27789723/prevalence-and-correlates-of-persistent-hiv-1-rna-in-cerebrospinal-fluid-during-antiretroviral-therapy
#6
Albert M Anderson, Jose A Muñoz-Moreno, Daniel McClernon, Ronald J Ellis, Debra Cookson, David B Clifford, Ann C Collier, Benjamin B Gelman, Christina M Marra, Justin C McArthur, J Allen McCutchan, Susan Morgello, Ned Sacktor, David M Simpson, Donald R Franklin, Robert K Heaton, Igor Grant, Scott L Letendre
BACKGROUND:  Neurocognitive disorders remain common among HIV+ adults, perhaps due to persistent HIV-1 RNA in cerebrospinal fluid (CSF) during antiretroviral therapy (ART). METHODS:  Using a single copy assay, we measured HIV-1 RNA in CSF and plasma from 220 HIV+ adults who were taking suppressive ART. Fifty-five participants were tested twice. RESULTS:  HIV-1 RNA was detected in 42.3% of CSF and 65.2% of plasma samples. Correlates of higher CSF HIV-1 RNA included higher nadir and current CD4+ counts, plasma HIV-1 RNA≥1 c/mL, and lower CPE values (Model p<0...
October 26, 2016: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27730543/microrna-133a-suppresses-the-proliferation-migration-and-invasion-of-laryngeal-carcinoma-cells-by-targeting-cd47
#7
Hui Li, Yan Wang, Yan-Zhong Li
The study aims to investigate the possible mechanisms of microRNA-133a (miR-133a) targeting CD47 on cell proliferation, apoptosis, migration, and invasion in laryngeal carcinoma. Forty-two laryngeal carcinoma tissue specimens confirmed by pathological examination from laryngeal carcinoma patients as the case group were collected, and 20 chronic laryngitis tissues were gathered as the control group. The human laryngeal carcinoma cell line Hep-2 was marked as the miR-133a mimic, negative control (NC), miR-133a inhibitor, CD47-siRNA, miR-133a inhibitor + CD47-siRNA, and Mock groups...
October 11, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/27667278/-effect-of-notch1-2-3-genes-silencing-on-notch-and-nuclear-factor-%C3%AE%C2%BAb-signaling-pathway-of-macrophages-derived-from-patients-with-coronary-artery-disease
#8
Z B Ruan, X L Fu, W Li, J Ye, R Z Wang, Y G Yin, L Zhu
Objective: To investigate the effects of Notch1, 2, 3 genes silencing by siRNA on Notch signaling pathway (Delta-like 4(DLL4), Jagged 1(JAG1)) and nuclear factor-κB (NF-κB) signaling pathway (IκBα, P52) of macrophages derived from patients with coronary artery disease (CAD), thus to explore the potential genetic treatment perspectives for CAD. Methods: Peripheral blood mononuclear cells of CAD patients were isolated by density gradient centrifugation and transformed by phorbol-12-myristate-13-acetate (PMA) to macrophages...
September 24, 2016: Zhonghua Xin Xue Guan Bing za Zhi
https://www.readbyqxmd.com/read/27665605/the-quick-and-the-dead-a-guide-to-fast-phasing-of-small-ribozyme-and-riboswitch-crystal-structures
#9
Jermaine L Jenkins, Joseph E Wedekind
Ribozymes and riboswitches are examples of non-protein-coding (nc)RNA molecules that achieve biological activity by adopting complex three-dimensional folds. Visualization of such molecules at near-atomic resolution can enhance our understanding of how chemical groups are organized spatially, thereby providing novel insight into function. This approach has its challenges, which mainly entail sample crystallization followed by the application of empirical, structure-determination methods that often include experimental "phasing" of X-ray diffraction data...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27636713/a-pilot-study-of-circulating-microrna-125b-as-a-diagnostic-and-prognostic-biomarker-for-epithelial-ovarian-cancer
#10
Tao Zhu, Wen Gao, Xi Chen, Ying Zhang, Meijuan Wu, Ping Zhang, Shihua Wang
OBJECTIVE: Early diagnosis of epithelial ovarian cancer is critical for patient survival. The objective of this pilot study is to identify a circulating micro (mi)RNA as a potential biomarker for epithelial ovarian cancer. METHODS: A total of 135 epithelial ovarian cancer patients and 54 benign ovarian tumor patients were recruited for this study. Using customized TaqMan low density miRNA arrays, we first screened expression levels of 48 miRNAs in sera from 18 epithelial ovarian cancer patients and 16 benign ovarian tumor patients...
September 15, 2016: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/27600599/histone-deacetylase-enzyme-silencing-using-shrnas-enhances-radiosensitivity-of-sw579-thyroid-cancer-cells
#11
Ye Wang, Tao Jin, Xueming Dai, Dongwang Yan, Zhihai Peng
The aim of the present study was to screen the enzymes that are associated with the radiosensitivity of SW579 thyroid cancer cells, and investigate whether radiation, combined with specific RNA interference on the screened enzymes, enhances radiosensitivity of SW579 thyroid cancer cells. Quantitative polymerase chain reaction (qPCR) was used to analyze epigenetic enzyme expression changes before and after radiotherapy, and four enzymes, histone deacetylase 1 (HDAC1), HDAC2, HDAC4 and HDAC6 were screened. Western blot analysis was performed to analyze the change in HDAC1, HDAC2, HDAC4 and HDAC6 protein expression following radiotherapy...
October 2016: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27578037/complete-genome-sequence-and-evolution-analysis-of-eimeria-stiedai-rna-virus-1-a-novel-member-of-the-family-totiviridae
#12
Caiyan Xin, Bin Wu, Jianhua Li, Pengtao Gong, Ju Yang, He Li, Xuepeng Cai, Xichen Zhang
Eimeria stiedai (E. stiedai) is a coccidian that infects the liver of the domestic rabbit and may cause severe hepatic coccidiosis. Virus-like particles in E. stiedai were discovered by Revets et al. However, the complete genome sequence of the E. stiedai virus has yet to be determined. A novel virus was isolated from E. stiedai in the present study. The complete genome sequence of the E. stiedai virus was 6219 bp in length and contained two open reading frames (ORFs) with a tetranucleotide overlap (AUGA)...
December 2016: Archives of Virology
https://www.readbyqxmd.com/read/27552763/targetm6a-identifying-n6-methyladenosine-sites-from-rna-sequences-via-position-specific-nucleotide-propensities-and-a-support-vector-machine
#13
Guang-Qing Li, Zi Liu, Hong-Bin Shen, Dong-Jun Yu
As one of the most ubiquitous post-transcriptional modifications of RNA, N6-methyladenosine (m6A) plays an essential role in many vital biological processes. The identification of m6A sites in RNAs is significantly important for both basic biomedical research and practical drug development. In this study, we designed a computational-based method, called TargetM6A, to rapidly and accurately target m6A sites solely from the primary RNA sequences. Two new features, i.e., position-specific nucleotide / dinucleotide propensities (PSNP / PSDP), are introduced and combined with the traditional nucleotide composition (NC) feature to formulate RNA sequences...
August 10, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27541140/the-rna-binding-specificity-of-human-apobec3-proteins-resembles-that-of-hiv-1-nucleocapsid
#14
Ashley York, Sebla B Kutluay, Manel Errando, Paul D Bieniasz
The APOBEC3 (A3) cytidine deaminases are antiretroviral proteins, whose targets include human immunodeficiency virus type-1 (HIV-1). Their incorporation into viral particles is critical for antiviral activity and is driven by interactions with the RNA molecules that are packaged into virions. However, it is unclear whether A3 proteins preferentially target RNA molecules that are destined to be packaged and if so, how. Using cross-linking immunoprecipitation sequencing (CLIP-seq), we determined the RNA binding preferences of the A3F, A3G and A3H proteins...
August 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27531476/-inhibitory-effect-of-rna-interference-targeting-gfi-1-on-the-proliferation-of-atypical-chronic-myelogenous-leukemia-nt1-cells
#15
X Yang, H Liu, Z H Lin, J Qian, X R Xu
OBJECTIVE: To investigate the inhibitory effects of RNA interference targeting GFI-1 on growth and proliferation of atypical chronic myelogenous leukemia (aCML) NT1 cells. METHODS: NT1 cells were transfected with PBS and liposome complex (vehicle group), scrambled siRNA and liposome complex (negative control, NC group), and GFI-1 siRNA and liposome complex (GFI-1 siRNA group), respectively. Real-time quantitative RT-PCR (qRT-PCR) and Western blot were performed to examine the expression levels of GFI-1 mRNA and protein, respectively...
August 2016: Zhonghua Zhong Liu za Zhi [Chinese Journal of Oncology]
https://www.readbyqxmd.com/read/27515235/characterization-of-the-interaction-between-the-hiv-1-gag-structural-polyprotein-and-the-cellular-ribosomal-protein-l7-and-its-implication-in-viral-nucleic-acid-remodeling
#16
Hala El Mekdad, Emmanuel Boutant, Hassan Karnib, Marina E Biedma, Kamal Kant Sharma, Iuliia Malytska, Géraldine Laumond, Marion Roy, Eléonore Réal, Jean-Christophe Paillart, Christiane Moog, Jean Luc Darlix, Yves Mély, Hugues de Rocquigny
BACKGROUND: In HIV-1 infected cells, the integrated viral DNA is transcribed by the host cell machinery to generate the full length HIV-1 RNA (FL RNA) that serves as mRNA encoding for the Gag and GagPol precursors. Virion formation is orchestrated by Gag, and the current view is that a specific interaction between newly made Gag molecules and FL RNA initiates the process. This in turn would cause FL RNA dimerization by the NC domain of Gag (GagNC). However the RNA chaperoning activity of unprocessed Gag is low as compared to the mature NC protein...
2016: Retrovirology
https://www.readbyqxmd.com/read/27514744/functional-and-structural-characterization-of-novel-type-of-linker-connecting-capsid-and-nucleocapsid-protein-domains-in-murine-leukemia-virus
#17
Michal Doležal, Romana Hadravová, Milan Kožíšek, Lucie Bednárová, Hana Langerová, Tomáš Ruml, Michaela Rumlová
The assembly of immature retroviral particles is initiated in the cytoplasm by the binding of the structural polyprotein precursor Gag with viral genomic RNA. The protein interactions necessary for assembly are mediated predominantly by the capsid (CA) and nucleocapsid (NC) domains, which have conserved structures. In contrast, the structural arrangement of the CA-NC connecting region differs between retroviral species. In HIV-1 and Rous sarcoma virus, this region forms a rod-like structure that separates the CA and NC domains, whereas in Mason-Pfizer monkey virus, this region is densely packed, thus holding the CA and NC domains in close proximity...
September 23, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27494068/down-regulation-of-21a-alu-rna-as-a-tool-to-boost-proliferation-maintaining-the-tissue-regeneration-potential-of-progenitor-cells
#18
Arianna Gigoni, Delfina Costa, Massimiliano Gaetani, Roberta Tasso, Federico Villa, Tullio Florio, Aldo Pagano
21A is an Alu non-coding (nc) RNA transcribed by RNA polymerase (pol) III. While investigating the biological role of 21A ncRNA we documented an inverse correlation between its expression level and the rate of cell proliferation. The downregulation of this ncRNA not only caused a boost in cell proliferation, but was also associated to a transient cell dedifferentiation, suggesting a possible involvement of this RNA in cell dedifferentiation/reprogramming. In this study, we explored the possibility to enhance proliferation and dedifferentiation of cells of interest, by 21A down-regulation, using a mixture of chemically modified Anti-21A RNAs...
September 16, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27412167/thinking-beside-the-box-should-we-care-about-the-non-coding-strand-of-the-16s-rrna-gene
#19
Jose F Garcia-Mazcorro, Jose R Barcenas-Walls
The 16S rRNA gene (16S rDNA) codes for RNA that plays a fundamental role during translation in the ribosome and is used extensively as a marker gene to establish relationships among bacteria. However, the complementary non-coding 16S rDNA (nc16S rDNA) has been ignored. An idea emerged in the course of analyzing bacterial 16S rDNA sequences in search for nucleotide composition and substitution patterns: Does the nc16S rDNA code? If so, what does it code for? More importantly: Does 16S rDNA evolution reflect its own evolution or the evolution of its counterpart nc16S rDNA? The objective of this minireview is to discuss these thoughts...
August 2016: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/27347072/effect-of-plc%C3%AE%C2%B5-gene-silencing-on-inhibiting-the-cancerous-transformation-of-ulcerative-colitis
#20
Kun Yang, Jing Yan, Lan Peng, Yu-Pei Zou, Fu-Qian He, Hua-Tian Gan, Xiao-Li Huang
The aim of the present study was to investigate the effect of phosphoinositide-specific phospholipase Cε (PLCε) gene silencing on the inhibition of cancer development in ulcerative colitis (UC) and to explore the pathogenesis and carcinogenic mechanism of UC, in order to facilitate the establishment of novel strategies for the treatment of UC, prevent the cancerous transformation of UC and discern the association between inflammation and cancer. A pGenesil-PLCε RNA interference vector was constructed and transfected into HEK293 cells (pGenesil-PLCε group)...
July 2016: Experimental and Therapeutic Medicine
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