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Author (up) Ambrosone, A.; Costa, A.; Leone, A.; Grillo, S. file  url
doi  openurl
  Title Beyond transcription: RNA-binding proteins as emerging regulators of plant response to environmental constraints Type Journal Article
  Year 2012 Publication Plant Science : an International Journal of Experimental Plant Biology Abbreviated Journal Plant Sci  
  Volume 182 Issue Pages 12-18  
  Keywords Abscisic Acid/metabolism; Acclimatization/*physiology; Gene Expression Regulation, Plant; Osmotic Pressure/physiology; *Plant Physiological Processes; Plants/genetics; RNA-Binding Proteins/genetics/metabolism/*physiology; Transcription, Genetic  
  Abstract RNA-binding proteins (RBPs) govern many aspects of RNA metabolism, including pre-mRNA processing, transport, stability/decay and translation. Although relatively few plant RNA-binding proteins have been characterized genetically and biochemically, more than 200 RBP genes have been predicted in Arabidopsis and rice genomes, suggesting that they might serve specific plant functions. Besides their role in normal cellular functions, RBPs are emerging also as an interesting class of proteins involved in a wide range of post-transcriptional regulatory events that are important in providing plants with the ability to respond rapidly to changes in environmental conditions. Here, we review the most recent results and evidence on the functional role of RBPs in plant adaptation to various unfavourable environmental conditions and their contribution to enhance plant tolerance to abiotic stresses, with special emphasis on osmotic and temperature stress.  
  Call Number Serial 1226  
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Author (up) Cabiscol, E.; Tamarit, J.; Ros, J. file  url
  Title Oxidative stress in bacteria and protein damage by reactive oxygen species Type Journal Article
  Year 2000 Publication International Microbiology : the Official Journal of the Spanish Society for Microbiology Abbreviated Journal Int Microbiol  
  Volume 3 Issue 1 Pages 3-8  
  Keywords Adaptation, Physiological; Aerobiosis; Amino Acids/chemistry; Bacteria/genetics/*metabolism; Bacterial Proteins/genetics/*metabolism/*physiology; DNA Damage; DNA, Bacterial/genetics/metabolism; *DNA-Binding Proteins; *Escherichia coli Proteins; Free Radicals; Gene Expression Regulation, Bacterial; Heat-Shock Proteins/metabolism; Iron-Sulfur Proteins/metabolism; Lipid Peroxidation; Oxidation-Reduction; Oxidative Stress/*genetics/physiology; Peroxides/metabolism; Reactive Oxygen Species/*metabolism; Repressor Proteins/genetics/*physiology; *Trans-Activators; Transcription Factors/genetics/*physiology; Transcription, Genetic  
  Abstract The advent of O2 in the atmosphere was among the first major pollution events occurred on earth. The reaction between ferrous iron, very abundant in the reductive early atmosphere, and oxygen results in the formation of harmful superoxide and hydroxyl radicals, which affect all macromolecules (DNA, lipids and proteins). Living organisms have to build up mechanisms to protect themselves against oxidative stress, with enzymes such as catalase and superoxide dismutase, small proteins like thioredoxin and glutaredoxin, and molecules such as glutathione. Bacterial genetic responses to oxidative stress are controlled by two major transcriptional regulators (OxyR and SoxRS). This paper reviews major key points in the generation of reactive oxygen species in bacteria, defense mechanisms and genetic responses to oxidative stress. Special attention is paid to the oxidative damage to proteins.  
  Call Number Serial 181  
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Author (up) Chen, X.; Qian, Y.; Yan, F.; Tu, J.; Yang, X.; Xing, Y.; Chen, Z. file  url
  Title 5'-triphosphate-siRNA activates RIG-I-dependent type I interferon production and enhances inhibition of hepatitis B virus replication in HepG2.2.15 cells Type Journal Article
  Year 2013 Publication European Journal of Pharmacology Abbreviated Journal Eur J Pharmacol  
  Volume 721 Issue 1-3 Pages 86-95  
  Keywords Base Sequence; DEAD-box RNA Helicases/*metabolism; DNA Replication/genetics; Hep G2 Cells; Hepatitis B Antigens/genetics/metabolism; Hepatitis B virus/*genetics/*physiology; Humans; Immunity, Innate; Interferon Type I/*biosynthesis/genetics; Polyphosphates/*chemistry; RNA Interference; RNA, Messenger/genetics; RNA, Small Interfering/chemistry/*genetics; Transcription, Genetic/genetics; Virus Replication/*genetics; 3-(4,5)-dimethylthiahiazol-2-y1)-2,5-diphenytetrazolium bromide; 3p-siRNA; 5â²-Triphosphated siRNA; 5â²-triphosphated siRNA; BF-siRNA; Ciap; Elisa; Hbv; HBV e antigen; HBV s antigen; HBeAg; HBsAg; Hcc; HepG2.2.15 cells; Hepatitis B virus; Ifn; Ifnî±/β; Mtt; NC-siRNA; Od; Prr; Rig-I; RNA interference; RNAi; Rt-Pcr; Tlr; bifunctional siRNA; calf intestine alkaline phosphatase; double strand DNA; double strand RNA; dsDNA; dsRNA; enzyme-linked immunosorbent assay; hepatitis B virus; hepatocellular carcinoma; interferon; negative control siRNA; optical density; pathogen-recognition receptor; retinoic acid-inducible gene I; reverse transcription PCR; siRNA; single strand RNA; small interfering RNA; ssRNA; toll-like receptor  
  Abstract Hepatitis B virus (HBV) infection often results in acute or chronic viral hepatitis and other liver diseases including cirrhosis and hepatocellular carcinoma. Current therapies for HBV usually have severe side effects and can cause development of drug-resistant mutants. An alternative and safe immunotherapeutic approach for HBV infection is urgently needed for effective anti-HBV therapy. In this study, we propose a new strategy for anti-HBV therapy that activates type-I interferon (IFN) antiviral innate immunity through stimulating pattern-recognition receptors with RNA interference (RNAi) using a 5'-end triphosphate-modified small interfering RNA (3p-siRNA). We designed and generated a 3p-siRNA targeting overlapping region of S gene and P gene of the HBV genome at the 5'-end of pregenomic HBV RNA. Our results demonstrated that 3p-siRNA induced a RIG-I-dependent antiviral type-I IFN response when transfected into HepG2.2.15 cells that support HBV replication. The 3p-siRNA significantly inhibited HBsAg and HBeAg secretion from HepG2.2.15 cells in a RIG-I-dependent manner, and the antiviral effect of 3p-siRNA was superior to that of siRNA. Furthermore, 3p-siRNA had more pronounced inhibition effects on the replication of HBV DNA and the transcription of mRNA than that of siRNA. Finally, 3p-siRNA displayed antiviral activity with long-term suppression of HBV replication. In conclusion, our findings suggest that 3p-siRNA could act as a powerful bifunctional antiviral molecule with potential for developing a promising therapeutic against chronic HBV infection.  
  Call Number Serial 1013  
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Author (up) Kass, S.U.; Pruss, D.; Wolffe, A.P. file  url
  Title How does DNA methylation repress transcription? Type Journal Article
  Year 1997 Publication Trends in Genetics : TIG Abbreviated Journal Trends Genet  
  Volume 13 Issue 11 Pages 444-449  
  Keywords Animals; Chromatin/chemistry/genetics; *DNA Methylation; Models, Genetic; *Transcription, Genetic  
  Abstract DNA methylation has an essential regulatory function in mammalian development, serving to repress nontranscribed genes stably in differentiated adult somatic cells. Recent data implicate transcriptional repressors specific for methylated DNA and chromatin assembly in this global control of gene activity. The assembly of specialized nucleosomal structures on methylated DNA helps to explain the capacity of methylated DNA segments to silence transcription more effectively than conventional chromatin. Specialized nucleosomes also provide a potential molecular mechanism for the stable propagation of DNA methylation-dependent transcriptional silencing through cell division.  
  Call Number Serial 1547  
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Author (up) McPheeters, D.S.; Wise, J.A. file  url
  Title Measurement of in vivo RNA synthesis rates Type Journal Article
  Year 2013 Publication Methods in Enzymology Abbreviated Journal Methods Enzymol  
  Volume 530 Issue Pages 117-135  
  Keywords Gene Expression Regulation, Fungal; RNA, Fungal/*genetics; Saccharomyces cerevisiae/*genetics; Schizosaccharomyces/*genetics; Transcription, Genetic; Immobilized DNA/RNA; Immobilized probes; In vivo RNA synthesis rates; Labeled RNA; Nascent transcripts  
  Abstract A technique is described to directly measure ongoing transcription from individual genes in permeabilized cells of either the budding yeast Saccharomyces cerevisiae or the fission yeast Schizosaccharomyces pombe. Transcription run-on (TRO) analysis is used to compare the relative rates of synthesis for specific transcripts in cells grown under different environmental conditions or harvested at different stages of development. As the amount of an individual RNA species present at any given time is determined by its net rate of synthesis and degradation, an accurate picture of transcription per se can be obtained only by directly measuring de novo synthesis of RNA (if you are interested in RNA degradation, see Method for measuring mRNA decay rate in Saccharomyces cerevisiae). Most techniques employed to measure changes in the relative levels of individual transcripts present under different conditions, including Northern analysis (see Northern blotting), RT-PCR (see Reverse-transcription PCR (RT-PCR)), nuclease protection assays (see Explanatory Chapter: Nuclease Protection Assays), and genome-wide assays, such as microarray analysis and high throughput RNA sequencing, measure changes in the steady-state level of a transcript, which may or may not reflect the actual changes in transcription of the gene. Recent studies carried out in fission yeast have demonstrated that increases in the steady-state level (accumulation) of many individual mRNAs occur without any significant changes in transcription rates (McPheeters et al., 2009), highlighting the important role of regulated RNA stability in determining gene expression programs (Harigaya et al., 2006).  
  Call Number Serial 1345  
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