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The 5 ' cap structure is added onto RNA polymerase II transcripts soon after initiation of transcription and modulates several post-transcriptional regulatory events involved in RNA maturation. It is also required for stimulating ...
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The 5 ' cap structure is added onto RNA polymerase II transcripts soon after initiation of transcription and modulates several post-transcriptional regulatory events involved in RNA maturation. It is also required for stimulating translation initiation of many cytoplasmic mRNAs and serves to protect mRNAs from degradation. These functional properties of the cap are mediated by several cap binding proteins (CBPs) involved in nuclear and cytoplasmic gene expression steps. The role that CBPs play in gene regulation, as well as the biophysical nature by which they recognize the cap, is quite intricate. Differences in mechanisms of capping as well as nuances in cap recognition speak to the potential of targeting these processes for drug development. In this review, we focus on recent findings concerning the cap epitranscriptome, our understanding of cap binding by different CBPs, and explore therapeutic targeting of CBP-cap interaction.
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In the binary projective spaces PG(n, 2) k-caps are called large if k > 2~(n-1) and small if k ≤ 2~(n-1). In this paper we propose new constructions producing infinite families of small binary complete caps.
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The eukaryotic mRNA 5' cap structure is indispensible for pre-mRNA processing, mRNA export, translation initiation, and mRNA stability. Despite this importance, structural and biophysical studies that involve capped RNA are challe...
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The eukaryotic mRNA 5' cap structure is indispensible for pre-mRNA processing, mRNA export, translation initiation, and mRNA stability. Despite this importance, structural and biophysical studies that involve capped RNA are challenging and rare due to the lack of a general method to prepare mRNA in sufficient quantities. Here, we show that the vaccinia capping enzyme can be used to produce capped RNA in the amounts that are required for large-scale structural studies. We have therefore designed an efficient expression and purification protocol for the vaccinia capping enzyme. Using this approach, the reaction scale can be increased in a cost-efficient manner, where the yields of the capped RNA solely depend on the amount of available uncapped RNA target. Using a large number of RNA substrates, we show that the efficiency of the capping reaction is largely independent of the sequence, length, and secondary structure of the RNA, which makes our approach generally applicable. We demonstrate that the capped RNA can be directly used for quantitative biophysical studies, including fluorescence anisotropy and high-resolution NMR spectroscopy. In combination with C-13-methyl-labeled S-adenosyl methionine, the methyl groups in the RNA can be labeled for methyl TROSY NMR spectroscopy. Finally, we show that our approach can produce both cap-0 and tap-1 RNA in high amounts. In summary, we here introduce a general and straightforward method that opens new means for structural and functional studies of proteins and enzymes in complex with capped RNA.
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The confined capping system, reported in this paper, provides a simple approach for compressive strength testing of high performance concrete cylinders. This method employs standard concrete laboratory testing equipment and an ine...
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The confined capping system, reported in this paper, provides a simple approach for compressive strength testing of high performance concrete cylinders. This method employs standard concrete laboratory testing equipment and an inexpensive customized capping apparatus for preparing the cylinder ends. The method ensures cap confinement without tight controls on the cylinder end roughness prior to capping, and on the cap thickness itself. This paper explains and documents the use of the method for testing concrete cylinders having strengths up to and exceeding 100 MPa.
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Human Nudt16 (hNudt16) is a member of the Nudix family of hydrolases, comprising enzymes catabolizing various substrates including canonical (d) NTPs, oxidized (d) NTPs, nonnucleoside polyphosphates, and capped mRNAs. Decapping ac...
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Human Nudt16 (hNudt16) is a member of the Nudix family of hydrolases, comprising enzymes catabolizing various substrates including canonical (d) NTPs, oxidized (d) NTPs, nonnucleoside polyphosphates, and capped mRNAs. Decapping activity of the Xenopus laevis (X29) Nudt16 homolog was observed in the nucleolus, with a high specificity toward U8 snoRNA. Subsequent studies have reported cytoplasmic localization of mammalian Nudt16 with cap hydrolysis activity initiating RNA turnover, similar to Dcp2. The present study focuses on hNudt16 and its hydrolytic activity toward dinucleotide cap analogs and short capped oligonucleotides. We performed a screening assay for potential dinucleotide and oligonucleotide substrates for hNudt16. Our data indicate that dinucleotide cap analogs and capped oligonucleotides containing guanine base in the first transcribed nucleotide are more susceptible to enzymatic digestion by hNudt16 than their counterparts containing adenine. Furthermore, unmethylated dinucleotides (GpppG and ApppG) and respective oligonucleotides (GpppG-16nt and GpppA-16nt) were hydrolyzed by hNudt16 with greater efficiency than were m7GpppG and m7GpppG-16nt. In conclusion, we found that hNudt16 hydrolysis of dinucleotide cap analogs and short capped oligonucleotides displayed a broader spectrum specificity than is currently known.
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The first example of the synthesis of new dinucleotide cap analog containing 2',3'-diacetyl group on m(7)guanosine moiety is described. The desired modified cap analog, m(7',2',3'-diacetyl)G[5]ppp[5']G has been obtained by the cou...
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The first example of the synthesis of new dinucleotide cap analog containing 2',3'-diacetyl group on m(7)guanosine moiety is described. The desired modified cap analog, m(7',2',3'-diacetyl)G[5]ppp[5']G has been obtained by the coupling reaction of triethylamine salt of m(7',2',3'-diacetyl)GDP with ImGMP in presence of ZnCl2 as a catalyst in 62% yield with high purity. The structure of new cap analog has been confirmed by H-1 and P-31 NMR and mass data.
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Around 3 millon people worldwide with end stage renal disease regularly need to use one of the established dialysis methods. The most common is haemodialysis but less irwasive is peritoneal dialysis where peritoneum takes the role...
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Around 3 millon people worldwide with end stage renal disease regularly need to use one of the established dialysis methods. The most common is haemodialysis but less irwasive is peritoneal dialysis where peritoneum takes the role of artificial kidney /1/. Using APD-Automatic peritoneal Dialysis, PD dialiser executes the whole cycle of successive charging and dialysis fuid discharging during the night. Connection of lines, solutions and patient to PD dialyser is done by use of connectors which are protected with caps that must be unscrewed sterly before use. In the production of disposable PDL lines the caps are screwed to connectors manually or automatically. Aulomatic screwing guarantees controlled and repetitive screwing conditions, as well as higher throughput. In the article we describe such a machine that we built. It is fuly automatic and needs to be occasionally reflled with material and reset to define new material lot. Process, as well as production, parameters are put-in through user friendly touch screen.
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The management and treatment of contaminated sediment is a worldwide problem and poses major technical and economic challenges. Nowadays, various attempts have been committed to investigating a cost-effective way in contaminated s...
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The management and treatment of contaminated sediment is a worldwide problem and poses major technical and economic challenges. Nowadays, various attempts have been committed to investigating a cost-effective way in contaminated sediment restoration. Among the remediation options, in situ capping turns out to be a less expensive, less disruptive, and more durable approach. However, by using the low adsorption capacity materials, traditional caps do not always fulfill the reduction of risks that can be destructive for human health, ecosystem, and even natural resources. Active caps, therefore, are designed to employ active materials (activated carbon, apatite, zeolite, organoclay, etc.) to strengthen their adsorption and degradation capacity. The active capping technology promises to be a permanent and cost-efficient solution to contaminated sediments. This paper provides a review on the types of active materials and the ways of these active materials employed in recent active capping studies. Cap design considerations including site-specific conditions, diffusion/advection, erosive forces, and active material selection that should be noticed in an eligible remediation project are also presented.
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Nowadays gene manipulation techniques (DNA therapy) undergo progressive development and become widely used in industry and medicine. Since new advances in mRNA technologies are capable for obtaining particles with increased stabil...
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Nowadays gene manipulation techniques (DNA therapy) undergo progressive development and become widely used in industry and medicine. Since new advances in mRNA technologies are capable for obtaining particles with increased stability and translational efficiency, RNA become an attractive alternative for advancement of DNA therapy. For the past years studies have been conducted to explore different modification in mRNA cap structure and its effect on RNA properties. Recently we have shown that modification of the cap structure at the N2 position of 7-methylguanosine leads to an enhancement in translation inhibition. Currently, we have decided to exploit translational properties of mRNA capped with the ARCA (anti-reversed cap) analogs modified within N2 position of purine moiety s. We designed and synthesized three new dinucleotide cap analogs and investigated them in the rabbit reticulocyte lysate (RRL) and the human embryonic kidney derived HEK293 cell line, in vitro translational model systems. The obtained data indicate that, in both translational assays, the cap analogs synthesized by us when incorporated into mRNA improved its translational properties compared to the ARCA capped transcripts. Furthermore, the introduced modifications enhanced stability of the capped transcripts in HEK293 cells, which become higher compared to that of the transcripts capped with regular cap or with ARCA. Additionally one of the synthesized cap analogs revealed strong translation inhibition potency in RRL system, with IC50 value 1.7 mu M.
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When bottled wine is opened, a completely different scenario occurs that can accelerate the oxidation of the product. This is called the secondary shelf life (SSL), which is generally shorter and less predictable than the primary ...
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When bottled wine is opened, a completely different scenario occurs that can accelerate the oxidation of the product. This is called the secondary shelf life (SSL), which is generally shorter and less predictable than the primary shelf life (PSL). In this context, the research aim was to evaluate the changes that occur in two types of red wine during two tests to evaluate the secondary shelf life as a function of the packaging systems. The variation of Total SO2 and Free SO2 and the other chemical parameters (polyphenols, anthocyanins, proanthocyanidins, color, and volatile acidity) were used to assess the oxidation rate of the packaging samples after opening during the SSL. In both tests and for the two types of stored red wine, the polymeric cap showed the best results. The other types of closure (screw cap, natural cork, crow cap, and Tetra Brik) showed a negative trend and a reduced SSL for both red wines. Finally, the sensory results confirmed that with the polymeric cap, the SSL increases considerably compared to other capping systems. These results may be due to the technical characteristics of polymeric materials, which tend to vary slightly in shape after repeated usage.
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