Relevant bibliographies by topics / RNA Synthesis

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'RNA Synthesis'

Author: Grafiati
Published: 4 June 2021
Last updated: 9 June 2025

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Journal articles on the topic "RNA Synthesis"

1

Cazenave, C., and O. C. Uhlenbeck. "RNA template-directed RNA synthesis by T7 RNA polymerase." Proceedings of the National Academy of Sciences 91, no. 15 (July 19, 1994): 6972–76. http://dx.doi.org/10.1073/pnas.91.15.6972.

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Sivakumaran, K., and C. Cheng Kao. "Initiation of Genomic Plus-Strand RNA Synthesis from DNA and RNA Templates by a Viral RNA-Dependent RNA Polymerase." Journal of Virology 73, no. 8 (August 1, 1999): 6415–23. http://dx.doi.org/10.1128/jvi.73.8.6415-6423.1999.

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ABSTRACT In contrast to the synthesis of minus-strand genomic and plus-strand subgenomic RNAs, the requirements for brome mosaic virus (BMV) genomic plus-strand RNA synthesis in vitro have not been previously reported. Therefore, little is known about the biochemical requirements for directing genomic plus-strand synthesis. Using DNA templates to characterize the requirements for RNA-dependent RNA polymerase template recognition, we found that initiation from the 3′ end of a template requires one nucleotide 3′ of the initiation nucleotide. The addition of a nontemplated nucleotide at the 3′ end of minus-strand BMV RNAs led to initiation of genomic plus-strand RNA in vitro. Genomic plus-strand initiation was specific since cucumber mosaic virus minus-strand RNA templates were unable to direct efficient synthesis under the same conditions. In addition, mutational analysis of the minus-strand template revealed that the −1 nontemplated nucleotide, along with the +1 cytidylate and +2 adenylate, is important for RNA-dependent RNA polymerase interaction. Furthermore, genomic plus-strand RNA synthesis is affected by sequences 5′ of the initiation site.
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Beerens, Nancy, Barbara Selisko, Stefano Ricagno, Isabelle Imbert, Linda van der Zanden, Eric J. Snijder, and Bruno Canard. "De Novo Initiation of RNA Synthesis by the Arterivirus RNA-Dependent RNA Polymerase." Journal of Virology 81, no. 16 (May 30, 2007): 8384–95. http://dx.doi.org/10.1128/jvi.00564-07.

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ABSTRACT All plus-strand RNA viruses encode an RNA-dependent RNA polymerase (RdRp) that functions as the catalytic subunit of the viral replication/transcription complex, directing viral RNA synthesis in concert with other viral proteins and, sometimes, host proteins. RNA synthesis essentially can be initiated by two different mechanisms, de novo initiation and primer-dependent initiation. Most viral RdRps have been identified solely on the basis of comparative sequence analysis, and for many viruses the mechanism of initiation is unknown. In this study, using the family prototype equine arteritis virus (EAV), we address the mechanism of initiation of RNA synthesis in arteriviruses. The RdRp domains of the members of the arterivirus family, which are part of replicase subunit nsp9, were compared to coronavirus RdRps that belong to the same order of Nidovirales, as well as to other RdRps with known initiation mechanisms and three-dimensional structures. We report here the first successful expression and purification of an arterivirus RdRp that is catalytically active in the absence of other viral or cellular proteins. The EAV nsp9/RdRp initiates RNA synthesis by a de novo mechanism on homopolymeric templates in a template-specific manner. In addition, the requirements for initiation of RNA synthesis from the 3′ end of the viral genome were studied in vivo using a reverse genetics approach. These studies suggest that the 3′-terminal nucleotides of the EAV genome play a critical role in viral RNA synthesis.
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Modahl, Lucy E., Thomas B. Macnaughton, Nongliao Zhu, Deborah L. Johnson, and Michael M. C. Lai. "RNA-Dependent Replication and Transcription of Hepatitis Delta Virus RNA Involve Distinct Cellular RNA Polymerases." Molecular and Cellular Biology 20, no. 16 (August 15, 2000): 6030–39. http://dx.doi.org/10.1128/mcb.20.16.6030-6039.2000.

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ABSTRACT Cellular DNA-dependent RNA polymerase II (pol II) has been postulated to carry out RNA-dependent RNA replication and transcription of hepatitis delta virus (HDV) RNA, generating a full-length (1.7-kb) RNA genome and a subgenomic-length (0.8-kb) mRNA. However, the supporting evidence for this hypothesis was ambiguous because the previous experiments relied on DNA-templated transcription to initiate HDV RNA synthesis. Furthermore, there is no evidence that the same cellular enzyme is involved in the synthesis of both RNA species. In this study, we used a novel HDV RNA-based transfection approach, devoid of any artificial HDV cDNA intermediates, to determine the enzymatic and metabolic requirements for the synthesis of these two RNA species. We showed that HDV subgenomic mRNA transcription was inhibited by a low concentration of α-amanitin (<3 μg/ml) and could be partially restored by an α-amanitin-resistant mutant pol II; however, surprisingly, the synthesis of the full-length (1.7-kb) antigenomic RNA was not affected by α-amanitin to a concentration higher than 25 μg/ml. By several other criteria, such as the differing requirement for the de novo-synthesized hepatitis delta antigen and temperature dependence, we further showed that the metabolic requirements of subgenomic HDV mRNA synthesis are different from those for the synthesis of genomic-length HDV RNA and cellular pol II transcripts. The synthesis of the two HDV RNA species could also be uncoupled under several different conditions. These findings provide strong evidence that pol II, or proteins derived from pol II transcripts, is involved in mRNA transcription from the HDV RNA template. In contrast, the synthesis of the 1.7-kb HDV antigenomic RNA appears not to be dependent on pol II. These results reveal that there are distinct molecular mechanisms for the synthesis of these two RNA species.
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Macnaughton, Thomas B., Stephanie T. Shi, Lucy E. Modahl, and Michael M. C. Lai. "Rolling Circle Replication of Hepatitis Delta Virus RNA Is Carried Out by Two Different Cellular RNA Polymerases." Journal of Virology 76, no. 8 (April 15, 2002): 3920–27. http://dx.doi.org/10.1128/jvi.76.8.3920-3927.2002.

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ABSTRACT Hepatitis delta virus (HDV) contains a viroid-like circular RNA that is presumed to replicate via a rolling circle replication mechanism mediated by cellular RNA polymerases. However, the exact mechanism of rolling circle replication for HDV RNA and viroids is not clear. Using our recently described cDNA-free transfection system (L. E. Modahl and M. M. Lai, J. Virol. 72:5449-5456, 1998), we have succeeded in detecting HDV RNA replication by metabolic labeling with [32P]orthophosphate in vivo and obtained direct evidence that HDV RNA replication generates high-molecular-weight multimeric species of HDV RNA, which are processed into monomeric and dimeric forms. Thus, these multimeric RNAs are the true intermediates of HDV RNA replication. We also found that HDV RNA synthesis is highly temperature sensitive, occurring most efficiently at 37 to 40°C and becoming virtually undetectable at temperatures below 30°C. Moreover, genomic HDV RNA synthesis was found to occur at a rate roughly 30-fold higher than that of antigenomic RNA synthesis. Finally, in lysolecithin-permeabilized cells, the synthesis of full-length antigenomic HDV RNA was completely resistant to high concentrations (100 μg/ml) of α-amanitin. In contrast, synthesis of genomic HDV RNA was totally inhibited by α-amanitin at concentrations as low as 2.5 μg/ml. Thus, these results suggest that genomic and antigenomic HDV RNA syntheses are performed by two different host cell enzymes. This observation, combined with our previous finding that hepatitis delta antigen mRNA synthesis is likely performed by RNA polymerase II, suggests that the different HDV RNA species are synthesized by different cellular transcriptional machineries.
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Röthlisberger, Pascal, Christian Berk, and Jonathan Hall. "RNA Chemistry for RNA Biology." CHIMIA International Journal for Chemistry 73, no. 5 (May 29, 2019): 368–73. http://dx.doi.org/10.2533/chimia.2019.368.

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Advances in the chemical synthesis of RNA have opened new possibilities to address current questions in RNA biology. Access to site-specifically modified oligoribonucleotides is often a pre-requisite for RNA chemical-biology projects. Driven by the enormous research efforts for development of oligonucleotide therapeutics, a wide range of chemical modifications have been developed to modulate the intrinsic properties of nucleic acids in order to fit their use as therapeutics or research tools. The RNA synthesis platform, supported by the NCCR RNA & Disease, aims to provide access to a large variety of chemically modified nucleic acids. In this review, we describe some of the recent projects that involved work of the platform and highlight how RNA chemistry supports new discoveries in RNA biology.
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ZACHLEDER, V., and I. ŠETLÍK. "Distinct controls of DNA replication and of nuclear division in the cell cycles of the chlorococcal alga Scenedesmus quadricauda." Journal of Cell Science 91, no. 4 (December 1, 1988): 531–39. http://dx.doi.org/10.1242/jcs.91.4.531.

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In the course of the cell cycle of Scenedesmus quadricauda, the syntheses of RNA and total protein occur in steps. Each step represents an approximate doubling of the preceding amount of RNA or protein per cell. The increase in protein content per cell runs parallel to, but with a constant delay behind, the corresponding RNA steps. When protein synthesis is suppressed (e.g. by maintaining the cells in the dark) after an RNA synthesis step has already occurred the cells double their DNA content, but no corresponding nuclear division occurs and uninuclear daughter cells with double the amount of DNA may be formed. Under conditions of phosphorus or nitrogen starvation RNA synthesis is stopped while protein synthesis continues. In this case, the number of DNA replication rounds corresponds to the reduced RNA content while the number of nuclear divisions tends to follow the number of protein synthesis steps until one genome per nucleus is attained. These results indicate that with each doubling of RNA content the cells become committed to DNA replication, while doubling of protein content is required for the commitment to the corresponding nuclear divisions.
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Doudna, Jennifer A., and Jack W. Szostak. "RNA-catalysed synthesis of complementary-strand RNA." Nature 339, no. 6225 (June 1989): 519–22. http://dx.doi.org/10.1038/339519a0.

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Illangasekare, M., G. Sanchez, T. Nickles, and M. Yarus. "Aminoacyl-RNA synthesis catalyzed by an RNA." Science 267, no. 5198 (February 3, 1995): 643–47. http://dx.doi.org/10.1126/science.7530860.

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Doudna, J. A., and J. W. Szostak. "RNA-catalysed synthesis of complementary strand RNA." Trends in Genetics 5 (1989): 323. http://dx.doi.org/10.1016/0168-9525(89)90125-x.

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Dissertations / Theses on the topic "RNA Synthesis"

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Peters, D. W. "RNA synthesis in Candida albicans." Thesis, University of Warwick, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.373051.

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Fritz, Sarah E. "Molecular basis of the DExH-box RNA helicase RNA helicase A (RHA/DHX9) in eukaryotic protein synthesis." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1437413252.

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Lackey, Jeremy. "New methods for the synthesis of RNA, novel RNA pro-drugs and RNA microarrays." Thesis, McGill University, 2010. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=92290.

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The demand for synthetic oligonucleotides has grown exponentially over the past decades as genome sequencing, functional genomics, polymerase chain reaction (PCR)-based detection methods, and gene silencing via RNA interference (RNAi) consume enormous numbers of DNA and RNA oligonucleotides. Although various RNA synthesis chemistries now allow oligoribonucleotides to be produced routinely, the higher complexity and cost of RNA (over DNA) has somewhat limited its availability.<br>A major goal of this thesis work was aimed at finding ribonucleoside synthons that potentially benefit two critical aspects of RNA manufacturing: yield and ease of post-synthesis processing. Towards these goals, we developed methods for the synthesis of RNA using 2'-O-Lv and 2'-O-acetal Lv (ALE) ribonucleoside derivatives. Deprotection of the RNA chains consisted of a three-step deprotection scheme, which eliminated the need for any harsh basic hydrolytic steps, generally composed of: (1) treatment with anhydrous NEt3 (r.t., 1 h) to deblock the phosphate's cyanoethyl groups; (2) hydrazinolysis (r.t., 30 min – 4 h) to simultaneously deprotect the nucleobases and 2'-OH positions, and (3) fluoride treatment (r.t., 30 min) to effect cleavage from the controlled pore glass solid support. Significantly, the rather mild conditions to remove 2'-O-Lv or 2'-O-ALE protecting groups did not lead to RNA strand scission. Furthermore, in the case of 2'-O-ALE protection, higher step-wise monomer coupling yields (~98.7%) was possible, since the ALE protection is less bulky than conventional silyl protection, i.e. TBDMS. Furthermore, both 2'-O-Lv or 2'O-ALE chemistries are completely compatible with the synthesis cycles used by all automated gene synthesizers.<br>With adjustments in protecting group strategies for the 5'-OH, exocyclic amino nucleobase groups and the development of a light-labile solid support, two other major goals were achieved: (1) the first in situ synthesis of RNA on microarrays, and (2) synthesis of chemically modified RNA strands with 2'-O-acetal ester and 2'-O-acetal ester pyrrolidines in order to increase lipophilicity and cellular permeability over native RNA. When RNA synthesis was carried out with 5'-O-NPPOC 2'-O-ALE monomers on a microarray ("chip"), deprotection typically involved (1) cleavage of the photolabile 5'-protecting group; (2) treatment with anhydrous NEt3 (r.t., 1 h) to deblock the phosphate's cyanoethyl groups; (3) hydrazinolysis (r.t., 30 min – 4 h) to simultaneously deprotect bases and 2'-OH positions. The latter step could also be accomplished with ethylenediamine at room temperature. An RNase A assay was performed as "proof-of-principle" to demonstrate the value of a DNA-RNA microarray for studying enzyme kinetics and specificity on oligonucleotide based libraries. We showed that RNase A acts effectively on a DNA-RNA substrate with measurable kinetics analogous to those of the reference substrates.<br>The novel 2'-O-modified RNA were tested as short interfering RNA pro-drugs ("pro-siRNA") that would cross the cell membrane and be hydrolyzed (at the 2'-O-ester groups) by ubiquitous esterases to release the active (siRNA) molecules. Indeed, both siRNA and pro-siRNA prepared via 2'-O-ALE chemistry were shown to be active in an RNAi luciferase gene knockdown assay, confirming the integrity of the synthesized RNA strands and the promise of the pro-siRNA approach.
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Johnston, Julie Catherine. "In vitro translation of cucumber necrosis virus RNA." Thesis, University of British Columbia, 1989. http://hdl.handle.net/2429/28969.

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The in vitro translation products directed by cucumber necrosis virus (CNV) RNA were analyzed in both rabbit reticulocyte lysate and wheat germ extract cell-free translation systems. In rabbit reticulocyte lysates, one major protein of ca. 33 Mr was produced. In wheat germ extracts, four proteins of ca. 41, 33, 21 and 20 Mr were produced. Hybrid-arrested translation (HART) studies using synthetic CNV antisense RNA corresponding to the entire CNV genome demonstrated that the four major proteins synthesized from CNV virion RNA in wheat germ extracts are virus-specific translation products. The genomic locations of the CNV in vitro translation products were determined using a number of experimental approaches including: (1) HART using antisense RNA corresponding to selected regions of the CNV genome; (2) in vitro translation of synthetic messenger-sense CNV transcripts; (3) immunoprecipitation of in vitro translation products with CNV polyclonal antisera and (4) in vitro translation of size-fractionated CNV virion RNA. Together, these experiments demonstrated that the ca. 33 Mr protein is derived from the 5' proximal coding region, the ca. 41 Mr protein is derived from an internal coding region, and that at least one but probably both of the ca. 20 and 21 Mr proteins are derived from the 3' terminal coding region(s) of the CNV genome. In addition, immunoprecipitation experiments provided further evidence that the ca. 41 Mr protein is the viral coat protein. The size, number, and genomic locations of the CNV in vitro translation products reported here are in agreement with those predicted from nucleotide sequence data (Rochon & Tremaine, 1989). The natural template for the expression of downstream cistrons in the CNV genome was investigated by in vitro translation of sucrose fractionated CNV virion RNA as well as in vitro translation of messenger-sense synthetic transcripts. These studies indicate that in vitro, both subgenomic and genomic-length CNV RNA molecules may act as templates for the synthesis of the ca. 41,21 and 20 Mr proteins as well as the ca. 33 Mr protein.<br>Land and Food Systems, Faculty of<br>Graduate
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Attwater, James. "Ice as a medium for RNA-catalysed RNA synthesis and evolution." Thesis, University of Cambridge, 2011. https://www.repository.cam.ac.uk/handle/1810/246525.

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A critical event in the origin of life is thought to have been the emergence of a molecule capable of self-replication and evolution. According to the RNA World hypothesis, this could have been an RNA polymerase ribozyme capable of generating copies of itself from simple nucleotide precursors. In vitro evolution experiments have provided modern examples of such ribozymes, such as the R18 RNA polymerase ribozyme, exhibiting basic levels of this crucial catalytic activity; R18’s activity, however, falls far short of that required of an RNA replicase, leaving unanswered the question of whether RNA can catalyse its self-replication. This thesis describes the development and use of a novel in vitro selection system, Compartmentalised Bead-Tagging (CBT), to isolate variants of the R18 ribozyme with improved sequence generality and extension capabilities. CBT evolution and engineering of polymerase ribozymes, together with RNA template evolution, allowed the synthesis of RNA molecules over 100 nucleotides long, as well as the RNA-catalysed transcription of a catalytic hammerhead ribozyme. This demonstrates the catalytic capabilities of ribozyme polymerases. The R18 ribozyme was also exploited as an analogue of a primordial replicase, to determine replicase behaviour in different reaction environments. Substantial ribozyme polymerisation occurred at −7˚C in the liquid eutectic phase of water-ice; increased ribozyme stability at these low temperatures allowed longer extension products to be generated than at ambient temperatures. The concentration effect of eutectic phase formation could also yield RNA synthesis from dilute solutions of substrates, and provide quasicellular compartmentalisation of ribozymes. These beneficial physicochemical features of ice make it a potential protocellular medium for the emergence of primordial replicases. Ice also could serve as a medium for CBT, allowing the isolation of a polymerase ribozyme adapted to the low temperatures in the ice phase, demonstrating the primordial potential and modern feasibility of ribozyme evolution in ice.
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Collis, Alana E. C. "The synthesis of vinylphosphonate-linked RNA." Thesis, University of Nottingham, 2008. http://eprints.nottingham.ac.uk/10541/.

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An introductory chapter discusses the steric block, RNase H and RNA interference antisense mechanisms and the application of antisense nucleic acids as therapeutic agents. Examples of existing chemical modifications of the sugar and backbone regions of nucleic acids are given, followed by the introduction of the vinylphosphonate modification. The vinylphosphonate has previously been examined in DNA and has been synthesised by either Pd(0) catalysed cross-coupling of an H-phosphonate with a vinyl bromide, or by the cross-metathesis of a vinylphosphonate with a terminal olefin. This thesis details the first examples of the vinylphosphonate modification in RNA. The initial aim of this project was the synthesis of a range of nucleosides where the 5'-C-O was replaced by a vinyl bromide carbon-carbon double bond. Starting from alpha-D-glucose, acid catalysed formation of the 1,2:5,6-diisopropylidene alpha-D-glucofuranose was carried out followed by protection of the 3-OH as an acetate. The 5,6-isopropylidene was then subjected to H5IO6 mediated one-pot hydrolysis-oxidative cleavage to obtain the 5-aldehyde. Wittig olefination using CBr4 and Ph3P led to the dibromo olefin which was then stereoselectively reduced using dimethyl phosphite and diisopropylamine to obtain the pure trans-vinyl bromide. Following hydrolysis of the acetate, the stereochemistry of the 3-OH was then inverted by sequential oxidation and reduction. With the correct stereochemistry, the 3-OH was protected as the 2-methylnaphthyl ether. The 1,2-isopropylidene moiety was then hydrolysed and acetylated to the bis-acetate which was subjected to Vorbruggen conditions obtaining the uridine (93%), adenosine (77%), cytidine (30) and guanosine (63%) vinyl bromide nucleosides. The 2'-OAc of the nucleosides were hydrolysed to the 2'-OH in yields of 74-92%. The uridine 2'-OH was protected as the 2'-OTBS ether (98%), analogous to the commercially available phosphoramidites used in automated oligonucleotide synthesis. Similarly, the adenosine and uridine nucleosides could also be blocked as the 2'-OMe (59% and 73% respectively). In the case of the uridine vinyl bromide, the 3'-O-(2-methylnaphthyl) protecting group was cleaved using DDQ, this then enabled the vinylphosphonate-linked uridine dinucleotides to be functionalised at the 3'-OH as the cyanoethyl phosphoramidite using N,N-diisopropyl-2-cyanoethyl-chlorophosphoramidite, DIPEA and DMAP in dichloromethane (2'-OTBS 74%, 2'-OMe 41%). These could then be used in automated solid phase oligonucleotide synthesis. The H-phosphonates were prepared in a single step form the commercially available phosphoramidites using a tetrazole. These were then coupled to the vinyl bromide nucleosides using standard conditions of Pd(OAc)2 (0.2 eq.), dppf (0.4 eq.) and propylene oxide (20 eq.) in THF at 70 oC in a sealed vial for 6 hours. A range of vinylphosphonate-linked dinucleotides were accessed in yields of 61-99%. A detailed experimental section at the end of this thesis describes the procedures used in the synthesis and the analysis of the structures obtained.
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Liu, Qi. "Synthesis of small molecules targeting RNA /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2004. http://wwwlib.umi.com/cr/ucsd/fullcit?p3142456.

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D'Abramo, Claudia M. "Biochemical characterization of the BVDV RNA-dependent RNA polymerase during initiation and elongation of RNA synthesis." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=111870.

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The RNA-dependent RNA polymerase (RdRp) of viruses belonging to the Flaviviridae family, including the hepatitis C virus (HCV) and bovine viral diarrhea virus (BVDV) is critical for viral replication. The major goal of this PhD study was to biochemically characterize the role of the polymerase during initiation and elongation of RNA synthesis, utilizing the BVDV RdRp as a model system. We showed that the BVDV polymerase efficiently incorporates chain-terminating nucleoside analogues, which ultimately arrest RNA synthesis. The incorporated chain-terminators, however, can be removed from the primer terminus in the presence of pyrophosphate (PPi). These results suggest that the phosphorolytic excision of incorporated chain-terminators is a possible mechanism that can diminish the efficiency of this class of compounds against viral RdRps. The chain-terminators then served as valuable tools in subsequent experiments to analyze the functional role(s) of the RdRp-associated GTP-specific binding site (G-site) and the consequences of GTP binding during the initiation of RNA synthesis. The results provide biochemical evidence for the existence of a G-site in the BVDV enzyme, and suggest that GTP binding controls template positioning during de novo initiation. Finally, through the development of a novel ribonuclease-based footprinting assay, it was determined that catalytically active complexes contact the newly synthesized RNA during elongation of RNA synthesis with approximately 6-7 base pairs. The polymerase moves along the template according to the position where RNA synthesis is arrested. Taken together, this study provides novel insight into mechanisms involved during initiation and elongation of RNA replication of viruses belonging to the Flaviviridae family. The ability of RdRps to excise incorporated chain-terminators points to possible shortcomings of nucleoside analogue inhibitors that are under development as antiviral agents for the treatment of infection with HCV.
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Repass, John F. "Studies of murine coronavirus cis-acting RNA elements that affect RNA synthesis /." Digital version accessible at:, 2000. http://wwwlib.umi.com/cr/utexas/main.

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Gilea, Manuela Aurora. "DNA and RNA synthesis in ionic liquids." Thesis, Queen's University Belfast, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485198.

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The solid-phase synthesis of oligonucleotide derivatives such as phosphorothioates and phosphoroselenoates was investigated. Some ionic liquids containing the trlbexyl(tetradecyl)phosphonium cation and various anions proved to be very effective in dissolving the chalcogens (sulfur and , selenium) and to prepare oligonucleoside chalcogenophosphates. The suitability ofionic liquid-based chalcogen-transfer mixtures for the synthesis of oligonucleoside chalcogenophosphates on solid-phase was evaluated and subsequently the structure-activity relationship studied in detail. The compatibility of ionic liquid-based chalcogen-transfer mixtures with diverse types of solid supports e.g. controlled-pore glass, poly(vinylacetate) and. different synthetic methods. e.g. phosphoramidite and H-phosphonate method makes them useful as replacement of the more expensive and relatively unstable commerciaily avai1able chalcogen-transfer reagents. The distillation of ionic liquids was also studied.
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Books on the topic "RNA Synthesis"

1

Peters, David William. RNA synthesis in 'Candida albicans'. [s.l.]: typescript, 1985.

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L, Hatfield Dolph, Lee Byeong J, and Pirtle Robert M, eds. Transfer RNA in protein synthesis. Boca Raton: CRC Press, 1992.

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James, Dahlberg, and Abelson John, eds. RNA processing. San Diego: Academic, 1989.

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Conn, Graeme L., ed. Recombinant and In Vitro RNA Synthesis. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-113-4.

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1953-, Krieg Paul A., ed. A laboratory guide to RNA: Isolation, analysis, and synthesis. New York: Wiley-Liss, 1996.

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A, Narang Saran, ed. Synthesis and applications of DNA and RNA. Orlando: Academic Press, 1987.

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Johnson, Moira A. Kinetics of RNA synthesis in rotavirus infected cells. [s.l.]: typescript, 1988.

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Lynne, Maquat, ed. Nonsense-mediated mRNA decay. Georgetown, Tex: Landes Bioscience, 2006.

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service), ScienceDirect (Online, ed. RNA turnover in bacteria, archaea and organelles. San Diego, Calif: Academic Press/Elsevier, 2008.

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Arnstein, H. R. V. Protein biosynthesis. [Oxford, England]: IRL Press at Oxford University Press, 1992.

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Book chapters on the topic "RNA Synthesis"

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Beckert, Bertrand, and Benoît Masquida. "Synthesis of RNA by In Vitro Transcription." In RNA, 29–41. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-59745-248-9_3.

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Johnson, Kyle L., and Peter Sarnow. "Viral RNA Synthesis." In Human Enterovirus Infections, 95–112. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818326.ch4.

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van den Born, Erwin, and Eric J. Snijder. "RNA Signals Regulating Nidovirus RNA Synthesis." In Nidoviruses, 115–31. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555815790.ch8.

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Engels, Joachim W., Dalibor Odadzic, Romualdas Smicius, and Jens Haas. "Chemical Synthesis of 2′-O-Alkylated siRNAs." In RNA Interference, 155–70. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-588-0_10.

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Frei, Julia, Natalia T. Jarzebska, Mark Mellett, Thomas M. Kündig, Steve Pascolo, and Andreas M. Reichmuth. "Design and Synthesis of Circular RNA Expression Vectors." In RNA Vaccines, 205–15. New York, NY: Springer US, 2024. http://dx.doi.org/10.1007/978-1-0716-3770-8_9.

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Snijder, Eric J. "Arterivirus RNA Synthesis Dissected." In Advances in Experimental Medicine and Biology, 241–53. Boston, MA: Springer US, 2001. http://dx.doi.org/10.1007/978-1-4615-1325-4_39.

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Höbartner, Claudia. "Chemical Synthesis of RNA." In Alternative pre-mRNA Splicing, 154–62. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527636778.ch14.

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Huq, Tamanna Binte, and Juan L. Vivero-Escoto. "Synthesis of Mesoporous Silica Nanoparticles for the Delivery of Nucleic Acid Nanostructures." In RNA Nanostructures, 205–10. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3417-2_13.

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Sproat, Brian S. "Chemical RNA Synthesis, Purification, and Analysis." In Handbook of RNA Biochemistry, 129–50. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2014. http://dx.doi.org/10.1002/9783527647064.ch7.

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Gößringer, Markus, Dominik Helmecke, Karen Köhler, Astrid Schön, Leif A. Kirsebom, Albrecht Bindereif, and Roland K. Hartmann. "Enzymatic RNA Synthesis Using Bacteriophage T7 RNA Polymerase." In Handbook of RNA Biochemistry, 1–28. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2014. http://dx.doi.org/10.1002/9783527647064.ch1.

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Conference papers on the topic "RNA Synthesis"

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Mehta, Richa, Azizbek Khurramov, Vinay Kumar Deolia, M. Vamsikrishna, Haider Alabdeli, and R. Gunasundari. "Beam Synthesis in O-RAN 5G: Operational Considerations." In 2024 International Conference on Communication, Computing and Energy Efficient Technologies (I3CEET), 199–205. IEEE, 2024. https://doi.org/10.1109/i3ceet61722.2024.10993633.

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Voloshin, A. A., E. A. Voloshin, A. I. Kovalenko, D. P. Yakovlev, E. S. Astakhov, I. S. Polygalin, and D. A. Romanov. "Algorithm of Automatic Synthesis of Optimal Solutions for Power Systems based on the Method of Dynamic Programming." In 2024 7th International Youth Scientific and Technical Conference on Relay Protection and Automation (RPA), 1–23. IEEE, 2024. https://doi.org/10.1109/rpa65165.2024.10932888.

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Obeyesekere, Nihal, and Thusitha Wickramarachchi. "Transition from Combinatorial Chemistry to Present Day Robotics in Product Development for Oil Field Chemicals." In MECC 2023, 1–15. AMPP, 2023. https://doi.org/10.5006/mecc2023-20245.

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Abstract In this paper, the slow evolution of combinatorial chemistry from its dawn in 1980’s to today’s oil field product development is discussed. Combinatorial chemistry comprises chemical synthetic methods that make it possible to prepare a vast number of compounds in a single process. These compound libraries can be made as mixtures, sets of individual compounds or chemical structures generated by computer software. This phenomenon was first invented by Arpad Furka (Lorand University, Budapest) in 1982. He described the principle of it, the combinatorial synthesis and a deconvolution procedure. The methodology was first used in drug discovery using a wide range of linear or wide range of macrocyclic chemical molecules: peptides, non-peptide oligomers, peptidomimetics, small-molecules, and natural product-like organic molecules. However, handling vast amounts of data and extremely small chemical recovery were a very difficult endeavor. To avoid this problem and help to refine the size of the chemical libraries, various software programs were utilized. This was achieved by utilizing a tool known as Design of Experiment (DoE). In this paper, the high throughput product screening to identify corrosion inhibitors was performed by utilizing critical micelle concentration (CMC). CMC was used to differentiate performance of libraries of chemical blends. Combinatorial synthesis (or blends) and combinatorial screening were performed by utilizing robotics methodologies. The corrosion inhibitor formulations predicted by DoE were built out by using combinatorial chemical methods and the arrays of chemical formulations were screened by utilizing high throughput robotics, using CMC as the selection guide. To validate the concept, several known corrosion inhibitor formulas were selected to optimize their efficacy. Each formula contained several active ingredients and a solvent package. These raw materials were blended in random but in a control, manner using combinatorial methodologies. After formulation of a vast array of formulation by using Design Expert solvent package. These raw materials were blended in random but in a control, manner using combinatorial methodologies. After formulation of a vast array of formulation by using Design Expert (DE) software, the products were screened for by CMC using automated surface tension workstation. Several formulations with lower CMC than the reference products were selected. The selected corrosion inhibitor formulations were identified and blended in larger scales. The efficacy of these products was tested by classical laboratory testing methods such as rotating cylinder electrode (RCE) and rotating cage autoclave (RCA) to determine their performance as anti-corrosion agents. These tests were performed against the original reference corrosion inhibitor. The testing indicated that several corrosion inhibitor formulations outperform the original blend thus validating the proof of concept.
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Kozlov, I. B., O. A. Gerasimov, O. Y. Domasheva, L. G. Bushina, and D. M. Fedoseeva. "PREPARATION AND APPLICATION OF SYNTHETIC RNA OLIGONUCLEOTIDE WITH 5’-TERMINAL PHOSPHATE." In XI МЕЖДУНАРОДНАЯ КОНФЕРЕНЦИЯ МОЛОДЫХ УЧЕНЫХ: БИОИНФОРМАТИКОВ, БИОТЕХНОЛОГОВ, БИОФИЗИКОВ, ВИРУСОЛОГОВ, МОЛЕКУЛЯРНЫХ БИОЛОГОВ И СПЕЦИАЛИСТОВ ФУНДАМЕНТАЛЬНОЙ МЕДИЦИНЫ. IPC NSU, 2024. https://doi.org/10.25205/978-5-4437-1691-6-243.

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Technologies for creating genotherapeutic drugs using synthetic 5’-phosphorylated RNA oligonucleotides are being actively developed. The synthesis of these oligonucleotides is complicated by the methods selection for post-synthetic purification using HPLC. We propose combination of HPLC methods for efficient purification of the target product. The structure of the obtained 5’-phosphorylated RNA oligonucleotides was confirmed by LC-MS.
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Bakhno, I. A. "DESIGN AND SYNTHESIS OF MODIFIED RNAS." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-294.

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RNA is a universal tool, it is involved in many cellular processes. Understanding the mechanisms of these processes is necessary not only to understand the fundamental principles of the structure of a living cell, but also to create drugs. In this regard, tools are required to create modified RNA analogs to study these processes.
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Smirnova, O. S., and I. D. Konstantinova. "CHEMO-ENZYMATIC SYNTHESIS OF NEW RIBAVIRIN ANALOGS." In OpenBio-2023. ИПЦ НГУ, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-51.

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Wachowius, Falk, Giuseppe Sicoli, Marina Bennati, and Claudia Höbartner. "Synthesis of spin-labeled RNA and probing of RNA secondary structures by pulsed EPR spectroscopy." In XVth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2011. http://dx.doi.org/10.1135/css201112336.

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Akama, Satoru, Masayuki Yamamura, and Takanori Kigawa. "Multi-Objective Robust Optimization for In Vitro RNA Synthesis." In Computational Intelligence and Bioinformatics / Modelling, Simulation, and Identification. Calgary,AB,Canada: ACTAPRESS, 2012. http://dx.doi.org/10.2316/p.2012.753-017.

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Akama, Satoru, Masayuki Yamamura, and Takanori Kigawa. "Multi-Objective Robust Optimization for In Vitro RNA Synthesis." In Computational Intelligence and Bioinformatics / Modelling, Simulation, and Identification. Calgary,AB,Canada: ACTAPRESS, 2011. http://dx.doi.org/10.2316/p.2011.753-017.

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Božilović, Jelena, Jan W. Bats, and Joachim W. Engels. "Synthesis and crystal structures of fluorinated indols as RNA analogues." In XIIIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2005. http://dx.doi.org/10.1135/css200507385.

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Reports on the topic "RNA Synthesis"

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Soell, D. [The first steps of chlorophyll synthesis: RNA involvement and regulation]. Office of Scientific and Technical Information (OSTI), January 1992. http://dx.doi.org/10.2172/6528189.

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Nilsson, Emil. Synthesis of Sulfamoyl??Aminoacyl Adenylate Analogs for use in Protein?RNA Structure Determination. Portland State University Library, May 2013. http://dx.doi.org/10.15760/honors.28.

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Walker, Richard T. Synthesis of Nucleoside Analogues with Potential Antiviral Activity against Negative Strand RNA Virus Targets. Fort Belvoir, VA: Defense Technical Information Center, November 1989. http://dx.doi.org/10.21236/ada229411.

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Soell, D. [The first steps of chlorophyll synthesis: RNA involvement and regulation]. Progress report, January 1990--June 1992. Office of Scientific and Technical Information (OSTI), December 1992. http://dx.doi.org/10.2172/10158546.

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Stern, David, and Gadi Schuster. Manipulating Chloroplast Gene Expression: A Genetic and Mechanistic Analysis of Processes that Control RNA Stability. United States Department of Agriculture, June 2004. http://dx.doi.org/10.32747/2004.7586541.bard.

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New potential for engineering chloroplasts to express novel traits has stimulated research into relevant techniques and genetic processes, including plastid transformation and gene regulation. This BARD-funded research dealt with the mechanisms that influence chloroplast RNA accumulation, and thus gene expression. Previous work on cpRNA catabolism has elucidated a pathway initiated by endonucleolytic cleavage, followed by polyadenylation and exonucleolytic degradation. A major player in this process is the nucleus-encoded exoribo-nuclease/polymerase polynucleotide phosphorylase (PNPase). Biochemical characterization of PNPase has revealed a modular structure that controls its RNA synthesis and degradation activities, which in turn are responsive to the phosphate (P) concentration. During the funding period, new insights emerged into the molecular mechanism of RNA metabolism in the chloroplast and cyanobacteria, suggesting strategies for improving agriculturally-important plants or plants with novel introduced traits.
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Schuster, Gadi, and David Stern. Integration of phosphorus and chloroplast mRNA metabolism through regulated ribonucleases. United States Department of Agriculture, August 2008. http://dx.doi.org/10.32747/2008.7695859.bard.

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New potential for engineering chloroplasts to express novel traits has stimulated research into relevant techniques and genetic processes, including plastid transformation and gene regulation. This proposal continued our long time BARD-funded collaboration research into mechanisms that influence chloroplast RNA accumulation, and thus gene expression. Previous work on cpRNA catabolism has elucidated a pathway initiated by endonucleolytic cleavage, followed by polyadenylation and exonucleolytic degradation. A major player in this process is the nucleus-encoded exoribonuclease/polymerasepolynucleotidephoshorylase (PNPase). Biochemical characterization of PNPase has revealed a modular structure that controls its RNA synthesis and degradation activities, which in turn are responsive to the phosphate (P) concentration. However, the in vivo roles and regulation of these opposing activities are poorly understood. The objectives of this project were to define how PNPase is controlled by P and nucleotides, using in vitro assays; To make use of both null and site-directed mutations in the PNPgene to study why PNPase appears to be required for photosynthesis; and to analyze plants defective in P sensing for effects on chloroplast gene expression, to address one aspect of how adaptation is integrated throughout the organism. Our new data show that P deprivation reduces cpRNA decay rates in vivo in a PNPasedependent manner, suggesting that PNPase is part of an organismal P limitation response chain that includes the chloroplast. As an essential component of macromolecules, P availability often limits plant growth, and particularly impacts photosynthesis. Although plants have evolved sophisticated scavenging mechanisms these have yet to be exploited, hence P is the most important fertilizer input for crop plants. cpRNA metabolism was found to be regulated by P concentrations through a global sensing pathway in which PNPase is a central player. In addition several additional discoveries were revealed during the course of this research program. The human mitochondria PNPase was explored and a possible role in maintaining mitochondria homeostasis was outlined. As polyadenylation was found to be a common mechanism that is present in almost all organisms, the few examples of organisms that metabolize RNA with no polyadenylation were analyzed and described. Our experiment shaded new insights into how nutrient stress signals affect yield by influencing photosynthesis and other chloroplast processes, suggesting strategies for improving agriculturally-important plants or plants with novel introduced traits. Our studies illuminated the poorly understood linkage of chloroplast gene expression to environmental influences other than light quality and quantity. Finely, our finding significantly advanced the knowledge about polyadenylation of RNA, the evolution of this process and its function in different organisms including bacteria, archaea, chloroplasts, mitochondria and the eukaryotic cell. These new insights into chloroplast gene regulation will ultimately support plant improvement for agriculture
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Sionov, Edward, Nancy Keller, and Shiri Barad-Kotler. Mechanisms governing the global regulation of mycotoxin production and pathogenicity by Penicillium expansum in postharvest fruits. United States Department of Agriculture, January 2017. http://dx.doi.org/10.32747/2017.7604292.bard.

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The original objectives of the study, as defined in the approved proposal, are: To characterize the relationship of CreA and LaeA in regulation of P T production To understand how PacC modulates P. expansumpathogenicity on apples To examine if other secondary metabolites are involved in virulence or P. expansumfitness To identify the signaling pathways leading to PAT synthesis Penicilliumexpansum, the causal agent of blue mould rot, is a critical health concern because of the production of the mycotoxinpatulin (PAT) in colonized apple fruit tissue. Although PAT is produced by many Penicilliumspecies, the factors activating its biosynthesis were not clear. This research focused on host and fungal mechanisms of activation of LaeA (the global regulator of secondary metabolism), PacC (the global pH modulator) and CreA (the global carbon catabolite regulator) on PAT synthesis with intention to establish P. expansumas the model system for understanding mycotoxin synthesis in fruits. The overall goal of this proposal is to identify critical host and pathogen factors that mechanistically modulate P. expansumgenes and pathways to control activation of PAT production and virulence in host. Several fungal factors have been correlated with disease development in apples, including the production of PAT, acidification of apple tissue by the fungus, sugar content and the global regulator of secondary metabolism and development, LaeA. An increase in sucrose molarity in the culture medium from 15 to 175 mM negatively regulated laeAexpression and PAT accumulation, but, conversely, increased creAexpression, leading to the hypothesis that CreA could be involved in P. expansumPAT biosynthesis and virulence, possibly through the negative regulation of LaeA. We found evidence for CreAtranscriptional regulation of laeA, but this was not correlated with PAT production either in vitro or in vivo, thus suggesting that CreA regulation of PAT is independent of LaeA. Our finding that sucrose, a key ingredient of apple fruit, regulates PAT synthesis, probably through suppression of laeAexpression, suggests a potential interaction between CreA and LaeA, which may offer control therapies for future study. We have also identified that in addition to PAT gene cluster, CreA regulates other secondary metabolite clusters, including citrinin, andrastin, roquefortine and communesins, during pathogenesis or during normal fungal growth. Following creation of P. expansumpacCknockout strain, we investigated the involvement of the global pH regulator PacC in fungal pathogenicity. We demonstrated that disruption of the pH signaling transcription factor PacC significantly decreased the virulence of P. expansumon deciduous fruits. This phenotype is associated with an impairment in fungal growth, decreased accumulation of gluconic acid and reduced synthesis of pectolytic enzymes. We showed that glucose oxidase- encoding gene, which is essential for gluconic acid production and acidification during fruit colonization, was significantly down regulated in the ΔPepacCmutant, suggesting that gox is PacC- responsive gene. We have provided evidence that deletion of goxgene in P. expansumled to a reduction in virulence toward apple fruits, further indicating that GOX is a virulence factor of P. expansum, and its expression is regulated by PacC. It is also clear from the present data that PacC in P. expansumis a key factor for the biosynthesis of secondary metabolites, such as PAT. On the basis of RNA-sequencing (RNA-seq) analysis and physiological experimentation, the P. expansumΔlaeA, ΔcreAand ΔpacCmutants were unable to successfully colonize apples for a multitude of potential mechanisms including, on the pathogen side, a decreased ability to produce proteolytic enzymes and to acidify the environment and impaired carbon/nitrogen metabolism and, on the host side, an increase in the oxidative defence pathways. Our study defines these global regulatory factors and their downstream signalling pathways as promising targets for the development of strategies to fight against this post-harvest pathogen.
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Wang, X. F., and M. Schuldiner. Systems biology approaches to dissect virus-host interactions to develop crops with broad-spectrum virus resistance. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134163.bard.

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More than 60% of plant viruses are positive-strand RNA viruses that cause billion-dollar losses annually and pose a major threat to stable agricultural production, including cucumber mosaic virus (CMV) that infects numerous vegetables and ornamental trees. A highly conserved feature among these viruses is that they form viral replication complexes (VRCs) to multiply their genomes by hijacking host proteins and remodeling host intracellular membranes. As a conserved and indispensable process, VRC assembly also represents an excellent target for the development of antiviral strategies that can be used to control a wide-range of viruses. Using CMV and a model virus, brome mosaic virus (BMV), and relying on genomic tools and tailor-made large-scale resources specific for the project, our original objectives were to: 1) Identify host proteins that are required for viral replication complex assembly. 2) Dissect host requirements that determine viral host range. 3) Provide proof-of-concept evidence of a viral control strategy by blocking the viral replication complex-localized phospholipid synthesis. We expect to provide new ways and new concepts to control multiple viruses by targeting a conserved feature among positive-strand RNA viruses based on our results. Our work is going according to the expected timeline and we are progressing well on all aims. For Objective 1, among ~6,000 yeast genes, we have identified 96 hits that were possibly play critical roles in viral replication. These hits are involved in cellular pathways of 1) Phospholipid synthesis; 2) Membrane-shaping; 3) Sterol synthesis and transport; 4) Protein transport; 5) Protein modification, among many others. We are pursuing several genes involved in lipid metabolism and transport because cellular membranes are primarily composed of lipids and lipid compositional changes affect VRC formation and functions. For Objective 2, we have found that CPR5 proteins from monocotyledon plants promoted BMV replication while those from dicotyledon plants inhibited it, providing direct evidence that CPR5 protein determines the host range of BMV. We are currently examining the mechanisms by which dicot CPR5 genes inhibit BMV replication and expressing the dicot CPR5 genes in monocot plants to control BMV infection. For Objective 3, we have demonstrated that substitutions in a host gene involved in lipid synthesis, CHO2, prevented the VRC formation by directing BMV replication protein 1a (BMV 1a), which remodels the nuclear membrane to form VRCs, away from the nuclear membrane, and thus, no VRCs were formed. This has been reported in Journal of Biological Chemistry. Based on the results from Objective 3, we have extended our plan to demonstrate that an amphipathic alpha-helix in BMV 1a is necessary and sufficient to target BMV 1a to the nuclear membrane. We further found that the counterparts of the BMV 1a helix from a group of viruses in the alphavirus-like superfamily, such as CMV, hepatitis E virus, and Rubella virus, are sufficient to target VRCs to the designated membranes, revealing a conserved feature among the superfamily. A joint manuscript describing these exciting results and authored by the two labs will be submitted shortly. We have also successfully set up systems in tomato plants: 1) to efficiently knock down gene expression via virus-induced gene silencing so we could test effects of lacking a host gene(s) on CMV replication; 2) to overexpress any gene transiently from a mild virus (potato virus X) so we could test effects of the overexpressed gene(s) on CMV replication. In summary, we have made promising progress in all three Objectives. We have identified multiple new host proteins that are involved in VRC formation and may serve as good targets to develop antiviral strategies; have confirmed that CPR5 from dicot plants inhibited viral infection and are generating BMV-resistance rice and wheat crops by overexpressing dicot CPR5 genes; have demonstrated to block viral replication by preventing viral replication protein from targeting to the designated organelle membranes for the VRC formation and this concept can be further employed for virus control. We are grateful to BARD funding and are excited to carry on this project in collaboration.
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Loebenstein, Gad, William Dawson, and Abed Gera. Association of the IVR Gene with Virus Localization and Resistance. United States Department of Agriculture, August 1995. http://dx.doi.org/10.32747/1995.7604922.bard.

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We have reported that localization of TMV in tobacco cultivars with the N gene, is associated with a 23 K protein (IVR) that inhibited replication of several plant viruses. This protein was also found in induced resistant tissue of Nicotiana glutinosa x Nicotiana debneyi. During the present grant we found that TMV production is enhanced in protoplasts and plants of local lesion responding tobacco cultivars exposed to 35oC, parallel to an almost complete suppression of the production of IVR. We also found that IVR is associated with resistance mechanisms in pepper cultivars. We succeeded to clone the IVR gene. In the first attempt we isolated a clone - "101" which had a specific insert of 372 bp (the full length gene for the IVR protein of 23 kD should be around 700 bp). However, attempts to isolate the full length gene did not give clear cut results, and we decided not to continue with this clone. The amino acid sequence of the N-terminus of IVR was determined and an antiserum was prepared against a synthetic peptide representing amino acids residues 1-20 of IVR. Using this antiserum as well as our polyclonal antiserum to IVR a new clone NC-330 was isolated using lamba-ZAP library. This NC-330 clone has an insert of about 1 kB with an open reading frame of 596 bp. This clone had 86.6% homology with the first 15 amino acids of the N-terminal part of IVR and 61.6% homology with the first 23 amino acids of IVR. In the QIA expression system and western blotting of the expressed protein, a clear band of about 21 kD was obtained with IVR antiserum. This clone was used for transformation of Samsun tobacco plants and we have presently plantlets which were rooted on medium containing kanamycin. Hybridization with this clone was also obtained with RNA from induced resistant tissue of Samsun NN but not with RNA from healthy control tissue of Samsun NN, or infected or healthy tissue of Samsun. This further strengthens the previous data that the NC 330 clone codes for IVR. In the U.S. it was shown that IVR is induced in plants containing the N' gene when infected with mutants of TMV that elicit the HR. This is a defined system in which the elicitor is known to be due to permutations of the coat protein which can vary in elicitor strength. The objective was to understand how IVR synthesis is induced after recognition of elicitor coat protein in the signal transduction pathway that leads to HR. We developed systems to manipulate induction of IVR by modifying the elicitor and are using these elicitor molecules to isolate the corresponding plant receptor molecules. A "far-western" procedure was developed that found a protein from N' plants that specifically bind to elicitor coat proteins. This protein is being purified and sequenced. This objective has not been completed and is still in progress. We have reported that localization of TMV in tobacco cultivars with the N gene, is associated with a 23 K protein (IVR) that inhibited replication of several plant viruses. This protein was also found in induced resistant tissue of Nicotiana glutinosa x Nicotiana debneyi.
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Lapidot, Moshe, and Vitaly Citovsky. molecular mechanism for the Tomato yellow leaf curl virus resistance at the ty-5 locus. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7604274.bard.

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Tomato yellow leaf curl virus (TYLCV) is a major pathogen of tomato that causes extensive crop loss worldwide, including the US and Israel. Genetic resistance in the host plant is considered highly effective in the defense against viral infection in the field. Thus, the best way to reduce yield losses due to TYLCV is by breeding tomatoes resistant or tolerant to the virus. To date, only six major TYLCV-resistance loci, termed Ty-1 to Ty-6, have been characterized and mapped to the tomato genome. Among tomato TYLCV-resistant lines containing these loci, we have identified a major recessive quantitative trait locus (QTL) that was mapped to chromosome 4 and designated ty-5. Recently, we identified the gene responsible for the TYLCV resistance at the ty-5 locus as the tomato homolog of the gene encoding messenger RNA surveillance factor Pelota (Pelo). A single amino acid change in the protein is responsible for the resistant phenotype. Pelo is known to participate in the ribosome-recycling phase of protein biosynthesis. Our hypothesis was that the resistant allele of Pelo is a “loss-of-function” mutant, and inhibits or slows-down ribosome recycling. This will negatively affect viral (as well as host-plant) protein synthesis, which may result in slower infection progression. Hence we have proposed the following research objectives: Aim 1: The effect of Pelota on translation of TYLCV proteins: The goal of this objective is to test the effect Pelota may or may not have upon translation of TYLCV proteins following infection of a resistant host. Aim 2: Identify and characterize Pelota cellular localization and interaction with TYLCV proteins: The goal of this objective is to characterize the cellular localization of both Pelota alleles, the TYLCV-resistant and the susceptible allele, to see whether this localization changes following TYLCV infection, and to find out which TYLCV protein interacts with Pelota. Our results demonstrate that upon TYLCV-infection the resistant allele of pelota has a negative effect on viral replication and RNA transcription. It is also shown that pelota interacts with the viral C1 protein, which is the only viral protein essential for TYLCV replication. Following subcellular localization of C1 and Pelota it was found that both protein localize to the same subcellular compartments. This research is innovative and potentially transformative because the role of Peloin plant virus resistance is novel, and understanding its mechanism will lay the foundation for designing new antiviral protection strategies that target translation of viral proteins. BARD Report - Project 4953 Page 2
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