Relevant bibliographies by topics / RNA Syntheis

Academic literature on the topic 'RNA Syntheis'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "RNA Syntheis"

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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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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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Harold, Cecelia M., Amber F. Buhagiar, Yan Cheng, and Susan J. Baserga. "Ribosomal RNA Transcription Regulation in Breast Cancer." Genes 12, no. 4 (March 29, 2021): 502. http://dx.doi.org/10.3390/genes12040502.

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Ribosome biogenesis is a complex process that is responsible for the formation of ribosomes and ultimately global protein synthesis. The first step in this process is the synthesis of the ribosomal RNA in the nucleolus, transcribed by RNA Polymerase I. Historically, abnormal nucleolar structure is indicative of poor cancer prognoses. In recent years, it has been shown that ribosome biogenesis, and rDNA transcription in particular, is dysregulated in cancer cells. Coupled with advancements in screening technology that allowed for the discovery of novel drugs targeting RNA Polymerase I, this transcriptional machinery is an increasingly viable target for cancer therapies. In this review, we discuss ribosome biogenesis in breast cancer and the different cellular pathways involved. Moreover, we discuss current therapeutics that have been found to affect rDNA transcription and more novel drugs that target rDNA transcription machinery as a promising avenue for breast cancer treatment.
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Harrington, C. A., and D. M. Chikaraishi. "Transcription of spacer sequences flanking the rat 45S ribosomal DNA gene." Molecular and Cellular Biology 7, no. 1 (January 1987): 314–25. http://dx.doi.org/10.1128/mcb.7.1.314-325.1987.

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The transcriptional activity of spacer sequences flanking the rat 45S ribosomal DNA (rDNA) gene were studied. Nascent RNA labeled in in vitro nuclear run-on reactions hybridized with both 5' and 3' spacer regions. The highest level of hybridization was seen with an rDNA fragment containing tandem repeats of a 130-base-pair sequence upstream of the 45S rRNA initiation site. Synthesis of RNA transcripts homologous to this internally repetitious spacer region was insensitive to high levels of alpha-amanitin, suggesting that it is mediated by RNA polymerase I. Analysis of steady-state RNA showed that these transcripts were present at extremely low levels in vivo relative to precursor rRNA transcripts. In contrast, precursor and spacer run-on RNAs were synthesized at similar levels. This suggests that spacer transcripts are highly unstable in vivo; therefore, it may be the process of transcription rather than the presence of spacer transcripts that is functionally important. Transcription in this upstream rDNA region may be involved in regulation of 45S rRNA synthesis in rodents, as has been suggested previously for frog rRNA. In addition, the presence of transcriptional activity in other regions of the spacer suggests that some polymerase I molecules may transcribe through the spacer from one 45S gene to the next on rodent rDNA.
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Harrington, C. A., and D. M. Chikaraishi. "Transcription of spacer sequences flanking the rat 45S ribosomal DNA gene." Molecular and Cellular Biology 7, no. 1 (January 1987): 314–25. http://dx.doi.org/10.1128/mcb.7.1.314.

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The transcriptional activity of spacer sequences flanking the rat 45S ribosomal DNA (rDNA) gene were studied. Nascent RNA labeled in in vitro nuclear run-on reactions hybridized with both 5' and 3' spacer regions. The highest level of hybridization was seen with an rDNA fragment containing tandem repeats of a 130-base-pair sequence upstream of the 45S rRNA initiation site. Synthesis of RNA transcripts homologous to this internally repetitious spacer region was insensitive to high levels of alpha-amanitin, suggesting that it is mediated by RNA polymerase I. Analysis of steady-state RNA showed that these transcripts were present at extremely low levels in vivo relative to precursor rRNA transcripts. In contrast, precursor and spacer run-on RNAs were synthesized at similar levels. This suggests that spacer transcripts are highly unstable in vivo; therefore, it may be the process of transcription rather than the presence of spacer transcripts that is functionally important. Transcription in this upstream rDNA region may be involved in regulation of 45S rRNA synthesis in rodents, as has been suggested previously for frog rRNA. In addition, the presence of transcriptional activity in other regions of the spacer suggests that some polymerase I molecules may transcribe through the spacer from one 45S gene to the next on rodent rDNA.
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Tian, Q., G. S. Kopf, R. S. Brown, and H. Tseng. "Function of basonuclin in increasing transcription of the ribosomal RNA genes during mouse oogenesis." Development 128, no. 3 (February 1, 2001): 407–16. http://dx.doi.org/10.1242/dev.128.3.407.

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Active protein synthesis during early oogenesis requires accelerated transcription of ribosomal RNA genes (rDNAs). In response to this demand, rDNAs are amplified more than 1000-fold early in Xenopus oogenesis. Here, we report evidence that rDNA is not amplified in mouse oocytes, but these cells may instead employ the zinc-finger protein basonuclin, a putative rDNA transcription factor, to enhance rRNA synthesis. This conclusion is based on observations that basonuclin is localized in the nucleolus in the mouse oocyte early in its growth phase, when rRNA transcription is highly active; and that the binding sites of basonuclin zinc fingers on the human and mouse rDNA promoters are homologous. In a co-transfection assay, basonuclin can elevate transcription from an rDNA promoter, and its zinc-finger domain can inhibit RNA polymerase I transcription, as detected by a run-on assay, in growing mouse oocytes.
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Bednarska, Elżbieta. "Ultrastructural and metabolic transformations of differentiating Hyacinthus orientalis L, pollen grain cells. I. RNA and protein synthesis." Acta Societatis Botanicorum Poloniae 53, no. 2 (2014): 145–58. http://dx.doi.org/10.5586/asbp.1984.014.

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RNA and protein synthesis were investigated in generative and vegetative cells during maturation of pollen grains. The rate of RNA and protein synthesis was analysed in reference to the successive interphase periods of the life cycle of pollen cells as well as against the background of the growth dynamics of the cell volume. The results of studies demonstrated that the pollen grain increases in size owing to the growth of the vegetative cell. The generative one does not grow. RNA synthesis and that of proteins in differentiating pollen cells has a different course. In the growing vegetative cell it lasts longer and is more intensive than in the generative cell which does not grow. RNA and protein synthesis in the vegetative cell take place in the period from the callose stage to the stage of lemon-shaped generative cell, that is in the period of phases G<sub>1</sub>, S and G<sub>2</sub>. This synthesis is positively correlated with the growth of the pollen grain. RNA and protein synthesis in the generative cell comprises the period from the callose-less lenticular stage to the stage of spherical generative cell, that is the phases S and early phase G<sub>2</sub>. These results suggest that in the vegetative cell RNA and protein synthesis is utilised above all to increase of its cell, instead in non growing generative cell protein synthese is probably limited mostly to a histones and enzymatic proteins serving for the DNA replication process.
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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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Izumikawa, Keiichi, Hideaki Ishikawa, Harunori Yoshikawa, Sally Fujiyama, Akira Watanabe, Hiroyuki Aburatani, Hiroyuki Tachikawa, et al. "LYAR potentiates rRNA synthesis by recruiting BRD2/4 and the MYST-type acetyltransferase KAT7 to rDNA." Nucleic Acids Research 47, no. 19 (September 2, 2019): 10357–72. http://dx.doi.org/10.1093/nar/gkz747.

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Abstract Activation of ribosomal RNA (rRNA) synthesis is pivotal during cell growth and proliferation, but its aberrant upregulation may promote tumorigenesis. Here, we demonstrate that the candidate oncoprotein, LYAR, enhances ribosomal DNA (rDNA) transcription. Our data reveal that LYAR binds the histone-associated protein BRD2 without involvement of acetyl-lysine–binding bromodomains and recruits BRD2 to the rDNA promoter and transcribed regions via association with upstream binding factor. We show that BRD2 is required for the recruitment of the MYST-type acetyltransferase KAT7 to rDNA loci, resulting in enhanced local acetylation of histone H4. In addition, LYAR binds a complex of BRD4 and KAT7, which is then recruited to rDNA independently of the BRD2-KAT7 complex to accelerate the local acetylation of both H4 and H3. BRD2 also helps recruit BRD4 to rDNA. By contrast, LYAR has no effect on rDNA methylation or the binding of RNA polymerase I subunits to rDNA. These data suggest that LYAR promotes the association of the BRD2-KAT7 and BRD4-KAT7 complexes with transcription-competent rDNA loci but not to transcriptionally silent rDNA loci, thereby increasing rRNA synthesis by altering the local acetylation status of histone H3 and H4.
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Dissertations / Theses on the topic "RNA Syntheis"

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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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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.
Land and Food Systems, Faculty of
Graduate
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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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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.
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.
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.
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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Brown, Michael Dean. "Genetic analysis of RNA splicing in the thymidylate synthase gene of bacteriophage T4." Diss., Georgia Institute of Technology, 1990. http://hdl.handle.net/1853/25390.

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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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9

Finnegan, Patrick Michael. "RNA synthesis in maize mitochondria : the identification of autonomously replicating RNA species and a kinetic analysis of transcript accumulation." Thesis, McGill University, 1989. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=75931.

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Transcription in mammalian and yeast mitochondria proceeds from a few well defined promoters, with processing of polycistronic transcripts producing the mature RNAs. The levels of different sequences in the steady-state RNA populations depend on differential promoter strengths, transcription attenuation and/or selective termination, and differential RNA stabilities. To gain insights into the processes governing transcription and RNA levels in plant mitochondria, a system using isolated maize mitochondria, which synthesize bona fide mitochondrial RNAs, was developed and partially characterized with respect to exogenous requirements and sensitivity to inhibitors of DNA-dependent RNA synthesis.
Although initiation and processing probably occur at reduced levels in isolated maize mitochondria, endogenous DNA templates are extensively transcribed at the same relative rates as in vivo. Isolated maize mitochondria were used to demonstrate that differential rates of both synthesis and turnover help determine the steady-state abundances of various mitochondrial RNA sequences and that mitochondria from certain lines possess an autonomously-replicating, RNA-based genetic system.
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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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Books on the topic "RNA Syntheis"

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

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Rabinovich, Peter M. Synthetic messenger RNA and cell metabolism modulation: Methods and protocols. New York: Humana Press, 2013.

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

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Rabinovich, Peter M., ed. Synthetic Messenger RNA and Cell Metabolism Modulation. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-260-5.

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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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1947-, Witkowski J. A., ed. The inside story: DNA to RNA to protein. Woodbury, N.Y: Cold Spring Harbor Laboratory Press, 2005.

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Ponchon, Luc. RNA scaffolds: Methods and protocols. New York: Humana Press, 2015.

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Book chapters on the topic "RNA Syntheis"

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Schächner, Christopher, Philipp E. Merkl, Michael Pilsl, Katrin Schwank, Kristin Hergert, Sebastian Kruse, Philipp Milkereit, Herbert Tschochner, and Joachim Griesenbeck. "Establishment and Maintenance of Open Ribosomal RNA Gene Chromatin States in Eukaryotes." In Ribosome Biogenesis, 25–38. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_2.

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AbstractIn growing eukaryotic cells, nuclear ribosomal (r)RNA synthesis by RNA polymerase (RNAP) I accounts for the vast majority of cellular transcription. This high output is achieved by the presence of multiple copies of rRNA genes in eukaryotic genomes transcribed at a high rate. In contrast to most of the other transcribed genomic loci, actively transcribed rRNA genes are largely devoid of nucleosomes adapting a characteristic “open” chromatin state, whereas a significant fraction of rRNA genes resides in a transcriptionally inactive nucleosomal “closed” chromatin state. Here, we review our current knowledge about the nature of open rRNA gene chromatin and discuss how this state may be established.
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Merkl, Philipp E., Christopher Schächner, Michael Pilsl, Katrin Schwank, Kristin Hergert, Gernot Längst, Philipp Milkereit, Joachim Griesenbeck, and Herbert Tschochner. "Analysis of Yeast RNAP I Transcription of Nucleosomal Templates In Vitro." In Ribosome Biogenesis, 39–59. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_3.

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AbstractNuclear eukaryotic RNA polymerases (RNAPs) transcribe a chromatin template in vivo. Since the basic unit of chromatin, the nucleosome, renders the DNA largely inaccessible, RNAPs have to overcome the nucleosomal barrier for efficient RNA synthesis. Gaining mechanistical insights in the transcription of chromatin templates will be essential to understand the complex process of eukaryotic gene expression. In this article we describe the use of defined in vitro transcription systems for comparative analysis of highly purified RNAPs I–III from S. cerevisiae (hereafter called yeast) transcribing in vitro reconstituted nucleosomal templates. We also provide a protocol to study promoter-dependent RNAP I transcription of purified native 35S ribosomal RNA (rRNA) gene chromatin.
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Liaqat, Anam, Maksim V. Sednev, and Claudia Höbartner. "In Vitro Selection of Deoxyribozymes for the Detection of RNA Modifications." In Ribosome Biogenesis, 167–79. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_10.

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AbstractDeoxyribozymes are artificially evolved DNA molecules with catalytic abilities. RNA-cleaving deoxyribozymes have been recognized as an efficient tool for detection of modifications in target RNAs and provide an alternative to traditional and modern methods for detection of ribose or nucleobase methylation. However, there are only few examples of DNA enzymes that specifically reveal the presence of a certain type of modification, including N6-methyladenosine, and the knowledge about how DNA enzymes recognize modified RNAs is still extremely limited. Therefore, DNA enzymes cannot be easily engineered for the analysis of desired RNA modifications, but are instead identified by in vitro selection from random DNA libraries using synthetic modified RNA substrates. This protocol describes a general in vitro selection stagtegy to evolve new RNA-cleaving DNA enzymes that can efficiently differentiate modified RNA substrates from their unmodified counterpart.
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Roberts-Galbraith, Rachel H. "RNAi Screening to Assess Tissue Regeneration in Planarians." In Methods in Molecular Biology, 509–27. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2172-1_27.

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AbstractOver the past several decades, planarians have emerged as a powerful model system with which to study the cellular and molecular basis of whole-body regeneration. The best studied planarians belong to freshwater flatworm species that maintain their remarkable regenerative capacity partly through the deployment of a population of adult pluripotent stem cells. Assessment of gene function in planarian regeneration has primarily been achieved through RNA interference (RNAi), either through the feeding or injection of double-stranded RNA (dsRNA). RNAi treatment of planarians has several advantages, including ease of use, which allows for medium-throughput screens of hundreds of genes over the course of a single project. Here, I present methods for dsRNA synthesis and RNAi feeding, as well as strategies for follow-up assessment of both structural and functional regeneration of organ systems of planarians, with a special emphasis on neural regeneration.
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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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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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Lee, Jaehyung, Andrew C. Keates, and Chiang J. Li. "Synthetic Biology and Bacteria-Based." In RNA Scaffolds, 267–80. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1499-0_19.

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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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Chan, Siu-Hong, and Bijoyita Roy. "Preparation of Synthetic mRNAs—Overview and Considerations." In RNA Technologies, 181–207. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-08415-7_9.

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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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Conference papers on the topic "RNA Syntheis"

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Saito, Hirohide, Ayako Yamada, Rei Ohmori, Yusho Kato, Toru Yamanaka, Kenichi Yoshikawa, and Tan Inoue. "Towards constructing synthetic cells: RNA/RNP evolution and cell-free translational systems in giant liposomes." In 2007 International Symposium on Micro-NanoMechatronics and Human Science. IEEE, 2007. http://dx.doi.org/10.1109/mhs.2007.4420868.

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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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Badelt, Stefan, Christoph Flamm, and Ivo Hofacker. "Computational Design of a Circular RNA with Prion-Like Behavior." In Artificial Life 14: International Conference on the Synthesis and Simulation of Living Systems. The MIT Press, 2014. http://dx.doi.org/10.7551/978-0-262-32621-6-ch091.

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Hlaing, Aye Mya, Win Pa Pa, and Ye Kyaw Thu. "Enhancing Myanmar Speech Synthesis with Linguistic Information and LSTM-RNN." In 10th ISCA Speech Synthesis Workshop. ISCA: ISCA, 2019. http://dx.doi.org/10.21437/ssw.2019-34.

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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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Rieder, Renate, Kathrin Lang, Barbara Puffer, Holger Moroder, Dagmar Graber, Ulrike Rieder, Jessica Steger, et al. "Chemical synthesis in RNA research: from riboswitch to ribosome function." In XIVth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2008. http://dx.doi.org/10.1135/css200810121.

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Dupouy, Christelle, Annabelle Biscans, Nicholas Ader, Georg Sczakiel, Jean-Jacques Vasseur, and Françoise Debart. "A straightforward synthesis of RNA prodrugs bearing biolabile pivaloyloxymethyl groups." In XVIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2014. http://dx.doi.org/10.1135/css201414133.

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Sekine, Mitsuo, Yoshiaki Masaki, Takeshi Yamada, Youdai Ishii, Keishi Yamamoto, Natsuki Okaniwa, Takeshi Kanamori, et al. "Synthesis and properties of base or sugar modified RNA derivatives." In XVIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2014. http://dx.doi.org/10.1135/css201414167.

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Reports on the topic "RNA Syntheis"

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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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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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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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Baudais, Virginie, Annelies Hickendorff, Jaïr van der Lijn, Igor Acko, Souleymane Maiga, and Hussein Yusuf Ali. EU Military Training Missions: A Synthesis Report. Stockholm International Peace Research Institute, May 2022. http://dx.doi.org/10.55163/lfle9658.

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This paper draws overarching conclusions based on a synthesis of previously published case studies that examined the impact of EU military training missions (EUTMs) in Somalia (EUTM Somalia, 2010–), Mali (EUTM Mali, 2013–), the Central African Republic (CAR) (EUTM RCA, 2016–). It concludes that EUTMs are relevant niche operations. Despite difficult circumstances beyond the control of the missions, EUTM training and advisory efforts have increased the effectiveness of partner armed forces. While these gains have been marginal in CAR and Somalia, they have been a bit more pronounced in Mali. Yet, broader security sector reform and defence sector reform efforts to improve the accountability and governance of defence and security sectors have become bogged down. The main challenge is that EUTMs are generally mandated to implement largely technical and tactical agendas in contexts where the ongoing armed conflict and the politics of the security sector are not conducive to building professional national security forces. As a consequence EUTMs find themselves caught up in interlinked and partially overlapping dilemmas. This study concludes with seven partly overlapping recommendations to EU member states and to EUTMs to address the main limitations that are restricting the impact of the missions.
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Granot, David, Scott Holaday, and Randy D. Allen. Enhancing Cotton Fiber Elongation and Cellulose Synthesis by Manipulating Fructokinase Activity. United States Department of Agriculture, 2008. http://dx.doi.org/10.32747/2008.7613878.bard.

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a. Objectives (a) Identification and characterization of the cotton fiber FRKs; (b) Generating transgenic cotton plants overproducing either substrate inhibited tomato FRK or tomato FRK without substrate inhibition; (c) Generating transgenic cotton plants with RNAi suppression of fiber expressed FRKs; (d) Generating Arabidopsis plants that over express FRK1, FRK2, or both genes, as additional means to assess the contribution of FRK to cellulose synthesis and biomass production. b. Background to the topic: Cellulose synthesis and fiber elongation are dependent on sugar metabolism. Previous results suggested that FRKs (fructokinase enzymes that specifically phosphorylate fructose) are major players in sugar metabolism and cellulose synthesis. We therefore hypothesized that increasing fructose phosphorylation may enhance fiber elongation and cellulose synthesis in cotton plants. Accordinlgy, the objectives of this research were: c. Major conclusions and achievements: Two cotton FRKs expressed in fibers, GhFRK2 and GhFRK3, were cloned and characterized. We found that GhFRK2 enzyme is located in the cytosol and GhFRK3 is located within plastids. Both enzymes enable growth on fructose (but not on glucose) of hexose kinase deficient yeast strain, confirming the fructokinase activity of the cloned genes. RNAi constructs with each gene were prepared and sent to the US collaborator to generate cotton plants with RNAi suppression of these genes. To examine the effect of FRKs using Arabidopsis plants we generated transgenic plants expressing either LeFRK1 or LeFRK2 at high level. No visible phenotype has been observed. Yet, plants expressing both genes simultaneously are being created and will be tested. To test our hypothesis that increasing fructose phosphorylation may enhance fiber cellulose synthesis, we generated twenty independent transgenic cotton plant lines overexpressing Lycopersicon (Le) FRK1. Transgene expression was high in leaves and moderate in developing fiber, but enhanced FRK activity in fibers was inconsistent between experiments. Some lines exhibited a 9-11% enhancement of fiber length or strength, but only one line tested had consistent improvement in fiber strength that correlated with elevated FRK activity in the fibers. However, in one experiment, seed cotton mass was improved in all transgenic lines and correlated with enhanced FRK activity in fibers. When greenhouse plants were subjected to severe drought during flowering and boll development, no genotypic differences in fiber quality were noted. Seed cotton mass was improved for two transgenic lines but did not correlate with fiber FRK activity. We conclude that LeFRK1 over-expression in fibers has only a small effect on fiber quality, and any positive effects depend on optimum conditions. The improvement in productivity for greenhouse plants may have been due to better structural development of the water-conducting tissue (xylem) of the stem, since stem diameters were larger for some lines and the activity of FRK in the outer xylem greater than observed for wild-type plants. We are testing this idea and developing other transgenic cotton plants to understand the roles of FRK in fiber and xylem development. We see the potential to develop a cotton plant with improved stem strength and productivity under drought for windy, semi-arid regions where cotton is grown. d. Implications, scientific and agricultural: FRKs are probably bottle neck enzymes for biomass and wood synthesis and their increased expression has the potential to enhance wood and biomass production, not only in cotton plants but also in other feed and energy renewable plants.
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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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Sharon, Amir, and Maor Bar-Peled. Identification of new glycan metabolic pathways in the fungal pathogen Botrytis cinerea and their role in fungus-plant interactions. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7597916.bard.

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The involvement of glycans in microbial adherence, recognition and signaling is often a critical determinant of pathogenesis. Although the major glycan components of fungal cell walls have been identified there is limited information available on its ‘minor sugar components’ and how these change during different stages of fungal development. Our aim was to define the role of Rhacontaining-glycans in the gray mold disease caused by the necrotrophic fungus B. cinerea. The research was built on the discovery of two genes, Bcdhand bcer, that are involved in formation of UDP-KDG and UDP-Rha, two UDP- sugars that may serve as donors for the synthesis of cell surface glycans. Objectives of the proposed research included: 1) To determine the function of B. cinereaBcDh and BcEr in glycan biosynthesis and in pathogenesis, 2) To determine the expression pattern of BcDH and BcERand cellular localization of their encoded proteins, 3) Characterize the structure and distribution of Rha- containing glycans, 4) Characterization of the UDP-sugar enzymes and potential of GTs involved in glycanrhamnosylation. To address these objectives we generated a series of B. cinereamutants with modifications in the bchdhand bcergenes and the phenotype and sugar metabolism in the resulting strains were characterized. Analysis of sugar metabolites showed that changes in the genes caused changes in primary and secondary sugars, including abolishment of rhamnose, however abolishment of rhamnose synthesis did not cause changes in the fungal phenotype. In contrast, we found that deletion of the second gene, bcer, leads to accumulation of the intermediate sugar – UDP- KDG, and that such mutants suffer from a range of defects including reduced virulence. Further analyses confirmed that UDP-KDG is toxic to the fungus. Studies on mode of action suggested that UDP-KDG might affect integrity of the fungal cell wall, possibly by inhibiting UDP-sugars metabolic enzymes. Our results confirm that bcdhand bcerrepresent a single pathway of rhamnose synthesis in B. cinerea, that rhamnose does not affect in vitro development or virulence of the fungus. We also concluded that UDP-KDG is toxic to B. cinereaand hence UDP-KDG or compounds that inhibit Er enzymes and lead to accumulation of UDP-KDG might have antifungal activity. This toxicity is likely the case with other fungi, this became apparent in a collaborative work with Prof. Bart Thomma of Wageningen University, NETHERLANDS . We have shown the deletion of ER mutant in Verticillium dahlia gave plants resistance to the fungal infection.
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