Relevant bibliographies by topics / MRNA

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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 'MRNA'

Author: Grafiati
Published: 4 June 2021
Last updated: 22 February 2025

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Journal articles on the topic "MRNA"

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Chiang, Chiayn, Guang-Wu Chen, and Shin-Ru Shih. "Mutations at Alternative 5′ Splice Sites of M1 mRNA Negatively Affect Influenza A Virus Viability and Growth Rate." Journal of Virology 82, no. 21 (September 3, 2008): 10873–86. http://dx.doi.org/10.1128/jvi.00506-08.

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ABSTRACT Different amino acid sequences of influenza virus proteins contribute to different viral phenotypes. However, the diversity of the sequences and its impact on noncoding regions or splice sites have not been intensively studied. This study focuses on the sequences at alternative 5′ splice sites on M1 mRNA. Six different mutations at the splice sites were introduced, and viral growth characteristics for those mutants generated by reverse genetics with 12 plasmids were examined, for which G12C (the G-to-C mutation at the first nucleotide of the intron for the mRNA3 5′ splice site), C51G (at the 3′ end of the exon of the M2 mRNA 5′ splice site), and G146C (for the first nucleotide of the intron for mRNA4) are lethal mutations. On the other hand, mutants with the mutation G11C (at the 3′ end of exon of the mRNA3 5′ splice site), G52C (for the first nucleotide of the intron for M2 mRNA), or G145A (at the 3′ end of the exon of mRNA4) were rescued, although they had significantly attenuated growth rates. Notably, these mutations did not change any amino acids in M1 or M2 proteins. The levels of precursor (M1 mRNA) and spliced products (M2 mRNA, mRNA3, and mRNA4) from the recombinant mutant virus-infected cells were further analyzed. The production levels of mRNA3 in cells infected with G11C, G52C, and G145A mutant viruses were reduced in comparison with that in wild-type recombinant virus-infected ones. More M2 mRNA was produced in G11C mutant virus-infected cells than in wild-type-virus-infected cells, and there was little M2 mRNA and none at all in G145A and G52C mutant virus-infected ones, respectively. Results obtained here suggest that introducing these mutations into the alternative 5′ splice sites disturbed M1 mRNA splicing, which may attenuate viral growth rates.
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Jackson, David, and Robert A. Lamb. "The influenza A virus spliced messenger RNA M mRNA3 is not required for viral replication in tissue culture." Journal of General Virology 89, no. 12 (December 1, 2008): 3097–101. http://dx.doi.org/10.1099/vir.0.2008/004739-0.

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Influenza A virus genome RNA segment 7 encodes three known mRNAs, two of which, M2 mRNA and M mRNA3, are derived by alternative splicing of the primary collinear mRNA transcript using alternative 5′ splice sites. The function of M mRNA3 is currently unknown, therefore we attempted to determine whether it is essential for virus replication. Recombinant viruses unable to produce M mRNA3 and/or M2 mRNA were created by mutating the shared 3′ splice site. Growth of the mutant viruses in M2-expressing MDCK cells was not significantly affected by the lack of M mRNA3. During the course of a wild-type virus infection, levels of M mRNA3 began to decrease while those of M2 mRNA increased, which may indicate a potential mechanism of alternative splicing control. These data suggest that neither M mRNA3 nor any potential protein product are essential for influenza virus replication in tissue culture.
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Ruepp, Marc-David, Chiara Aringhieri, Silvia Vivarelli, Stefano Cardinale, Simona Paro, Daniel Schümperli, and Silvia M. L. Barabino. "Mammalian pre-mRNA 3′ End Processing Factor CF Im68 Functions in mRNA Export." Molecular Biology of the Cell 20, no. 24 (December 15, 2009): 5211–23. http://dx.doi.org/10.1091/mbc.e09-05-0389.

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Export of mRNA from the nucleus is linked to proper processing and packaging into ribonucleoprotein complexes. Although several observations indicate a coupling between mRNA 3′ end formation and export, it is not known how these two processes are mechanistically connected. Here, we show that a subunit of the mammalian pre-mRNA 3′ end processing complex, CF Im68, stimulates mRNA export. CF Im68 shuttles between the nucleus and the cytoplasm in a transcription-dependent manner and interacts with the mRNA export receptor NXF1/TAP. Consistent with the idea that CF Im68 may act as a novel adaptor for NXF1/TAP, we show that CF Im68 promotes the export of a reporter mRNA as well as of endogenous mRNAs, whereas silencing by RNAi results in the accumulation of mRNAs in the nucleus. Moreover, CF Im68 associates with 80S ribosomes but not polysomes, suggesting that it is part of the mRNP that is remodeled in the cytoplasm during the initial stages of translation. These results reveal a novel function for the pre-mRNA 3′ end processing factor CF Im68 in mRNA export.
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Noble, Scott L., Brittany L. Allen, Lai Kuan Goh, Kristen Nordick, and Thomas C. Evans. "Maternal mRNAs are regulated by diverse P body–related mRNP granules during early Caenorhabditis elegans development." Journal of Cell Biology 182, no. 3 (August 11, 2008): 559–72. http://dx.doi.org/10.1083/jcb.200802128.

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Processing bodies (P bodies) are conserved mRNA–protein (mRNP) granules that are thought to be cytoplasmic centers for mRNA repression and degradation. However, their specific functions in vivo remain poorly understood. We find that repressed maternal mRNAs and their regulators localize to P body–like mRNP granules in the Caenorhabditis elegans germ line. Surprisingly, several distinct types of regulated granules form during oocyte and embryo development. 3′ untranslated region elements direct mRNA targeting to one of these granule classes. The P body factor CAR-1/Rap55 promotes association of repressed mRNA with granules and contributes to repression of Notch/glp-1 mRNA. However, CAR-1 controls Notch/glp-1 only during late oogenesis, where it functions with the RNA-binding regulators PUF-5, PUF-6, and PUF-7. The P body protein CGH-1/Rck/Dhh1 differs from CAR-1 in control of granule morphology and promotes mRNP stability in arrested oocytes. Therefore, a system of diverse and regulated RNP granules elicits stage-specific functions that ensure proper mRNA control during early development.
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Yu, Jia, and J. Eric Russell. "Structural and Functional Analysis of an mRNP Complex That Mediates the High Stability of Human β-Globin mRNA." Molecular and Cellular Biology 21, no. 17 (September 1, 2001): 5879–88. http://dx.doi.org/10.1128/mcb.21.17.5879-5888.2001.

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ABSTRACT Human globins are encoded by mRNAs exhibiting high stabilities in transcriptionally silenced erythrocyte progenitors. Unlike α-globin mRNA, whose stability is enhanced by assembly of a specific messenger RNP (mRNP) α complex on its 3′ untranslated region (UTR), neither the structure(s) nor the mechanism(s) that effects the high-level stability of human β-globin mRNA has been identified. The present work describes an mRNP complex assembling on the 3′ UTR of the β-globin mRNA that exhibits many of the properties of the stability-enhancing α complex. The β-globin mRNP complex is shown to contain one or more factors homologous to αCP, a 39-kDa RNA-binding protein that is integral to α-complex assembly. Sequence analysis implicates a specific 14-nucleotide pyrimidine-rich track within its 3′ UTR as the site of β-globin mRNP assembly. The importance of this track to mRNA stability is subsequently verified in vivo using mice expressing human β-globin transgenes that contain informative mutations in this region. In combination, the in vitro and in vivo analyses indicate that the high stabilities of the α- and β-globin mRNAs are maintained through related mRNP complexes that may share a common regulatory pathway.
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Robb, Nicole C., and Ervin Fodor. "The accumulation of influenza A virus segment 7 spliced mRNAs is regulated by the NS1 protein." Journal of General Virology 93, no. 1 (January 1, 2012): 113–18. http://dx.doi.org/10.1099/vir.0.035485-0.

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The influenza A virus M1 mRNA is alternatively spliced to produce M2 mRNA, mRNA3, and in some cases, M4 mRNA. Splicing of influenza mRNAs is carried out by the cellular splicing machinery and is thought to be regulated, as both spliced and unspliced mRNAs encode proteins. In this study, we used radioactively labelled primers to investigate the accumulation of spliced and unspliced M segment mRNAs in viral infection and ribonucleoprotein (RNP) reconstitution assays in which only the minimal components required for transcription and replication to occur were expressed. We found that co-expression of the viral NS1 protein in an RNP reconstitution assay altered the accumulation of spliced mRNAs compared with when it was absent, and that this activity was dependent on the RNA-binding ability of NS1. These findings suggest that the NS1 protein plays a role in the regulation of splicing of influenza virus M1 mRNA.
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Schmidt, Edward E., Eric S. Hanson, and Mario R. Capecchi. "Sequence-Independent Assembly of Spermatid mRNAs into Messenger Ribonucleoprotein Particles." Molecular and Cellular Biology 19, no. 5 (May 1, 1999): 3904–15. http://dx.doi.org/10.1128/mcb.19.5.3904.

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ABSTRACT During mammalian spermatogenesis, meiosis is followed by a brief period of high transcriptional activity. At this time a large amount of mRNA is stored as messenger ribonucleoprotein (mRNP) particles. All subsequent processes of sperm maturation occur in the complete absence of transcription, primarily using proteins which are newly synthesized from these stored mRNAs. By expressing transgene mRNAs in the early haploid spermatids of mice, we have investigated the sequence requirements for determining whether specific mRNAs in these cells will be stored as mRNP particles or be assembled into polysomes. The results suggest that mRNAs which are transcribed in spermatids are assembled into mRNP particles by a mechanism that acts independently of mRNA sequence. Our findings reveal a fundamental similarity between the mechanisms of translational control used in spermatogenesis and oogenesis.
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Kleene, Kenneth C., and Danielle L. Cullinane. "Maybe repressed mRNAs are not stored in the chromatoid body in mammalian spermatids." REPRODUCTION 142, no. 3 (September 2011): 383–88. http://dx.doi.org/10.1530/rep-11-0113.

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The chromatoid body is a dynamic organelle that is thought to coordinate the cytoplasmic regulation of mRNA translation and degradation in mammalian spermatids. The chromatoid body is also postulated to function in repression of mRNA translation by sequestering dormant mRNAs where they are inaccessible to the translational apparatus. This review finds no convincing evidence that dormant mRNAs are localized exclusively in the chromatoid body. This discrepancy can be explained by two hypotheses. First, experimental artifacts, possibly related to peculiarities of the structure and function of the chromatoid body, preclude obtaining an accurate indication of mRNA localization. Second, mRNA is not stored in the chromatoid body, because, like perinuclear P granules in Caenorhabditis elegans, the chromatoid body functions as a center for mRNP remodeling and export to other cytoplasmic sites.
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Mili, Stavroula, Hong Jun Shu, Yingming Zhao, and Serafı́n Piñol-Roma. "Distinct RNP Complexes of Shuttling hnRNP Proteins with Pre-mRNA and mRNA: Candidate Intermediates in Formation and Export of mRNA." Molecular and Cellular Biology 21, no. 21 (November 1, 2001): 7307–19. http://dx.doi.org/10.1128/mcb.21.21.7307-7319.2001.

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ABSTRACT Nascent pre-mRNAs associate with hnRNP proteins in hnRNP complexes, the natural substrates for mRNA processing. Several lines of evidence indicate that hnRNP complexes undergo substantial remodeling during mRNA formation and export. Here we report the isolation of three distinct types of pre-mRNP and mRNP complexes from HeLa cells associated with hnRNP A1, a shuttling hnRNP protein. Based on their RNA and protein compositions, these complexes are likely to represent distinct stages in the nucleocytoplasmic shuttling pathway of hnRNP A1 with its bound RNAs. In the cytoplasm, A1 is associated with its nuclear import receptor (transportin), the cytoplasmic poly(A)-binding protein, and mRNA. In the nucleus, A1 is found in two distinct types of complexes that are differently associated with nuclear structures. One class contains pre-mRNA and mRNA and is identical to previously described hnRNP complexes. The other class behaves as freely diffusible nuclear mRNPs (nmRNPs) at late nuclear stages of maturation and possibly associated with nuclear mRNA export. These nmRNPs differ from hnRNPs in that while they contain shuttling hnRNP proteins, the mRNA export factor REF, and mRNA, they do not contain nonshuttling hnRNP proteins or pre-mRNA. Importantly, nmRNPs also contain proteins not found in hnRNP complexes. These include the alternatively spliced isoforms D01 and D02 of the hnRNP D proteins, the E0 isoform of the hnRNP E proteins, and LRP130, a previously reported protein with unknown function that appears to have a novel type of RNA-binding domain. The characteristics of these complexes indicate that they result from RNP remodeling associated with mRNA maturation and delineate specific changes in RNP protein composition during formation and transport of mRNA in vivo.
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Yang, Feng, Yong Peng, Elizabeth L. Murray, Yuichi Otsuka, Nancy Kedersha, and Daniel R. Schoenberg. "Polysome-Bound Endonuclease PMR1 Is Targeted to Stress Granules via Stress-Specific Binding to TIA-1." Molecular and Cellular Biology 26, no. 23 (September 18, 2006): 8803–13. http://dx.doi.org/10.1128/mcb.00090-06.

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ABSTRACT The generalized process of mRNA decay involves deadenylation followed by release from translating polysomes, decapping, and exonuclease decay of the mRNA body. In contrast the mRNA endonuclease PMR1 forms a selective complex with its translating substrate mRNA, where it initiates decay by cleaving within the mRNA body. In stressed cells the phosphorylation of the α subunit of eukaryotic initiation factor 2 causes translating mRNAs to accumulate with stalled 48S subunits in large subcellular structures termed stress granules (SGs), wherein mRNAs undergo sorting for reinitiation, storage, or decay. Given the unique relationship between translation and PMR1-mediated mRNA decay, we examined the impact of stress-induced dissociation of polysomes on this process. Arsenite stress disrupts the polysome binding of PMR1 and its substrate mRNA but has no impact on the critical tyrosine phosphorylation of PMR1, its association with substrate mRNA, or its association with the functional ∼680-kDa mRNP complex in which it normally resides on polysomes. We show that arsenite stress drives PMR1 into an RNase-resistant complex with TIA-1, and we identify a distinct domain in the N terminus of PMR1 that facilitates its interaction with TIA-1. Finally, we show that arsenite promotes the delayed association of PMR1 with SGs under conditions which cause tristetraprolin and butyrate response factor 1, proteins that facilitate exonucleolytic mRNA, to exit SGs.
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Dissertations / Theses on the topic "MRNA"

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Brogna, Saverio. "Nonsense-mediated mRNA reduction and pre-mRNA processing in Drosophila." Thesis, Open University, 2000. http://oro.open.ac.uk/54807/.

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Zhou, Yang. "Regulation of pre-mRNA splicing and mRNA degradation in Saccharomyces cerevisiae." Doctoral thesis, Umeå universitet, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet), 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-138142.

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Messenger RNAs are transcribed and co-transcriptionally processed in the nucleus, and transported to the cytoplasm. In the cytoplasm, mRNAs serve as the template for protein synthesis and are eventually degraded. The removal of intron sequences from a precursor mRNA is termed splicing and is carried out by the dynamic spliceosome. In this thesis, I describe the regulated splicing of two transcripts in Saccharomyces cerevisiae. I also describe a study where the mechanisms that control the expression of magnesium transporters are elucidated. The pre-mRNA retention and splicing (RES) complex is a spliceosome-associated protein complex that promotes the splicing and nuclear retention of a subset of pre-mRNAs. The RES complex consists of three subunits, Bud13p, Snu17p and Pml1p. We show that the lack of RES factors causes a decrease in the formation of N4-acetylcytidine (ac4C) in tRNAs. This phenotype is caused by inefficient splicing of the pre-mRNA of the TAN1 gene, which is required for the formation of ac4C in tRNAs. The RES mutants also show growth defects that are exacerbated at elevated temperatures. We show that the temperature sensitive phenotype of the bud13Δ and snu17Δ cells is caused by the inefficient splicing of the MED20 pre-mRNA. The MED20 gene encodes a subunit of the Mediator complex. Unspliced pre-mRNAs that enter the cytoplasm are usually degraded by the nonsense-mediated mRNA decay (NMD) pathway, which targets transcripts that contain premature translation termination codons. Consistent with the nuclear retention function of the RES complex, we find that NMD inactivation in the RES mutants leads to the accumulation of both TAN1 and MED20 pre-mRNAs. We also show that the cis-acting elements that promote RES-dependent splicing are different between the TAN1 and MED20 pre-mRNAs. The NMD pathway also targets transcripts with upstream ORFs (uORFs) for degradation. The ALR1 gene encodes the major magnesium importer in yeast, and its expression is controlled by the NMD pathway via a uORF in the 5’ untranslated region. We show that the ribosome reaches the downstream main ORF by a translation reinitiation mechanism. The NMD pathway was shown to control cellular Mg2+ levels by regulating the expression of the ALR1 gene. We further show that the NMD pathway targets the transcripts of the vacuolar Mg2+ exporter Mnr2p and the mitochondrial Mg2+ exporter Mme1p for degradation. In summary, we conclude that the RES complex has a role in the splicing regulation of a subset of transcripts. We also suggest a regulatory role for the NMD pathway in maintaining the cellular Mg2+ concentration by controlling the expression of Mg2+ transporters.
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SPEDALIERI, Gaetana. "Translation of Leaderless mRNAs and Structure of cspD mRNA in E. coli." Doctoral thesis, Università degli Studi di Camerino, 2010. http://hdl.handle.net/11581/401866.

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Part I: Translation of leaderless mRNA in E. coli Spedalieri G., Kashrer C., RajBhandary U.L. Leaderless mRNAs are present in all three domains of life. They do not have a 5' untranslated region (5'UTR), they start directly with the initiation codon, AUG in most cases. In Escherichia coli these mRNAs are very rare and show inefficient translation. In contrast, leaderless mRNAs are quite prevalent in archaea, where they are translated as efficiently as the ''leadered'' mRNAs containing the typical Shine-Dalgarno sequence. In leaderless translation initiation 70S ribosomes are thought to be used without a typical pre-initiation complex involving a 30S ribosomal subunit. In this study, the goal is to answer two fundamental questions: (i) Is AUG strictly required as initiation codon? (ii) Is the formylmethionyl-tRNAfMet (fMet-tRNAfMet) required as initiator tRNA? Is the amino acid ''methionine'' important? Using a chloramphenicol acetyltransferase reporter system for studying in vivo translation of leaderless mRNAs in E. coli, we have found that the initiation codon AUG is not absolutely required and the amino acid ''methionine'' plays a fundamental role. Part II: Structural and functional characterization of cspD mRNA in Escherichia coli Gaetana Spedalieri, Anna Brandi and Anna Maria Giuliodori Expression of cspD, a gene belonging to the csp family of Escherichia coli, is exclusively induced at 37°C during stationary-phase or upon glucose starvation and does not increase during cold-shock. To shed light on the mechanisms responsible for the regulation of cspD expression, I have elucidated by enzymatic and chemical probing the secondary structure of cspD mRNA as a function of temperature. The structure, which was also validated by mutagenesis, demonstrates that cspD mRNA does not undergo any temperature-dependent structural rearrangement. Functional analyses suggest that the presence of a helix occluding the initiation codon might be partly responsible for the scarce translation of cspD mRNA and that RNase III is likely involved in the regulation of cspD gene expression. Overall, these data suggest that induction of cspD, like that of many other csp gene of E. coli, is controlled also at a posttranscriptional level.
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Ruscica, Vincenzo [Verfasser]. "GIGYF recruits mRNA decay factors to repress target mRNA expression / Vincenzo Ruscica." Tübingen : Universitätsbibliothek Tübingen, 2021. http://d-nb.info/1225740169/34.

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Deneke, Carlus. "Theory of mRNA degradation." Phd thesis, Universität Potsdam, 2012. http://opus.kobv.de/ubp/volltexte/2012/6199/.

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One of the central themes of biology is to understand how individual cells achieve a high fidelity in gene expression. Each cell needs to ensure accurate protein levels for its proper functioning and its capability to proliferate. Therefore, complex regulatory mechanisms have evolved in order to render the expression of each gene dependent on the expression level of (all) other genes. Regulation can occur at different stages within the framework of the central dogma of molecular biology. One very effective and relatively direct mechanism concerns the regulation of the stability of mRNAs. All organisms have evolved diverse and powerful mechanisms to achieve this. In order to better comprehend the regulation in living cells, biochemists have studied specific degradation mechanisms in detail. In addition to that, modern high-throughput techniques allow to obtain quantitative data on a global scale by parallel analysis of the decay patterns of many different mRNAs from different genes. In previous studies, the interpretation of these mRNA decay experiments relied on a simple theoretical description based on an exponential decay. However, this does not account for the complexity of the responsible mechanisms and, as a consequence, the exponential decay is often not in agreement with the experimental decay patterns. We have developed an improved and more general theory of mRNA degradation which provides a general framework of mRNA expression and allows describing specific degradation mechanisms. We have made an attempt to provide detailed models for the regulation in different organisms. In the yeast S. cerevisiae, different degradation pathways are known to compete and furthermore most of them rely on the biochemical modification of mRNA molecules. In bacteria such as E. coli, degradation proceeds primarily endonucleolytically, i.e. it is governed by the initial cleavage within the coding region. In addition, it is often coupled to the level of maturity and the size of the polysome of an mRNA. Both for S. cerevisiae and E. coli, our descriptions lead to a considerable improvement of the interpretation of experimental data. The general outcome is that the degradation of mRNA must be described by an age-dependent degradation rate, which can be interpreted as a consequence of molecular aging of mRNAs. Within our theory, we find adequate ways to address this much debated topic from a theoretical perspective. The improvements of the understanding of mRNA degradation can be readily applied to further comprehend the mRNA expression under different internal or environmental conditions such as after the induction of transcription or stress application. Also, the role of mRNA decay can be assessed in the context of translation and protein synthesis. The ultimate goal in understanding gene regulation mediated by mRNA stability will be to identify the relevance and biological function of different mechanisms. Once more quantitative data will become available, our description allows to elaborate the role of each mechanism by devising a suitable model.
Ein zentrales Ziel der modernen Biologie ist es, ein umfassendes Verständnis der Genexpression zu erlangen. Die fundamentalen Prozesse sind im zentralen Dogma der Genexpression zusammengefasst: Die genetische Information wird von DNA in Boten-RNAs (mRNA) transkribiert und im Prozess der Translation von mRNA in Proteine übersetzt. Zum Erhalt ihrer Funktionalität und der Möglichkeit von Wachstum und Fortpflanzung muss in jeder Zelle und für jedes Gen die optimale Proteinkonzentration akkurat eingestellt werden. Hierzu hat jeder Organismus detaillierte Regulationsmechanismen entwickelt. Regulation kann auf allen Stufen der Genexpression erfolgen, insbesondere liefert der Abbau der mRNA-Moleküle einen effizienten und direkten Kontrollmechanismus. Daher sind in allen Lebewesen spezifische Mechanismen - die Degradationsmechanismen - entstanden, welche aktiv den Abbau befördern. Um ein besseres Verständnis von den zugrunde liegenden Prozessen zu erlangen, untersuchen Biochemiker die Degradationsmechanismen im Detail. Gleichzeitig erlauben moderne molekularbiologische Verfahren die simultane Bestimmung der Zerfallskurven von mRNA für alle untersuchten Gene einer Zelle. Aus theoretischer Perspektive wird der Zerfall der mRNA-Menge als exponentieller Zerfall mit konstanter Rate betrachtet. Diese Betrachtung dient der Interpretation der zugrunde liegenden Experimente, berücksichtigt aber nicht die fundierten Kenntnisse über die molekularen Mechanismen der Degradation. Zudem zeigen viele experimentelle Studien ein deutliches Abweichen von einem exponentiellen Zerfall. In der vorliegenden Doktorarbeit wird daher eine erweiterte theoretische Beschreibung für die Expression von mRNA-Molekülen eingeführt. Insbesondere lag der Schwerpunkt auf einer verbesserten Beschreibung des Prozesses der Degradation. Die Genexpression kann als ein stochastischer Prozess aufgefasst werden, in dem alle Einzelprozesse auf zufällig ablaufenden chemischen Reaktionen basieren. Die Beschreibung erfolgt daher im Rahmen von Methoden der stochastischen Modellierung. Die fundamentale Annahme besteht darin, dass jedes mRNA-Molekül eine zufällige Lebenszeit hat und diese Lebenszeit für jedes Gen durch eine statistische Lebenszeitverteilung gegeben ist. Ziel ist es nun, spezifische Lebenszeitverteilungen basierend auf den molekularen Degradationsmechanismen zu finden. In dieser Arbeit wurden theoretische Modelle für die Degradation in zwei verschiedenen Organismen entwickelt. Zum einen ist bekannt, dass in eukaryotischen Zellen wie dem Hefepilz S. cerevisiae mehrere Mechanismen zum Abbau der mRNA-Moleküle in Konkurrenz zueinander stehen. Zudem ist der Abbau durch mehrere geschwindigkeitsbestimmende biochemische Schritte charakterisiert. In der vorliegenden Arbeit wurden diese Feststellungen durch ein theoretisches Modell beschrieben. Eine Markow-Kette stellte sich als sehr erfolgreich heraus, um diese Komplexität in eine mathematisch-fassbare Form abzubilden. Zum anderen wird in Kolibakterien die Degradation überwiegend durch einen initialen Schnitt in der kodierenden Sequenz der mRNA eingeleitet. Des Weiteren gibt es komplexe Wechselwirkungen mit dem Prozess der Translation. Die dafür verantwortlichen Enzyme - die Ribosomen - schützen Teile der mRNA und vermindern dadurch deren Zerfall. In der vorliegenden Arbeit wurden diese Zusammenhänge im Rahmen eines weiteren spezifischen, theoretischen Modells untersucht. Beide Mechanismen konnten an experimentellen Daten verifiziert werden. Unter anderem konnten dadurch die Interpretation der Zerfallsexperimente deutlich verbessert und fundamentale Eigenschaften der mRNA-Moleküle bestimmt werden. Ein Vorteil der statistischen Herangehensweise in dieser Arbeit liegt darin, dass theoretische Konzepte für das molekulare Altern der mRNAs entwickelt werden konnten. Mit Hilfe dieser neuentwickelten Methode konnte gezeigt werden, dass sich die Komplexität der Abbaumechanismen in einem Alterungsprozess manifestiert. Dieser kann mit der Lebenserwartung von einzelnen mRNA-Molekülen beschrieben werden. In dieser Doktorarbeit wurde eine verallgemeinerte theoretische Beschreibung des Abbaus von mRNAMolek ülen entwickelt. Die zentrale Idee basiert auf der Verknüpfung von experimentellen Zerfallsmessungen mit den biochemischen Mechanismen der Degradation. In zukünftigen experimentellen Untersuchungen können die entwickelten Verfahren angewandt werden, um eine genauere Interpretation der Befunde zu ermöglichen. Insbesondere zeigt die Arbeit auf, wie verschiedene Hypothesen über den Degradationsmechanismus anhand eines geeigneten mathematischen Modells durch quantitative Experimente verifiziert oder falsifiziert werden können.
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Cumberbatch, Marcus G. "mRNA export and cancer." Thesis, University of Sheffield, 2016. http://etheses.whiterose.ac.uk/13480/.

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Sadlon, Timothy John. "Regulation of the rat 5-aminolevulinate synthase mRNA : the role of mRNA stability /." Title page, contents and summary only, 1995. http://web4.library.adelaide.edu.au/theses/09PH/09phs126.pdf.

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Swisher, Kylie. "Assembly of mRNP Complexes During Stress and Nonsense-Mediated mRNA Decay Quality Control in Saccharomyces cerevisiae." Diss., The University of Arizona, 2011. http://hdl.handle.net/10150/204068.

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In eukaryotes, mRNA is in constant flux between an actively translating state and translationally repressed states. Specifically, mRNA degradation and repression factors compete with translation factors to direct mRNAs out of translation for storage or decay. This process often leads to formation of cytoplasmic aggregates. P-bodies are granules that contain mRNA and degradation factors, suggesting they are sites of mRNA decay or storage. Stress granules form in response to stress conditions and contain mRNAs and translation factors.P-bodies and stress granules consist of mRNPs of different compositions, believed to mature and transition between the states. It is proposed that mRNAs transition between the two granules. In the work described below, we use Saccharomyces cerevisiae to demonstrate that a decay factor, Dhh1 is capable of existing in both P-body and stress granule mRNPs. This suggests that a decay factor can be part of two different mRNP complexes. Additionally, we identify two novel components of the stress granule mRNPs, Pbp4 and Lsm12, and determine that they are not essential for stress granule formation. Lastly, we show that the stress granule mRNP factor, Pab1, is not absolutely required for stress granule formation.An important aspect of cytoplasmic mRNA regulation is mRNA quality control. One example of this is nonsense-mediated mRNA decay (NMD), whereby aberrant mRNAs containing premature termination codons are targeted for decay, and can be localized to P-bodies. Upf1-3 and the mRNA decapping complex, Dcp2/Dcp1 are essential for NMD, which requires Upf1 interaction with stalled ribosomal/mRNA complexes to target aberrant mRNA for decapping and degradation. How Dcp2/Dcp1 is recruited to aberrant mRNA is poorly understood.Here, we show by yeast two-hybrid assays that an interaction between Dcp2 and Upf1 is mediated by the decapping stimulator Edc3. Interestingly, Edc3 and Upf2 share overlapping binding sites on the Upf1 N-terminal domain. The decapping stimulator, Pat1, also interacts on the Upf1 N-terminus, but Edc3 and Pat1 are not essential for NMD. Surprisingly, the Upf1-Edc3 interaction does not promote or negatively regulate NMD. Thus, the Upf1-Edc3 and Upf1-Pat1 interactions likely regulate a subset of mRNA transcripts, or are essential for proper NMD under different environmental conditions.
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Wilson, Timothy Craig. "The role of mRNA stability and Fos protein in transient c-fos mRNA accumulation." Thesis, University of Cambridge, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.304567.

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Brown, Cheryl Yvette. "Regulation of cytokine mRNA stabilty /." Title page, contents and summary only, 1996. http://web4.library.adelaide.edu.au/theses/09PH/09phb877.pdf.

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Thesis (Ph. D.)--University of Adelaide, Dept. of Microbiology and Immunology and Div. of Human Immunology, Hanson Centre for Cancer Research, Institute of Medical and Veterinary Science, 1996.
Copies of author's previously published works inserted. Includes bibliographical references.
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Books on the topic "MRNA"

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Rhoads, Robert E., ed. Synthetic mRNA. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3625-0.

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Shi, Yongsheng, ed. mRNA Processing. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7204-3.

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Lamandé, Shireen R., ed. mRNA Decay. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7540-2.

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Yu, Dong, and Benjamin Petsch, eds. mRNA Vaccines. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-18070-5.

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Wery, Maxime, ed. mRNA Decay. New York, NY: Springer US, 2025. http://dx.doi.org/10.1007/978-1-0716-4176-7.

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Lamond, Angus I., and R. G. Landes Company. Pre-mRNA Processing. Berlin, Heidelberg: Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/978-3-662-22325-3.

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Lamond, Angus I. Pre-mRNA processing. New York: Springer-Verlag, 1995.

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Lamond, Angus I. Pre-mRNA processing. Austin: R.G. Landes Co., 1995.

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Schoenberg, Daniel R. mRNA Processing and Metabolism. New Jersey: Humana Press, 2004. http://dx.doi.org/10.1385/1592597505.

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Hertel, Klemens J., ed. Spliceosomal Pre-mRNA Splicing. Totowa, NJ: Humana Press, 2014. http://dx.doi.org/10.1007/978-1-62703-980-2.

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Book chapters on the topic "MRNA"

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Roy, Bijoyita. "Effects of mRNA Modifications on Translation: An Overview." In Methods in Molecular Biology, 327–56. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1374-0_20.

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AbstractThe mRNA epitranscriptome imparts diversity to gene expression by installing chemical modifications. Advances in detection methods have identified chemical modifications in eukaryotic, bacterial, and viral messenger RNAs (mRNAs). The biological functions of modifications in mRNAs still remain to be understood. Chemical modifications are introduced in synthetic mRNAs meant for therapeutic applications to maximize expression from the synthetic mRNAs and to evade the host immune response. This overview provides a background of chemical modifications found in mRNAs, with an emphasis on pseudouridine and its known effects on the mRNA life cycle, its potential applications in synthetic mRNA, and the methods used to assess its effects on mRNA translation.
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Khanfer, Riyad, John Ryan, Howard Aizenstein, Seema Mutti, David Busse, Ilona S. Yim, J. Rick Turner, et al. "mRNA." In Encyclopedia of Behavioral Medicine, 1266. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-1005-9_101108.

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Arnemann, J. "mRNA." In Springer Reference Medizin, 1689. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-48986-4_3535.

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Arnemann, J. "mRNA." In Lexikon der Medizinischen Laboratoriumsdiagnostik, 1. Berlin, Heidelberg: Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-662-49054-9_3535-1.

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Niazi, Sarfaraz K. "RNA Therapeutics." In mRNA Therapeutics, 67–106. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9781003248156-4.

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Niazi, Sarfaraz K. "The Genome Machine." In mRNA Therapeutics, 19–40. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9781003248156-2.

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Niazi, Sarfaraz K. "Nucleoside Vaccines." In mRNA Therapeutics, 107–54. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9781003248156-5.

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Niazi, Sarfaraz K. "Understanding Nucleic Acids." In mRNA Therapeutics, 41–66. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9781003248156-3.

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Niazi, Sarfaraz K. "Regulatory Guidance." In mRNA Therapeutics, 197–240. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9781003248156-7.

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Niazi, Sarfaraz K. "Background." In mRNA Therapeutics, 1–18. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9781003248156-1.

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Conference papers on the topic "MRNA"

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Alevras, Dimitris, Mihir Metkar, Takahiro Yamamoto, Vaibhaw Kumar, Triet Friedhoff, Jae-Eun Park, Mitsuharu Takeori, Mariana LaDue, Wade Davis, and Alexey Galda. "mRNA Secondary Structure Prediction Using Utility-Scale Quantum Computers." In 2024 IEEE International Conference on Quantum Computing and Engineering (QCE), 488–99. IEEE, 2024. https://doi.org/10.1109/qce60285.2024.00064.

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Kabardaeva, K. V., O. N. Mustafaev, I. V. Deineko, A. V. Suhorukova, and I. V. Goldenkova-Pavlova. "Finding of regulatory codes in 5`-UTR of A. thaliana mRNAs by polysome profiling method." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.107.

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The polysome profiling method was used to separate mRNAs depending on their loading by ribosomes into polysomal and monosomal fractions. Pools separation of such mRNAs and analysis of transcripts (mRNAs) which are associated with each mRNA pool due to RNA sequencing allowed to get an idea of the translational efficiency of individual mRNAs. Moreover, subsequent in silico analysis make possible searching of regulatory contexts in the 5'-UTR of plant A. thaliana, which may be potentially important for efficient translation of mRNA.
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Sakaruassen, K. S., J. S. Powell, E. W. Raines, and R. Ross. "SELECTIVE EXPRESSION OF PLATELET-DERIVED GROWTH FACTOR B-CHAIN mRNA BY HUMAN ENDOTHELIAL CELLS AND BY HUMAN PERIPHERAL BLOOD MONOCYTES, BUT NOT BY HUMAN SMOOTH MUSCLE CELLS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643752.

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Vascular injury may occur by a variety of mechanisms. Episodes of local hypoxia or conditions leading to local generation of thrombin may influence local cells to release growthregulatory molecules such as platelet-derivedgrowth factor (PDGF) in the surrounding connective tissue. The roles of the cells and of PDGF in these processes are not entirely understood, and this prompted us to investigate effects of hypoxia (5% O2) on cultured human saphenous vein endothelial cells andhuman thoracic aorta smooth muscle cells. Freshly isolated human peripheral blood monocytes were exposed to 3.0 U/ml a-thrombin. PDGF-A and PDGF-B mRNAs were analyzed by Northern blots, and their levels were assessed by dot blots utilizing 32P nick-translated cDNA probes. Selective expressionof PDGF-B mRNA occurred in endothelial cells during hypoxia and in monocytes exposed to thrombin. Genes coding for PDGF-A and PDGF-B are expressed cons tit utively, in endothelium, and after 48 hr of hypoxia a nine-fold increase of PDGF-B mRNA is detected (9 pg mRNA/ug total RNA). No detectable levels of mRNA encoding PDGF-A and PDGF-B were observed in freshly isolated monocytes; however, a 4-hr exposure to a-thrombin resulted in a selective and transitory increase in PDGF-B mRNA, amountingto 1 pg mRNA/ug toted RNA. No PDGF-B mRNA wasdetected after 20 hr. Hypoxic conditions did not trigger any selective expression of PDGF-B mRNA in smooth muscle, including arterialsmooth muscle derived from 1-day- and 3-month-old individuals, or from adult venous smoot muscle. However, constitutive expression of PDGF-A mRNA was observed in each of these, amounting to 0.4 pg mRNA/ug total RNA in the 1-day- and 3-month-old cells, and 0.2 pg mRNA/ugtotal RNA in the venous smooth muscle. Our datashow that endothelium and monocytes selectively express PDGF-B mRNA in vitro in response to conditions mimicking those encountered during vascular injury in some in-vivo situation.The data imply that both endothelial cells and monocyte/macrophages may be sources for mitogens that induce intimal hyperplasia and eventually plaque formation.
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Ahmed, Ahmed, Muhammad Alkataan, and Asmaa Shetawi. "Cathelicidin (LL37) in Metabolic Syndrome Patients in Mosul City." In 5th International Conference on Biomedical and Health Sciences. Cihan University-Erbil, 2024. http://dx.doi.org/10.24086/biohs2024/paper.1339.

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Abstract—Background: LL37 exhibits a salient role in the innate immunity. This study tried to assess mRNA expression of LL37 in patients with metabolic syndrome and correlate it to different parameters. Methods and Results: The study included 50 patients with metabolic syndrome and 50 control subjects. LL37, VDR and IL6 mRNA relative expression was measured using qPCR for all subjects. BMI, total serum cholesterol, triglyceride, HDL cholesterol and HbA1c were estimated. Patients’ parameters were correlated using Pearson correlation with LL37 mRNA relative expression. Results Showed a significant down regulation of both blood LL37 and VDR mRNA relative expression among patients compared to controls (P-value <0.0001). While Patients IL6 mRNA relative expression significantly upregulated (p-value <0.0001). BMI, HbA1c, total serum cholesterol, and serum triglyceride showed a significant higher concentration among patients than controls (p-value <0.0001) for each parameter. Serum vitamin D and HDL-cholesterol were significantly lower among patients with P-value <0.0001 and = 0.0005 respectively. The LL37 mRNA relative expression was significantly correlated with VDR mRNA relative expression r was 0.636 and P-value was 0.0006. IL6 mRNA expression, BMI, HbA1c, serum total cholesterol, serum triglyceride, serum HDL-cholesterol and serum vitamin D didn't show a significant correlation with the LL37 mRNA relative expression. Conclusion: Patients with MTS has a significant lower blood mRNA relative expression of LL37 in comparison to control, which significantly correlated with blood VDR mRNA relative expression, but not correlated with the other patients’ parameters.
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Rhee, Wonjong, Hanjoong Jo, and Gang Bao. "Live Cell Detection of Specific Messenger RNA for Molecular Analysis of Plaque Formation." In ASME 2007 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2007. http://dx.doi.org/10.1115/sbc2007-176737.

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The ability to visualize mRNA in single living cells and monitor in real-time the changes of mRNA level and localization in response to shear flow can provide unprecedented opportunities for the molecular analysis of atherosclerosis. We carried out an extensive study of the design of molecular beacons to target BMP-4 mRNA, which plays important roles in proatherogenic development in response to unstable flow conditions. Specifically, we selected an optimal molecular beacon design, and found that the fluorescent intensity from targeting BMP-4 mRNA correlated well with the GFP signal after up-regulating BMP-4 and co-expressing GFP using adenovirus. The knock-down of BMP-4 mRNA using siRNA significantly reduced the beacon signal, further demonstrating detection specificity. We found that, due to target accessibility, molecular beacons designed with different target sequences gave very different signal levels, and establishing molecular beacon design rules has significant implications to live cell mRNA detections, especially to the studies of BMP-4 mRNA in endothelial cells under shear flow.
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Bharti, Alok. "HPV mRNA-based diagnostic tools." In 10th National Conference of Asia Oceania Research Organisation on Genital Infections and Neoplasia, India. AOGIN 2021, 2021. http://dx.doi.org/10.7869/aogin45.

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Arioua, Khalil. "CD16A and CD16B mRNA levels as a potential immunological marker in prostate cancer." In Наука России: Цели и задачи. Наука России, 2021. http://dx.doi.org/10.18411/sr-05-12-2021-06.

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Introduction and purpose Understanding the movement of immune cells in prostate cancer is the best solution for development antitumor therapy. In our study, we will evaluate level mRNA CD16А (FCGR3A) and mRNA CD16B (FCGR3B) in patients diagnosing benign hyperplasia and patients diagnosing prostate cancer (Pc). Materials and methods In the study, we analyzed 240 samples of mRNA, 49 was the blood of healthy donors, 37 was the blood of prostate cancer patients and 62 tumors of prostate, 37 were blood of hyperplasia and 55 was tissue of hyperplasia, all patients treated in the Hospital 33 (Niznhy Novgord, Russia). The relative level of mRNA in peripheral blood and tumors was determined by the method of reverse transcription-polymerase chain reaction in real time. Results In the peripheral blood of patients with prostate cancer and patients with hyperplasia, the level of mRNA FCGR3A and FCGR3B was statistically significantly lower than in healthy individuals. The normalization of the CD16 level in the blood of healthy donors was higher The relative level of mRNA FCGR3A, FCGR3B was the highest in patients with Prostate antigen specific (PSA) from 10Ng/ml to 20Ng/ml. The higher level mRNA FCGR3A and FCGR3B was for patients with higher testosterone ≥8mmol/L. also a higher level of FCGR3A, FCGR3B was found in patients diagnosed with an adenopathy:, a higher size prostate and a higher Gleason Scores. The results of Classification based on the degree of differentiation shows that the level of mRNA FCGR3A and FCGR3B in patients with medium differentiation was higher and statistically significant than in patient with lower differentiation. Conclusion. The Changes in the mRNA level of genes encoding CD16A (FCGR3A) and CD16B (FCGR3A) was detected in blood and tumor samples. The results indicate the potential use of these indicators as monitoring immunological markers in hyperplasia and prostate cancer.
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Zadorozhny, A. M., S. V. Sharabrin, A. P. Rudometov, and L. I. Karpenko. "CONSTRUCTION OF A DNA TEMPLATE FOR THE PRODUCTION OF MRNA ENCODING RBD OF THE S PROTEIN OF THE SARS-COV-2 OMICRON BA.2 VIRUS." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-77.

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The work is devoted to the construction of DNA templates for in vitro production of mRNAs encoding the receptor-binding domain (RBD) of the S protein of the SARS-CoV-2 virus, the genetic variant Omicron BA.2. Three plasmids DNA templates were obtained that encode the RBD protein gene, but differ in that they carry different 5’UTRs and 3’UTRs. A variant of the DNA template was chosen, which provides the synthesis of mRNA-RBD most effectively expressed in eukaryotic cells.
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Pandit, V., R. S. Nesbitt, J. Macione, and S. P. Kotha. "Reprogramming of cells using modified mRNA." In 2011 37th Annual Northeast Bioengineering Conference (NEBEC). IEEE, 2011. http://dx.doi.org/10.1109/nebc.2011.5778580.

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Del Fabbro, Cristan, Francesco Vezzi, and Alberto Policriti. "mrNA: The MPI Randomized Numerical Aligner." In 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2011. http://dx.doi.org/10.1109/bibm.2011.17.

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Reports on the topic "MRNA"

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Kencono Wungu, Citrawati Dyah. In mRNA we trust. Edited by Ria Ernunsari. Monash University, April 2022. http://dx.doi.org/10.54377/93ec-d46b.

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Abcouwer, Steve P. Demonstration that a mRNA Binding Protein is Responsible for GADD45 mRNA Destabilization. Fort Belvoir, VA: Defense Technical Information Center, May 2003. http://dx.doi.org/10.21236/ada418512.

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Stern, David B., and Gadi Schuster. Manipulation of Gene Expression in the Chloroplast: Control of mRNA Stability and Transcription Termination. United States Department of Agriculture, December 1993. http://dx.doi.org/10.32747/1993.7568750.bard.

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Chloroplasts are the site of photosynthesis and of other essential biosynthetic activities in plant cells. Chloroplasts are semi-autonomous organelles, since they contain their own genomes and protein biosynthetic machinery, but depend on the coordinate expression of nuclear genes to assemble macromolecular complexes. The bioeingineering of plants requires manipulation of chloroplast gene expression, and thus a knowledge of the molecular mechanisms that modulate mRNA and protein production. In this proposal the heterotrophic green alga Chlamydomonas reinhardtii has been used as a model system to understand the control and interrelationships between transcription termination, mRNA 3' end processing and mRNA stability in chloroplasts. Chlamydomonas is a unique and ideal system in which to address these issues, because the chloroplast can be easily manipulated by genetic transformation techniques. This research uncovered new and important information on chloroplast mRNA 3' end formation and mRNA stability. In particular, the 3' untranslated regions of chloroplast mRNAs were shown not to be efficient transcription terminators. The endonucleolytic site in the 3' untranslated region was characterized by site directed mutagensis and the role of several 3' untranslated regions in modulating RNA stability and translation has been studied. This information will allow us to experimentally manipulate the expression of chloroplast genes in vivo by post-transcriptional mechanisms, and should be widely applicable to other higher plant systems.
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Wickstrom, Eric. Oncogene mRNA Imaging with Radionuclide-PNA-Peptides. Office of Scientific and Technical Information (OSTI), March 2008. http://dx.doi.org/10.2172/925560.

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Yu, Jindan. Role of mRNA Methylation in Prostate Cancer. Fort Belvoir, VA: Defense Technical Information Center, February 2015. http://dx.doi.org/10.21236/ada614407.

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Leibowitz, Michael J., Francis P. Barbone, and Denise E. Georgopoulos. Factors Determining Translational Efficiency of mRNA in Yeast,. Fort Belvoir, VA: Defense Technical Information Center, January 1991. http://dx.doi.org/10.21236/ada249298.

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Standiford, David M. In Vivo Analysis of Alternative Pre-mRNA Splicing. Fort Belvoir, VA: Defense Technical Information Center, October 1996. http://dx.doi.org/10.21236/adb225042.

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Stern, D. B. Differential regulation of plastid mRNA stability. Progress report. Office of Scientific and Technical Information (OSTI), September 1993. http://dx.doi.org/10.2172/10175480.

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Stern, David, and Gadi Schuster. Manipulation of Gene Expression in the Chloroplast. United States Department of Agriculture, September 2000. http://dx.doi.org/10.32747/2000.7575289.bard.

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The steady-state level of a given mRNA is determined by its rates of transcription and degradation. The stabilities of chloroplast mRNAs vary during plant development, in part regulating gene expression. Furthermore, the fitness of the organelle depends on its ability to destroy non-functional transcripts. In addition, there is a resurgent interest by the biotechnology community in chloroplast transformation due to the public concerns over pollen transmission of introduced traits or foreign proteins. Therefore, studies into basic gene expression mechanisms in the chloroplast will open the door to take advantage of these opportunities. This project was aimed at gaining mechanistic insights into mRNA processing and degradation in the chloroplast and to engineer transcripts of varying stability in Chlamydomonas reinhardtii cells. This research uncovered new and important information on chloroplast mRNA stability, processing, degradation and translation. In particular, the processing of the 3' untranslated regions of chloroplast mRNAs was shown to be important determinants in translation. The endonucleolytic site in the 3' untranslated region was characterized by site directed mutagensis. RNA polyadenylation has been characterized in the chloroplast of Chlamydomonas reinhardtii and chloroplast transformants carrying polyadenylated sequences were constructed and analyzed. Data obtained to date suggest that chloroplasts have gene regulatory mechanisms which are uniquely adapted to their post-endosymbiotic environment, including those that regulate RNA stability. An exciting point has been reached, because molecular genetic studies have defined critical RNA-protein interactions that participate in these processes. However, much remains to be learned about these multiple pathways, how they interact with each other, and how many nuclear genes are consecrated to overseeing them. Chlamydomonas is an ideal model system to extend our understanding of these areas, given its ease of manipulation and the existing knowledge base, some of which we have generated.
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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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