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Dissertations / Theses on the topic 'TRNA-modification'

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Published: 4 June 2021

Last updated: 4 February 2022

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1

Kessler, Alan Christopher Kessler. "tRNA subcellular dynamics dictates modification and nutrient sensing." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1513786086369393.

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2

Wohlgamuth-Benedum, Jessica M. "MODIFICATION AND EDITING IN MITOCHONDRIAL TRYPTOPHAN tRNA OF TRYPANOSOMES." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1245097409.

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3

Swinehart, William E. Jr. "A Biochemical Investigation of Saccharomyces cerevisiae Trm10 and Implications of 1-methylguanosine for tRNA Structure and Function." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1429867956.

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4

Hernandez, Diana Raquel. "Regulation of Expression of a Neisseria Gonorrhoeae tRNA-Modification Enzyme (Gcp)." Diss., The University of Arizona, 2012. http://hdl.handle.net/10150/242381.

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Neisseria gonorrhoeae (Ng) encounters different microenvironments during its life-cycle. Some of these niches have different concentrations of oxygen, which influences the rate of Ng growth; as well as iron, an element essential for Ng survival. Differential expression of several proteins allows the bacteria to adapt to the diverse conditions it comes encounters. One protein affected by environmental changes during Ng growth is Gcp, a tRNA-modification enzyme essential for protein synthesis. To study the regulation of expression of Gcp, we first analyzed the sequence of its ORF, gcp. Orthologs

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5

Bou, Nader Charles. "Structural and Functional characterization of flavoenzymes involved in posttranscriptional modification of tRNA." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066205/document.

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La modification posttranscriptionnelle des acides ribonucléiques (ARNs) est une étape de maturation conservée dans tous les domaines du vivant. Mes travaux de thèse ont porté sur la caractérisation fonctionnelle et structurale de flavoenzymes impliquées dans la modification des ARN de transfert (ARNt) : les dihydrouridines synthases (Dus) dictant la formation de dihydrouridine via la flavine mononucléotide (FMN) et TrmFO responsable de la méthylation en C5 de l'uridine 54 via la flavine adénosine dinucléotide (FAD) ainsi que le methylènetétrahydrofolate. Afin d'élucider le mécanisme de TrmFO,

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6

Joardar, Archi. "GUIDE RNA-DEPENDENT AND INDEPENDENT tRNA MODIFICATIONS IN ARCHAEA." OpenSIUC, 2012. https://opensiuc.lib.siu.edu/dissertations/625.

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Stable RNAs undergo a wide variety of post-transcriptional modifications, that add to the functional repertoire of these molecules. Some of these modifications are catalyzed by stand-alone protein enzymes, while some others are catalyzed by RNA-protein complexes. tRNAs from all domains of life contain many such modifications, that increase their structural stability and refine their decoding properties. Certain regions of tRNAs are more frequently modified than others. Two such regions are the anticodon loop, and the TψC stem. In the halophilic euryarchaeon Haloferax volcanii, tRNATrp and tRNA

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7

Gaston, Kirk W. "Editing and Modification of Threonyl-tRNAs in Kinetoplastids." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1248965851.

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8

Russell, Susan P. "Characterizing Modified Nucleosides in RNA by LC/UV/MS." University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1353951985.

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9

Harrison, Jesse. "Physiological relevance of a trna-dependent mechanism for membrane modification in enterococcus faecium." Honors in the Major Thesis, University of Central Florida, 2012. http://digital.library.ucf.edu/cdm/ref/collection/ETH/id/565.

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Enterococci were once thought to be harmless, commensal organisms that colonize the gastrointestinal tract of humans and other mammals. In the last 30 years, however, concern has grown in the clinical setting over two particular species, Enterococcus faecalis and Enterococcus faecium, which are frequently found to be the etiologic agents of nosocomial infections. Aminoacyl-phosphatidylglycerol synthases (aaPGSs) are integral membrane proteins that add amino acids to phosphatidylglycerol (PG) in the cellular envelope of bacteria. Addition of amino acids to PG confers resistance to various thera

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10

Nist, Richard Neil. "Maturation of tRNA in Haloferax volcanii." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1308066223.

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11

Bimai, Louise. "Etude biochimique et structurale de deux enzymes de thiolation des ARNt dépendantes d’un centre [4Fe-4S] : la s2U54-ARNt thiolase TtuA et la s2U34-ARNt thiolase NcsA." Electronic Thesis or Diss., Paris Sciences et Lettres (ComUE), 2018. https://theses.hal.science/tel-03270824.

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Les ARN de transfert (ARNt) sont des composants essentiels de la machinerie de traduction génétique. Pour être fonctionnels, ces ARNt subissent des modifications chimiques post-transcriptionnelles. Ces modifications permettent d’améliorer la reconnaissance entre l’ARNt et ses partenaires durant la traduction et assurent ainsi la fidélité et l’efficacité de la traduction. Le soufre est présent dans plusieurs nucléosides au sein de ces ARNt, comme dérivé de la thiouridine (s4U8, s2U34, m5s2U54), de la 2-thioadénosine (ms2i6A37, ms2t6A37) et la 2-thiocytidine (s2C32).Mon projet a consisté en l’ét

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12

McKenney, Katherine Mary. "Investigating the basis of tRNA editing and modification enzyme coactivation in Trypanosoma brucei." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu152266963775877.

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13

Xu, Hao. "Functional aspects of modified nucleosides in tRNA." Doctoral thesis, Umeå universitet, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-109491.

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Transfer ribonucleic acids (tRNAs) are extensively modified, especially their anticodon loops. Modifications at position 34 (wobble base) and 37 in these loops affect the tRNAs’ decoding ability, while modifications outside the anticodon loops, e.g. m1A58 of tRNAMeti, may be crucial for tRNA structure or stability. A number of gene products are required for the formation of modified nucleosides, e.g. at least 26 proteins (including Elongator complex) are needed for U34 modifications in yeast, and methyl transferase activity of the Trm6/61p complex is needed to form m1A58. The aim of the studie

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14

Fu, Lihua. "Identification of tRNA modifications in T. thermophilus: wild type HB8 and mutant DTTHA1897 by LC-UV-MS/MS." University of Cincinnati / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1445342537.

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15

Navarro, González María del Carmen. "Caenorhabditis elegans as a research tool to study mitochondrial diseases associated with defects in tRNA modification." Doctoral thesis, Universitat Politècnica de València, 2016. http://hdl.handle.net/10251/61978.

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[EN] Post-transcriptional modification of the wobble uridine (U34) of a tRNA set is an evolutionary conserved process, produced by homologous proteins from the MnmA/MTU1, MnmE/GTPBP3 and MnmG/MTO1 families. Mutations in the human genes MTU1 and GTPBP3 or MTO1 produce acute infantile liver failure, and hypertrophic cardiomyopathy and lactic acidosis, respectively, which usually cause lethality in the first months of life. It is assumed that the primary cause of these diseases is the lack of the modifications introduced by the MTU1 protein in position 2 (tiol) and GTPBP3 and MTO1 proteins (tauri

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16

Krishnamohan, Aiswarya Lakshmi. "Biochemical characterization of catalytic mechanism and substrate recognition by the atypical SPOUT tRNA methyltransferase, Trm10." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1512039838462506.

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17

Cargill, James Stuart. "Characterisation of the essential t⁶A tRNA modification enzymes and evaluation as a potential novel antimicrobial target." Thesis, University of Dundee, 2014. https://discovery.dundee.ac.uk/en/studentTheses/62f60b8c-44be-4af4-b5d9-3eec06700690.

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Modified bases in RNA molecules are common, with over one-hundred individual modifications reported to date. In transfer RNA (tRNA), these modifications help hold the molecule in its proper conformation, allow the aminoacyl-synthetases to attach the amino acid to the correct tRNA for transfer to the ribosome, and in the correct matching of the codon-anticodon pair at the ribosome. Two positions on the tRNA molecule are significant in this last action; positions 34 and 37. Position 34 is the first base in the anticodon, and pairs with the last base in the codon during translation; modifications

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18

Young, Anthony Peter, and Anthony Peter Young. "Characterization of 4-demethylwyosine Synthase, a Radical S-adenosyl-l-methionine Enzyme Involved in the Modification of tRNA." Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/621437.

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Wyosine derivatives are highly complex modified ribonucleic acid (RNA) bases found in archaea and eukarya. They are a modification of a genetically encoded guanosine found at position 37 of phenylalanine encoding transfer ribonucleic acid (tRNA). The second step in the biosynthesis of all wyosine derivatives, in both archaea and eukarya, is the transformation of N-methylguanosine to 4-demethylwyosine by the radical S-adenosyl-l-methionine enzyme TYW1. When these studies were initiated, the substrate of TYW1 was unknown. Four possible substrates; acetyl CoA, acetyl phosphate, phosphoenolpyruvat

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19

Yu, Ningxi. "Post-transcriptional Modification Characterizing and Mapping of Archaea tRNAs Using Liquid Chromatography with Tandem Mass Spectrometry." University of Cincinnati / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1552379526695035.

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20

Chatterjee, Kunal. "A TALE OF TWO METHYLATION MODIFICATIONS IN ARCHAEAL RNAs." OpenSIUC, 2014. https://opensiuc.lib.siu.edu/dissertations/806.

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In all the three domains of life, most RNAs undergo post transcriptional modifications both on the bases as well as the ribose sugars of the individual ribonucleotides. 2'-O-methylation of ribose sugars and isomerization of Uridines to Pseudouridines are two most predominant modifications in rRNAs and tRNAs across all domains of life. Besides 2'-O-methylation of ribose sugars, methylation of pseudouridine (Ø) at position 54 of tRNA, producing m1Ø, is a hallmark of many archaeal species but the specific methylase involved in the formation of this modification had yet to be characterized. A comp

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21

Dare, Kiley Elizabeth. "Changes in the Physiology of Bacillus subtilis and Listeria monocytogenes Upon tRNA-dependent Phospholipid Modification with Lysine." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1343793765.

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22

Deutsch, Christopher Wayne. "Discovery and Characterization of the Proteins Involved in the Synthesis of N⁶-Threonylcarbamoyl Adenosine, a Nucleoside Modification of tRNA." PDXScholar, 2016. http://pdxscholar.library.pdx.edu/open_access_etds/3080.

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N6-threonylcarbamoyl adenosine (t6A) is a universally conserved tRNA modification found at position 37 of tRNAs which decode ANN codons. Structural studies have implicated its presence as a requirement for the disruption of a U-turn motif in certain tRNAs, leading to the formation of properly structured anticodon stem loop. This structure is proposed to enhance the base pairing between U36 of tRNA and A1 of the codon which aids in translational frame maintenance. Despite significant effort since its discovery in the 1970s the enzymes involved in its biosynthesis remained undiscovered. Bioinfor

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23

Di, Santo Rachael Teresa Ann. "A basic region in the Elp1 subunit of the budding yeast Elongator complex is essential for wobble uridine tRNA modification." Thesis, University of Dundee, 2013. https://discovery.dundee.ac.uk/en/studentTheses/1a4fb1c9-4bac-4dc8-a3bc-f3d29ec73503.

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24

Létoquart, Juliette. "Etudes structurales et fonctionnelles de complexes entre Trm112 et différentes méthyltransférases impliquées dans la traduction." Thesis, Paris 11, 2014. http://www.theses.fr/2014PA114821/document.

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La traduction représente un processus central au sein de la cellule, elle assure le transfert de l’information génétique de l’ARNm vers les protéines. De nombreux acteurs y sont impliqués directement ou indirectement et parmi eux, chez les eucaryotes, la petite protéine Trm112. Celle-ci participe à la modification de plusieurs acteurs directs en interagissant et en activant quatre MTases. Le facteur de terminaison eRF1 est méthylé par le complexe Mtq2-Trm112, l’ARNr 18S par Bud23-Trm112 et certains ARNt par les complexes Trm9-Trm112 et Trm11-Trm112. Au cours de ce travail, les structures crist

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25

Guelorget, Amandine. "Etude de la structure et de la région-spécificité de la m1A57/58 méthyltransférase d'ARNt de l'archée Pyrococcus abyssi." Phd thesis, Université Paris Sud - Paris XI, 2011. http://tel.archives-ouvertes.fr/tel-00612159.

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La méthylation de l'adénine en position 58 des ARNt (m1A58) est présente dans les trois domaines de vie et joue un rôle crucial chez plusieurs organismes. Sa formation est catalysée par la méthyltransférase SAM-dépendante TrmI. Alors que chez les eucaryotes et les bactéries, TrmI est site-spécifique pour l'adénine en position 58, chez l'archée Pyrococcus abyssi, TrmI est région-spécifique puisqu'elle catalyse également la méthylation de l'adénine en position 57. Nous nous sommes intéressés à cette enzyme, PabTrmI, pour comprendre cette différence de spécificité par rapport à ses homologues euc

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26

Fleming, Ian Murray Cameron. "Studies on RNA Modification and Editing in Trypanosoma brucei." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1452245560.

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27

Sample, Paul J. "Characterization of two unique pathways for wyosine biosynthesis in Kinetoplastids." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1397733440.

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28

Galvanin, Adeline. "Use of high-throughput sequencing for the characterization of extracellular RNA and to study the dynamics of bacterial RNA modification." Thesis, Université de Lorraine, 2019. http://www.theses.fr/2019LORR0095/document.

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Le séquençage à haut débit est une technique très utile pour l’étude des ARN. Pendant mon doctorat, nous l’avons utilisé pour la caractérisation des ARN extracellulaire (ARNex) du plasma humain. Les ARNex du plasma sont retrouvés soit à l’état soluble sous forme de complexes ribonucléoprotéiques (RNP) ou encapsulés au sein de vésicules extracellulaires (VE) de diverses origines (exosomes, microvesicles, …). Dans ce projet, j’ai démontré que le plasma contenait principalement des micro ARN, le fragment hY4 et des ARN ribosomiques dégradés. Par ailleurs, après chromatographie à exclusion de tail

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29

Leipuviene, Ramune. "Frameshifting as a tool in analysis of transfer RNA modification and translation." Doctoral thesis, Umeå universitet, Molekylärbiologi (Teknat- och Medfak), 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-302.

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Studies of ribosomal reading frame maintenance are often based on frameshift mutation suppression experiments. In this thesis, suppression of a frameshift mutation in Salmonella enterica serovar Typhimurium by a tRNA and a ribosomal protein are described. The +1 frameshift mutation hisC3072 (that contains an extra G in a run of Gs) is corrected by mutations in the argU gene coding for the minor tRNAArgmnm5UCU. The altered tRNAArgmnm5UCU has a decreased stability and reduced aminoacylation due to changed secondary and/or tertiary structure. Protein sequencing revealed that during the translatio

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30

Cao, Xiaoyu. "Mass Exclusion list for RNA modification mapping using LC-MS/MS." University of Cincinnati / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1495807992024166.

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31

BOUDOVÁ, Michala. "The role of Q tRNA modification in the virulence of \kur{Leishmania mexicana}." Master's thesis, 2018. http://www.nusl.cz/ntk/nusl-390822.

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The aim of the thesis was to indentify the orthologues of TGT1 and TGT2 genes in Leishmania mexicana and to verify the involvement of the respective gene products in the formation of Q-tRNAs in this species. Additionally, infection experiments in vitro as well as in vivo were carried out in order to test the plausible effect of Q-tRNA modification presence and/or absence on the virulence of the parasite.

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32

Yu, Ming-Chen, and 余明真. "Effects of Iron Status on tRNA Thio-modification in Muscle and Liver of Rat." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/15609648646018048857.

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碩士<br>國立臺灣大學<br>生化科技學系<br>101<br>Transfer RNA (tRNA) are the most highly modified RNAs. To date, more than 100 species of tRNA modification have been reported. The majority of these modifications in tRNA have been found at the anticodon first (wobble) position 34, and at position 37 3’-adjacent to the anticodon. In eukaryotes, the wobble base of the tRNAs for Glu, Gln and Lys are universally modified to 5-methyl-2-thiouridine derivatives (xm5s2U), such as 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) in cytoplasmic tRNAs. The 2-thio modification xm5s2U plays a critical role in protein synthe

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33

Hsu, Yi-Shen, and 許義申. "The Effect Of Iron Chelator Deferoxamine Treatment On TRNA Thio-modification In Rat L6 Skeletal Muscle Cell." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/52531693091648347554.

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碩士<br>輔仁大學<br>營養科學系<br>100<br>In eukaryotes, the uridine in wobble position of tRNALys, tRNAGlu and tRNAGln molecules will be modified to 5-methoxycarbonylmethyl-2-thiour -idine (mcm5s2U), and these thio-modifications could affect the decoding of mRNA codon and translation rate. Recently, the study had showed that the iron-sulfur cluster (ISC) biogenesis proteins, such as Nfs1/IscS, Isu/IscU and Nbp35/Nubp1 were required for thio-modification of cytosolic thiouri -dine-containing tRNAs in yeast. Therefore, we used the rat L6 muscle cell model to investigate the cellular iron status on thio-mod

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34

Denmon, Andria. "The Role of Base Modifications on Tyrosyl-tRNA Structure, Stability, and Function in Bacillus subtilis and Bacillus anthracis." Thesis, 2013. http://hdl.handle.net/1911/71946.

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tRNA molecules contain more than 80 chemically unique nucleotide base modifications that contribute to the chemical and physical diversity of RNAs as well as add to the overall fitness of the cell. For instance, base modifications have been shown to play a critical role in tRNA molecules by improving the fidelity and efficiency of translation. Most of this work has been carried out extensively in Gram-negative bacteria, however, the role of modified bases in tRNAs as they relate to thermostability, structure, and transcriptional regulation in Gram-positive bacteria, such as Bacillus subtilis a

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35

Naumann, Peter-Thomas. "Versuche zur Strukturaufklärung bakterieller Thiouridin Synthetasen." Doctoral thesis, 2006. http://hdl.handle.net/11858/00-1735-0000-0006-AC64-1.

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