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Chen, Xing. "EVOLUTION OF GROUP I INTRONS IN THE NUCLEAR RIBOSOMAL RNA GENES OF DOTHIDEOMYCETES." Bowling Green State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1288376350.
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Cooper, Lizette. "Evolutionary investigation of group I introns in nuclear ribosomal internal transcribed spacers in Neoselachii." Bowling Green State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu154229759945368.
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Benavides, Edgar. "Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal." Diss., CLICK HERE for online access, 2006. http://contentdm.lib.byu.edu/ETD/image/etd1652.pdf.
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Vogel, Laura Sanders. "The decline of Fowler's Toad (Bufo fowleri) in southern Louisiana: molecular genetics, field experiments and landscape studies." ScholarWorks@UNO, 2007. http://scholarworks.uno.edu/td/579.
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Two of the most pervasive threats to species biodiversity are invasive species and habitat loss and degradation. Invasive species are often relatively insensitive to disturbance and many expand their range into disturbed and fragmented habitats. This dissertation uses an interdisciplinary approach to investigate how anthropogenic habitat disturbance is precipitating a range expansion in an invasive toad species, Bufo nebulifer, which is driving a decline in its native congener, B. fowleri. I employed a remote sensing and GIS study using historical data to compare changes in the two species distributions and habitat changes, a molecular genetic study to identify interspecific hybrids and their potential effects on the parental species, and an experimental ecology study to look at the effects of competition and predation on the two species. The results of the landscape level analyses of species' distributional changes in different disturbance levels showed that both species' distributions have changed significantly. The distributions of the two species are inversely affected by habitat disturbance; the distribution of B. fowleri in highly degraded habitat has contracted while the expansion of B. nebulifer increased substantially. The molecular genetic study successfully demonstrated the use of nuclear and mitochondrial markers to identify cryptic hybrids and their maternal lineage. Three hybrids were detected using nuclear introns and a morphologically cryptic hybrid was identified using mitochondrial DNA as the progeny of a cross that was previously thought to be inviable. Although relatively few hybrids were currently found, the identification of a cryptic hybrid implies that the rate of historical hybridization may have been drastically underestimated. Ecological studies showed that competition with B. nebulifer tadpoles had a negative effect on both body size measures and survival to metamorphosis for B. fowleri tadpoles. The addition of predators to experiment did not favor the survival of B. fowleri over B. nebulifer. Bufo fowleri's inability to compete with its invasive congener could be a driving mechanism for the decline of B. fowleri and the expansion of B. nebulifer. The methods discussed in this dissertation offer promising and practical new approaches for evaluating and managing changes in the distribution of species of conservation concern.
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Till, Bradley J. "A nucleus-encoded protein required for the splicing of the maize chloroplast atpF group II intron /." view abstract or download file of text, 2000. http://wwwlib.umi.com/cr/uoregon/fullcit?p9998022.
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Thesis (Ph. D.)--University of Oregon, 2000.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 56-59). Also available for download via the World Wide Web; free to University of Oregon users.
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Jenkins, Bethany Diane. "Identification of nucleus-encoded factors required for group II intron splicing in chloroplasts /." view abstract or download file of text, 2000. http://wwwlib.umi.com/cr/uoregon/fullcit?p9963446.
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Thesis (Ph. D.)--University of Oregon, 2000.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 110-117). Also available for download via the World Wide Web; free to University of Oregon users. Address: http://wwwlib.umi.com/cr/uoregon/fullcit?p9963446.
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Aggarwal, Neha. "Characterization of a microRNA Harboring Intron for pre-mRNA Splicing and microRNA Processing." Cleveland State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=csu1275407397.
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Baboo, Sabyasachi. "Nuclear translation." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:5266f049-d576-44fd-ab26-11cf7a27f678.
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In bacteria, protein synthesis can occur tightly coupled to transcription. In eukaryotes, it is believed that translation occurs solely in the cytoplasm; I test whether some occurs in nuclei and find: (1) L-azidohomoalanine (Aha) – a methionine analogue (detected by microscopy after attaching a fluorescent tag using ‘click’ chemistry) – is incorporated within 5 s into nuclei in a process sensitive to the translation inhibitor, anisomycin. (2) Puromycin – another inhibitor that end-labels nascent peptides (detected by immuno-fluorescence) – is similarly incorporated in a manner sensitive to a transcriptional inhibitor. (3) CD2 – a non-nuclear protein – is found in nuclei close to the nascent RNA that encodes it (detected by combining indirect immuno-labelling with RNA fluorescence in situ hybridization using intronic probes); faulty (nascent) RNA is destroyed by a quality-control mechanism sensitive to translational inhibitors. I conclude that substantial translation occurs in the nucleus, with some being closely coupled to transcription and the associated proof-reading. Moreover, most peptides made in both the nucleus and cytoplasm are degraded soon after they are made with half-lives of about one minute. I also collaborated on two additional projects: the purification of mega-complexes (transcription ‘factories’) containing RNA polymerases I, II, or III (I used immuno-fluorescence to confirm that each contained the expected constituents), and the demonstration that some ‘factories’ specialize in transcribing genes responding to tumour necrosis factor α – a cytokine that signals through NFκB (I used RNA fluorescence in situ hybridization coupled with immuno-labelling to show active NFκB is found in factories transcribing responsive genes).
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Nicolas, Antoine. "UNDERSTANDING EVOLUTIONARY RELATIONSHIPS IN THE ANGIOSPERM ORDER APIALES BASED ON ANALYSES OF ORGANELLAR DNA SEQUENCES AND NUCLEAR GENE DUPLICATIONS." VCU Scholars Compass, 2009. http://scholarscompass.vcu.edu/etd/1701.
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I studied evolutionary history in the angiosperm order Apiales, with a special emphasis on interactions between form, time, and space. Four broad categories of problems were addressed: interfamilial relationships in Apiales, the assignment of genera traditionally assigned to the Apiaceae subfamily Hydrocotyloideae, the estimation of divergence times of the major clades, and the reconstruction of the biogeographic history of Apiales. We used molecular markers with different evolutionary properties and rates derived from the plastid (trnD-trnT and rpl16), nuclear (RPB2), and mitochondrial (nad1 intron 2) genomes, from more than 250 species representing all major clades in the order. The nuclear RPB2 region exhibited evidence of at least six duplication events in Apiales and provided a rich source of information for understanding the origins of polyploid lineages, especially in Araliaceae. Sequence comparisons among the copies show that exon regions are highly conserved. All copies appear to be functional but may have undergone subfunctionalization. Phylogenetic analyses of the three genomes suggest that Hydrocotyloideae should be divided into as many as six evolutionary lineages, but that most taxa should be included in subfamilies Azorelloideae and Mackinlayoideae. Relationships among and within the major clades of Azorelloideae need further analyses since many genera appeared non-monophyletic (e.g., Azorella, Schizeilema, and Eremocharis). Mackinlayoideae appeared as the earliest diverging lineage of Apiaceae, but the plastid and nuclear trees were incongruent in the placement of the Platysace clade relative to Mackinlayoideae and the rest of Apiaceae. Among the remaining clades of suborder Apiineae, Myodocapaceae appeared sister to Apiaceae in both plastid and nuclear trees, preceded by the divergence of Araliaceae and then Pittosporaceae. At the base of the gene trees in Apiales, Griseliniaceae and Torricelliaceae formed successive sisters to Apiineae. The placement of Pennantiaceae as sister to the rest of Apiales was confirmed by plastid data, but was not found in the nuclear trees. The order appears to have originated in the Cretaceous, with Apiineae having an age of c. 100 Mya. Australasia appears to be the most likely center of origin for Apiineae and most of its major clades, except Azorelloideae (South America) and Apioideae-Saniculoideae (sub-Saharan Africa).
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Hushek, Stephen Gerard. "Quantitative analysis of intro-operative magnetic resonance images and tissue survival for laserthermia of 9L gliosarcoma." Thesis, Massachusetts Institute of Technology, 1994. http://hdl.handle.net/1721.1/28078.
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Greaver, Liane Raynette. "GEOGRAPHIC POPULATION STRUCTURE AND TAXONOMIC IDENTITY OF RHINICHTHYS OSCULUS, THE SANTA ANA SPECKLED DACE, AS ELUCIDATED BY NUCLEAR DNA INTRON SEQUENCING." CSUSB ScholarWorks, 2019. https://scholarworks.lib.csusb.edu/etd/931.
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Rhinichthys osculus (Cyprinidae), the speckled dace, is the most widely distributed freshwater fish in the western United States. The southern California populations of R. osculus are identified as the Santa Ana speckled dace (SASD), though the SASD has not yet been formally recognized as a distinct taxon. Current mtDNA analysis performed in the Metcalf Lab has shown a reciprocally monophyletic relationship among three California regions; southern, central coast, and Owens Valley. Similarly, microsatellite genotyping has shown significant levels of geographic population structure. The purpose of this study was to provide nuclear DNA sequence data to determine the taxonomic status of the SASD to elucidate their evolutionary history and the relationships among the three regions, and to further define their evolutionary trajectory by comparing SASD sequence data to that of speckled dace from the Colorado River of Arizona. To examine this, three EPIC intron markers were sequenced on 54 samples representing all four regions. Based on the mtDNA and microsatellite data alone, there is strong support that the southern California populations of R. osculus are a reproductively isolated taxon at the species level. My study confirms this by showing the SASD to be reciprocally monophyletic for nuclear DNA markers, in conjunction with the mitochondrial DNA marker analyses. Because they are evolutionarily independent and face increased incidence of drought, fire, and flood, endangered species status should be considered.
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Alexander, Rashada Corine. "INSIGHTS INTO ENZYMATIC MANIPULATIONS OF NUCLEIC ACIDS." UKnowledge, 2005. http://uknowledge.uky.edu/gradschool_diss/283.
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This dissertation details three studies dealing with the manipulation of nucleicacids. In the first investigation, each of the four natural nucleobases were analyzed for theability to serve as a universal template at the ligation junction of a T4 DNA ligasereaction. This resulted in the first instance of sequence-independent ligation catalyzed byany DNA ligase. Although all of the nucleobases display universal templatingcapabilities, thymidine and guanosine provided the most effective results. In addition,lowered MgCl2 and ATP concentrations, as well as the inclusion of DMSO, also aided inthe sequence-independent ligation reported here. In the course of these studies, currentmethods of removing urea from denaturing-gel purified nucleic acids provedcumbersome. Therefore, in the second study simple butanol extraction was examined as ameans to eliminate urea from nucleic acid solutions. Stepwise butanol extraction was themost effective approach to solving this problem and provided a much needed techniquefor nucleic acid purification. This type of extraction also does not result in significantlosses of nucleic acid sample. The third study exploits the molecular recognition andcatalytic properties inherent in an autocatalytic group I intron to develop a ribozyme thatcan replace the 5' end of an RNA substrate with a different RNA. This 5' replacementsplicing reaction can potentially repair mutations on the 5' ends of RNA transcripts thatlead to a variety of genetic mutations. The model system was a common mutation in asmall model mimic of the k-ras gene in vitro, which predisposes individuals to lungcancer. This 5' replacement splicing reaction occurred in vitro using this small modelsystem; the reaction was also enhanced by the alteration of the molecular interactionsinvolved. The results and implications of each of these studies are detailed in thisdissertation.
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Bifano, Abby Lynn Shumaker. "The Role of a Nuclear-Encoded DEAD-box Protein from Saccharomyces cerevisiae in Mitochondrial Group I Intron Splicing." Case Western Reserve University School of Graduate Studies / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1283302534.
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Prikryl, Jana 1976. "Functions of organelle-specific nucleic acid binding protein families in chloroplast gene expression." Thesis, University of Oregon, 2009. http://hdl.handle.net/1794/10614.
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xii, 83 p. : ill. A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number.My dissertation research has centered on understanding how nuclear encoded proteins affect chloroplast gene expression in higher plants. I investigated the functions of three proteins that belong to families whose members function solely or primarily in mitochondrial and chloroplast gene expression; the Whirly family (ZmWHY1) and the pentatricopeptide repeat (PPR) family (ZmPPR5 and ZmPPR10). The Whirly family is a plant specific protein family whose members have been described as nuclear DNA-binding proteins involved in transcription and telomere maintenance. I have shown that ZmWHY1 is localized to the chloroplast where it binds nonspecifically to DNA and also binds specifically to the atpF group II intron RNA. Why1 mutants show reduced atpF intron splicing suggesting that WHY1 is directly involved in atpF RNA maturation. Why1 mutants also have aberrant 23S rRNA metabolism resulting in a lack of plastid ribosomes. The PPR protein family is found in all eukaryotes but is greatly expanded in land plants. Most PPR proteins are predicted to localize to the mitochondria or chloroplasts where they are involved in many RNA-related processes including splicing, cleavage, editing, stabilization and translational control. Our results with PPR5 and PPR10 suggest that most of these activities may result directly from the unusually long RNA binding surface predicted for PPR proteins, which we have shown imparts two biochemical properties: site-specific protection of RNA from other proteins and site-specific RNA unfolding activity. I narrowed down the binding site for PPR5 and PPR10 to ∼45 nt and 19 nt, respectively. I showed that PPR5 contributes to the splicing of its group II intron ligand by restructuring sequences that are important for splicing. I used in vitro assays with purified PPR10 to confirm that PPR10 can block exonucleolytic RNA decay from both the 5' and 3' directions, as predicted by prior in vivo data. I also present evidence that PPR10 promotes translation by restructuring its RNA ligand to allow access to the ribosome. These findings illustrate how the unusually long RNA interaction surface predicted for PPR proteins can have diverse effects on RNA metabolism. This dissertation includes both previously published and unpublished co-authored material.
Committee in charge: Eric Selker, Chairperson, Biology; Alice Barkan, Advisor, Biology; Victoria Herman, Member, Biology; Karen Guillemin, Member, Biology; J. Andrew Berglund, Outside Member, Chemistry
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Kotovic, Kimberly Marie. "Co-transcriptional recruitment of the U1 snRNP." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2004. http://nbn-resolving.de/urn:nbn:de:swb:14-1103190658062-33439.
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It is currently believed that the splicing of most pre-mRNAs occurs, at least in part, co-transcriptionally. In order to validate this principle in yeast and establish an experimental system for monitoring spliceosome assembly in vivo, I have employed the chromatin immunoprecipitation (ChIP) assay to study co-transcriptional splicing events. Here, I use ChIP to examine key questions with respect to the recent proposal that RNA polymerase II (Pol II) recruits pre-mRNA splicing factors to active genes. In my thesis, I address: 1) whether the U1 snRNP, which binds to the 5¡¦ splice site of each intron, is recruited co-transcriptionally in vivo and 2) if so, where along the length of active genes the U1 snRNP is concentrated. U1 snRNP accumulates on downstream positions of genes containing introns but not within promoter regions or along intronless genes. More specifically, accumulation correlated with the presence and position of the intron, indicating that the intron is necessary for co-transcriptional U1 snRNP recruitment and/or retention (Kotovic et al., 2003). In contrast to capping enzymes, which bind directly to Pol II (Komarnitsky et al., 2000; Schroeder et al., 2000), the U1 snRNP is poorly detected in promoter regions, except in genes harboring promoter-proximal introns. Detection of the U1 snRNP is dependent on RNA synthesis and is abolished by intron removal. Microarray data reveals that intron-containing genes are preferentially selected by ChIP with the U1 snRNP furthermore indicating recruitment specificity to introns. Because U1 snRNP levels decrease on downstream regions of intron-containing genes with long second exons, our lab is expanding the study to 3¡¦ splice site factors in hopes to address co-transcriptional splicing. In my thesis, I also focus on questions pertaining to the requirements for recruitment of the U1 snRNP to sites of transcription. To test the proposal that the cap-binding complex (CBC) promotes U1 snRNP recognition of the 5¡¦ splice site (Colot et al., 1996), I use a ?´CBC mutant strain and determine U1 snRNP accumulation by ChIP. Surprisingly, lack of the CBC has no effect on U1 snRNP recruitment. The U1 snRNP component Prp40p has been identified as playing a pivotal role in not only cross-intron bridging (Abovich and Rosbash, 1997), but also as a link between Pol II transcription and splicing factor recruitment (Morris and Greenleaf, 2000). My data shows that Prp40p recruitment mirrors that of other U1 snRNP proteins, in that it is not detected on promoter regions, suggesting that Prp40p does not constitutively bind the phosphorylated C-terminal domain (CTD) of Pol II as previously proposed. This physical link between Pol II transcription and splicing factor recruitment is further tested in Prp40p mutant strains, in which U1 snRNP is detected at normal levels. Therefore, U1 snRNP recruitment to transcription units is not dependent on Prp40p activity. My data indicates that co-transcriptional U1 snRNP recruitment is not dependent on the CBC or Prp40p and that any effects of these players on spliceosome assembly must be reflected in later spliceosome events. My data contrasts the proposed transcription factory model in which Pol II plays a central role in the recruitment of mRNA processing factors to TUs. According to my data, splicing factor recruitment acts differently than capping enzyme and 3¡¦ end processing factor recruitment; U1 snRNP does not accumulate at promoter regions of intron-containing genes or on intronless genes rather, accumulation is based on the synthesis of the intron. These experiments have lead me to propose a kinetic model with respect to the recruitment of splicing factors to active genes. In this model, U1 snRNP accumulation at the 5¡¦ splice site requires a highly dynamic web of protein-protein and protein-RNA interactions to occur, ultimately leading to the recruitment and/or stabilization of the U1 snRNP.
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Dijon, Aurore. "Evolution de la collectivité autour du 68Ni : rôle des états intrus." Phd thesis, Université de Caen, 2012. http://tel.archives-ouvertes.fr/tel-00728430.
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L'évolution des nombres magiques en fonction du nombre de neutrons est aujourd'hui un axe de recherche majeur en physique nucléaire. Cette évolution qui se traduit par des modifications profondes de la structure de ces noyaux exotiques, se manifeste expérimentalement par des changements rapides de collectivité et de forme. Dans cette thèse nous avons étudié les noyaux situés autour du 68Ni produits par collisions dites profondément inélastiques au GANIL. Les noyaux d'intérêts ont été sélectionnés et identifiés grâce au spectromètre VAMOS. Les rayonnements gamma permettant d'étudier leur structure ont été détectés par EXOGAM autour du point cible ainsi que par un dispositif spécifique installé au plan focal de VAMOS afin d'identifier les isomères pour une des deux expériences. Dans la première, nous avons observé un nouvel état isomère dans le 68Ni dont la configuration basée sur un état intrus proton nous renseigne sur les effets de couches Z=28 et N=40. De nouvelles transitions ont également été identifiées dans les noyaux de Co, Fe et Mn de masse impaire. Dans la seconde expérience, nous avons mesuré la durée de vie des premiers états excités des noyaux 63,65Co en utilisant une méthode utilisant l'effet Doppler. La mesure de ces temps de vie nous permet d'accéder aux probabilités de transitions électromagnétiques, donc à la collectivité. Des comparaisons avec différents modèles théoriques (modèle en couches et champs moyen) nous permettent d'aller plus loin dans l'interprétation et d'avoir des informations supplémentaires sur l'interaction entre les protons et les neutrons ainsi que sur l'évolution de la collectivité dans cette région de masse.
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Goasduff, Alain. "Etats intrus dans les noyaux de la couche sd : de 1p-1t à np-nt dans les isotopes de Si." Phd thesis, Université de Strasbourg, 2012. http://tel.archives-ouvertes.fr/tel-00796884.
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Des calculs de type modèle en couches ont été réalisés dans un espace de valence 1¯hω complet pour les noyaux de la couche sd. Ces calculs ont permis pour la première fois de prédire la durée de vie des états de parité positive et négative des noyaux riches en neutrons de la couche sd. Les durées de vie prédites (1 - 100 ps) sont mesurables par la méthode de décalage Doppler différentiel.Le démonstrateur du détecteur γ européen de nouvelle génération, AGATA, en coïncidence avec le spectromètre magnétique PRISMA du LNL (Italie) et le plunger de l'Université de Cologne ont été utilisés pour mesurer les durées de vie des états excités dans 32,33Si et 35,36S. Les structures plus complexes, à n¯hω ont également été étudiées dans le 28Si. Ce dernier est un noyau important pour comprendre la compétition entre les structures de type champ moyen et les structures en agrégats. La réaction résonante de capture radiative d'ions lourds-légers 12C+16O a été réalisée à des énergies sous-coulombiennes. La décroissance γ complète depuis les résonances peuplées par laréaction jusqu'au niveau fondamental de 28Si a été mesurée pour la première fois à ces énergies et montre une forte alimentation d'états intermédiaires autour de 10 MeV. Les comparaisons avec des études de captures radiatives au-dessus de la barrière de Coulomb ont été effectuées et les résultats ont été interprétés en termes de l'alimentation favorisée d'états à isospin T = 1 dans le noyau autoconjugué 28Si.
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Bouhelal, Mouna. "Application du modèle en couches à l'étude des états intrus de parité négative des noyaux sd moyennant la nouvelle interaction PSDPF." Phd thesis, Université de Strasbourg, 2010. http://tel.archives-ouvertes.fr/tel-00651110.
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La structure nucléaire des noyaux de la couche sd a été bien étudiée expérimentalement à proximité de la ligne de stabilité et, plus récemment, l'intérêt a porté sur les noyaux riches en neutrons. Les états normaux de parité positive sont bien décrits à l'aide de l'interaction USD dans l'espace sd (espace 0ħω) avec un cœur de 16O. Cette interaction a été récemment réajustée et les nouveaux Hamiltonians obtenus sont appelés USDA et USDB. Les spectres expérimentaux montrent l'existence, en plus des états normaux, d'un ensemble d'états de parité négative nommé "états intrus", résultant de l'excitation d'un nucléon de la couche p vers sd, pour les noyaux près de 16O ou de la couche sd vers pf pour les noyaux proches de 40Ca. Au milieu de la couche sd il y a compétition entre les deux types d'excitations pour les intrus. Avant notre travail, il n'existait pas de description unifiée des états de parité négative à travers toute la couche sd. Pour étudier les états intrus, nous avons élargi l'espace modèle de l'espace sd (cœur 16O) à l'espace complet p-sd-pf (cœur 4He) appelé espace 1ħω. Cela nécessite la construction d'une nouvelle interaction compatible avec cette extension de l'espace modèle. Cette procédure est maintenant possible en raison de l'augmentation de la puissance de calcul. Nous avons ainsi mis au point pour la première fois une interaction 1ħω appelée PSDPF, qui comporte cinq parties distinctes: p, sd et pf en plus des termes croisés p-sd et sd-pf. Les trois interactions fixes pour p, sd et pf sont respectivement: CK, USDB et SDPF-NR, cette dernière contient également les éléments de matrice à deux corps sd-pf, l'interaction p-sd est considérée comme étant l'interaction PSDT. Nous avons modifié les contributions p-sd et sd-pf pour reproduire l'évolution en énergie des états intrus de différents spins à travers toute la couche sd. Cette nouvelle interaction a été utilisée pour calculer les états intrus dans les noyaux sd avec N = Z et Z + 1. Les spectres en énergie des états + et - dans tous les noyaux sd ont aussi été calculés. La comparaison expérience-théorie montre un très bon accord et donne ainsi du crédit à notre nouvelle interaction proposée pour décrire les états intrus de la couche sd. Des états de parité - ont été attribués certains niveaux de Jπ inconnus. Les probabilités de transitions électromagnétiques réduites E2 et E3 des premiers états de parité + et -, avec Jπ = 2+ et 3- dans les noyaux pair-pairs, ont été également calculées et les charges effectives pour les transitions E3 ont été étudiées pour la première fois.
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Bretes, Rodrigues Hugo. "Etude de la régulation du métabolisme des ARN messagers chez la levure Saccharomyces cerevisiae." Thesis, Paris 11, 2012. http://www.theses.fr/2012PA112209.
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Au cours de la transcription, plusieurs facteurs sont assemblés sur les ARN messagers pour former des Ribonucléoparticules de messagers (mRNPs), et contrôler leur maturation, leur stabilité et leur devenir dans le cytoplasme. Afin d’assurer la production de protéines fonctionnelles, la cellule dispose de plusieurs mécanismes de régulation et de contrôle de qualité assurant la fidélité de l’information génétique transmise au niveau ARN messager et protéine.Chez la levure Saccharomyces cerevisiae, un ensemble de protéines associées au pore nucléaire, incluant la SUMO protéase Ulp1, a été impliqué dans un contrôle de qualité des mRNPs régulant leur export vers le cytoplasme. Ces données suggéraient que l’export des ARN messagers pourrait être contrôlé par la modification post-traductionnelle par le polypeptide SUMO d’un ou de plusieurs effecteurs au sein des mRNPs. Afin de mieux comprendre ces processus, nous avons combiné plusieurs approches visant à identifier ces protéines SUMOylées. En particulier, nous avons mis en place un crible protéomique visant à identifier les protéines dont l’association sur les mRNPs dépend d’Ulp1. Ce crible nous a permis de mettre en évidence une régulation par Ulp1 de l’assemblage du complexe THO sur les ARN messagers. Ce complexe, recruté sur les gènes et les mRNPs, est connu pour contribuer à l’efficacité de la transcription, prévenir l’instabilité génétique liée à la formation d’hybrides ADN matrice – ARN messager (dénommés R-loops) et permettre l’export des mRNPs. En combinant l’analyse biochimique de différentes catégories de mRNPs à des expériences d’immunoprécipitation de l’ARN, nous avons montré que l’activité de la SUMO-protéase Ulp1 est nécessaire à l’association du complexe THO sur différents ARN messagers. De plus, nous avons montré que le complexe THO est SUMOylé sur le domaine C-terminal de sa sous-unité Hpr1, et que Ulp1 régule cette modification. Enfin, cet événement de SUMOylation du complexe THO régule son association avec les mRNPs. L’analyse fonctionnelle de mutants affectant la SUMOylation du complexe THO révèle que des défauts de SUMOylation de ce complexe compromettent ses fonctions dans la transcription sans affecter l’export. De manière intéressante, nous avons observé que la présence d’un intron sur des rapporteurs LacZ diminue la sensibilité de leur expression à des inactivations ou des défauts de SUMOylation du complexe THO. Ce phénotype entraine une augmentation relative des niveaux d’ARN pré-messagers dans ces mutants, un phénomène rendant compte de la fuite cytoplasmique apparente d’ARN non épissés précédemment observée dans le mutant ulp1. L’ensemble de ces données caractérise pour la première fois un rôle de la SUMOylation dans le contrôle de l’assemblage et du devenir cellulaire des mRNPsDuring transcription, several factors associate with mRNA to form messenger Ribonucleoparticles (mRNPs), thereby controlling their processing, their stability, and their cytoplasmic fate. To ensure the production of functional proteins from these mRNAs, eukaryotic cells contain numerous regulatory and quality control systems in order to prevent aberrant mRNP accumulation and export.In the yeast Saccharomyces cerevisiae, several nuclear pore associated proteins, including the SUMO isopeptidase Ulp1, have been involved in a mRNP quality control regulating their nuclear export. These data suggested that post-translational modification by SUMO of one or several mRNP components could regulate mRNA export. In order to understand the molecular mechanisms underlying this process, we undertook several approaches to identify these SUMOylated factors. In particular, we have set up a proteomic screen to identify mRNP components whose assembly onto mRNPs depends on Ulp1 activity.This proteomic survey revealed an Ulp1-dependent regulation of THO complex assembly to mRNPs. This complex, recruited to transcribed genes and mRNPs, is known to regulate transcription elongation by preventing DNA-RNA hybrids formation (termed R-loops), and mRNP export. Through a combination of proteomic analysis of mRNPs assembled in Ulp1 mutant cells, with RNA / chromatin immunoprecipitation experiments, we demonstrate that Ulp1 controls specifically the recruitment of the THO complex within mRNPs. SUMOylation analysis further reveals that Ulp1 targets the THO complex subunit Hpr1 on its C-terminal domain for deSUMOylation. We further show that this SUMOylation event regulates THO complex association within mRNPs. Finally, functional analysis reveal that impaired deSUMOylation of the THO complex do not affect mRNP export, but disturbs expression of LacZ reporter genes, a phenotype classically associated with THO complex dysfunction. Intriguingly, the transcriptional effect of inactivation or impaired deSUMOylation of the THO complex on LacZ expression is alleviated by the presence of an intron, providing a molecular basis for previously reported pre-mRNA leakage phenotypes. Our data therefore unravels for the first time a function of SUMO in the control of mRNP assembly contributing to proper mRNP homeostasis
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Haponski, Amanda E. "Molecular, morphological, and biogeographic resolution of cryptic taxa in the Greenside Darter Etheostoma blennioidescomplex." Connect to full text in OhioLINK ETD Center, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=toledo1196866050.
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Thesis (M.S.)--University of Toledo, 2007.Typescript. "Submitted as partial fulfillment of the requirements for The Master of Science Degree in Biology (Ecology-track)." "A thesis entitled"--at head of title. Bibliography: leaves 35-47.
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Li, Fei. "Nuclear genes that promote splicing of the chloroplast group-I 23S rRNA intron and an organelle intron database, FUGOID." 2002. http://wwwlib.umi.com/cr/utexas/fullcit?p3099478.
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Nyberg, Tarah Michelle. "In vivo studies of yeast mitochondrial intron splicing ectopic branching and a screen for nuclear encoded splicing factors." 2006. http://www4.utsouthwestern.edu/library/ETD/etdDetails.cfm?etdID=195.
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Li, Youyang. "Phylogeny of the lamprey genus Lethenteron Creaser and Hubbs 1922 and closely related genera using the mitochondrial cytochrome b gene and nuclear gene introns." 2014. http://hdl.handle.net/1993/23657.
Full textAbstract:
The phylogeny of lampreys is controversial, because they possess few taxon-distinctive morphological characters. This is especially true of the relationships among the genus Lethenteron and the closely related genera Eudontomyzon and Lampetra. Thus, the first objective of this thesis was to use DNA sequences of the mitochondrial cytochrome b gene and two nuclear gene introns to infer the phylogeny among these three genera. I found that: 1) Lethenteron plus Eudontomyzon morii without Lethenteron ninae, Lethenteron zanandreai, and Lethenteron sp. S (a distinct cryptic species in the Lethenteron reissneri complex) was monophyletic; 2) Lampetra from the Pacific drainage of North America and Lampetra aepyptera should each be separated, as distinct genera, from Lampetra (including Lethenteron ninae and Lethenteron zanandreai) from the Atlantic drainage of Eurasia; and 3) the remaining Eudontomyzon and the Atlantic Lampetra clustered together in all analyses. The second objective of this thesis was to resolve the relationship among closely related Lethenteron species. Lampreys are either parasitic or non-parasitic, and each non-parasitic (satellite) species is believed to have been derived independently from the parasitic (stem) ancestor. In the phylogenetic analysis, the parasitic Arctic lamprey Lethenteron camtschaticum and its four satellite species were not reciprocally monophyletic. Since network methods are generally more useful for closely related haplotypes than bifurcating trees, a haplotype network of these five Lethenteron species was generated using the cytochrome b gene sequences; Lethenteron appendix showed haplotype frequency distribution differences but there was little support for recognizing the other four taxa as distinct species.
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Luo, Liming 1967. "Genetic mapping of nuclear suppressors of splicing-deficient chloroplast introns, and a novel rhodanese-domain protein required for chloroplast translation in Chlamydomonas." Thesis, 2010. http://hdl.handle.net/2152/ETD-UT-2010-12-2200.
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Although many group I (GI) introns can self-splice in vitro, their splicing is promoted by proteins in vivo. Only a few splicing factors that specifically promote GI intron splicing have been identified, however, none are from chloroplasts, which is the subject of this study. In previous work from our lab, a strategy was developed to identify splicing factors for chloroplast GI introns of Chlamydomonas by using suppressor genetics. A mutant with reduced splicing of the chloroplast 23S rRNA intron (Cr.LSU) was generated. Then, 3 nuclear suppressors (7120, 71N1 and 7151) with substantially restored splicing of Cr.LSU were isolated and partially characterized. However, the suppressor gene(s) were not identified. In this study, I have used genetic mapping to make a renewed attempt to isolate these genes. Using polymorphisms between the 137C strain that was used for suppressor isolation, and a new strain of C.reinhardtii (S1D2), the nuclear suppressor mutations in 7120 and 71N1 were mapped to a region on chromosome III that is essentially devoid of recombination. Based on the recombination maps, the suppressor gene in 7120 is located within a ~418-kb region from bp 2,473,064 to 2,891,232, whereas the suppressor in 71N1 is likely located within a ~236-kb subregion from bp 2,473,064 to 2,709,377. It is possible that these mutations are in the same gene; however, the maps could not be refined further due to the lack of recombination in this 418-kb region.
I also attempted to compare the genomic sequence of the 7120 suppressor, which was obtained by next-generation sequencing, with the Chlamydomonas reference genome (JGI, v.4). Next-generation sequencing of 7120 revealed the existence of abundant repetitive sequences and transposable elements clustered in a ~40-kb subregion of the recombinationally suppressed 418-kb region on chromosome III. I suggest that the high frequency of repetitive sequences and transposable elements in this region may be the reason for the suppressed recombination.
Searching for candidate genes in the mapped region led me to examine a novel protein that was predicted to have a putative chloroplast transit-peptide, and an RNA binding domain. Further bioinformatic analysis revealed a single rhodanese domain with an active-site cysteine. The protein was expressed in E.coli as the full-length and predicted mature forms, plus a small His-tag. The purified mature protein had rhodanese catalytic activity, based on the fact that it was able to transfer sulfur from thiosulfate to cyanide. Also, western blot analysis with a polyclonal antibody produced in rabbits showed that the cellular protein migrated on SDS gels close to the mature protein and faster than the full-length protein, indicative of an organelle-targeted protein. The antibody also showed that the cellular protein co-fractionated with chloroplasts. To gain insight into its in vivo function, the gene was knocked down using the tandem RNAi system (Rohr et al., 2004), which produced strains (5) with reductions of 31% to 76% in the mRNA level, and ~30% to ~60% in the protein level. These strains were sensitive to bright light, and had reduced rates of growth under all conditions, which are characteristics of chloroplast translation mutants. Thus, chloroplast protein synthesis was examined by radioisotope pulse-labeling in the presence of cycloheximide, which showed that the RNAi strains were broadly and negatively affected, and RT-PCR and northern blot revealed only normal chloroplast mRNA levels. These data have identified a new rhodanese-family enzyme that is required for chloroplast translation, which I have designated “CRLT”, for chloroplast rhodanese-like translation.text
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Kierlin-Duncan, Monique Natasha. "Using Nucleic Acids to Repair β-Globin Gene Mutations." Diss., 2007. http://hdl.handle.net/10161/178.
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Nucleic acids are an emerging class of therapeutics with the capacity to repair
both DNA and RNA mutations in clinically relevant targets. We have used two
approaches, mobile group II introns and Spliceosome Mediated RNA Trans-splicing
(SMaRT), to correct β-globin mutations at the DNA and RNA levels respectively. We
show that the group II intron inserts site-specifically into its DNA target, even when
similar targets are available. Experiments transitioning this therapeutic into mammalian
cell systems are then described. We also illustrate how SMaRT RNA repair can be used
to correct β-globin mutations involved in sickle cell disease and some forms of β-
thalassemia. We uncovered diverse repair efficiencies when targeting sickle cell versus β-
thalassemia transcripts in mammalian cells. Possible reasons for this and how it might
direct target choice for the SMaRT therapeutic approach are both discussed. The
therapeutic molecule in SMaRT, a Pre-Trans-splicing Molecule or PTM, is also delivered
via lentivirus to erythrocyte precursors cultured from the peripheral blood of sickle cell
patients. Preliminary results from these experiments are discussed.Dissertation
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Kierlin-Duncan, Monique Natasha. "Using nucleic acids to repair [beta] -globin gene mutations." Diss., 2007. http://hdl.handle.net/10161/178.
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Yu, Hsiao-Chi, and 喻筱琪. "Role of the Hepatitis B Virus (HBV) Intron and Posttranscriptional Regulatory Element (PRE) in Nuclear Export of HBV RNAs." Thesis, 2000. http://ndltd.ncl.edu.tw/handle/84407384190906844998.
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碩士國立陽明大學
微生物暨免疫學研究所
88
The hepatitis B virus posttranscriptional regulatory element (PRE) is an cis-element that is required for high-level expression of viral surface gene transcripts and appears to function by activating mRNA export to the cytoplasm. In this study, we found that the PRE not only increase the amount of the intronless surface RNA in the cytoplasm, but also increase the amount of the 3.5-kb RNA and 2.2-kb singly-spliced RNA in the cytoplasm. The PRE mutation results in a 92%, 59% and 70% decreasing in cytoplasmic accumulation of surface RNA, 3.5-kb RNA and 2.2-kb singly-spliced RNA, respectively. The cytoplasmic accumulation of 3.5-kb RNA is also affected by splice-site mutation. An approximate 26% , 16% and 25% decreasing in cytoplasmic 3.5-kb RNA, respectively, was observed when mutation was introduced into splice acceptor sites (SA1562 and SA1769), splice donor site (SD549) or both. Furthermore, in combination with PRE mutation, the cytoplasmic 3.5-kb RNA could be decreased further to 80%, 50% and 65%, respectively. In addition, these effects were also reflected on their protein products, i.e., the production of surface antigen and e antigen. On the other hand, when the splicing efficiency of 3.5-kb RNA was enhanced by changing its splice donor at nt547 to a consensus sequence, the production of 2.2-kb singly-spliced RNA increased. Under this condition, the effect of PRE on the accumulation of this species of spliced RNA was still observed. This study shows that HBV PRE element can enhance not only the cytoplsmic accumulation of intronless RNA, but also those of 3.5-kb RNA with potential intron and 2.2-kb RNA that being spliced efficiently.
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Liu, Shu-Chun, and 劉淑君. "Using intron 2 and exon 1 sequences of GFAP (glial fibrilary acidic protein) gene as novel nuclear markers to study the phylogeny of closely related primate and suborder Scombroidei species." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/59035533077407580269.
Full textAbstract:
碩士國立臺灣大學
分子與細胞生物學研究所
99
In recent years, mitochondrial DNA and microsatellite sequences are often used as the molecular markers for studying species evolution and population structure. However, to date, appropriate molecular markers for distinguishing closely related species have not been well-established. Our previous study demonstrated that the gene sequences of intermediate filaments (IFs) proteins, one of the major types of cytoskeleton, could separate vertebrates and invertebrates into two different groups in phylogenetic reconstruction. In addition, each of the vertebrate IF genes was separated into different subgroups corresponding to their IF types. Furthermore, within each subgroup, the evolutionary relationship of different species is parallel to that of species. These results suggested that the evolution of IF genes is closely related to the evolution of vertebrate species. In this study, the gene of type III intermediate filament protein GFAP (glial fibrillary acidic protein) was selected as the molecular marker. Due to its specific expression in the central nervous system, it is postulated that its selective pressure from the external environment is minimum, thus it is more likely to maintain neutral. To prove that the GFAP gene is an appropriate molecular marker, we collected the GFAP sequences of each species from the Ensembl database. Subsequently, we generated the phylogenetic tree of the GFAP gene sequences of 19 animal species by Bayesian inference (BI). The results was in agree with the currently accepted classification. Therefore, the validity of GFAP gene as a molecular marker is confirmed. Recently, it has been shown that introns have relatively large nucleotide variability, and can be easily amplified with primers placed in the adjacent exons. Thus, there are increasing number of studies using intronic sequence to investigate the phylogenetic relationship of species. In 2010, Igea et al., by applying several reasonable filters, selected 224 intronic sequences that belongs to several mammalian species, including human, chimpanzee, macaque, dog and cattle, and successfully distinguish the phylogenetic relationship of these species. Therefore, in this study, it is anticipated to characterize the appropriate introns of GFAP gene for distinguishing the closely related species. By aligning the 8 intronic sequence of GFAP gene of five primate species, including human, chimpanzee, gorilla, gibbon and macaque, it was revealed that the length of the intron 2 fragment are the same among five primate species. In addition, the phylogenetic tree of these five primate species reconstructed with GFAP intron 2 by UPGMA method was also in consensus with currently established phylogenetic relationship. Thus, the intron 2 sequence was selected as the molecular marker for the current study. The traditional classification for mammals is based on fossil evidence. On the other hand, classification of fishes is mainly based on morphology of the extant species. Thus, the aim of this study is to examine the phylogenetic relationship of species under a unified standard by examining GFAP intron 2 sequences of primates and fishes. In our study, fishes of several different families and genera in the suborder Scombroidei were selected, and their GFAP genes sequences were amplified by PCR. After sequencing, their lengths and variation were compared. The results revealed the length of GFAP intron 2 is different in each of the five fish families. Surprisingly, although from the same family of Scombridae, the length of GFAP intron 2 of the yellowfin tuna, bigeye tuna, albacore tuna,, Pacific bluefin tuna (Thunnus) and the seer fish (Scomberomorus) is distinct from that of spotted mackerel (Scomber) and frigate mackerel (Auxis). Then, we reconstructed the phylogenetic tree by intron 2 sequence from each of the fishes, the results revealed one single group among the four fishes of Scombridae and fishes of Trichiuridae. Moreover, among the Scombridae, spotted mackerel and frigate mackerel are closer to each other, but are distinct from the Thunns and seer fish. Taken together, the results suggest that the evolutionary relationship of Scombridae and Trichiuridae are closer than the currently accepted phylogenetic classification. Furthermore, it is also proposed that spotted mackerel, frigate mackerel should be separated from Thunns, seer fish, and regrouped into a new family. Besides, the protein coding region of GFAP exon 1 was also included in our analysis. The results showed that the evolutionary rate of exon 1 is higher than intron 2, thus it can be used to clarify the phylogenetic relationship of closely related fish species. In summary, the current study confirmed the validity of GFAP intron 2 and exon 1 as the molecular marker for closely related species. We have also re-examined the phylogenetic relationship of mammals and fishes, and the results shows that GFAP may have the potential to serve as one of the species barcode genes.