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Buender, Til. "Structural, biochemical and genetic dissection of RPS19 function." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609522.
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Thomas, Franck. "Expression des gènes rpl23, rpl2, rps19 et rps19' du génome chloroplastique d'épinard : identification des produits de quelques gènes de protéines ribosomiques." Grenoble 1, 1987. http://www.theses.fr/1987GRE10171.
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Le genome chloroplastique d'epinard est constitue d'une molecule d'adn circulaire (140 kbp) organisee en 4 regions: une sequence unique (lsc) et une petite sequence unique (ssc) separees par deux regions inversees repetees (ira et irb). L'expression des genes rp12, rps19 et rps19' est etudie. Les techniques de clonage et de cartographie a la nuclease s1 ont peris de montrer que le gene rps19' n'est pas exprime "in vivo" dans le chloroplaste en raison de la co-transcription sur l'autre brin des genes psba et trn h-gug. Les genes rp12 et rps19 codent respectivement pour les proteines ribosomiques chloroplastiques d'epinard l4 et s23 fortement homologues aux l2 et s19 d'e. Coli
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Drager, Robert Gray. "Structure and transcript processing of a Euglena gracilis chloroplast operon encoding genes rps2, atpI, atpH, atpF, atpA and rps18." Diss., The University of Arizona, 1993. http://hdl.handle.net/10150/186334.
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A 9.8 kbp region of the Euglena gracilis chloroplast genome has been cloned, sequenced and analyzed. This region contains six genes, rps2, rps18, atpI, atpH, atpF and atpA which encode ribosomal proteins S2 and S18 and ATP synthase subunits CFₒIV, CFₒIII, CFₒI and CF₁α, respectively. The linear order of these genes, 5'-rps2-atpI-atpH-atpF-atpA-rps18-3', is similar to that of land plant chloroplasts. These six genes are co-transcribed with two tRNA genes which are 5' to rps2. A fully spliced, 5.5 kb transcript containing all six genes accumulates. The spliced hexa-cistronic transcript is processed by intercistronic cleavage to mono-cistronic mRNAs. The 5' ends of the accumulated mono-cistronic transcripts map to single-stranded regions of the most stable secondary structure for each intercistronic sequence. There is no evidence for initiation of transcription in this region of the Euglena gracilis chloroplast genome. This Euglena chloroplast operon is interrupted by 17 introns. Nine of the introns are group III and seven are group II. All of the group III introns have potential secondary structures near their 3' ends which resemble domain VI of group II introns. The remaining intron is a complex twintron excised as four group III introns. This intron is comprised of two group III introns within the internal intron of a group III twintron. Two of the internal introns are excised from multiple splice sites. Two of the internal introns interrupt the domain VI-like structure of the host group III intron. The 16S rRNA sequence of Euglena chloroplasts is phylogenetically related to the 16S rRNA sequence of chromophyte chloroplasts, while the Euglena derived atpA amino acid sequence is more closely related to atpA sequences of chlorophyte chloroplasts than to atpA sequences of chromophyte chloroplasts. Too few chloroplast ribosomal protein sequences are available in the databases to perform meaningful phylogenetic analysis of rps2 or rps18. Although clustering of rps2 with the ATP synthase genes in chloroplasts of chlorophytes, rhodophytes, chromophytes and euglenophytes, but not prokaryotes, is evidence that chloroplasts are of mono-phyletic origin.
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Binder, Ann-Kathrin [Verfasser]. "Die prognostische Bedeutung von RPS15 Mutationen in der chronischen lymphatischen Leukämie / Ann-Kathrin Binder." Ulm : Universität Ulm, 2021. http://d-nb.info/1239180381/34.
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HILDEBRAND, MARK MICHAEL. "MOLECULAR CHARACTERIZATION OF STREPTOMYCIN RESISTANCE AND THE TRANS-SPLICING RPS12 GENE IN NICOTIANA TABACUM CHLOROPLASTS." Diss., The University of Arizona, 1987. http://hdl.handle.net/10150/184063.
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Streptomycin resistance in E. coli ribosomes is conferred by alterations in the amino acid sequence of 30S ribosomal protein S12. The alterations result from point mutations at specific locations in the rps12 gene. A point mutation at a conserved nucleotide in the 16S rRNA gene, originally identified in Euglena gracilis chloroplasts, also confers streptomycin resistance to prokaryotic-like ribosomes. The Nicotiana tabacum mutant "SR1" possesses a chloroplast-linked streptomycin resistance allele. The results presented in this thesis identify a mutation in SR116S rRNA, which occurs at the same position as in streptomycin resistant Euglena mutants. The tobacco chloroplast rps12 gene has been characterized. This gene is expressed in a unique way; two separate transcripts encoding different portions of the gene undergo a bimolecular (trans-) splicing event during mRNA maturation. C-terminal rps12 exons 2 and 3 were identified in the inverted repeat regions of the tobacco chloroplast genome. Complementary DNA sequencing of mature rps12 mRNA allowed deduction of the remaining N-terminal (exon 1) sequence. Hybridizations with synthetic oligodeoxyribonucleotide primers complementary to the deduced RNA sequence located the coding region of exon 1 to be 29 kilobasepairs (kbp) downstream of the nearest copy, and 69 kbp away from, and on the opposite DNA strand of, the distal copy, of exons 2 and 3. Northern hybridization analysis and primer extension sequencing of cDNA of rps12 transcripts indicate that exon 1 and exons 2-3 are encoded on separate transcripts. Exon 1 and exons 2-3 are covalently ligated in mature rps12 mRNA. Therefore, the separate transcripts encoding exon 1 and exons 2-3 undergo a trans-splicing event during the maturation of rps12 mRNA. A complete cloned library of tobacco chloroplast DNA was obtained, consisting of overlapping Bam HI restriction fragments. Three new restriction maps of tobacco chloroplast DNA, for the enzymes Sma I, Kpn I, and Bam HI, were derived by two-dimensional gel analysis and a novel computer-aided mapping technique.
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Loc'h, Jérôme. "Etude structurale et fonctionnelle du sous-complexe Fap7-Rps14 impliqué dans la biogenèse du ribosome." Thesis, Paris 5, 2013. http://www.theses.fr/2013PA05P628.
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Plus de 200 facteurs pré-ribosomiques sont impliqués dans la maturation des ribosomes. La majorité de ces facteurs sont essentiels à la survie cellulaire, mais la fonction précise de la plupart d’entre eux demeure inconnue. Une des dernières étapes de maturation de la petite sous-unité du ribosome est le clivage du pré-ARNr 20S en ARNr 18S mature. Ce clivage est réalisé par l'endonucléase Nob1 et nécessite également la présence de la NTPase Fap7 ainsi que d’une pléthore d’autres facteurs pré-ribosomiques. La fonction de Fap7 est particulièrement intrigante, car l'homologue humain hCINAP possède une activité adénylate kinase, activité enzymatique qui n’est généralement pas liée à la biogenèse des particules ribonucléoprotéiques. En outre, la fonction de Fap7 est intimement liée à son interaction avec la protéine ribosomique Rps14. La partie C-terminale de Rps14 est essentielle pour le clivage au niveau du site D et est située à proximité de l’extrémité 3’ de l’ARNr 18S dans le ribosome mature. La suppression de cette protéine provoque le syndrome 5q qui est phénotypiquement proche de l’anémie de Diamond-Blackfan. Ces deux protéines interviennent également au niveau d’une voie de régulation de p53 qui est dérégulée dans de nombreux cancers. La combinaison d’études structurales par cristallographie aux rayons X, d’études enzymatiques sur des protéines recombinantes ainsi que des tests de maturation in vitro réalisés sur des pré-ribosomes purifiés, nous a permis de mieux appréhender la fonction de Fap7 au sein de la sous-unité pré-40S du ribosome. Nous avons également montré que l'interaction Fap7-Rps14 est impliquée dans un changement conformationnel majeur au cœur des pré-ribosomes et que cette réorganisation est nécessaire afin d'exposer le site D pour le clivage par l’endonucléase Nob1Over 200 pre-ribosomal factors involved in the maturation of ribosomes. Most of these factors are essential to cell survival, but the precise function of most of these factors remains elusive. One of the last steps of maturation of the small subunit of the ribosome is the cleavage of 20S pre-rRNA in 18S rRNA in the cytoplasm. This cleavage is carried out by the endonuclease Nob1 and also requires the presence of other factors such as the methyltransferase Dim1, and a plethora of NTPases including the Rio protein kinases, Prp43 and its cofactor Pfa1, the Ltv1 GTPase and the Fap7 NTPase. The function of Fap7 is especially intriguing since the human homologue bears Adenylate activity, an enzymatic activity not usually linked to ribonucleoprotein biogenesis. In addition, the function of Fap7 is intimately linked its interaction with the Rps14 ribosomal protein. The Rps14 C-terminal is essential of D site cleavage and is located in proximity to the 18S C-terminus in the mature ribosome. The deletion of this protein causes the 5q syndrome that is phenotypically close to Diamond Blackfan anemia. The link between the enzymatic activity of Fap7 and its role in ribosome biogenesis remains enigmatic. Using a combination of structural studies by X-ray crystallography, small angle X-ray scattering (SAXS) in solution, enzymatic studies on purified proteins, and in vitro D site cleavage reaction assays on purified pre-ribosomes, we were able to uncover the function of Fap7 within pre-40S ribosomes. We show that the Fap7/Rps14 interaction is involved in a major conformational change at the heart of the pre-ribosomes and that this structural rearrangement is necessary to expose the D-site for cleavage by the endonuclease Nob1
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Matsson, Hans. "Studies of the Ribosomal Protein S19 in Erythropoiesis." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4283.
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Burlacu, Elena. "Probing ribosomal RNA structural rearrangements : a time lapse of ribosome assembly dynamics." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/17072.
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Ribosome synthesis is a very complex and energy consuming process in which pre-ribosomal RNA (pre-rRNA) processing and folding events, sequential binding of ribosomal proteins and the input of approximately 200 trans-acting ribosome assembly factors need to be tightly coordinated. In the yeast Saccharomyces cerevisiae, ribosome assembly starts in the nucleolus with the formation of a very large 90S-sized complex. This ~2.2MDa pre-ribosomal complex is subsequently processed into the 40S and 60S assembly intermediates (pre-40S and pre-60S), which subsequently mature largely independently. Although we have a fairly complete picture of the protein composition of these pre-ribosomes, still very little is known about the rRNA structural rearrangements that take place during the assembly of the 40S and 60S subunits and the role of the ribosome assembly factors in this process. To address this, the Granneman lab developed a method called ChemModSeq, which made it possible to generate nucleotide resolution maps of RNA flexibility in ribonucleoprotein complexes by combining SHAPE chemical probing, high-throughput sequencing and statistical modelling. By applying ChemModSeq to ribosome assembly intermediates, we were able to obtain nucleotide resolution insights into rRNA structural rearrangements during late (cytoplasmic) stages of 40S assembly and for the early (nucleolar) stages of 60S assembly. The results revealed structurally distinct cytoplasmic pre-40S particles in which rRNA restructuring events coincide with the hierarchical dissociation of assembly factors. These rearrangements are required to trigger stable incorporation of a number of ribosomal proteins and the completion of the head domain. Rps17, one of the ribosomal proteins that fully assembled into pre-40S complexes only at a later assembly stage, was further characterized. Surprisingly, my ChemModSeq analyses of nucleolar pre-60S complexes indicated that most of the rRNA folding steps take place at a very specific stage of maturation. One of the most striking observations was the stabilization of 5.8S pre-rRNA region, which coincided with the dissociation of the assembly factor Rrp5 and stable incorporation of a number of ribosomal proteins.
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Dias, Sandra Martha Gomes. "Identificação, clonagem, estrutura e transcrição do loco genico mitocondrial nad3-rps12 de Coix lacryma-job L." [s.n.], 1999. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316477.
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Orientador: Anete Pereira de SouzaDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Com o objetivo de identificar e clonar um gene novo do DNA mitocondrial (DNAmt) de Coix lacryma-jobi L. (coix), utilizou-se a estratégia da hibridização heteróloga. Para tanto amplificou-se por PCR um fragmento correspondente a um quadro de leitura aberto ("open reading frame"-oif), denominado orf167, presente no DNAmt da briófita Marchantia polymorpha, e tido como um possível gene. Marcou-se radioativamente e utilizou-se esta sequência como sonda em hibridizações com o DNAmt de coix digerido com várias enzimas. Identificou-se um fragmento homólogo Bgl II/ Bgl II de 1,4 kb, o qual foi clonado em pBluescript. Elaborou-se o mapa de restrição deste fragmento e localizou-se nele a exata região de homologia com a orf167. A região de homologia estava presente em um fragmento interno de 0,5 kb Spe I / Pvu II. Este fragmento de 0,5 kb, homólogo à orf167, foi utilizado em hibridizações com o DNArmt de várias espécies de plantas superiores (alfafa, batata, coix, couve-flor, ervilha, milho e soja), verificando-se que o mesmo correspondia a uma seqüência altamente conservada. Este mesmo fragmento foi também hibridizado em membranas contendo o RNAmt tota de oix e de outras espécies de plantas superiores (milho e couve flor). Os resultados revelaram que ele é transcrito na mitocôndria das espécies analisadas. O fragmento original de 1,4 kb Bgl II / Bgl II foi divido em 5 subfragmentos, os quais foram clonados e sequenciados. Após a análise da homologia desta sequência com outras presentes nos bancos de dados, verificou-se que o fragmento de 1,4 kb Bgl II./ Bgl II, isolado do DNAmt de coix, contém um "cluster" gênico onde estão presentes o gene que codifica o tRNA serina (tRNAScr), um pseudo-gene provavelmente originado do tRNA fenilananina (tRNAPhe), os genes nad3 e rps12. Tais genes presentes em coix são muito similares àqueles presentes em trigo e milho, os quais se organizam também em um "c1uster" gênico muito similar ao existente em coix. Estudos de expressão realizados através de "Northern Blotting" e RT ¿PCR mostraram que os genes tRNA ser, nad3 e rps12 são transcritos, sendo os dois últimos cotranscritos. Vinte e três elones de cDNA dos transcritos dos genes nad3 e rps12 foram seqüenciados, e tiveram suas sequências comparadas com a seqüência genômica. Encontrou-se 21 sítios de edição nos transcritos do gene nad3 e 8 sítios nos transcritos do gene rps12. Após comparações entre a sequência de aminoácidos predita a partir do clone genômico e do cDNA, observou-se que todas as edições modificam o aminoácido especificado pelo codon onde O evento de edição foi detectado, tornando a sequência de aminoácidos editada diferente da prevista pela sequência genômica. Vinte sítios de edição no gene nad3, e 6 no gene rps12, alteram a identidade do codon, de modo a especificar um aminoácido mais conservado durante a evolução entre diferentes espécies vegetais. Os outros três sítios, sendo I no gene nad3 e 2 no gene rps12, acarretam mudanças raras, espécie-específicas e não conservativas. Todos os 23 elones de cDNA investigados estavam diferentemente editados, predominando os cDNAs com sítios parcialmente editados. Não foi encontrada nenhuma orientação preferencial (5' para 3', ou 3' para 5') para o processamento da edição. Discute-se os motivos do reconhecimento do gene nad3 de coix pela orf167 de M. polymorpha
Abstract: We have cloned and sequenced the nad3 and rps12 mithocondrial genes from Coix lacryma-jobi L., whose sequence were found to be similar to the corresponding genes in wheat and maize. In addition, we have indentified a tRNA Ser and a pseudo-tRNA genes on the 5¿ upstream of nad3, generating a locus organization which is identical to what has been observed in wheat and maize. The locus identification was performed with a heterologous hibridization using the mitochondrial probe orf167 from Marchantia polymorpha. The gene expression was analysed using NoI1hern hybridization and RT -PCR, indicating that nad3 and rps12 gene were cotranscribed in a 1.3 kb RNA molecule. Concernig the RNA editing, we have found 21 and 8 sites in the nad3 and rps12 genes respectively. In general terms, the observed coix mRNA editing has changed the codon identities in such a way that the NAD3- and RPS12- protein aminoacid sequence was kept closer to the corresponding ones in other organisms. However, we have detected three specie-specific editing sites which were not conservative. As for the editing processing, we have analysed 23 cDNA clones which showed different editing pattems. A predominance of partial editing was observed where the edited sites were randomly distributed.
Mestrado
Genetica Vegetal e Melhoramento
Mestre em Genética e Biologia Molecular
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Elorza, Godoy Alvaro. "Etude de l'expression des gènes nucléaires codant pour les protéïnes͏ mitochondriales RPS14 et SDH2 chez Arabidopsis thaliana." Bordeaux 2, 2004. http://www.theses.fr/2004BOR21094.
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La biogenèse mitochondriale dépend de l'expression du génome nucléaire. Nous avons étudié l'expression chez Arabidopsis thaliana du gène pour la protéine ribosomale S14 (RPS14) et des 3 gènes SDH2 de la sous-unité fer-soufre du complexe II de la chaîne respiratoire (succinate déshydrogénase). RPS14, SDH2-2 s'expriment dans tous les organes des plantes adultes. Leurs transcrits sont plus abondants dans les fleurs et en particulier dans le tapis et le pollen des anthères, en accord avec le rôle connu dans les mitochondries dans le développement floral. L'analyse des promoteurs a montré que les séquences responsables de l'expression dans les anthères sont différentes chez SDH2-1 et SDH2-2, et que les 2 gènes s'expriment de façon différente dans les extrémités des racines. Le troisième SDH2 s'exprime seulement au cours de la maturation de l'embryon, contrôlé par une région du promoteur comprise entre - 220 et - 65. Le niveau du transcrit est élevé dans les graines sèches mais diminue rapidement au cours de la germination. L'expression différentielle des trois gènes SDH2 constitue la première évidence pour des rôles physiologiques différentsMitochondrial biogenesis requires expression of nuclear genes. We have characterized the expression of the gene encoding the S14 ribosomal protein (RPS14) and of the three SDH2 genes for the iron-sulfur subunit of respiratory complex II (succinate deshydrogenase) in Arabidopsis thaliana. RPS14, SDH2-1 and SDH2-2 are expressed in all organs from adult plants. Their transcript levels are higher in flowers, particularly in pollen and tapetum, in agreement with the known mitochondrial role in flower development. Promoter analysis showed that different promoter sequences are responsible for another expression in SDH2-1 and SDH2-2, and that both genes are differentially expressed in root tips. The third SDH2 gene is expressed only during embryo maturation, under the control of a promoter region located between - 220 and - 65. Opposite to SDH2-1, SDH2-2 and RPS14, SDH2-3 transcript level is high in dry seeds but decreases during germination. This is the first evidence for non-redundant functions of the three SDH2 genes. Our results show that expression of the nuclear genes for the mitochondrial proteins RPS14 and SDH2 is regulated during A. Thaliana development
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Balmant, Kelly Mayrink. "Identificação de um fator do hospedeiro, RPS5A, envolvido na interação com a proteína de movimento (MP) de geminivírus." Universidade Federal de Viçosa, 2011. http://locus.ufv.br/handle/123456789/4743.
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The movement protein MP from bipartite geminivirus (begomovirus) facilitates the cell-to-cell and long-distance transport of viral DNA in addition to affecting viral pathogenicity. To identify host factors that interact with MP, initially a cDNA library prepared from CaLCuV (Cabbage leaf curl virus)-infected Arabidopsis leaf mRNA was generated in a pEXPAD502 vector. To select for interactions between the bait BD-MP and cDNA library-encoded proteins, double transformants (BD-MP+ cDNA-AD) were plated on medium lacking histidine but supplemented with 3-aminotriazole (3-AT). From 5 x 105 transformants screened, two clones, encoding AtEXL3 (Exordium Like 3), a cell wall protein, and AtRPS5A, ribosomal protein S5A, displayed histidine/adenine auxotrophy and activate LacZ expression, on X-gal indicator plates. Expression of a full-length RPS5A cDNA fused to the Gal4 activation domain in yeast carrying BD-MP promoted growth of the double transformants in the absence of histidine and presence of 3-AT, in addition to activating high levels of LacZ expression. Furthermore, the interaction between MP and RPS5A was confirmed in vitro by pull down assays. Analysis of RPS5A gene expression by qRT-PCR demonstrated that the accumulation of rpS5A transcripts is suppressed by geminivirus infection. Based on these results and others, a functional model for the MP-RPS5A interaction is discussed.
A proteína de movimento (MP) de geminivírus bissegmentados (begomovirus) facilita o movimento célula-célula, bem como o movimento a longas distâncias do DNA viral, além de influenciar na patogenicidade viral. Com o objetivo de identificar fatores do hospedeiro que interagem com MP, inicialmente foi construída uma biblioteca de cDNA a partir de mRNAs de folhas de Arabidopsis infectadas com CaLCuV (Cabbage leaf curl virus) no vetor pEXPAD502. Para selecionar por interações entre a proteína quimérica BD-MP e proteínas codificadas pelos cDNAs da biblioteca, transformantes duplos (BDMP+ cDNA-AD) foram plaqueados em meio deficiente de histidina e suplementados com 3-amino triazol (3-AT). De um total de 5 x 105 transformantes escrutinados, dois clones, codificando EXL3 (Exordium Like 3), uma proteína de parede celular, e RPS5A, proteína ribossomal S5A, apresentaram auxotrofia a histidina e expressão do gene repórter LacZ, em placas indicadoras de X-gal. Expressão do cDNA completo de RPS5A fusionado ao domínio de ativação de Gal-4 em leveduras, carreando BD-MP, promoveu crescimento dos transformantes na ausência de histidina e presença de 3-AT, além de ativar altos níveis de expressão de LacZ.. Além disso, a interação entre MP e RPS5A foi confirmada in vitro por ensaios de pull down. Análises de expressão do gene RPS5A por meio de qRT-PCR demonstraram que o acúmulo de seus transcritos é reprimido por geminivírus. Baseado nestes resultados e de outros, um modelo funcional para interação de MP com RPS5A é discutido.
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Aguissa, Toure Almass-Houd. "Bases moléculaires de l'anémie de Diamond-Blackfan : étude structure-fonction de la protéine ribosomique RPS19 chez Saccharomyces cerevisiae." Toulouse 3, 2008. http://thesesups.ups-tlse.fr/427/.
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L'anémie de Diamond-Blackfan (ADB) est une érythroblastopénie congénitale rare associée à des mutations mono-alléliques dans plusieurs gènes de protéine ribosomique. Cette liaison suggère une relation causale entre l'altération de la biogenèse ou de la fonction des ribosomes et cette pathologie. Le gène RPS19 est le plus fréquement muté (25% des patients). Pour comprendre l'impact des mutations, en particulier les mutations ponctuelles faux-sens, nous avons engagé une étude structure-fonction de l'homologue de la protéine RPS19 chez la levure Saccharomyces cerevisiae. Parallèlement, nous avons mené un travail collaboratif pour déterminer la structure cristalline de l'homologue de RPS19 de l'archeae Pyrococcus abyssi. Nos résultats distinguent deux types de mutations : certaines, enfouies dans la structure, affectent le repliement et la stabilité de la protéine, tandis que d'autres, en surface de la protéine, inhibent l'incorporation de RPS19 dans les particules pré-ribosomiques 40S. Par ailleurs, nous avons déterminé la séquence de localisation nucléaire et les déterminants moléculaires de l'adressage nucléaire de RPS19. Les différentes mutations de RPS19 n'interfèrent pas avec ce mécanisme de transport. Ainsi, les mutations faux-sens de la protéine RPS19 affectent en premier lieu la capacité de la protéine à être incorporée dans les pré-ribosomes, ce qui altère la biogenèse des ribosomes. Ceci pourrait d'une part activer une réponse de stress et d'autre part conduire à un déficit en ribosomes, deux facteurs qui pourraient être fatals dans certains processus physiologiques comme l'érythropoïèse. Ce mécanisme peut être étendu à toute protéine ribosomique mutée dans l'ADBDiamond-Blackfan Anaemia (DBA) is a rare congenital erythroblastopenia associated with mono-allelic mutations in several ribosomal protein genes. This linkage suggests a causal relationship between alteration of ribosome biogenesis or functions and this pathology. ?The RPS19 gene is the most frequently mutated (25% of patients). To understand the impact of the mutations, especially missense mutations, we undertook a structure-function study of RPS19 homolog in yeast Saccharomyces cerevisiae and we conducted a collaborative work to determine the crystal structure of archeae Pyrococcus abyssi RPS19. Our results distinguish two types of mutations: some affect residues buried in the structure and alter the protein folding and stability, while others change amino acids at the protein surface and prevent incorporation of RPS19 into 40S pre-ribosomal particles. In addition, we determined the nuclear localization sequence and the molecular determinants of RPS19 transport to the nucleus. Mutations linked to DBA do not interfere with the nuclear localization of the protein. Thus, missense mutations in RPS19 primarily affect the ability of the protein to be incorporated into pre-ribosomes, which alters ribosome biogenesis. This could on the one hand activate a stress response and on the other hand lead to ribosome shortage, two events that could be fatal to some physiological processes like erythropoiesis. A similar mechanism can be proposed for any ribosomal protein mutated to the DBA
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Atluri, Sruthi. "Evolutionary Status of Mitochondrial Ribosomal Protein Genes rps19 and rpl2 and their Transfer to the Nucleus in Grasses." Thesis, Université d'Ottawa / University of Ottawa, 2015. http://hdl.handle.net/10393/32268.
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Massive mitochondrial gene transfer to the nucleus occurred very early during eukaryotic evolution following endosymbiosis, and is still ongoing in plants. Tracking recent gene transfer events can give us insight into the evolutionary processes by which a transferred gene becomes functional in the nucleus and how its protein gets targeted back into the mitochondrion, where it is needed. Rps19 and rpl2 are two such ribosomal protein genes that are known to have been transferred to the nucleus, many times independently during flowering plant evolution. My research project focusses on determining the status and expression of rps19 and rpl2 in the mitochondrion and nucleus of selected grasses and in particular brome (close relative to agronomically important crops such as wheat, rye and barley). My results at the level of DNA and RNA (PCR and RT-PCR, respectively) show that the mitochondrial brome rpl2 copy is a pseudogene while its functional gene is in the nucleus. The brome mitochondrial genome has a copy of rps19 which is transcribed and C-U edited. Surprisingly, the brome nuclear genome also has functional copies of rps19.The targeting sequence for the nuclear rps19 gene was acquired from duplication of mitochondrial targeting heat shock protein (hsp70) presequence. Comparative analysis strongly suggests that a functional rps19 gene was transferred to the nucleus before rice and maize lineages split and now that brome rps19 has been found to be present in both compartments, this implies a transition stage of about 60 million years. Oats was found to have a functional rps19 copy in the nucleus and has a novel presequence due to lineage specific rearrangements and exon shuffling. Functional paralogous copies were found in wheat, and maize while barley lost one of the copy. Thus, following transfer, duplication of rps19 gene must have occurred in the ancestor of barley and wheat clade. Maize might have had a recent duplication or gene conversion events along its lineage as its paralogous copies are very similar to each other. More information is needed to determine if this duplication event extends to wheat-brome, wheat-oats or even before rice and maize split. Barley was also found to have a recent independent DNA mediated transfer in addition to the common transfer, as it possesses an unedited nuc-mt rps19 in its nuclear genome. This suggests that barley must also have had a transition stage for ~60MY and lost its mitochondrial copy very recently.
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Skorski, Patricia. "Initiation de la traduction et autorégulation du gène rpsA chez Escherichia coli." Paris 6, 2006. http://www.theses.fr/2006PA066318.
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Ljungström, Viktor. "Exploring next-generation sequencing in chronic lymphocytic leukemia." Doctoral thesis, Uppsala universitet, Experimentell och klinisk onkologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-302026.
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Next-generation sequencing (NGS) techniques have led to major breakthroughs in the characterization of the chronic lymphocytic leukemia (CLL) genome with discovery of recurrent mutations of potential prognostic and/or predictive relevance. However, before NGS can be introduced into clinical practice, the precision of the techniques needs to be studied in better detail. Furthermore, much remains unknown about the genetic mechanisms leading to aggressive disease and resistance to treatment. Hence, in Paper I, the technical performance of a targeted deep sequencing panel including 9 genes was evaluated in 188 CLL patients. We were able to validate 143/155 (92%) selected mutations through Sanger sequencing and 77/82 mutations were concordant in a second targeted sequencing run, indicating that the technique can be introduced in clinical practice. In Paper II we screened 18 NF-κB pathway genes in 315 CLL patients through targeted deep sequencing which revealed a recurrent 4 base-pair deletion in the NFKBIE gene. Screening of NFKBIE in 377 additional cases identified the mutation in ~6% of all CLL patients. We demonstrate that the lesion lead to aberrant NF-κB signaling through impaired interaction with p65 and is associated with unfavorable clinical outcome. In Paper III we sought to delineate the genetic lesions that leads to relapse after fludarabine, cyclophosphamide, and rituximab treatment. Through whole-exome sequencing of pre-treatment and relapse samples from 41 cases we found evidence of frequent selection of subclones harboring driver mutations and subsequent clonal evolution following treatment. We also detected mutations in the ribosomal protein RPS15 in 8 cases (19.5%) and characterization of the mutations through functional assays point to impaired p53 regulation in cells with mutated RPS15. Paper IV aimed at characterizing 70 patients assigned to three major subsets (#1, #2, and #4) through whole-genome sequencing. Besides recurrent exonic driver mutations, we report non-coding regions significantly enriched for mutations in subset #1 and #2 that may facilitate future molecular studies. Collectively, this thesis supports the potential of targeted sequencing for mutational screening of CLL in clinical practice, provides novel insight into the pathobiology of aggressive CLL, and demonstrates the clinical outcome and cellular effects of NFKBIE and RPS15 mutations.
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Sampaio, Fernanda. "Hipóteses filogenéticas de espécies sul americanas do gênero Lippia Spp. (Verbenacea) com base em sequências nucleotídicas." Universidade Federal de Juiz de Fora (UFJF), 2009. https://repositorio.ufjf.br/jspui/handle/ufjf/3846.
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O gênero Lippia é um dos principais da família Verbenaceae e em sua maior parte está concentrado no Brasil, México, Paraguai e Argentina com poucas espécies endêmicas na África. O objetivo deste trabalho foi a construção de uma hipótese filogenética para 39 espécies do gênero Lippia ocorrentes no Brasil, Argentina, Bolívia, Paraguai e Uruguai com base em dados moleculares das regiões ITS, Waxy, TrnL-F e trnQ-rps16. As sequências foram amplificadas e purificadas para posterior seqüenciamento. As análises foram feitas utilizando-se Máxima Verossimilhança e Inferência Bayesiana. O presente trabalho revelou, pela primeira vez, aspectos filogenéticos de espécies do gênero Lippia com base em caracteres moleculares. De modo geral, as árvores filogenéticas baseadas nas diferentes regiões gênicas estudadas revelaram questões importantes como é o caso do monofiletismo da seção Goniostachyum. Outro ponto importante envolve a falta de resolução das seções Dipterocalix, Rhodolippia e Zapania. Dentre elas destaca-se a seção Zapania que constitui em vários aspectos estudados, a seção mais diversa. Embora o presente trabalho tenha mostrado aspectos inéditos com relação à organização filogenética de espécies e seções do gênero Lippia, a questão da especiação no gênero permanece em aberto. É possível que para resolver este problema sejam necessários estudos populacionais e filogeográficos, embasados por uma análise filogenética com maior número de genes e principalmente, envolvendo um maior número de espécies.
Lippia is one of the most important genus of the Verbenaceae family. It is mainly concentrated in Brazil, Mexico, Paraguay and Argentina with few endemic species in Africa. The present study was done in order to construct a phylogenetic hypothesis for 39 species of the genus Lippia from Brazil, Argentina, Bolivia, Paraguay and Uruguay based on molecular data of regions ITS, Waxy, TrnL-F and rps16-trnQ. The sequences were amplified and purified for subsequent sequencing. The phylogenetic analyses were done using the Maximum Likelihood and Bayesian Inference. It was possible to show for the first time, phylogenetic aspects of the genus Lippia based on molecular data. In general, the phylogenetic trees based on different gene regions revealed important points such as the monophyly of Goniostachyum section. Another important point involves the lack of resolution of the sections Dipterocalix, Rhodolippia and mainly Zapania which is the most diverse among them. Although this work has shown new aspects about the phylogenetic organization of sections and species of the genus Lippia, the speciation process of the genus remains an open question. To resolve this problem, additional studies using phylogeographic and population genetics approaches, based on a phylogenetic analysis with greater numbers of genes and mainly involving a great number of species should be necessary.
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Ghosh, Arnab. "Coevolution of Ribosomes and The Translational Apparatus: The Structure and Function of Eukaryotic Ribosomal Protein uS7 from Yeast, Saccharomyces cerevisiae." Cleveland State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=csu1435159279.
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C, G. GUALBERTO JOSE MANUEL. "Etude des genes nad3, rps12, orf156 et coxiii du genome mitochondrial du ble (triticum aestivum) : structure, expression et edition de leurs transcrits." Strasbourg 1, 1990. http://www.theses.fr/1990STR13091.
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Deux regions transcrites du genome mitochondrial du ble ont ete sequencees et analysees. Une de ces regions correspond a une unite de transcription contenant les genes nad3 et rps12, codant respectivement pour la sous-unite 3 de la nadh deshydrogenase et pour la proteine ribosomale s12. Ces deux genes sont precedes par un gene de trna (trns-gcu) et par un pseudo-gene de trna. Trois phases ouvertes de lecture, orf299, orf86 et orf156, sont presentes en aval de rps12. Des anticorps specifiques detectent in vivo les produits de rps12 et de l'orf156. L'autre region etudiee contient les genes coxiii et trne-uuc, codant respectivement pour la sous-unite 3 de la cytochrome oxydase et pour un trna#g#l#u. La transcription de ces sequences a ete etudiee. L'analyse de l'utilisation des codons cgg dans nad3, rps12 et coxiii a permis de demontrer qu'une activite d'edition du rna, qui remplace specifiquement des cytidines en uridines, existe dans les mitochondries vegetales. Les sites d'edition dans les genes nad3, rps12, orf299, orf156 et coxiii ont ete determines. Des similarites de sequence autour des sites d'edition suggerent que des rna anti-sens sont impliques dans la specificite de l'edition. Des clones partiellement edites de nad3 et rps12 ont ete identifies. L'ensemble des resultats montre que l'edition est un processus post-transcriptionnel qui permet la conservation des proteines mitochondriales chez les plantes superieures
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Calixte, Sophie. "RNA processing of the ccmFn-rps1 and rpl5-Psirps14-cox3 loci in wheat mitochondria during seedling development." Thesis, University of Ottawa (Canada), 2008. http://hdl.handle.net/10393/27580.
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Plant mitochondria possess a gene expression system in which post-transcriptional events, such as transcript end maturation and turnover mechanisms play a key role in regulating the transcriptome. In addition, during early developmental stages of embryo germination, differing transcript profiles have been seen. This research focuses on two loci in wheat mitochondria, ccmFn-rps1 and rpl5-Psirps14-cox3, to elucidate the transcription and post-transcriptional events involved in their expression. Northern analysis of the ccmFN-rps1 genes during early seed-to-seedling development reveals a 3.2 kb primary transcript and a 2.7 kb bicistronic mRNA. A 0.7 kb monocistronic rps1 mRNA is detectable up to 2d but there is no detectable monocistronic ccmFN transcript during the stages examined. Transcript ends were mapped using circular-RT-PCR and phosphatase treatment at three different developmental stages and revealed two processing sites as well as a single 3' end common to all three transcripts. The 5' ends of the processed rps1 transcripts are heterogeneous and do not always include the start codon, questioning the rps1 transcript functionality.
Gene order varies between plant species due to the high recombination rate in mitochondrial genomes, as is seen for rpl5-Psirps14 in wheat and rice. In both plants, the functional rps14 gene is encoded in the nucleus and the mitochondrial rps14 copy is a pseudogene. In wheat, rpl5-Psirps14 are co-transcribed with cox3 as two RNA species of 3.5 kb and 2.7 kb at 24hr post-imbibition and exhibit developmentally-specific differences in abundance in seedlings. Two promoter regions were mapped in wheat upstream of rpl5 and both transcripts have the same 3' end. In rice 24hr and 6d however, rpl5-Psirps14 are co-transcribed as a 1.4 kb bicistronic mRNA. This presumably reflects the different regulatory signals used in different species. In addition, rpl5 has been subject to several independent gene transfers to the nucleus in the cereal lineages. For example, there is a functional copy of rpl5 in the mitochondria and the nucleus in wheat but it is absent from the mitochondria in rye and maize. In oat mitochondria, rpl5 appears to be a pseudogene and in barley, rearrangements at the 3' end and low transcript levels question its functionality.
The characterization of transcription initiation sites, processing sites and 3' ends for these two loci reflect the relaxed nature and flexibility of signals exploited by plant mitochondria. This research supports the significant role of post-transcriptional events in the regulation of gene expression in plant mitochondria.
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Raoelijaona, Raivoniaina. "Compréhension des rôles des complexes Nob1/Pno1 et RPS14/Cinap dans la maturation cytoplasmique de la petite sous-unité ribosomique (pré-40S) chez les eucaryotes." Thesis, Bordeaux, 2019. http://www.theses.fr/2019BORD0221/document.
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Les ribosomes sont des complexes nucléoproétiques responsables de la traduction. Chez les eucaryotes, la biogenèse du ribosome est un processus complexe très régulé qui fait intervenir un nombre important de facteurs d’assemblages (~200). La construction d’un ribosome est initiée dans le nucléole puis continue dans le nucléoplasme et se termine dans le cytoplasme. La maturation cytoplasmique de la petite sous-unité ribosomale implique la dissociation séquentielle des facteurs d’assemblage tardifs et la maturation finale de l’ARNr 18S. Ce processus est catalysé par l’endonucléase Nob1 qui assure la coupure de l’extrémité 3’ du précurseur de l’ARNr 18S (pré-18S) aboutissant à sa forme mature. Ce mécanisme est coordonné par la protéine Pno1 qui est le partenaire de Nob1. Des informations détaillées sur l’architecture des particules pré-ribosomiques nous ont permis de mieux comprendre les différents intermédiaires de la biogenèse. Cependant, certains aspects fonctionnels comme la conformation adoptée par Nob1 pour assurer la coupure du site D du pre-18S reste encore flou. L’objectif de mon travail a été de mieux comprendre les aspects très tardifs de la maturation cytoplasmique du ribosome. Pour ce faire, nous avons redéfini l’organisation modulaire de l’endonucléase Nob1 chez les eucaryotes pour ensuite étudier son mode d’interaction avec son partenaire Pno1. Des tests fonctionnels in vitro ont été effectués pour étudier le rôle de Pno1 dans la régulation de la coupure par Nob1.Nos résultats nous ont permis de montrer que le domaine catalytique de Nob1 adopte une conformation atypique. En effet le domaine PIN est composé de deux fragments (res 1-104 and 230-255) séparé par une boucle interne qui est importante pour la reconnaissance avec son partenaire Pno1. Nos études nous ont également montré que Pno1 inhibe l’activité de Nob1 probablement en reconnaissant directement l’ARNr substrat, masquant ainsi le site de coupure de l’endonucléase. Ces résultats sont complémentaires et cohérents avec les données structurales de cryo-EM de la particule pré-40S humaine récemment publiées. En effet, Nob1 est dans une conformation incapable de couper le pré-ARNr puisque son domaine catalytique se retrouve à une distance d’environ 30Å de son ARN substrat. Ce phénomène implique donc des changements de conformations ou encore la nécessité de protéine accessoire pour déplacer certains facteurs. La protéine Cinap est impliqué dans la maturation de l’ARNr 18S. Nos études d’interaction avec les protéines localisées au niveau de la plateforme (à savoir RPS14, RPS26, le complexe Nob1/Pno1) ont permis de montrer que Cinap pouvait former un complexe tripartite avec l’endonucléase Nob1 et son partenaire Pno1. De plus, Cinap est capable de reconnaitre RPS26 dans un complexe RPS14-dépendant. Il est important de noter que RPS26 est un composant de la petite sous-unité qui remplace Pno1 dans le ribosome mature. De ce fait le recrutement de RPS26 au sein du pré-ribosome nécessite la dissociation de Pno1 et cet échange serait assurée par Cinap. Sur la base des travaux effectués, nous pouvons proposer un modèle de maturation où la formation du complexe Cinap/Pno1 induirait un changement de conformation permettant à Nob1 de reconnaitre son substrat et donc de catalyser la coupure du site D qui aboutit à la maturation de l’ARNr 18S et donc à la production de la sous-unité 40S matureRibosomes are translational machineries universally responsible of protein synthesis. In eukaryote, ribosome assembly is a complex and highly regulated process that requires coordinated action of more than 200 biogenesis factors. Ribosome assembly is initiated in the nucleolus, continues in the nucleoplasm and terminates in the cytoplasm. The cytoplasmic maturation events of the small ribosomal subunit are associated with sequential release of the late assembly factors and concomitant maturation of the pre-rRNA. During final maturation of the small subunit, the pre-18S rRNA is cleaved off by the endonuclease Nob1, which activity is coordinated by its binding partner Pno1. Detailed information on pre-ribosomal particle architectures have been provided by structural snapshots of maturation events. However, key functional aspects such as the architecture required for pre-rRNA cleavage have remained elusive. In order to better understand these late steps of cytoplasmic pre-40S maturation, we first redefine the domain organization of Nob1, then study its binding mode with Pno1 using different tools such as sequence analysis, structure prediction and biochemical experiments and, we then performed functional assay to elucidate the role played by Pno1 during the pre-18S rRNA maturation.Our results have shown that eukaryotic Nob1 adopts an atypical PIN domain conformation: two fragments (res 1-104 and 230-255) separated by an internal loop, which is essential for Pno1 recognition. We also found out that Pno1 inhibits Nob1 activity likely by masking the cleavage site. Our findings further support the recently published cryo-EM structure of the pre-40S, where Nob1 displays an inactive conformation. Moreover, 18S rRNA 3’-end cleavage has to happen and this implies structural rearrangement or requirement of some accessory proteins such as Cinap, an atypical kinase involved in pre-18S processing. Studying the interplay between proteins localized in the pre-40S platform (RPS14, RPS26, Nob1/Pno1 complex) has shown that Cinap is able to form a trimeric complex with Nob1 and its binding partner Pno1. Furthermore, Cinap can recognize RPS26 in a RPS14-dependent manner, which had already been studied with its yeast counterpart. It is important to note that RPS26 is the ribosomal protein replacing Pno1 in the mature ribosome. Our finding clearly suggests a mechanism where RPS26 recruitment to the ribosome requires Pno1 dissociation. This exchange would be carried out by Cinap. Therefore, we can suggest a simplified model as follow: upon binding with Pno1, the newly formed complex (Cinap/Pno1) will trigger a conformational change, which will allow the endonuclease Nob1 to reach its substrate (D-site) and perform its cleavage resulting in mature 18 rRNA generation
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Esklual, Ghalia A. Y. [Verfasser]. "A phylogenetic study of Crepis L. species sect. Barkhausia (Asteraceae) using low-copy nuclear genes (gsh1, sqs) and plastid genes (rps16, matK1) / Ghalia A. Y. Esklual." Gießen : Universitätsbibliothek, 2017. http://d-nb.info/1127506722/34.
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Esklual, Ghalia [Verfasser]. "A phylogenetic study of Crepis L. species sect. Barkhausia (Asteraceae) using low-copy nuclear genes (gsh1, sqs) and plastid genes (rps16, matK1) / Ghalia A. Y. Esklual." Gießen : Universitätsbibliothek, 2017. http://d-nb.info/1127506722/34.
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Villain, Patricia. "Fonction transcriptionnelle du site 1 : élément cis du gène nucléaire d'épinard RPS1 codant pour la protéine ribosomique plastidiale CS1." Université Joseph Fourier (Grenoble), 1995. http://www.theses.fr/1995GRE10187.
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La boite site 1, element de liaison du facteur nucleaire de feuilles d'epinard s1f, a ete identifiee, dans notre laboratoire, au niveau du promoteur du gene d'epinard rps1. Ce gene nucleaire code pour une proteine ribosomique plastidiale, cs1. L'etude des elements cis et de leurs facteurs trans, identifies au niveau des promoteurs de ce type de gene, constitue un bon modele pour la comprehension des mecanismes d'action, au niveau genetique, des facteurs internes (lies au type cellulaire) de la differenciation plastidiale. L'expression des genes nucleaires codant pour les proteines ribosomiques plastidiales est, en effet, regulee au niveau transcriptionnel, selon le type d'organe et de maniere independante de la lumiere. Nous avons etudie le site 1 in vivo, par la realisation de tabacs transgeniques, et in vitro par des experiences d'interactions proteines/adn (gels retards). Nos resultats in vivo montrent que l'element site 1 a une fonction specifique au sein des organes contenant des amyloplastes, comme les racines, et differente de celle observee dans les feuilles: dans les premiers, il fonctionne apparemment comme un element negatif de transcription, mais d'apres les experiences d'interactions in vitro, ce serait plutot un element positif faible de transcription. Cette fonction differente de l'element site 1 est correlee a une activite de liaison a cette boite, in vitro, qui est differente selon l'organe etudie. Les experiences de gel retard montrent, en effet, qu'il existe dans les racines, un facteur de liaison a l'element site 1, qui possede une specificite et une affinite de liaison relativement plus faibles que celles du facteur de feuille: nous l'avons appele s1r. Nous avons etudie l'homologie, pour la liaison, in vitro, de facteurs proteiques, de la boite site 1 avec d'autres elements cis: elle est homologue a la boite site 3 (element cis du promoteur du gene rps1), et elle est apparentee, mais non identique, a l'element box ii (element cis du promoteur du gene rbcs-3a de pois). Comme pour l'element site 1, ce travail a permis de mettre en evidence, dans les racines, une activite de liaison a l'element box ii differente de celle caracterisee dans les feuilles: ce facteur, gt-1r, a une specificite de liaison relativement plus faible que celle du facteur de feuille. Nos resultats montrent qu'il pourrait exister, dans les racines, une activite inhibitrice i qui permettrait a gt-1r de se fixer a l'element box ii dans cet organe. D'apres ces resultats, nous proposons deux modeles, qui decrivent in vivo et selon l'organe, la nature des activites de liaison aux boites site 1 et box ii, et les fonctions de ces boites et de leurs facteurs pour l'expression des genes rps1 et rbcs-3a
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Brown, Catherine. "The phylogeography, biomass allocation and phenology of Salicornia tegetaria (S. Steffen, Mucina & G. Kadereit) Piirainen & G. Kadereit, an endemic salt marsh species in South Africa." University of the Western Cape, 2018. http://hdl.handle.net/11394/6248.
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Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv & Cons Biol)Salicornia tegetaria is an endemic salt marsh macrophyte that is widely distributed in estuaries along the South African coast. The aims of the study were to understand the phylogeography of the species, compare the biomass allocation in two regions and to determine phenological patterns of S. tegetaria between the warm and cool temperate biogeographical regions. The phylogeography of S. tegetaria was studied using the noncoding chloroplast DNA region rpS16 and nuclear rDNA ITS region. Five samples each were collected from eighteen estuaries stretching from Orange River in the Northern Cape to Mngazana Estuary in the Eastern Cape. Above- and belowground biomass was collected and physico-chemical conditions measured at Olifants, Berg and Langebaan Estuaries in the cool temperate, and Heuningnes, Nahoon and Kwelera Estuaries in the warm temperate biogeographical regions. The growth and flowering phenology of S. tegetaria in relation to environmental conditions was investigated in the cool temperate Langebaan Estuarine Embayment and compared to findings in the warm temperate, permanently open Kowie Estuary. The physico-chemical gradient found between the cool and warm temperate biogeographical regions may be useful to study climate change effects on plant species. The comparison of similar habitats in each region may provide insight into how different climate regimes may affect biomass allocation and phenology.
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Brown, Catherine Eileen. "The phylogeography, biomass allocation and phenology of Salicornia tegetaria (S. Steffen, Mucina & G. Kadereit) Piirainen & G. Kadereit, an endemic salt marsh species in South Africa." University of the Western Cape, 2018. http://hdl.handle.net/11394/6391.
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Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv & Cons Biol)Salicornia tegetaria is an endemic salt marsh macrophyte that is widely distributed in estuaries along the South African coast. The aims of the study were to understand the phylogeography of the species, compare the biomass allocation in two regions and to determine phenological patterns of S. tegetaria between the warm and cool temperate biogeographical regions. The phylogeography of S. tegetaria was studied using the noncoding chloroplast DNA region rpS16 and nuclear rDNA ITS region. Five samples each were collected from eighteen estuaries stretching from Orange River in the Northern Cape to Mngazana Estuary in the Eastern Cape. Above- and belowground biomass was collected and physico-chemical conditions measured at Olifants, Berg and Langebaan Estuaries in the cool temperate, and Heuningnes, Nahoon and Kwelera Estuaries in the warm temperate biogeographical regions. The growth and flowering phenology of S. tegetaria in relation to environmental conditions was investigated in the cool temperate Langebaan Estuarine Embayment and compared to findings in the warm temperate, permanently open Kowie Estuary. The physico-chemical gradient found between the cool and warm temperate biogeographical regions may be useful to study climate change effects on plant species. The comparison of similar habitats in each region may provide insight into how different climate regimes may affect biomass allocation and phenology.
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Badhai, Jitendra. "Ribosomal proteins in diamond-blackfan anemia Insights into failure of ribosome function /." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-110070.
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Toscano, Guerra Emily Marisol. "Detección de ácido pirazinoico como biomarcador de resistencia a pirazinamida en Mycobacterium tuberculosis mediante dos inmunoensayos empleando nanopartículas magnéticas, tmRNA y RpsA." Bachelor's thesis, Universidad Nacional Mayor de San Marcos, 2018. https://hdl.handle.net/20.500.12672/7298.
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Diseña un sistema que detecte al ácido pirazinoico (POA), el cual es producto del metabolismo de la bacteria y principio activo de la droga. Cuando una bacteria es sensible al tratamiento con pirazinamida, produce POA en los cultivos a determinado ratio, sin embargo, aquellas resistentes no producen o producen muy poco. Se logró ensamblar dos sistemas de detección, el Sistema I consistió en acoplar la proteína RpsA y su tmRNA a una nanopartícula magnética de estreptavidina a través del tmRNA biotinilado, mientras que el Sistema II, consistió en acoplar las mismas moléculas a una nanopartícula magnética de cobalto, pero a través de la cola de histidinas de la proteína RpsA. Estos sistemas fueron enfrentados de forma preliminar, a POA comercial. Como resultado se obtuvo que el primer sistema logró detectar hasta cinco picomoles del ácido, sin embargo, estos resultados no lograron ser reproducibles. El segundo sistema logró detectar hasta 750 picomoles del ácido, y se logró reproducir en dos ocasiones. Los sistemas fueron estables y demostraron estar ensamblados correctamente, sin embargo, la variabilidad en los resultados de detección de POA, aquí presentados, estarían indicando que la interacción entre el RpsA y el POA no es tan fuerte como se mencionó en estudios anteriores. El resultado de este trabajo estaría confirmando lo reportado en un último estudio publicado en Nature, el cual refuta la hipótesis de que el ácido pirazinoico se une a RpsA con gran afinidad.Innóvate Perú
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Gunadi, Andika. "Characterization of Rps8 and Rps3 Resistance Genes to Phytophthora sojae through Genetic Fine Mapping and Physical Mapping of Soybean Chromosome 13." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1354640151.
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Fröjmark, Anne-Sophie. "Molecular Studies of Diamond-Blackfan Anemia and Congenital Nail Dysplasia." Doctoral thesis, Uppsala universitet, Institutionen för genetik och patologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-128067.
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The aim of this thesis is to investigate the effect of genetic mutations on the pathophysiology of two human disorders: Diamond-Blackfan Anemia (DBA) and isolated congenital nail dysplasia. The first part of this thesis (Paper I-III) investigates the mechanism associated with DBA. DBA is a rare bone marrow failure syndrome characterized by the absence or decrease of erythroid precursor cells. The disease is further associated with growth retardation, malformations, predisposition to malignant disease and heterozygous mutations in ribosomal protein (RP) genes. The second part of this thesis (Paper IV) investigates the genetic basis of isolated autosomal recessive nail dysplasia characterized by pachyonychia and onycholysis of both finger- and toenails. It further dissects the molecular mechanisms regulating nail development. In the first study, we investigated the previously reported RPS19/PIM-1 interaction by generating a combined Rps19/Pim-1 knockout mouse model. We found that allelic Rps19 insufficiency and Pim-1 deficiency have a cooperative effect on murine hematopoiesis resulting in increased myeloid cellularity associated with cell cycle alterations and reduced apoptosis. In the second study, we analyzed primary fibroblasts from DBA patients with truncating mutations in RPS19 or RPS24 and observed a marked delay in cellular growth associated with specific cell cycle defects. In the third study, we discovered that recombinant RPS19 binds its own mRNA and that the binding is altered when two DBA-associated RPS19 mutations are introduced. In the fourth study, we identified mutations in the WNT signaling receptor Frizzled 6 (FZD6). We observed that the nonsense mutant fails to interact with the first downstream effector Dishevelled. Fzd6 mutant mice displayed claw malformations and we detected a transient Fzd6 expression in the distal digits at the embryonic time point for nail development. In summary, this thesis elucidates several mechanisms in the etiology of DBA and congenital nail dysplasia and mechanisms regulating nail development.
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Kronhamn, Jesper. "Genetic analysis of genes found on the 4th chromosome of Drosophila - emphasizing the developmental context of Pax6." Doctoral thesis, Umeå universitet, Molekylärbiologi (Teknat- och Medfak), 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-287.
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The small size and the lack of recombination set the fourth chromosome of Drosophila melanogaster apart from the other chromosomes. I have shown that the Minute gene on chromosome 4, earlier named Minute-4, encodes the ribosomal protein RpS3A. Two Pax6 genes, eyeless (ey) and twin of eyeless (toy) are also located on chromosome 4. Pax6 genes are important in head and eye development in both mammals and Drosophila. I have focused much of the study on ey and toy. The first mutant of toy that was characterized showed a headless phenotype. This indicates that Toy is important for the development of both the eye and antennal discs. The phenotype of the null mutation in toy is temperature sensitive due to that transcription of ey is temperature dependent in the eye-antennal primordium in absence of Toy. This temperature dependence was used to find out that the phenocritical period for ey in the adult head development is during embryonic stage 12-16 when ey first is expressed in the eye-antennal primordium. I also conclude that ey is activated by Toy in the eye-antennal primordium. The strong eyD mutation was molecularly characterized and it was finally settled that it is an allele in the ey locus. I also show that eyD homozygotes have a headless phenotype, much stronger than the earlier ey mutations.
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Cortese, Diego. "Genomic and transcriptomic sequencing in chronic lymphocytic leukemia." Doctoral thesis, Uppsala universitet, Institutionen för immunologi, genetik och patologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-303703.
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Identification of recurrent mutations through next-generation sequencing (NGS) has given us a deeper understanding of the molecular mechanisms involved in chronic lymphocytic leukemia (CLL) development and progression and provided novel means for risk assessment in this clinically heterogeneous disease. In paper I, we screened a population-based cohort of CLL patients (n=364) for TP53, NOTCH1, SF3B1, BIRC3 and MYD88 mutations using Sanger sequencing, and confirmed the negative prognostic impact of TP53, SF3B1 or NOTCH1 aberrations, though at lower frequencies compared to previous studies. In paper II, we assessed the feasibility of targeted NGS using a gene panel including 9 CLL-related genes in a large patient cohort (n=188). We could validate 93% (144/155) of mutations with Sanger sequencing; the remaining were at the detection limit of the latter technique, and technical replication showed a high concordance (77/82 mutations, 94%). In paper III, we performed a longitudinal study of CLL patients (n=41) relapsing after fludarabine, cyclophosphamide and rituximab (FCR) therapy using whole-exome sequencing. In addition to known poor-prognostic mutations (NOTCH1, TP53, ATM, SF3B1, BIRC3, and NFKBIE), we detected mutations in a ribosomal gene, RPS15, in almost 20% of cases (8/41). In extended patient series, RPS15-mutant cases had a poor survival similar to patients with NOTCH1, SF3B1, or 11q aberrations. In vitro studies revealed that RPS15mut cases displayed reduced p53 stabilization compared to cases wildtype for RPS15. In paper IV, we performed RNA-sequencing in CLL patients (n=50) assigned to 3 clinically and biologically distinct subsets carrying stereotyped B-cell receptors (i.e. subsets #1, #2 and #4) and revealed unique gene expression profiles for each subset. Analysis of SF3B1-mutated versus wildtype subset #2 patients revealed a large number of splice variants (n=187) in genes involved in chromatin remodeling and ribosome biogenesis. Taken together, this thesis confirms the prognostic impact of recurrent mutations and provides data supporting implementation of targeted NGS in clinical routine practice. Moreover, we provide evidence for the involvement of novel players, such as RPS15, in disease progression and present transcriptome data highlighting the potential of global approaches for the identification of molecular mechanisms contributing to CLL development within prognostically relevant subgroups.
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Popp, Magnus. "Disentangling the Reticulate History of Polyploids in Silene (Caryophyllaceae)." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3918.
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El-Habbak, Mohamed H. "OVEREXPRESSION/SILENCING OF SELECTED SOYBEAN GENES ALTERS RESISTANCE TO PATHOGENS." UKnowledge, 2013. http://uknowledge.uky.edu/plantpath_etds/8.
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Plant diseases remain a major obstruction to meeting the world’s increased demand for soybean oil and protein. Reducing the losses caused by diseases in order to improve crop production is a high priority for agricultural research. The need for novel strategies for plant disease control cannot be overstated. In the present study, selected defense-related genes were silenced and/or overexpressed in soybean using a virus-based vector and the resultant plants were tested for their responses to pathogens. The first part of the study focused on Rps1k (Resistance to Phytophthora sojae) gene. The two conserved domains encoding ‘P-Loop NTPase’ and ‘PLN03210’ of Rps1k were independently overexpressed. Stem inoculation assays for the overexpressing plants showed significant resistance to virulent races; 90% standing plants compared to 10% in controls. Lesion length was greatly restricted only in case of plants overexpressing ‘PLN03210’. Simultaneous silencing of Rps1k-1 and Rps1k-2 resulted in remarkable susceptibility to avirulent races when tested by a detached-leaf assay. The second part of the study entailed silencing/overexpression of the chlorophyllase genes GmCLH1 and GmCLH2 and testing the responses of the silenced/overexpressing plants to the sudden death pathogen Fusarium virguliforme. Four weeks post root inoculation, GmCLH2-silenced plants showed enhanced resistance while the GmCLH2-overexpressing plants exhibited markedly increased susceptibility when compared to empty vector control. RT-PCR assay of PR genes revealed elevated expression of PR2 and PR4 in GmCLH2-silenced plants. In the third part of the study, soybean plants silenced for a leucine-rich repeat receptor-like kinase (GmRLK3) gene were examined for their responses to different pathogens. Silencing of GmRLK3 enhanced susceptibility to infection with Alternaria tenuissima or Sclerotinia sclerotiorum as revealed by rapid disease progress on treated leaves. Surprisingly, silencing of GmRLK3 in known susceptible soybean cultivars rendered the silenced plants resistant to P. sojae. The ensuing partial resistance to P. sojae was consistent with results of RT-PCR assays that showed a significant increase in the transcript level of the osmotin-encoding gene (PR5a) in the GmRLK3-silenced plants. PR5a is considered a marker for systemic acquired resistance.
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Backlund, Maria. "Phylogenetic Studies in the Gentianales – Approaches at Different Taxonomic Levels." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6124.
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Eggens, Frida. "Systematics in Sileneae (Caryophyllaceae) : taxonomy and phylogenetic patterns /." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7380.
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Franzetti, Bruno. "Structure, fonction et expression de la protéine ribosomique chloroplastique CS1." Grenoble 1, 1992. http://www.theses.fr/1992GRE10099.
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Le controle de l'initiation de la traduction est une etape importante de l'expression des genes chloroplastiques et fait intervenir, chez e. Coli, la proteine ribosomique (proteine-r) s1. Afin d'etudier l'etape d'initiation de la traduction chez le chloroplaste, nous avons caracterise chez spinacia oleracea une proteine (cs1) apparentee a la proteine s1. Nous avons isole un adnc codant pour le precurseur de la proteine-r cs1. Cs1 est considerablement plus courte que sa contrepartie bacterienne. Un noyau central homologue se compose de trois repetitions degenerees qui presentent de l'homologie principalement avec le domaine de liaison a l'arn de la proteine s1 d'e. Coli. Cs1 a ete surproduite dans e. Coli et purifiee. Nous avons etudie les proprietes de liaison a l'arn de la proteine cs1 au sein de la sous-unite ribosomique 30s et de la proteine isolee. Nous montrons que cs1 joue un role actif dans la liaison des arnm durant l'initiation de la traduction. Les implications de ces resultats pour la comprehension du systeme traductionnel du chloroplaste sont discutees. Dans la seconde partie de ce travail, nous avons montre que l'arnm codant pour la proteine-r cs1 est synthetise tres precocement durant les premieres etapes du developpement des plantes et est accumule meme en absence de lumiere. Nous avons clone et sequence la totalite de la region codante ainsi que la region 5 regulatrice du gene nucleaire unique (rps1) codant pour cs1. Nous avons observe la presence de deux departs de transcription. L'arnm le plus long code par le gene rps1 est specifiquement transcrit dans les feuilles. Ces resultats sont a relier a une accumulation differentielle de l'arnm cs1 dans les racines et dans les feuilles. Ces observations nous amenent a conclure que le gene de menage rps1 est regule transcriptionnellement de maniere tissu-specifique
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"Ribosomal protein mutants and their effects on plant growth and development." Thesis, 2012. http://hdl.handle.net/10388/ETD-2012-10-758.
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Ribosomes, large enzymatic complexes containing an RNA catalytic core, drive protein synthesis in all living organisms. 80S cytoplasmic eukaryotic ribosomes are comprised of four rRNAs and approximately 80 ribosomal proteins (r-proteins). R-proteins are encoded by gene families with large families (average of twelve members) predominating in mammals and smaller families (two to seven members) in plants. Increased ribosome heterogeneity is possible in plant ribosomes due to multiple transcriptionally active members in each family, whereas, in mammalian r-protein gene families, only one member is typically active. Multiple functional paralogs provide for greater plasticity in response to environmental/developmental cues, as well as, increasing the possibility of individual paralogs procuring or retaining extraribosomal functions. This research investigated the effects of r-protein mutations on plant growth and development. Through RNA interference (RNAi) mediated knockdown (KD) of type I (cytoplasmic: RPS15aA/D and F) and type II (non-cytosolic: RPS15aB and E) RPS15a family members I was able to confirm the delineation between the two types. Subcellular localization of the type I isoforms was nuclear/nucleolar while localization of type II isoforms was non-mitochondrial and probably cytosolic. Illumina sequencing of two r-protein mutant transcriptomes, pfl1 (rps18a) and pfl2 (rps13a), identified a novel set of up and down regulated genes, previously unknown or linked to r-protein mutants. The 20 genes identified were classified into four groups (1) plant defense, (2) transposable elements, (3) nitrogen metabolism and (4) genes with unknown function. Illumina miRNOME analysis revealed no changes in the miRNA profile of pfl1 and pfl2 plants. These data do not support the previously proposed theory that a disruption in ribosome biogenesis (by decreased r-protein synthesis) disrupts miRNA-mediated degradation of a range of auxin response genes. Finally, a novel double r-protein mutant, rps18a:HF/RPL18B, presented a late flowering/thickened bolt phenotype not seen in a rps13a:HF/RPL18B mutant, suggesting that RPS18A has an extraribosomal role in plant growth and development in Arabidopsis.
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Mei, Hsu Chen, and 徐珍梅. "The relationship between streptomycin resistance and the chloroplast rps12 gene of Nicotiana plumbaginifolia." Thesis, 1993. http://ndltd.ncl.edu.tw/handle/68434421486840717838.
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Wu, San-pin, and 吳上賓. "Studies on the promoter-specific binding protein of the chloroplast psaA-psaB-rps14 operon." Thesis, 1996. http://ndltd.ncl.edu.tw/handle/06212535716452319995.
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"Identificação, clonagem, estrutura e transcrição do loco genico mitocondrial nad3-rps12 de Coix lacryma-job L." Tese, Biblioteca Digital da Unicamp, 1999. http://libdigi.unicamp.br/document/?code=vtls000188404.
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Aidoo, Francisca Ama. "Understanding the Mechanism of Aberrant FLVCR1 Splicing and Disrupted erythropoiesis in Diamond-Blackfan Anemia." Thesis, 2012. http://hdl.handle.net/1807/32515.
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Diamond Blackfan Anemia (DBA) is a congenital disorder characterized by a specific reduction in erythroid progenitor cells. Approximately 55% of patients have heterozygous mutations in ribosomal protein with 25% of these mutations in RPS19. However, it is unclear how a defect in ribosomal proteins specifically disrupts erythroid development. FLVCR1, a heme exporter, has been implicated as a potential DBA factor. FLVCR1 is essential for erythropoiesis as its disruption leads to apoptosis and disrupted erythroid differentiation. Though no FLVCR1 mutations have been found in DBA patients, our lab has shown that it is aberrantly spliced in DBA erythroid cells. Using RPS19 reduced K562 erythroid cells, I found that disruption of RPS19 leads to aberrant FLVCR1 splicing, disrupted erythropoiesis and reduced Tra2-β, ASF2 and SRp30c protein expression. This was specific to DBA as I did not find these features in a cell culture model of Shwachmann Diamond Syndrome, another ribosomal disorder.
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Chen, Wei-Jyun, and 陳韋君. "SNP Genotypes of GH, KRT5, RPS8 and COL1A1 Genes Associated with Velvet Antlers Traits in Formosan Sambar." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/88956796323245788280.
Full textAbstract:
碩士中興大學
動物科學系所
99
Formosan sambar (Rusa unicolor swinhoei) is endemic subspecies in Taiwan. The price of the velvet antlers is higher than other livestock products. The study was performed to analysis the genotypes in association with velvet antlers production of the GH (growth hormone), KRT5 (keratin 5), RPS8 (ribosomal protein S8), and COL1A1 (collagen, type I, alpha 1) genes by LIS-SSCP and PCR-RFLP. The specific primers were designed by Primer Express software to amplify the target DNA fragments from Formosan sambar genomic DNA by PCR, and followed by SSCP analysis. Single nucleotide polymorphisms (SNPs) were found by sequencing technology, and then processed PCR-RFLP and multiplex minisequencing method for genotyping. Further study was to investigate the correlation between genotypes and performance in Formosan sambar by SAS program. The results showed that, in the SNP C222T of GH gene, the velvet antler weight in 1st-10th saw with CC type seemed to higher than the CT and TT types in Formosan sambar (P < 0.20) , and velvet antler weight in 1st-3rd saw with CC type was significant higher than the CT and TT types (P < 0.05) ; In the SNP G323A, the velvet antler weight in 1st-3rd saw with AA type seemed to higher than the GA and GG types, but in 4th-6th saw with GA type seemed to higher than the GG type, and in 7th-10th saw with GA type seemed to higher than the AA type (P < 0.20). In the SNP C88T of RPS8 gene, the velvet antler weight in 1st-3rd saw with CC type seemed to higher than the TT type (P < 0.20). The velvet antler weight in 1st-10th saw of CC type of COL1A1 gene seemed to higher than the TT type, but in 7th-10th saw, CC type seemed to higher than the CT type (P < 0.20). These genes may involve in the formation of velvet antler, but need increase the sample size to confirm the results. The results may be useful in Formosan sambar breeding.