The work presented explored the in vivo and in vitro synthesis of ribosomal RNA in the Gram positive, spore-forming bacterium Bacillus subtilis. The investigation began with a study of rRNA synthesis in B. subtilis during steady state growth and under nutritional shift-up conditions. The percent of transcription which is ribosomal RNA was measured by hybridization of pulse labeled RNA to a specific DNA probe carrying the 3' end of the 23S RNA gene. The fractional rate of ribosomal RNA synthesis increased with cellular growth rate, and showed a rapid increase after a nutritional shift up. RNA synthesis during infection with an amber mutant of bacteriophage SP01 was also examined. Infected cells continued to synthesize rRNA at the preinfection rate, but could not respond to media enrichment by increasing the percent rRNA-synthesis. The latter study suggested the existence of a specific RNA polymerase that transcribed ribosomal RNA genes. The conclusions from the in vivo study led to an analysis of rRNA transcription in vitro. The isolation of the putative ribosomal RNA specific RNA polymerase was attempted by affinity chromatography on cellulose complexed with plasmid DNA containing the promoter region of the B. subtilis rrnB rRNA operon, and by sedimentation through a glycerol gradient. No difference in activity profile was observed when transcription activity at the rRNA tandem promoters was compared to activity at a non-ribosomal promoter. Since in vivo analysis of the control of rRNA synthesis in Escherichia coli suggested that regulation occurs at the level of transcription initiation, in vitro transcription initiation at the B. subtilis rRNA promoters was investigated using the single round transcription assay. Initial rates of transcription were different at each of the two tandem promoters of the B. subtilis rrnB operon: the upstream promoter, PI, initiated slowly, while the downstream promoter, P2, initiated faster. In addition, transcription initiation at the two promoters appeared to be linked. The formation of a heparin resistant complex at the PI promoter affected the stability of the heparin resistant complex formed at the P2 promoter. The kinetics of transcription initiation at the tandem rRNA promoters were examined using the tau plot analysis. RNA polymerase had a high affinity for both rRNA promoters, but the rate of initiation at these promoters was relatively slow when compared to non-ribosomal promoters. Finally, transcription initiation on two artificial tandem promoter constructs was compared with initiation on the native tandem promoter construct. In general, PI was shown to have a positive effect on transcription from downstream promoters, but had specific effects on different promoters. / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

Diss. (sammanfattning) Stockholm : Karol inst., 2003. / Härtill 4 uppsatser.

Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 70-81).

S:Als darrers 10 anys, el nostre coneixement de l'evolució dels animals ha estat objecte d'una revolució degut a l'aplicació de la Biologia Molecular al camp de la Filogènia, que ha rebutjat algunes hipòtesis antigues i n'ha proposat de noves. Un dels canvis més importants és el que subdivideix a tots els animals amb simetria bilateral (els Bilateria) en tres grups: els Lophotrochozoa, els Ecdysozoa y els Deuterostomata. Malgrat el gran cabdal d'informació que han suposat, les dades moleculars no han estat capaces de resoldre totes les relacions entre els fílums. Al començament, això era degut al l'ús de pocs marcadors moleculars, que no portaven prou informació i que patien artefactes metodològics com el Long Branch Atraction. L'objectiu d'aquest projecte és obtenir una filogènia molecular dels bilaterals el més resolta possible, mitjançant l'aplicació de dues aproximacions. La primera fa us de la gran quantitat de dades disponibles dels gens nuclears del RNA ribosomal (18S i 28S) a l'hora que es minimitza l'impacte dels artefactes filogenètics; s'ha obtingut una matriu de 104 representants dels bilaterals, pertanyents a 28 fílums i amb 3.700 parells de bases de longitud. Aquesta matriu s'ha analitzat mitjançant mètodes d'inferència filogenètica de tipus probabilístic (Maxima Versemblança i Inferència Bayesiana), tot fent servir models evolutius sofisticats i compartimentant les anàlisis pels grups problemàtics. La segona aproximació pretén construir una matriu dels bilaterals que maximitzi tant el nombre de marcadors com el de fílums representats. S'han seleccionat 13 gens candidat i recollit mostres per un total de 96 espècies de 31 fílums. S'han obtingut un total de 135 seqüències, que junt amb seqüències de les bases de dades, s'han fet servir per construir una matriu de 90 representants de 27 fílums amb 8.880 parells de bases de longitud i un 40% de missing data. Aquesta matriu s'ha analitzat amb mètodes d'inferència probabilístics.Els resultats principals dels dos estudis son: 1) es comprova la monofilia dels tres grans grups de bilaterals, així com la posició d'Acoela i Nemertodermatida com a bilaterals basals, 2) s'obté una filogènia resolta dels deuteròstoms, mentre que la filogènia dels ecdisozous resulta en una tricotomia i 3) s'obté una nova filogènia dels lofotrocozous, a on cal destacar als gnatostomulats i gastrotrics com els fílums més basals, la posició dels platihelmints com a grup germà de la resta d'animals espirals i la parafilia dels espirals degut a la posició de braquiòpodes i foronidis com a grup germà dels mol·luscs, 4) la filogènia obtinguda situa a Xenoturbella dins dels deuteròstoms, tot i que amb un suport molt baix, i no es pot descartar una posició més basal dins dels bilaterals, 5) els Chaetognatha pertanyen als ecdisozous, tot i que la posició exacta dins dels mateixos és dubtosa, i 6) la filogènia obtinguda ens ha permès especular sobre l'evolució de determinades característiques del patró corporal, mostrant la gran plasticitat de la seva aparició i la prevalença de l'adquisició independent d'algunes d'elles. / "Bilaterian molecular phylogeny: a multigenic approach"TEXT:Resolving the relationships among animal phyla is a key biological problem that remains to be solved. Morphology has been unable to determine the relationships among most phyla. During the past decade studies based on a limited number of markers established new hypotheses such as the existence of three bilaterian superclades (Deuterostomia, Ecdysozoa and Lophotrochozoa) but left major questions unresolved.The aim of this project is to obtain a well resolved bilaterian phylogeny applying two approaches. The first uses the great quantity of information available for 18S and 28S genes, while overcoming their pitfalls by combining several methods suggested in previous studies. A matrix was built, comprising 104 bilaterian representatives for 28 phyla and it is 3,700 base pairs long. The methods used include Maximum Likelihood and Bayesian Inference, the application of models with rate-heterogeneity across sites, wide taxon sampling, and compartmentalized analyses for each problematic clade. The second approach is based on maximizing the number of markers and the number of representatives. 13 genes were chosen as candidates and tissues for 96 species belonging to 31 phyla were sampled. 135 sequences were obtained, and used together with databases sequences to build a matrix 8,880 base pairs long, with 90 representatives for 27 bilaterian phyla and bears 40% of missing data.The results obtained show 1) the monophyly of the three superclades and the basal position of a paraphyletic Acoelomorpha, 2) a well resolved deuterostomates phylogeny, while ecdysozoan relationships turn up as a tricotomy, 3) a new lophotrochozoan phylogeny is obtained with gnathostomulids and gastrotrichs as the most basal phyla, flatworms as sistergroup to spiralians animals, and spiralians are paraphyletic due to the position of brachiopods and phoronids as sistergroup to molluscs, 4) Xenoturbella is shown within deuterostomates, though a more basal position cannot be rejected, 5) Chaetognatha belong to Ecdysozoa, though its exact position cannot be solved, and 6) the obtained phylogeny was used for a speculative discussion on morphological traits evolution, showing their great evolving plasticity.

by Wai-Man Tong. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 155-174). / Abstracts in English and Chinese. / ABSTRACT --- p.I-IV / Chapter 1. --- INTRODUCTION / Chapter 1.1. --- General / Chapter 1.1.1. --- Ribosome Inactivating Protein --- p.1 / Chapter 1.1.1.1. --- Ricin --- p.2 / Chapter 1.1.1.2. --- Trichosanthin --- p.5 / Chapter 1.1.2. --- In Vitro Study of RIP --- p.6 / Chapter 1.2. --- Uptake of Ribosome Inactivating Proteins / Chapter 1.2.1. --- Suicide Transport --- p.7 / Chapter 1.2.1.1 . --- Endocytic Uptake of Ricin --- p.8 / Chapter 1.2.1.2. --- Endocytic Uptake of Trichosanthin --- p.11 / Chapter 1.2.2. --- Pervious Studies in This Laboratory --- p.11 / Chapter 1.3. --- Apoptosis And Ribosome Inactivation / Chapter 1.3.1. --- Apoptosis / Chapter 1.3.1.1. --- Morphological Feature of Apoptosis --- p.14 / Chapter 1.3.1.2. --- Molecular Changes of Apoptosis --- p.15 / Chapter 1.3.2. --- Toxicity of Ribosome Inactivating Protein / Chapter 1.3.2.1. --- Toxicity of Ricin --- p.20 / Chapter 1.3.2.2. --- Toxicity of Trichosanthin --- p.21 / Chapter 2. --- MATERIALS AND METHODS / Chapter 2.1. --- GENERAL / Chapter 2.1.1. --- Cell Culture / Chapter 2.1.1.1 . --- Schwann Cell Culture --- p.23 / Chapter 2.1.1.2. --- Dorsal Root Ganglion Neuron Culture --- p.24 / Chapter 2.1.1.3. --- Identification of Schwann Cell and Dorsal Root Ganglion Neuron --- p.25 / Chapter 2.1.2. --- Labeling of Toxins --- p.26 / Chapter 2.1.3. --- Administration of Toxin --- p.27 / Chapter 2.2. --- UPTAKE OF RIBOSOME INACTIVATING PROTEINS / Chapter 2.2.1. --- Real-Time Observation of Toxin Uptake by Neurons --- p.27 / Chapter 2.3. --- APOPTOSIS STUDY OF RIBOSOME INACTIVATING PROTEINS' TOXICITY / Chapter 2.3.1. --- TUNEL Staining --- p.28 / Chapter 2.3.2. --- Annexin V Staining --- p.30 / Chapter 2.4. --- MOLECULAR STUDY OF THE DEATH MECHANISM OF RIBOSOME INACTIVATING PROTEINS / Chapter 2.4.1. --- NIH/3T3 Cell Line Culture --- p.33 / Chapter 2.4.2. --- Differential Display / Chapter 2.4.2.1. --- Differential Display --- p.34 / Chapter 2.4.2.2. --- Cloning and Sequencing --- p.38 / Chapter 2.4.2.3. --- RT-PCR --- p.42 / Chapter 2.4.3. --- Two Dimension Gel Electrophoresis --- p.43 / Chapter 2.4.4. --- Ribosomal RNA Analysis --- p.48 / Chapter 3. --- RESULTS / Chapter 3.1. --- General / Chapter 3.1.1. --- Cell Culture / Chapter 3.1.1.1 . --- Schwann Cell Culture --- p.50 / Chapter 3.1.1.2. --- Dorsal Root Ganglion Neuron Culture --- p.51 / Chapter 3.1.1.3. --- Identification of Schwann Cell and Dorsal Root Ganglion Neuron --- p.51 / Chapter 3.1.2. --- RIPs Labeling --- p.52 / Chapter 3.2. --- Uptake of Ribosome Inactivating Protein / Chapter 3.2.1. --- Real-Time Observation of Toxin Uptake --- p.53 / Chapter 3.3. --- Apoptosis Study of Ribosome Inactivating Proteins' Toxicity / Chapter 3.3.1. --- TUNEL Staining --- p.55 / Chapter 3.3.2. --- Annexin V Assay / Chapter 3.3.2.1. --- Schwann Cell Culture --- p.57 / Chapter 3.3.2.2. --- Dorsal Root Ganglion Neuron Culture --- p.58 / Chapter 3.3.2.3. --- Unique Observable Pattern --- p.60 / Chapter 3.4. --- Molecular Study of the Death Mechanism of Ribosome Inactivating Proteins / Chapter 3.4.1. --- NIH/3T3 Cell Line Culture --- p.60 / Chapter 3.4.1.1. --- TUNEL Staining --- p.61 / Chapter 3.4.1.2. --- Annexin V Staining --- p.61 / Chapter 3.4.2. --- Differential Display / Chapter 3.4.2.1. --- Observation --- p.61 / Chapter 3.4.2.2. --- Primer Combination --- p.62 / Chapter 3.4.2.3. --- Differential Display --- p.62 / Chapter 3.4.3. --- Two-Dimensional Gel Electrophoresis / Chapter 3.4.3.1. --- Observation --- p.63 / Chapter 3.4.3.2. --- Comparison of Gels --- p.63 / Chapter 3.4.4. --- Ribosomal RNA Analysis --- p.63 / Chapter 4. --- DISCUSSION / Chapter 4.1. --- General / Chapter 4.1.1. --- The Selection of In Vitro Model / Chapter 4.1.1.1. --- Schwann Cell Culture --- p.65 / Chapter 4.1.1.2. --- Dorsal Root Ganglion Neuron Culture --- p.66 / Chapter 4.1.2. --- Labeling of Toxins with Fluorochromes --- p.67 / Chapter 4.1.3. --- Dosage Used in In Vitro Study --- p.68 / Chapter 4.2. --- Uptake of Ribosome Inactivating Proteins / Chapter 4.2.1. --- Real-Time Examination of Toxin Uptake --- p.69 / Chapter 4.3. --- Involvement of Apoptosis in Ribosome Inactivating Proteins' Intoxication / Chapter 4.3.1. --- TUNEL Staining --- p.75 / Chapter 4.3.2. --- Annexin V and Propidium Iodide Staining --- p.77 / Chapter 4.3.3. --- Special Pattern of Fluorescence Signal in Neuronal Cell Bodies --- p.82 / Chapter 4.4. --- Molecular Study of Death Mechanism of Ribosome Inactivating Proteins / Chapter 4.4.1. --- NIH/3T3 Cell Line Culture --- p.84 / Chapter 4.4.2. --- Differential Display --- p.84 / Chapter 4.4.3. --- Two Dimensional Polyacrylamide Gel Electrophoresis --- p.86 / Chapter 4.4.4. --- Ribosomal RNA Alternation --- p.88 / Chapter 5. --- CONCLUSIONS --- p.89 / Chapter 6. --- "FIGURES, GRAPHS AND LEGENDS" --- p.91 / Chapter 7. --- REFERENCES --- p.155 / APPENDIX / Appendix A Materials --- p.175 / Appendix B Source of Chemicals and Equipments --- p.184 / ACKNOWLEDGEMENTS --- p.186

Diss. (sammanfattning) Linköping : Linköpings universitet, 2008. / Härtill 5 uppsatser.

No description available.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2006. / Härtill 3 uppsatser.

Dbp2p, a member of the large family of DEAD-box proteins and a yeast homolog of human p68, was shown to interact with Upf1p, an essential component of the nonsense-mediated mRNA decay pathway. Dbp2p:Upf1p interaction occurs within a large conserved region in the middle of Upf1p that is largely distinct from its Nmd2p and Sup35/45p interaction domains. Deletion of DBP2, or point mutations within its highly conserved DEAD-box motifs, increased the abundance of nonsense-containing transcripts, leading us to conclude that Dbp2p also functions in the nonsense-mediated mRNA decay pathway. Dbp2p, like Upf1p, acts before or at decapping, is predominantly cytoplasmic, and associates with polyribosomes. Interestingly, Dbp2p also plays an important role in rRNA processing. In dbp2Δ cells, polyribosome profiles are deficient in free 60S subunits and the mature 25S rRNA is greatly reduced. The ribosome biogenesis phenotype, but not the mRNA decay function, of dbp2Δ cells can be complemented by the human p68 gene. We propose a unifying model in which Dbp2p affects both nonsense-mediated mRNA decay and rRNA processing by altering rRNA structure, allowing specific processing events in one instance and facilitating dissociation of the translation termination complex in the other.

Neste trabalho realizamos a análise das variações na expressão gênica global durante a fase de esporulação do fungo aquático Blastocladiella emersonii utilizando a tecnologia dos microarranjos de cDNA em lâminas contendo 3.773 genes distintos. Ao todo 615 genes foram classificados como induzidos enquanto 645 foram classificados como reprimidos ao longo da esporulação. As categorias funcionais mais representadas entre os genes induzidos foram: microtúbulo e citoesqueleto, transmissão de sinal, atividade de ligação ao íon Ca2+, proteólise (apenas no início da esporulação) e biogênese e organização do cromossomo (apenas no final da esporulação). Dentre os genes reprimidos, as categorias funcionais mais representadas foram: biossíntese de proteína, transporte de carboidratos e metabolismo energético. A comparação dos dados de expressão gênica da esporulação com aqueles obtidos recentemente em nosso laboratório para a germinação mostrou um grande número de genes regulados inversamente ao longo das duas fases de diferenciação do ciclo de vida de B. emersonii. Muitos genes induzidos na esporulação são reprimidos na germinação e vice versa. Analisamos também o efeito de glicose e triptofano sobre a expressão gênica durante a formação dos zoósporos, tendo em vista que tais nutrientes são capazes de inibir a esporulação de B. emersonii. Nossos resultados mostraram que na presença de glicose (1%) genes envolvidos na composição e atividade do citoesqueleto foram superexpressos, enquanto na presença do aminoácido triptofano houve um aumento na expressão de genes envolvidos no processo de enovelamento de proteínas e proteólise, e na resposta ao estresse oxidativo. Além disso, genes envolvidos no processo de esporulação propriamente dito foram reprimidos durante o tratamento com triptofano. Investigamos também a via de sinalização por GMP cíclico (cGMP), cujos níveis aumentam consideravelmente durante a esporulação de B. emersonii. Iniciamos o estudo com uma busca no banco de ESTs de B. emersonii (http://blasto.iq.usp.br) por seqüências que codificassem enzimas envolvidas na síntese e degradação de cGMP. Foram encontradas três ESTs que codificam domínios catalíticos que parecem pertencer a três diferentes guanilato ciclases e uma EST codificando uma fosfodiesterase com alta similaridade com fosfodiesterases que possuem alta afinidade por cGMP. Experimentos de microarranjos de cDNA validados por RT-PCR quantitativo em tempo real mostraram que os quatro transcritos são expressos durante esporulação, com picos de indução durante a fase tardia da esporulação, momento em que ocorre a biogênese dos zoósporos. Além disso, dados obtidos a partir de experimentos in vivo e in vitro utilizando inibidores das enzimas guanilato ciclase e óxido nítrico sintase, sugeriram a participação do íon Ca2+ e do radical livre óxido nítrico (•NO) na atividade de guanilato ciclase, em uma via do tipo Ca2+-•NO-cGMP. / In the present work, we analyzed global gene expression changes during the sporulation phase of the aquatic fungus Blastocladiella emersonii using cDNA microarray technology with chips containing 3773 distinct genes. A total of 615 genes were upregulated and 645 were down-regulated along the sporulation of the fungus. The overrepresented functional categories among the induced genes were: microtubule and cytoskeleton, signal transduction, Ca2+ binding activity, proteolysis (only at the beginning of sporulation), and chromosome biogenesis and organization (only at the end of sporulation). Among the down-regulated genes, the over-represented functional categories were: protein biosynthesis, carbohydrate transport, and energetic metabolism. Sporulation gene expression data were compared with those obtained recently in our laboratory for the germination phase, showing that a great number of genes are inversely regulated along the two differentiation stages of B. emersonii life cycle. We also analyzed the effects of glucose and tryptophan on gene expression during biogenesis of the zoospores, as such nutrients are able to inhibit B. emersonii sporulation. Our results showed that in the presence of glucose (1%) genes related to activity and composition of cytoskeleton were over-expressed, while in the presence of tryptophan genes involved in protein folding, proteolysis and oxidative stress were induced. In addition, genes involved in the sporulation process per se were downregulated by tryptophan treatment. We also investigated the cyclic GMP signaling pathway, as the levels of this cyclic nucleotide increase considerably during B. emersonii sporulation. Firstly, we searched for sequences encoding enzymes involved in cGMP synthesis and degradation using the B. emersonii EST databank (http://blasto.iq.usp.br). Three sequences were found encoding distinct guanylate cyclase catalytic domains, and one showed high similarity with phosphodiesterases that exhibit high affinity for cGMP. Microarray experiments, validated by real time quantitative RT-PCR, showed that the four transcripts are induced during sporulation, reaching maximum levels at the late stages of sporulation, when zoospore biogenesis occurs. In addition, data obtained from in vivo and in vitro experiments using inhibitors for the enzymes guanylate cyclase and nitric oxide synthase indicated the involvement of the ion Ca2+ and the free radical nitric oxide (•NO) in guanylate cyclase activity, suggesting the existence of a Ca2+-• NO-cGMP signaling pathway.