<p>The stringent response plays a significant role in the survival of bacteria during different environmental conditions. It is activated by the binding of stringent factor (SF) to stalled ribosomes that have an unacylated tRNA in the ribosomal A-site which leads to the synthesis of (p)ppGpp. ppGpp binds to the RNA polymerase, resulting in a rapid down-regulation of rRNA and tRNA transcription and up-regulation of mRNAs coding for enzymes involved in amino acid biosynthesis. The importance of the A-site and unacylated tRNA in the activation of SF was confirmed by chemical modification and subsequent primer extension experiments (footprinting experiments) which showed that binding of SF to ribosomes resulted in the protection of regions in 23S rRNA, the A-loop and helix 89 that are involved in the binding of the A-site tRNA. An in vitro assay showed that the ribosomal protein L11 and its flexible N-terminal part was important in the activation of SF. Interestingly the N-terminal part of L11 was shown to activate SF on its own and this activation was dependent on both ribosomes and an unacylated tRNA in the A-site. The N-terminal part of L11 was suggested to mediate an interaction between ribosome-bound SF and the unacylated tRNA in the A-site or interact with SF and the unacylated tRNA independently of each other. Footprinting experiments showed that SF bound to the ribosome protected bases in the L11 binding domain of the ribosome that were not involved in an interaction with ribosomal protein L11. The sarcin/ricin loop, in close contact with the L11 binding domain on the ribosome and essential for the binding and activation of translation elongation factors was also found to be protected by the binding of SF. Altogether the presented results suggest that SF binds to the factor-binding stalk of the ribosome and that activation of SF is dependent on the flexible N-terminal domain of L11 and an interaction of SF with the unacylated tRNA in the A-site of the 50S subunit.</p>

The stringent response plays a significant role in the survival of bacteria during different environmental conditions. It is activated by the binding of stringent factor (SF) to stalled ribosomes that have an unacylated tRNA in the ribosomal A-site which leads to the synthesis of (p)ppGpp. ppGpp binds to the RNA polymerase, resulting in a rapid down-regulation of rRNA and tRNA transcription and up-regulation of mRNAs coding for enzymes involved in amino acid biosynthesis. The importance of the A-site and unacylated tRNA in the activation of SF was confirmed by chemical modification and subsequent primer extension experiments (footprinting experiments) which showed that binding of SF to ribosomes resulted in the protection of regions in 23S rRNA, the A-loop and helix 89 that are involved in the binding of the A-site tRNA. An in vitro assay showed that the ribosomal protein L11 and its flexible N-terminal part was important in the activation of SF. Interestingly the N-terminal part of L11 was shown to activate SF on its own and this activation was dependent on both ribosomes and an unacylated tRNA in the A-site. The N-terminal part of L11 was suggested to mediate an interaction between ribosome-bound SF and the unacylated tRNA in the A-site or interact with SF and the unacylated tRNA independently of each other. Footprinting experiments showed that SF bound to the ribosome protected bases in the L11 binding domain of the ribosome that were not involved in an interaction with ribosomal protein L11. The sarcin/ricin loop, in close contact with the L11 binding domain on the ribosome and essential for the binding and activation of translation elongation factors was also found to be protected by the binding of SF. Altogether the presented results suggest that SF binds to the factor-binding stalk of the ribosome and that activation of SF is dependent on the flexible N-terminal domain of L11 and an interaction of SF with the unacylated tRNA in the A-site of the 50S subunit.

MicroRNAs are small noncoding RNAs that post-transcriptionally reduce protein output from most human mRNAs by mechanisms that are still obscure. This thesis provides insights into three aspects of microRNA biogenesis and function described below. MicroRNA precursors are excised from primary transcripts by the Microprocessor complex containing Drosha and DGCR8. Although most microRNAs are located in introns of protein-coding and noncoding genes, the mechanisms coordinating microprocessing and splicing are unclear. MiR-211 is a microRNA expressed from intron 6 of melastatin, a suspected melanoma tumor suppressor. We demonstrate that miR-211, and not melastatin, is responsible for the tumor suppressive function of this locus, that Drosha-mediated processing of the miR-211 precursor promotes splicing of melastatin exon 6-exon 7 junctions, and that perturbing 5' splice site recognition by the U1 snRNP reduces Drosha recruitment to intron 6 specifically and intronic microRNA levels globally. Thus we identify a novel physical and functional coupling between microprocessing and splicing. Typically, Agos stabilize mature microRNAs and as a complex stoichiometrically bind to complementary mRNAs. We demonstrate an alternative order of events in which Agos bind and repress pre-formed imperfect microRNA-mRNA duplexes in processing bodies of live cells, and cleave pre-formed perfect microRNA-mRNA duplexes in vitro. Our data support a novel catalytic model whereby Agos first deposit microRNAs onto mRNAs and dissociate, thus priming multiple microRNA-mRNA duplexes for concurrent repression by a single Ago. Despite key roles in development and pathogenesis, effectors and regulators of microRNA-mediated repression are still poorly characterized. An RNAi screen revealed that depletion of ribosomal proteins of either small or large ribosomal subunit dissociates microRNA-containing complexes from mRNAs repressed at translation initiation, increasing their polysome association, translation, and stability relative to untargeted mRNAs. Thus ribosomal proteins globally regulate microRNA function. Another RNAi screen revealed that Akt3 phosphorylates Ago2, which negatively regulates cleavage and positively regulates translational repression of microRNA-targeted mRNAs. Thus Ago2 phosphorylation is a molecular switch between its mRNA cleavage and translational repression activities. The following pages will place these novel insights into biological and disease-relevant context, will describe what was known prior to these studies, and will provide perspectives for future studies.

Fluorescence-based techniques are widely used in bioscience, offering a high sensitivity and versatility. In this work, fluorescence electronic energy migration/ transfer is applied to measure intramolecular distances in two types of systems and under various conditions. The main part of the thesis utilizes the process of donor-acceptor energy transfer to probe distances within the ribosomal protein S16. Proteins are essential to all organisms. Therefore, it is of great interest to study protein structure and function in order to understand and prevent protein malfunction. Moreover, it is also important to try to study the proteins in an environment which resembles its natural habitat. Here two protein homologs were investigated; S16Thermo and S16Meso, isolated from a hyperthemophilic bacterium and a mesophilic bacterium, respectively. It was concluded that the chemically induced unfolded state ensemble of S16Thermo is more compact than the corresponding ensemble of S16Meso. This unfolded state compaction may be one reason for the increased thermal stability of S16Thermo as compared to S16Meso. The unfolded state of S16 was also studied under highly crowded conditions, mimicking the environment found in cells. It appears that a high degree of crowding, induced by 200 mg/mL dextran 20, forces the unfolded state ensemble of S16Thermo to become even more compact. Further, intramolecular distances in the folded state of five S16 mutants were investigated upon increasing amounts of dextran 20. We found that the probed distances in S16Thermo are unaffected by increasing degree of crowding. However, S16Meso shows decreasing intramolecular distances for all three studied variants, up to 100 mg/mL dextran. At higher concentrations, the change in distance becomes anisotropic. This suggests that marginally stable proteins like s16Meso may respond to macromolecular crowding by fine-tuning its structure. More stable proteins like S16Thermo however, show no structural change upon increasing degree of crowding. We also investigated the possibility of local specific interactions between the protein and crowding agent, by means of fluorescence quenching experiments. Upon increasing amounts of a tyrosine labelled dextran, a diverse pattern of fluorescence quantum yield and lifetime suggests that specific, local protein-crowder interactions may occur. In a second studied system, electronic energy migration between two donor-groups, separated by a rigid steroid, was studied by two-photon excitation depolarization experiments. Data were analysed by using recent advances, based on the extended Förster theory, which yield a reasonable value of the distance between the two interacting donor-groups. To the best of our knowledge, this is the first quantitative analysis of energy migration data, obtained from two-photon excited fluorescence.

Aspergillus fumigatus is a foodborne and airborne human pathogen which produces mycotoxins such as gliotoxin, helvolic acid, fumigallin, and fumigaclavin. The most common disease caused by A. fumigatus is aspergillosis, which is often fatal, especially among AIDS, cancer, and organ-transplant patients. In this study, random cDNA cloning was performed from a cDNA library of A. fumigatus (IMI 385708) constructed on &amp / #955 / ZAP Express. Some of these clones were selected according to their insert sizes and were further subjected to sequence analysis. The sequences were then analyzed by a BLAST search (NCBI Genome Database) to determine the possible functions of these genes. Two of the clones were identified as the primase and 60S ribosomal protein L1-b genes. These genes and a third gene corresponding to the antigenic cell wall galactomannoprotein gene of A. fumigatus were used for the design of three distinct primer pairs. For the primer design, a software was written to differentiate nonconserved regions by multiple sequence alignment. Designed primers were employed in PCR experiments against genomic DNAs of different Aspergillus species. Unique bands were obtained only against A. fumigatus genomic DNA. It was concluded that this PCR-based detection method can be further developed for the rapid detection of A. fumigatus spores from air and food samples.

Thesis (Ph. D.) -- University of Texas Southwestern Medical Center at Dallas, 2006. / Embargoed. Vita. Bibliography: 104-116.

Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2012-08-01T18:14:31Z No. of bitstreams: 1 Melissa Moura Abbehusen Estudo da imunogenicidade de vacinas de....pdf: 867164 bytes, checksum: 4ef801f12d349f64700eea900fccfc9b (MD5) / Made available in DSpace on 2012-08-01T18:14:31Z (GMT). No. of bitstreams: 1 Melissa Moura Abbehusen Estudo da imunogenicidade de vacinas de....pdf: 867164 bytes, checksum: 4ef801f12d349f64700eea900fccfc9b (MD5) Previous issue date: 2011 / Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, Bahia, Brasil / A Proteína ácida ribossomal de Leishmania infantum (L. infantum) - LiP0 é um componente estrutural da subunidade maior do ribossomo e já foi descrita como um antígeno imunodominante, que participa na síntese de outras proteínas e é capaz de induzir resposta imune humoral específica em soro de pacientes e cães infectados com Leishmania chagasi (L. chagasi). Mycobacterium smegmatis (M. smegmatis), é uma micobactéria oportunista, que apresenta crescimento rápido e uma poderosa capacidade adjuvante, já sendo utilizado como vetor de expressão para diversos antígenos. Neste trabalho avaliamos a capacidade imunoprotetora do Mycobacterium smegmatis recombinante (rM.smegmatis) expressando o gene que codifica a LiP0, bem como o plasmídeo e/ou proteína LiP0 utilizando estratégia homóloga (composta de plasmídeo de DNA) e heteróloga (composta de plasmídeo de DNA adicionado a proteína recombinante e CpG), contra a infecção causada por L. chagasi em hamsters. Hamsters foram imunizados e posteriormente infectados com L. chagasi por via endovenosa. Os animais imunizados com a micobactéria, apesar de apresentarem resposta imune humoral anti-M. smegmatis, não produziram anticorpo contra LiP0, que só foram detectados no soro dos animais que receberam a estratégia heteróloga de imunização. Na análise de citocinas, observou-se que os animais imunizados com rM.smegmatis LiP0 apresentaram maior concentração de IFN-γ e menor quantidade de TGF-ß e IL-10 quando comparado aos grupos controle, sugerindo uma resposta Th1. Em diferentes momentos após o desafio, o grau de proteção avaliado pela carga parasitária em órgãos alvo, foi estimado por ensaio de diluição limitante. Nenhuma diferença foi observada na carga parasitaria do baço, fígado e linfonodo em hamsters imunizados ou controles em todos os pontos da avaliação, sugerindo que a LiP0, não protegeu hamsters imunizados tanto com o Mycobacterium expressando o gene que codifica a proteína, nem como vacina de DNA utilizando a estratégia homóloga ou heteróloga contra infecção por L.chagasi. / The acid ribosomal protein of Leishmania infantum (L. infantum) - LiP0 is a structural component of the ribosomal subunit and it was described as an immunodominant antigen recognized either by serum of patients and dogs infected by Leishmania chagasi (L. chagasi) and cooperates in the synthesis of other proteins. Mycobacterium smegmatis (M. smegmatis) is a opportunistic bacteria, which presents rapid growth, is a potent adjuvant and has been used as carrier of antigens in several different experimental models of immunoprotection. In this work we evaluate the immunoprotective capacity of recombinant M. smegmatis (rM. smegmatis) carrying the gene of LiP0 and the DNA or protein of LiP0 using homologous strategy (composed of plasmid DNA) and heterologous (consisting of plasmid DNA and recombinant protein more CpG) to immunize hamsters against infection by L. chagasi. The immunized animals produced anti-M.smegmatis antibodies but they did not produce antibody against LiP0, detected only in animals who received the heterologous strategy of vaccination. In the analysis of cytokines, we observed that animals immunized with rM.smegmatis LiP0 had higher concentration of IFN-γ and lower amounts of TGF-ß and IL-10 compared to control groups, suggesting a Th1 response. At different times after challenge, the degree of protection, evaluated by parasite load in the target organs, was estimated by limiting dilution assay. No difference was observed in the parasite load in the spleen, liver and lymph node between immunized hamsters and controls at all points of evaluation. There was no protection in animals immunized with rM. smegmatis expressing the acidic ribosomal protein gene, suggesting that LiP0 did not protect hamsters immunized with either Mycobacterium expressing the gene encoding the protein or DNA as a vaccine strategy using homologous or heterologous against infection L.chagasi.

No description available.

No description available.

No description available.