A significant focus of nucleic acids research is on the reactivity of electrophilic species with DNA to form addition products (adducts). Phenols are known to be able to form adducts at the C8 site of deoxyguanosine (dG). This dissertation studies the oxygen (O)-linked class of phenolic dG adducts for their hydrolytic stability as well as their structural impact on the DNA duplex. To determine the effect of C8 O-linked phenolic dG adducts on glycosidic bond stability spectrophotometric determination of hydrolysis kinetics was performed. The kinetics establish the adducts to be less stable than native dG in acid, but surprisingly stable under physiological conditions. Then to assess the modified duplex structure, a C8 O-linked phenolic dG adduct was incorporated into a DNA duplex. Thermal melting analysis establish the adduct as having a destabilizing effect on the regularly paired duplex and the conformational analysis suggests the phenolic lesion to be weakly mutagenic. / NSERC

Trichomonas vaginalis é o protozoário flagelado que parasita o sistema urogenital humano causando a tricomoníase, a doença sexualmente transmissível não viral mais comum no mundo, sendo registrados aproximadamente 276 milhões de novos casos a cada ano. O sucesso da colonização das células hospedeiras e desenvolvimento da infecção envolve um complexo processo que culmina em citoaderência e citotoxicidade. Nucleotídeos e nucleosídeos são liberados para o espaço extracelular por células em situações de estresse ou lesão tecidual e desencadeiam seus efeitos sinalizadores através da ativação de purinoceptores. Ainda, a hidrólise sequencial de nucleotídeos pelas ectonucleotidases, nucleosídeo trifosfato difosfoidrolase (NTPDase) e ecto-5’-nucleotidase leva à formação de nucleosídeos que são essenciais para o metabolismo de purinas do parasito. Efeitos antagônicos são desencadeados por nucleotídeos e nucleosídeos, respectivamente próinflamatórios e anti-inflamatórios, na mediação de respostas imunes. A atividade dessas enzimas sobre os nucleotídeos da guanina e o efeito de restrição metabólica sobre a hidrólise de nucleotídeos foi avaliada. Além disso, a participação da sinalização mediada pelos nucleotídeos e nucleosídeos também foi avaliada em um modelo de citotoxicidade. Os resultados demonstram que os nucleotídeos GTP, GDP e GMP são substratos para as ectonucleotidases de T. vaginalis com parâmetros cinéticos compatíveis para enzimas dessa família. A condição de restrição de soro aumentou a atividade da NTPDase e da ecto-5’-nucleotidase e o aumento da expressão gênica das TvNTPDase 2 e 4 pode justificar o aumento da atividade. A recaptação de guanosina extracelular foi menor do que a recaptação de adenosina, demonstrada pela razão isotópica C12/C13 no nucleosídeo detectada no DNA dos parasitos. A fim de investigar um possível papel biológico para o acúmulo de guanosina extracelular, bem como avaliar o envolvimento da sinalização purinérgica na citotoxicidade mediada pelo parasito, diferentes isolados de T. vaginalis foram testados frente à capacidade de promover citólise. Todos os isolados foram capazes de promover efeito citolítico em alguma proporção, com destaque para o isolado TV-LACM6, que apresenta um perfil de hidrólise ATP, GTP > AMP > GMP. Quando nucleotídeos e nucleosídeos foram testados, o efeito citotóxico produzido pelo isolado foi potencializado na presença de ATP e GTP. Por outro lado, o efeito foi revertido na presença de eritro-9-(2-hidroxi-3-nonil) adenina (EHNA), um inibidor da adenosina deaminase. Importante, guanosina não foi capaz de reverter o efeito citotóxico produzido pelos trofozoítos, resultado que corrobora com o perfil de hidrólise de nucleotídeos e acúmulo de guanosina exracelular, sendo uma vantagem para o parasito. A possível participação dos receptores de adenosina foi avaliada, entretando os receptores ADORA1 e ADORA2A não parecem estar envolvidos no efeito protetor mediado pela adenosina. Considerando o potencial farmacológico desempenhado por essas enzimas no metabolismo de purinas em protozoários bem como no controle de respostas imunes, a modulação da hidrólise de nucleotídeos pode ser um alvo terapêutico importante e representar um mecanismo sinérgico na atividade antiparasiária de compostos ativos. Nesse sentido, o estudo demonstrou a atividade anti-T. vaginalis de três compostos, e em especial o isoaustrobrasilol B, com IC50 de 38 μM. O composto não apresentou efeitos hemolíticos frente a eritrócitos humanos e apesar de ter demonstrado efeito citotóxico in vitro frente à linhagem de células epiteliais vaginais humanas (HMVII), nenhuma citotoxicidade foi demonstrada no modelo in vivo. Isoaustrobrasilol B foi o único composto que inibiu significativamente as atividades da NTPDase e ecto-5’-nucleotidase e o efeito imune atribuído ao acúmulo extracelular de nucleotídeos foi avaliado. A produção de espécies reativas de oxigênio e interelucina-6 (IL-6) por neutrófilos estimulados por T.vaginalis não foi afetada pelo tratamento com o composto. Por outro lado, a liberação de interleucina-8 (IL-8), a principal interleucina produzida por neutrófilos na tricomoníase, foi aumentada. O efeito sinérgico de redução de viabilidade de trofozoítos e modulação da NTPDase e ecto-5’-nucleotidase pode aumentar a suscetibilidade do T. vaginalis frente à resposta imune do hospedeiro e consequentemente, sua eliminação do sítio de infecção. / Trichomonas vaginalis is a flagellate protozoan that parasitizes the human urogenital tract causing trichomoniasis, the most common non-viral sexually transmitted disease, infecting approximately 276 million people worldwide annually. To achieve success in parasitism trichomonads develop a complex process against the host cells that culminate in cytoadherence and cytotoxicity. Nucleotides and nucleosides are released into the extracellular space by cells under stress or injury and they exert their signaling effects through activation of the purinoceptors. Moreover, the ectonucleotidases, nucleoside triphosphate diphosphohydrolase (NTPDase) and ecto-5'-nucleotidase, are capable of hydrolyzing the nucleotides producing nucleosides that are essential to the parasite purine metabolism. The enzymatic cascade mediated by ectonucleotidases is relevant in controlling nucleotides and nucleosides levels as these molecules play antagonistic roles in inflammation, as proinflamatory and anti-inflammatory mediators, respectively. This study investigated the hydrolysis profile of guanine nucleotides in T. vaginalis as the effect of serum limitation condition in the enzymatic cascade. Furthermore, we investigated the influence of extracellular nucleotides and nucleosides on the modulation of the host cell cytotoxicity mediated by T. vaginalis. Results show that guanine nucleotides GTP, GDP, GMP are substrates for T. vaginalis ectonucleotidases, with expected kinetic parameters for this enzyme family. The metabolic restriction condition enhanced NTPDase and ecto-5’-nucleotidase activities and the highest gene expressions found for TvNTPDase 2 and 4 which may explain the enzymatic activity enhance. The extracellular guanosine uptake was lower than that observed for adenosine into parasite DNA measured by isotopic ratio C12/C13 of the nucleosides. In order to investigate the possible biological role for extracellular guanosine accumulation as well as to evaluate the involvment of purinergic signaling in the citotoxicity promoted by the parasite, a collection of T. vaginalis isolates were tested against a human epithelial vaginal cell line (HMVII). Fresh clinical T. vaginalis isolates produced cytolytic effect against human vaginal epithelial cells in a heterogeneous profile. The most cytotoxic isolate, TV-LACM6, presents the hydrolysis profile ATP, GTP > AMP > GMP. When the nucleotides and nucleosides were tested, the cytotoxic effect elicited by TV-LACM6 was increased in presence of nucleotides ATP and GTP. In contrast, the cytotoxicity was reversed by adenosine in presence of erythro-9-(2-hydroxy-3-nonyl) adenine (EHNA), but not by guanosine, which is in agreement with the accumulation of extracellular guanosine and the hydrolysis profile, acting as an advantage for the parasite. ADORA1 and ADORA2A are not involved in the protective mechanism of adenosine. Considering the pharmacological potential that ectonucleotidases play in the context of purine metabolism and in the imune response modulation, nucleotide hydrolysis may represent a therapeutic target as an additional mechanism in association with anti T.vaginalis compounds. The study demonstrated promissing activities for three derivatvies with isoaustrobrasilol B the most activity compound with IC50 38 μM. The compound did not demonstrate any hemolytic activity and although induced cytotoxicity against human epithelial vaginal cells (HMVII), absence of toxicity was obtained when in vivo model was studied. Isoaustrobrasilol B was the only compound that significantly inhibited NTPDase and ecto-5’-nucleotidase activities and the immune modulation attributed to extracellular nucleotide accumulation was evaluated. Reactive oxygen species production and interleukin-6 (IL-6) release by T.vaginalis stimulated neutrophils were not affected by phloroglucinol treatment. On the other hand, interleukin-8 (IL-8), the primarily cytokine produced by neutrophils during trichomoniasis, was significantly enhanced. The associative mechanism of trophozoites death and NTPDase and ecto-5’-nucleotidase modulation may increase the susceptibility of T. vaginalis to host immune responses and, consequently, the elimination from the infection site.

Xue, Yan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 95-102). / Abstract also in Chinese. / Thesis committe --- p.2 / Statement --- p.3 / Abstract --- p.4 / Acknowledgement --- p.8 / General abbreviations --- p.10 / Abbreviations of chemicals --- p.13 / List of figures --- p.15 / List of tables --- p.16 / Table of contents --- p.17 / Chapter Chapter 1 --- General Introduction / Chapter 1.1 --- Impact of bacterial blight on rice production --- p.25 / Chapter 1.2 --- The plant immune system --- p.25 / Chapter 1.2.1 --- Preformed resistance --- p.25 / Chapter 1.2.2 --- PAMP triggered immunity (PTI) --- p.26 / Chapter 1.2.3 --- Effecter triggered immunity (ETI) --- p.27 / Chapter 1.2.3.1 --- R genes --- p.27 / Chapter 1.2.3.2 --- Hypersensitive responses (HR) --- p.27 / Chapter 1.2.3.3 --- Systemic acquired resistance (SAR) --- p.28 / Chapter 1.2.3.3.1 --- Salicylic acid is required for SAR establishment --- p.28 / Chapter 1.2.3.3.2 --- Involvement of lipid-based molecules in SAR signaling --- p.28 / Chapter 1.2.3.3.3 --- NPR1: the master regulator of SAR --- p.29 / Chapter 1.2.3.3.4 --- Expression of pathogenesis related (PR) genes --- p.29 / Chapter 1.2.4 --- Interaction between SA and JA --- p.29 / Chapter 1.2.5 --- Other important signaling components in plant defense responses --- p.30 / Chapter 1.2.5.1 --- G proteins --- p.30 / Chapter 1.2.5.2 --- G proteins in defense responses --- p.30 / Chapter 1.3 --- OsGAPl is a C2 (protein kinase C conserved region 2) domain harboring GTPase activating protein --- p.32 / Chapter 1.4 --- OsYchFl is a GTPase and an interacting partner of OsGAPl --- p.32 / Chapter 1.5 --- Hypothesis and objectives of this research --- p.33 / Chapter Chapter 2 --- materials and methods / Chapter 2.1 --- Materials --- p.35 / Chapter 2.1.1 --- Chemicals and reagents --- p.39 / Chapter 2.1.2 --- Commercial kits --- p.40 / Chapter 2.1.3 --- Primers used --- p.41 / Chapter 2.1.4 --- Equipment and facilities used: --- p.47 / Chapter 2.1.5 --- "Buffer, solution, gel and medium:" --- p.47 / Chapter 2.2 --- Methods: --- p.51 / Chapter 2.2.1 --- Culture of bacterial strains --- p.51 / Chapter 2.2.2 --- Composition of medium used in this work for cultivating bacterial strains: --- p.51 / Chapter 2.2.3 --- Plant growth and treatment --- p.52 / Chapter 2.2.3.1 --- Surface sterilization of Arabidopsis thaliana seeds --- p.52 / Chapter 2.2.3.2 --- Seed germination and Arabidopsis plant growth --- p.52 / Chapter 2.2.4 --- Generation of transgenic Arabidopsis --- p.53 / Chapter 2.2.4.1 --- Agrobacterium-mediated Arabidopsis transformation --- p.53 / Chapter 2.2.5 --- Pathogen inoculation test --- p.54 / Chapter 2.2.6 --- Molecular cloning --- p.54 / Chapter 2.2.6.1 --- DNA sequencing: --- p.55 / Chapter 2.2.6.2 --- Transformation of E. coli strains: --- p.55 / Chapter 2.2.6.3 --- Transformation of Agrobacteria by electroporation --- p.55 / Chapter 2.2.7 --- DNA and RNA extraction --- p.56 / Chapter 2.2.7.1 --- Plasmid DNA extraction from bacterial cells --- p.56 / Chapter 2.2.7.2 --- Genomic DNA extraction from plant tissues --- p.56 / Chapter 2.2.7.3 --- RNA extraction from plant tissues --- p.56 / Chapter 2.2.8 --- Northern blot --- p.57 / Chapter 2.2.9 --- Subcellular localization studies --- p.58 / Chapter 2.2.9.1 --- Transformation of tobacco BY-2 cells --- p.58 / Chapter 2.2.9.2 --- Maintenance of transgenic tobacco BY-2 cells --- p.59 / Chapter 2.2.9.3 --- Confocal microscopy --- p.59 / Chapter 2.2.9.4 --- Electron microscopy --- p.59 / Chapter 2.2.10 --- Bimolecular fluorescence complementation studies (BiFC) --- p.60 / Chapter 2.2.10.1 --- Construct making --- p.61 / Chapter 2.2.10.2 --- Preparation of rice protoplasts --- p.61 / Chapter 2.2.10.3 --- PEG-mediated transfection --- p.62 / Chapter 2.2.10.4 --- Detection of protein-protein interaction --- p.62 / Chapter Chapter 3 --- Results / Chapter 3.1 --- OsGAPl interacts with OsYchFl in vivo --- p.63 / Chapter 3.1.1 --- Construction of vectors for BiFC transient assay in rice protoplasts --- p.64 / Chapter 3.1.2 --- BiFC assay in rice protoplasts revealed in vivo interaction between the OsGAPl and the OsYchFl proteins --- p.66 / Chapter 3.2.1 --- Subcellular localization of OsGAPl --- p.68 / Chapter 3.2.2 --- Localization of OsGAPl and OsYchFl in rice leaves revealed by electron microscopy --- p.70 / Chapter 3.3 --- Functional characterization of OsYchFl / Chapter 3.3.1 --- Characterization of Arabidopsis YchF1 knockdown mutant --- p.75 / Chapter 3.3.2 --- Complementation of AtYchF1 knockdown Arabidopsis --- p.77 / Chapter 3.3.3.1 --- Pathogen inoculation test --- p.80 / Chapter Chapter 4 --- Discussion / Chapter 4.1 --- Significance of the project --- p.85 / Chapter 4.2 --- In vivo interaction between OsGAPl and OsYchFl --- p.86 / Chapter 4.3 --- OsGAPl is located either inside the cytosol or on the plasma membrane in transgenic tobacco BY-2 cells --- p.87 / Chapter 4.4 --- Study of wounding effect on the subcellular localization of OsGAPl and OsYchFl at whole plant level by EM --- p.88 / Chapter 4.5 --- OsYchFl functions as a negative regulator of defense responses in A.thaliana --- p.90 / Chapter 4.6 --- Conclusion --- p.92 / References --- p.95 / Appendix --- p.103

<p>A synthetic pathway towards the cap-structure of 2,2,7-trimethylguanosine containing a methylene modified triphosphate bridge have been investigated. The modification to the triphosphate bridge is hoped to slow down cap degradation and give the connected  oligunucleotide an increased lifetime. This could result in an better understanding of nuclear transport of oligonucleotides and could thereby helping to develop new treatments for different diseases. The synthesis relies on a coupling reaction between the 2,2,7-trimethylguanosine 5’phosphate and 2’-<em>O</em>-methyladenosine with a 5’-pyrophosphate where the central oxygen has been replaced by a methylene group. The reaction pathway consists of 9 steps of which 8 steps have been successfully performed. The last step, which includes a coupling reaction, was attempted but without successful identification and isolation of the cap-structure, and will need further attention. The reaction has been performed in a milligram scale with various yields.</p> / Presentation utförd

During protein synthesis, elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA (aa-tRNA) to the A-site of mRNA-programmed ribosomes in a GTP-dependent manner. To enable future studies on the functional and structural requirement of EF-Tu’s function, a Cysteine-free variant of EF-Tu was constructed suitable for subsequent labelling of the protein and use in kinetic studies. Here, the kinetic properties of three Cysteine-less EF-Tu variants are reported, demonstrating that only the variant with the Alanine substitution in position 81 retains wild-type activity with respect to the interaction with guanine nucleotides, aa-tRNA and the ribosome. To explore a possible tRNA independent pathway for the GTPase activation signal, three residues in domain II of EF-Tu (Arginine 279, Glycine 280, Arginine 283) were mutated; the activity of EF-Tu variants were analyzed. Results suggest that these residues are indeed required for efficient ribosome-dependent stimulation of the GTPase activity of EF-Tu. / x, 85 leaves : ill. (some col.) ; 29 cm

RelA is a guanosine tetraphosphate synthetase which catalyzes the production of (p)ppGpp during the stringent response in Escherichia coli. RelA consists of an N-terminus, which is responsible for the catalytic activity, and a C-terminus, which is thought to be involved in the regulation of RelA activity. Furthermore, the C-terminus has dimerization and ribosome binding ability. ‘RelA-2, which is a fragment of C-terminus, is a major domain responsible for dimerization and ribosome binding. In this study, it was demonstrated that combination of two mutations (C612G, D637R) in ‘RelA-2 significantly reduced the dimerization. This dimerization-defective mutant still bound to ribosomes both in vivo and in vitro, indicating that dimerization is not required for its ribosome binding and that the dimerizaton domain is separated from its ribosome binding domain. The overexpression of the dimerization-defective mutant in amino acid starved cells inhibited chromosome-encoded wild type RelA activity. As a result, the starved cells did not show a stringent response. This finding does not support the oligomerization model proposed by Gropp group. Previous studies in this laboratory have shown, and were confirmed here, that the overexpressed ‘RelA-3, another fragment of C-terminus, which is devoid of dimerization and ribosome binding ability, did not inhibit the RelA activity when cells are under amino acid starvation. This evidence supports the hypothesis that ribosome binding is somehow involved in the regulation of RelA activity. It was demonstrated in this study that RelA was localized to the 50S subunit in vivo by Western Blot analysis. This result confirmed a previous study showing that the 50S subunit had the enzymatic activity in vitro, but not the 30S subunit. However, an in vitro study using pure 50S and 30S ribosomal subunits for the binding experiments indicated that RelA mainly bound to the 30S subunit and weakly to the 50S subunit. A model has been proposed to explain the possible mechanism of ribosome association for RelA. The involvement of L11 and EF-G in the regulation of RelA activity was also investigated. Three residues (C38, G131, and G137) in L11 have been identified to be crucial for the regulation of RelA activity. Three residues (T89, L438, and G628) in EF-G have been identified to be involved in the regulation of RelA activity. These preliminary studies implicate that the regulation of RelA inside amino acid-starved E. coli is complex.

Thesis (Ph. D.)--Ohio State University, 2007.

Thesis (doctoral)--Karolinska Institutet, Stockholm, 1988. / Extra t.p. with thesis statement inserted. Includes bibliographical references.

Thesis (M.S.)--Naval Postgraduate School, 1981. / Cover title. "September 1981." Includes bibliographical references (leaves 108-120).

Objetivos: Desenvolver um modelo de isquemia e reperfusão (I-R) ocular baseado no aumento da pressão intraocular (PIO) em ratos Wistar, e utilizar este modelo para investigar o efeito da guanosina (GUA) na captação de glutamato (GLU) nas retinas destes ratos em condições de I-R. Métodos: Desenvolvemos um modelo de I-R ocular e utilizamos este modelo para investigar 30 ratos Wistar, divididos em 3 grupos de 10 animais. Em cada rato, o olho direito foi submetido à elevação da PIO, gerando isquemia retiniana por 45 minutos, sem nenhuma intervenção no olho esquerdo (controle). No grupo 1, os animais não receberam GUA. No grupo 2, os animais receberam injeção intraperitoneal de GUA 30 minutos antes da isquemia e, no grupo 3, os animais receberam GUA na água durante 1 semana antes e 1 semana após a isquemia. Todos os animais foram mortos 7 dias após a isquemia e suas retinas foram coletadas para quantificar a captação de GLU. Resultados: As captações de GLU nas retinas controle foram semelhantes em todos os grupos. No grupo 1, a captação de GLU foi reduzida pela I-R. Esta redução foi abolida pela GUA administrada na água (grupo 3) e, no grupo 2, a captação de GLU aumentou com a administração intraperitoneal de GUA (P<0.001; ANOVA). Conclusões: Estes resultados sugerem que a I-R ocular gerada em nosso modelo experimental diminuiu a captação de GLU nas retinas de ratos Wistar e que a GUA aboliu tal redução ou, até mesmo, aumentou a captação de GLU. Este efeito da GUA está de acordo com estudos prévios que revelaram comportamento neuroprotetor da GUA no sistema nervoso central, por estimular a captação de GLU por astrócitos. Na retina, este efeito pode ser devido à ação da GUA estimulando a captação de GLU pelas células de Müller. / Purpose: To devise an experimental model of ocular ischemia-reperfusion (I-R) based on intraocular pressure (IOP) elevation in Wistar rats, and use this model to investigate the effect of guanosine (GUA) on glutamate (GLU) uptake in retinas of Wistar rats submitted to such ocular I-R injuries. Methods: We devised an experimental model of ocular I-R and applied this model to investigate 30 Wistar rats, divided in 3 groups of 10 rats. Each rat was submitted to IOP elevation in the right eye generating retinal ischemia during 45 minutes with no intervention in the left eye (control retina). In group 1, animals did not receive any GUA. In group 2, animals received an intraperitoneal injection of GUA 30 minutes before ischemia and, in group 3, animals received GUA in water during 1 week before and 1 week after ischemia. All animals were killed 7 days after ischemia and retina samples were obtained. Glutamate uptakes were performed from these retina samples. Results: GLU uptake in control retina was similar in all groups. In group 1, GLU uptake was significantly reduced by I-R; this reduction was abolished by GUA administration in water (group 3) and GLU uptake increased with intraperitoneal GUA (group 2).(P<0.001; ANOVA) Conclusions: These results point that I-R generated by our experimental model decreased GLU uptake in retinas of Wistar rats and that GUA abolished or even overcomed this decrease. These GUA effects are in agreement to previous results, which show that GUA administration presents neuroprotection in central nervous system by stimulating GLU uptake, mainly by astrocytes. In retina, this effect may be due to GUA stimulation of GLU uptake exerted mainly by Müller cells.