Rayleigh-Taylor instability has been an area of active research in fluid dynamics for the last twenty years, but relatively little attention has been paid to the dynamics of problems where Rayleigh-Taylor instability plays a role, but is only one component of a more complex system. Here, Rayleigh-Taylor instability between miscible fluids is examined in situations where it is confined by various means: by geometric restriction, by penetration into a stable linear stratification, and by impingement on a stable density interface. Water-based experiments are modelled using a variety of techniques, ranging from simple hand calculation of energy exchange to full three-dimensional numerical simulation. Since there are well known difficulties in modelling unconfined Rayleigh-Taylor instability, the confined test cases have been sequenced to begin with dynamically simple benchmark systems on which existing modelling approaches perform well, then they progress to more complex systems and explore the limitations of the various models. Some work on the phenomenology of turbulent mixing is also presented, including a new experimental technique that allows mixed fluid to be visualised directly, and an analysis of energy transport and mixing efficiency in variable density flows dominated by mixing.

This diploma thesis deals with the possibilities of stress resistance analysis of the Cupriavidus necator H16 and PHB-4 bacterial cells by spectroscopic methods and by testing the suitability of acridine orange as a viable dye. Based on research in literature, suitable analytical methods have been proposed, namely flow cytometer and fluorescence microscope. The first part of the experimental work was focused on the fluorescence microscope, which confirmed the basic character of acridine orange. Three stress factors, 50% and 70% ethanol, and acidic pH (pH = 1) were selected for viability monitoring. The bacteria fluoresced with green color after exposure to ethanol and red spots were found next to the cells, indicating their loss of integrity. In an acidic environment, the bacteria fluoresced red because of a partial DNA breakdown. The results were verified by the combination of propidium iodide with SYTO9 and the acridine orange suitability proved to be useful in this method. Image records were processed using image analysis. In the second part, acridine orange was used to monitor fluorescence using a flow cytometer. The result of the measurement was fluorescence expressed as histograms for individual channels, where fluorescence was characterized by median and mean intensity. By comparing the methods used, the acridine orange appears to be a more suitable fluorescent dye for the microscope than for a flow cytometer in which it was more difficult to obtain cell viability information. In the last part of the experimental work interesting photophysical properties of acridine orange were investigated.

No description available.

No description available.

The interaction of the protein Rev with Rev Response Element (RRE) RNA is critical to the HIV-1 life cycle as this complex is required for the export of singly-spliced and unspliced mRNAs from the nucleus to the cytoplasm. Disruption of this interaction is considered to be a powerful strategy towards the development of HIV-1 therapeutics. Therefore, we have developed several branched peptide libraries containing unnatural amino acids to target the high-affinity binding site of RRE RNA (RRE IIB), with the idea that branching in peptides can provide multivalent contacts with folded RNA structures and boost binding affinity and selectivity for the target. Unnatural amino acids were incorporated into the library design to encourage non-canonical interactions with the RNA and to improve proteolytic stability. The on-bead high-throughput screening of our first branched peptide library (46,656 sequences) against HIV-1 RRE RNA generated hit peptides with binding affinities in the low micromolar range. We demonstrated that branching in the peptide is required for efficient binding and selectivity towards the RNA, and that the peptides bind a large surface area of RRE IIB. Introduction of boronic acids into branched peptides boosted selectivity of the peptides for RRE IIB, and proved to be a novel and tunable mode of binding towards RNA. Additionally, we revealed that these branched peptide boronic acids (BPBAs) were cell permeable and non-toxic. One BPBA (BPBA3) bound RRE IIB selectively and was able to inhibit HIV-1 replication in vitro, revealing enzymatic cleavage of the RNA upon binding. A second generation BPBA library that introduced acridinyl lysine as an intercalator (4,096 sequences) was screened against RRE IIB. Several hit compounds bound in the low nanomolar regime, and a significant number of compounds inhibited HIV-1 replication in vitro. These BPBAs were also found to severely inhibit the microbial growth of bacteria and fungus, with MICs as low as 1 µg/mL against Staphylococcus aureus, Candida albicans, and Escherichia coli. These compounds were also found to significantly inhibit biofilm formation and growth, and were non-hemolytic. High-throughput screening of a third generation BPBA library containing all unnatural amino acids (46,656 sequences) revealed several hits that bound RRE IIB RNA in the nanomolar range. Sequence motifs present in the hit peptides suggested that the location and composition of amino acids within the branched peptide structure were important for recognizing the RNA target. In particular, lead compounds 2C5 and 4B3 demonstrated selectivity towards RRE, and footprinting experiments combined with SHAPE experiments revealed different interactions of the peptides with the RNA Toxicity assays revealed no impact on cell viability for the majority of hit sequences tested up to 100 µM, and several compounds also demonstrated inhibition of HIV-1 replication. / Ph. D.

La carbamazépine (CBZ) est un antiépileptique largement consommé, peu dégradé dans les stations de traitement des eaux usées et donc rejeté dans les eaux de surface. Cette thèse vise à étudier le devenir de CBZ et de deux métabolites, l'oxcarbazépine (OxCBZ) et l'acide 9-carboxylique acridine (9-CAA), sous irradiation par la lumière solaire dans des eaux naturelles douces et salées. Les suivis cinétiques ont permis de mettre en évidence des comportements différents en fonction des composés mais aussi des types d’eaux et impliquant des mécanismes de phototransformation directe et induite mais aussi des réactions d’atténuation naturelle. Pour approfondir ces résultats, la spectrophotométrie d’absorption résolue en temps et l’utilisation d’une sonde chimique ont souligné la formation d’espèces réactives (radicaux hydroxyles, carbonates et halogénés) et des réactions de compétition ont permis de mesurer leur réactivité avec les composés étudiés.La formation de dérivés issus de processus d’hydroxylation, d’oxydation, de perte de la fonction latérale, d’ouverture et/ou contraction de cycle aromatique (etc.) et de sous-produits halogénés dans les eaux salées ont été identifiés lors de la photodégradation de CBZ, OxCBZ et 9-CAA. Enfin, l’écotoxicité aiguë et chronique de CBZ, OxCBZ et 9-CAA a été évaluée individuellement et en mélange à dose environnementales sur 3 espèces vivantes de différents niveaux trophiques en mesurant les paramètres suivants : luminescence sur la bactérie Vibrio fischeri, phytométabolites sur la lentille d'eau Lemna minor et altération aux niveaux population, cellulaire et moléculaire sur le cnidaire Hydra circumcincta. / Carbamazepine (CBZ) is a widely consumed anti-epileptic pharmaceutical drug, inefficiently removed in activated sludge secondary treatment process. Consequently, it is almost completely rejected in its original form into surface waters. Hence, this thesis aimed to study the fate of CBZ and two of its known bio-metabolites, i.e. oxcarbazepine (OxCBZ) and 9-carboxylic acridine acid (9-CAA), under solar light irradiation in fresh and salty waters. Kinetic monitoring revealed different behaviours both compounds and water types dependent implying photolysis, induced photodegradation but also natural attenuation reactions. To deeper understand these results, laser flash photolysis experiments and the use of a chemical probe highlighted the formation of reactive species (hydroxyl, carbonate and halogenated radicals). By implementing competition reactions, the rate constants of each compound with each chemical radical species were determined.The formation of derivatives from hydroxylation, oxidation, ring contraction, loss of side function, aromatic ring opening (etc.) and also halogenated by-products in salty waters were identified throughout CBZ, OxCBZ and 9-CAA phototransformations.Finally, acute and chronic ecotoxicity of CBZ, OxCBZ and 9-CAA individually and in mixture at environmental concentration levels were investigated on 3 living species from different trophic levels. The following endpoints were monitored: luminescence on the bacteria Vibrio fischeri, growth and development and phytometabolites on the duckweed Lemna minor and alterations at the population, cellular and molecular levels on the cnidarian Hydra circumcincta.

O óxido nítrico (NO) é biossintetizado em diferentes células do organismo animal, relacionando-se com inúmeros processos fisiológicos. Existe, aparentemente, uma relação entre os efeitos mediados pelo NO e o microambiente celular. Desta forma, a resposta observada depende da localização da molécula radicalar, da duração da exposição e da sua concentração. Assim, observa-se um efeito antagônico do NO no que tange a biologia de tumores, admitindo-se que baixas concentrações de NO estimulam a proliferação de células tumorais e altas concentrações propiciam a atividade tumoricida. Nesse sentido, o presente trabalho visou ao desenvolvimento de um novo complexo de rutênio doador de óxido nítrico coordenado ao ligante fluorescente Alaranjado de Acridina. A coordenação do rutênio ao ligante heterocíclico de nitrogênio permitiu a obtenção do composto fluorescente [Ru(NO2)(bpy)(AO)2NO](PF6)2, em que bpy = 2,2\'bipiridina e AO = Alaranjado de Acridina. O complexo foi caracterizado por UV-vis, FITR e espectrometria de massas. Experimentos fotoquímicos revelaram que o complexo [Ru(NO2)(bpy)(AO)2NO](PF6)2 apresentou um valor de rendimento quântico de fluorescência em etanol inferior ao do ligante livre. No entanto, o rendimento quântico de produção de oxigênio singleto em água foi maior em relação ao Alaranjado de Acridina. Avaliações de fotoestabilidade por espectroscopia de emissão e absorção no UV-vis demonstraram que [Ru(NO2)(bpy)(AO)2NO](PF6)2 é mais fotoestável nas condições avaliadas e a fluorescência apresenta menor redução, quando irradiado em 470 nm comparado ao Alaranjado de Acridina. Ensaios de avaliação do potencial citotóxico dos compostos com irradiação em 470 nm, na dose de 5 J cm-², demonstraram que o corante Alaranjado de Acridina apresenta maior citotoxicidade frente à linhagem celular tumoral metastática estudada (B16/F10). Isso se relaciona, possivelmente, ao fato de o Alaranjado de Acridina livre direcionar-se para o núcleo e promover intercalação com os pares de base do DNA. A avaliação por microscopia de fluorescência revelou a predileção do complexo [Ru(NO2)(bpy)(AO)2NO](PF6) pelo núcleo. Os dados obtidos enfatizam a importância do grupo ligante para a localização do complexo, bem como para a atividade antitumoral do mesmo. / Nitric Oxide is biosynthesized in different cells of the animal organism. It is related to numerous physiological processes. There is apparently a relationship between the effects mediated by NO and the microenvironment. Thus, the cellular response observed depends on the location of the radical molecule, the duration of exposure and its concentration. Thus, an antagonistic effect of NO is observed with respect to the biology of tumors, admitting that low concentrations of NO stimulate the proliferation of tumor cells and high concentrations promote the tumoricidal activity. In this sense, the present work aimed the development of a new ruthenium complex donor of nitric oxide coordinated to the fluorescent ligand of Acridine. The coordination of Ruthenium to the nitrogen heterocyclic ligand allowed to obtain the fluorescent compound [Ru(NO2)(bpy)(AO)2NO](PF6)2, where bpy = 2,2\' bipyridine and AO = Acridine Orange, which was characterized by UV-Vis, FITR and mass spectrometry. Photochemical experiments revealed that the [Ru(NO2)(bpy) (AO)2NO](PF6) 2 complex presented a fluorescence quantum yield value, in ethanol, about 20 % lower than the free binder. However, the quantum yield of singlet oxygen in water was approximately 40 % higher compared to Acridine Orange. UV-vis emission spectroscopy and UV-vis absorption spectroscopy have shown that [Ru (NO2)(bpy)(AO)2NO](PF6) 2 is apparently more photostable and suffers less fluorescence suppression when irradiated at 470 nm compared with Acridine Orange. Cell cytotoxicity assays with irradiation using dose of 5 J cm-2 demonstrated that the coordination of Acridine Orange dye to the complex decreases its cytotoxicity against the metastatic tumor cell line studied, possibly by preventing the mechanism of intercalation of the planar ligand to DNA. Monitoring by fluorescence microscopy revealed the preferential localization of the compound [Ru(NO2)(bpy) (AO)2NO] (PF6) by the cell nucleus possibly due to coordinated Acridine Orange, which has a tropism by DNA. These results emphasize the importance of the ligand group for the localization of the complex, as well as for the cytotoxic activity of the same

Submitted by Cristhiane Guerra (cristhiane.guerra@gmail.com) on 2017-02-03T14:26:05Z No. of bitstreams: 1 arquivototal.pdf: 1920368 bytes, checksum: a0cab7d082218cd820a2d1c4f4b184f7 (MD5) / Made available in DSpace on 2017-02-03T14:26:05Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 1920368 bytes, checksum: a0cab7d082218cd820a2d1c4f4b184f7 (MD5) Previous issue date: 2015-02-27 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Cancer is a major public health problem worldwide and is considered a group of diseases characterized by uncontrolled growth and multiplication of abnormal cells that can invade various tissues. Treatment has been benefited from research that seek to reduce toxicity and increase the effectiveness of different anticancer drugs. Acridine derivatives have a number of proven biological activities, and amsacrine, an antineoplastic used for the treatment of leukemias and lymphomas, is the main representative of the group. This study aimed to evaluate the toxicity and antitumor activity of acridine- derived N’-(2-chloro-6-methoxy-acridin-9-yl)-2-cyano-3-(4-dimethylaminophenyl)-acrilohydrazide (ACS-AZ10). In the assessment of cytotoxicity in mouse erythrocytes it was observed that ACS-AZ10 did not cause hemolysis at the concentrations tested (up to 1250 μg / ml), suggesting low toxicity in erythrocytes. After acute administration of ACS-AZ10 (2000 mg / kg) in mice intraperitoneally (ip), characteristic effects of changes in the central nervous system among them, writhing and abduction of the legs of the rear train, were observed. The estimated LD50 (dose that produces death in 50% of experimental animals) was around 2500 mg / kg. The ACS-AZ10 (15 or 30 mg / kg), after a nine days treatment (ip) showed significant antitumor activity in vivo in Ehrlich ascites carcinoma model (EAC), considering the volume parameters, mass, viability and total cell count. Treatment at the dose 7.5 mg/kg induced an increase in sub-G1 peak, with a consequent reduction in the percentage of cells in G0/G1 and S phases of cell cycle, suggesting death by apoptosis. However, treatment with 15 mg/kg induced cell cycle arrest in G2/M phase and a reduction of the fraction G0/G1 and S, suggesting a pre-mitotic blockade. The treatment with different doses of ACS-AZ10 significantly reduced the angiogenic capacity of the EAC, thus it can be inferred that the ACS-AZ10´s antitumor mechanism of action involves, at least in part, an anti-angiogenic effect. The toxicological analysis indicated that after nine days of treatment with ACS-AZ10, low haematological and biochemical toxicity were observed. Histopathological analysis indicated liver damage following treatment with ACS-AZ10, however, the damage was considered mild and reversible. ACS-AZ10 induced no increase in the quantity of micronucleated erythrocyte in micronucleus test, indicating the absence of genotoxic under the conditions evaluated. Therefore, it is possible to infer that the ACS-AZ10 has potent antitumor activity in vivo with low toxicity. / O câncer é um importante problema de saúde pública em nível mundial, sendo considerado um grupo de doenças caracterizadas pelo crescimento descontrolado e multiplicação de células modificadas que podem invadir diversos tecidos. Seu tratamento tem se beneficiado das pesquisas que buscam reduzir a toxicidade e aumentar a eficácia de diferentes fármacos antineoplásicos. Os derivados da acridina possuem diversas atividades biológicas comprovadas, sendo a amsacrina, um antineoplásico usado para o tratamento de leucemias e linfomas, o principal representante do grupo. Esse trabalho teve como objetivo avaliar a toxicidade e atividade antitumoral do derivado acridínico N’-(2-cloro-6-metoxi-acridin-9-yl)-2-ciano-3-(4-dimetilaminofenil)-acrilohidrazida (ACS-AZ10). Na avaliação da citotoxicidade em eritrócitos de camundongos foi possível observar que o ACS-AZ10 em concentração de até 1250 g/mL não causou dano direto a membrana de eritrócitos de camundongos, sugerindo atividade intracelular em hemácias. Após administração aguda do ACS-AZ10 (2000 mg/kg) em camundongos por via intraperitoneal (i.p.), foram observados efeitos característicos de alterações no Sistema Nervoso Central dentre estes, contorções abdominais e abdução das patas do trem posterior. O valor estimado da DL50 (dose que produz morte de 50% dos animais experimentais) foi em torno de 2500 mg/kg. O ACS-AZ10 (15 ou 30 mg/kg), após nove dias de tratamento (i.p.), mostrou significante atividade antitumoral in vivo em modelo de Carcinoma Ascítico de Ehrlich (CAE), considerando os parâmetros volume, massa, viabilidade e total celular. O tratamento na dose 7,5 mg/kg induziu um aumento do pico sub-G1, com consequente redução da percentagem de células nas fases G0/G1 e S do ciclo celular, o que sugere morte por apoptose. No entanto, o tratamento com a dose de 15 mg/kg induziu parada do ciclo celular na fase G2/M e diminuição da fração G0/G1 e S, o que sugere um bloqueio pré-mitótico. O tratamento com as diferentes doses de ACS-AZ10 diminuiu significativamente a capacidade angiogênica do CAE, desta forma, pode-se inferir que o mecanismo de ação antitumoral do ACS-AZ10 envolve, pelo menos parcialmente, um efeito antiangiogênico. As análises toxicológicas indicaram que, após nove dias de tratamento com ACS-AZ10 foi observada baixa toxicidade hematológica e bioquímica. A análise histopatológica indicou danos hepáticos após o tratamento com ACS-AZ10, entretanto, os danos foram considerados leves e reversíveis. O ACS-AZ10 não induziu aumento na quantidade de eritrócitos micronucleados no ensaio do micronúcleo, o que indica ausência de genotoxicidade, nas condições avaliadas. Portanto, é possível inferir que o ACS-AZ10 apresenta potente atividade antitumoral in vivo com baixa toxicidade.

Prokaryotic cells such as Escherichia coli use glucose as their preferred carbon source. In the absence of glucose, these cells resort to other sources to generate glucose and this process of de novo synthesis of glucose is termed gluconeogenesis. Phosphoenolpyruvate carboxykinase (Pck) is one of the three enzymes important in regulating gluconeogenesis. It converts oxaloacetic acid (OAA) from the Krebs cycle to phosphoenolpyruvate (PEP), a glycolytic intermediate. The Pck structural gene (pckA) is regulated by catabolite repression. There is a 100-fold induction of pckA-lacZ fusions at the onset of stationary phase concurrent with induction of glycogen synthesis. Mutants affecting the expression of pckA were analysed to shed some light on the mechanism of its genetic regulation.<p>Spontaneous mutants isolated with Pck- (lack of PEP carboxykinase activity) and Suc- (inability to utilise succinate as carbon source) phenotypes were previously characterised as atpG mutants defective in the ã subunit of ATP synthase.<p>In this work we find by reverse transcriptase and real time quantitative PCR that levels of pckA mRNA are normal in the atpG mutants and that the defects in expression of pckA are therefore likely at the level of translation, protein assembly and/or protein degradation. As expected, ATP synthase activity and proton pumping in inside-out membrane vesicles were defective in these atpG mutants. It is likely that one of these defects is affecting regulation or expression of the pckA gene. It was observed that atpG mutants were defective in calcium-dependent transformation although they could be made competent for electroporation. The atpG mutants were also defective for growth of P1 bacteriophage although they could serve as recipients for P1-dependent generalised transduction. These latter phenotypes are also likely due to defects in energy metabolism.

Prokaryotic cells such as Escherichia coli use glucose as their preferred carbon source. In the absence of glucose, these cells resort to other sources to generate glucose and this process of de novo synthesis of glucose is termed gluconeogenesis. Phosphoenolpyruvate carboxykinase (Pck) is one of the three enzymes important in regulating gluconeogenesis. It converts oxaloacetic acid (OAA) from the Krebs cycle to phosphoenolpyruvate (PEP), a glycolytic intermediate. The Pck structural gene (pckA) is regulated by catabolite repression. There is a 100-fold induction of pckA-lacZ fusions at the onset of stationary phase concurrent with induction of glycogen synthesis. Mutants affecting the expression of pckA were analysed to shed some light on the mechanism of its genetic regulation.<p>Spontaneous mutants isolated with Pck- (lack of PEP carboxykinase activity) and Suc- (inability to utilise succinate as carbon source) phenotypes were previously characterised as atpG mutants defective in the ã subunit of ATP synthase.<p>In this work we find by reverse transcriptase and real time quantitative PCR that levels of pckA mRNA are normal in the atpG mutants and that the defects in expression of pckA are therefore likely at the level of translation, protein assembly and/or protein degradation. As expected, ATP synthase activity and proton pumping in inside-out membrane vesicles were defective in these atpG mutants. It is likely that one of these defects is affecting regulation or expression of the pckA gene. It was observed that atpG mutants were defective in calcium-dependent transformation although they could be made competent for electroporation. The atpG mutants were also defective for growth of P1 bacteriophage although they could serve as recipients for P1-dependent generalised transduction. These latter phenotypes are also likely due to defects in energy metabolism.