Current excessive use and abuse of antibiotics has resulted in increasing bacterial resistance to common treatment options which is threatening to deprive us of a pillar of modern medicine. In this work methods to optimize the use of existing antibiotics and to help development of new antibiotics were developed and applied. Semi-mechanistic pharmacokinetic-pharmacodynamic (PKPD) models were developed to describe the time course of the dynamic effect and interaction of combinations of antibiotics. The models were applied to illustrate that colistin combined with a high dose of meropenem may overcome meropenem-resistant P. aeruginosa infections. The results from an in vivo dose finding study of meropenem was successfully predicted by the meropenem PKPD model in combination with a murine PK model, which supports model based dosage selection. However, the traditional PK/PD index based dose selection was predicted to have poor extrapolation properties from pre-clinical to clinical settings, and across patient populations. The precision of the model parameters, and hence the model predictions, is dependent on the experimental design. A limited study design is dictated by cost and, for in vivo studies, ethical reasons. In this work optimal design (OD) was demonstrated to be able to reduce the experimental effort in time-kill curve experiments and was utilized to suggest the experimental design for identification and estimation of an interaction between antibiotics. OD methods to handle inter occasion variability (IOV) in optimization of individual PK parameter estimates were proposed. The strategy was applied in the design of a sparse sampling schedule that aim to estimate individual exposures of colistin in a multi-centre clinical study. Plasma concentration samples from the first 100 patients have been analysed and indicate that the performance of the design is close to the predicted. The methods described in this thesis holds promise to facilitate the development of new antibiotics and to improve the use of existing antibiotics.

Made available in DSpace on 2014-06-11T19:32:53Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-11-17Bitstream added on 2014-06-13T20:24:17Z : No. of bitstreams: 1 aoki_ee_dr_arafcf.pdf: 506585 bytes, checksum: 218b2c8e86bf9f798b9b0d4d716e2401 (MD5) / Universidade Estadual Paulista (UNESP) / O efeito de amoxicilina e ciprofloxacino, agentes antimicrobianos com diferentes mecanismos de ação, sobre alguns fatores relacionados à sua virulência em Staphylococcus aureus ATCC 25923 foi comparado. Efeito pós-antimicrobiano, atividade hemolítica para hemácias de carneiro, atividade de citolisinas extracelulares para células McCoy, susceptibilidade à fagocitose dependente e não dependente de opsonização, por neutrófilos de Rattus albinus norvegicus, foram avaliados em bactérias crescidas na presença de concentração subinibitória (½ CIM) do antimicrobiano e a capacidade de induzir estresse oxidativo foi determinada diretamente sobre as células bacterianas através da detecção da produção de ânion superóxido. Amoxicilina e ciprofloxacino demonstraram efeito sobre o crescimento de S. aureus estatisticamente significativo em relação ao controle, sendo maior para amoxicilina. A atividade hemolítica foi diminuída na presença de amoxicilina e ambos antimicrobianos induziram aumento na atividade de citolisinas extracelulares. A técnica de quimiluminescência dependente de luminol, utilizada para avaliar susceptibilidade à fagocitose através do burst oxidativo de polimorfonucleares neutrófilos, demonstrou que amoxicilina influenciou positivamente a fagocitose dependente de opsoninas e ciprofloxacino estimulou a fagocitose não opsonizada. Visto o burst oxidativo ser um método indireto para a demonstração de fagocitose, a confirmação de células bacterianas fagocitadas/aderidas foi realizada através da observação de esfregaços corados em microscopia ótica comum (1000 x). Apesar de ambos antimicrobianos induzirem aumento de ânion superóxido intracelular, detectado em ensaios de redução de nitroblue tetrazolium (NBT), o ciprofloxacino induziu maior quantidade que a amoxicilina. A demonstração de que diferentes antimicrobianos possam atuar sobre...( Resumo completo, clicar acesso eletrônico abaixo) / Amoxycillin and ciprofloxacin are antimicrobials with dissimilar mechanisms of action against bacteria. This is a comparative study of how each of these agents affects some of the factors related to the virulence of the pathogenic strain of Staphylococcus aureus ATCC 25923. The post-antibiotic effect, hemolytic activity against sheep erythrocytes, cytolysin activity against McCoy cells and susceptibility to opsonin-dependent and independent phagocytosis by neutrophils from Rattus albinus norvegicus were assessed in bacteria grown in a subinhibitory concentration (½ MIC) of each agent. Induction of oxidative stress was observed directly by detecting superoxide production in response to the bacteria. Both the antimicrobials exerted effect on the growth of S. aureus, which was significantly different from the growth of controls, though amoxycillin had the stronger effect. Hemolytic activity was diminished in the presence of amoxycillin, but both agents induced an increase in the activity of secreted cytolysins. By employing luminol-dependent chemiluminescence to assess the susceptibility of the bacteria to phagocytosis by detecting the respiratory burst in polymorphonuclear neutrophils, it was shown that amoxycillin had a positive effect on opsonin-dependent phagocytosis, while ciprofloxacin stimulated non-opsonized phagocytosis. Since detection of the respiratory burst is an indirect demonstration of phagocytosis, direct observation of stained slides under the light microscope at 1000 × magnification was used to confirm the presence of bacteria ingested by and adhering to neutrophils. While both agents induced a rise in the intracellular level of superoxide, assayed by nitroblue tetrazolium reduction, ciprofloxacin produced the stronger response. The demonstration that distinct antimicrobials... (Complete abstract click electronic access below)

O presente trabalho aborda a biodegradação de sulfametoxazol e ciprofloxacino em 2 reatores anaeróbios horizontais de leito fixo (RAHLF). Os reatores foram operados e mantidos em regime permanente com um tempo de detenção hidráulica de 16 a 17 horas com uma água residuária sintética que simula o esgoto sanitário na temperatura de 25°C. Foi avaliado o estado dos reatores como ponto de referência para os próximos passos. A contaminação com sulfametoxazol e ciprofloxacino iniciou-se, então, e o comportamento dos reatores foi avaliado. As concentrações dos antimicrobianos foram analisadas por extração em fase sólida acoplada com espectrometria de massa. Ambos antimicrobianos foram degradados pelos reatores até níveis abaixo do limite de quantificação dos métodos de análise. Utilizando os dados de DQO e as análises dos antimicrobianos, junto com dados cinéticos obtidos, foi determinado que o RAHLF tem resistência a estes compostos e concentrações até uma ordem de magnitude acima das encontradas em condições reais. A degradação do sulfametoxazol foi muito eficiente e é previsto que um RAHLF típico em operação consegue degradar mais que 99% do sulfametoxazol. A degradação do ciprofloxacino foi menos eficiente, com remoção prevista para RAHLF típico de 80% a 90%. / The present project approaches sulfamethoxazole and ciprofloxacin biodegradation in two horizontal anaerobic immobilized sludge (HAIS) reactors. The reactors were operated and maintained at dynamic stability with a hydraulic retention time of 16 to 17 hours using synthetic wastewater, which simulates domestic wastewater, at 25°C. The dynamically stable state was evaluated as a control for the following steps. The reactors were then continuously fed with synthetic wastewater contaminated with sulfamethoxazole and ciprofloxacin, independently, and their behaviors were observed. The antibiotics\' concentrations were analyzed by solid phase extraction couples with mass spectrometry. Both antibiotics were degraded in the bioreactors to below quantification limits. Using COD and antibiotic data and derived kinetic constants, it was shown that a typical operating HAIS reactor with a hydraulic retention time of 6 to 8 hours should be capable of removing over 99% of sulfamethoxazole in its influent. Ciprofloxacin removal was less efficient, but was nevertheless promising, with a removal rate of 80% to 90% in typical conditions.

L'application des biomatériaux est de plus en plus élargie. Le progrès médical suggère l'utilisation des biomatériaux (verres bioactifs, apatites,..) en tant qu'implants selon le besoin de l'organisme. L'objectif de notre travail est de mettre en évidence l'influence biologique des molécules organiques (bisphosphonates, biopolymères et antibiotiques) incorporés dans des matrices de verres bioactifs. De même, notre étude vise à optimiser les meilleures techniques de synthèse et d'association des verres bioactifs à ces molécules. La détoxification des rats mâles de souche « Wistar » exposés au chlorure de nickel par une apatite synthétique a aussi fait l'objet de ce travail. Suite à une perte osseuse provoquée, nous avons démontré que l'utilisation des antibiotiques associés à des verres bioactifs en tant qu'implants osseux, chez des rattes ovariectomisées, permet d'éliminer certains effets indésirables par voie systémique. Ceci a été mis en évidence par l'évaluation des paramètres biochimiques et histologiques du foie et du rein. Aucune variation significative en comparaison avec ceux du témoin négatif n'a été révélée. L'étude in vitro a montré d'une part que l'introduction du Chitosan et surtout de l'antibiotique dans la matrice vitreuse font augmenter l'activité antibactérienne in vitro. Cette étude in vitro a montré d'autre part que la Ciprofloxacine induit un effet néfaste sur les cellules ostéoblastiques et endothéliales. Cet effet est local lorsqu'il s'agit des expérimentations in vivo. Ceci est mis en évidence lors des évaluations du statut oxydant. Les marqueurs du remodelage osseux, l'histologie de l'os et les paramètres physico-chimiques montrent l'effet retardateur de cet antibiotique sur la dissolution de l'implant et par conséquent sur son ossification. La synthèse par le procédé de sol-gel provoque une bioactivité plus importante que celle obtenue par fusion. La bioactivité des verres bioactifs étudiés diffère selon la molécule introduite. Celle-ci est réduite dans le cas de l'association du Clodronate et de Ciprofloxacine in vitro et in vivo. Alors que, le Polyvinyl Alcohol et surtout le Chitosan font modifier la cinétique de cette bioactivité in vivo. Concernant l'hydroxyapatite, nous avons essayé d'explorer son effet détoxifiant chez des rats reçevant le chlorure de nickel. Nos résultats ont montré que le nickel induit un stress oxydant au niveau du foie, du rein, de la rate et du culot érythrocytaire. Des troubles physiologiques ont été observés chez les rats exposés au nickel. Cependant, l'implantation de l'hydroxyapatite protège les rats intoxiqués par le nickel contre ses effets toxiques en diminuant l'état du stress. Le biomatériau utilisé s'avère efficace pour corriger l'équilibre ferrique et phosphocalcique, protéger les fonctions rénale et hépatique, abaisser le taux du nickel osseux et corriger l'anémie. / The application of biomaterials is increasingly widened. Medical progress suggest the use of biomaterials (bioactive glasses, apatites,..) as implants according to the need of the body. The aim of our work is to highlight the biological influence of organic molecules (bisphosphonates, biopolymers and antibiotics) incorporated into matrix of bioactive glasses. Similarly, our study aims to optimize the best synthesis and combination technique of bioactive glasses to these molecules. The detoxification of male rats strain "Wistar" exposed to nickel chloride by a synthetic apatite also has been the object of this work. Following the bone loss induced, we have demonstrated that the use of antibiotics associated with bioactive glass as bone implants, in ovariectomised rats, eliminates some adverse effects systemic. This has been highlighted by the evaluation of biochemical and histological parameters of liver and kidney. Any significant changes in comparison with those of the negative control was revealed. The in vitro study showed in the one hand that the introduction of Chitosan and especially of the antibiotic in the glass matrix can increase antibacterial activity. This in vitro study showed in the other hand that the Ciprofloxacin induces a negative effect on osteoblastic and endothelial cells. This effect is local when it has been an in vivo experiments. This is highlighted by the oxidative status evaluation. Markers of bone turnover, bone histology and physicochemical parameters show the retarding effect of this antibiotic on the dissolution of the implant and consequently on its bone formation. Synthesis by sol-gel method causes a more important bioactivity than melting. The bioactivity of elaborated bioactives glasses will differ depending on the molecule introduced. It is reduced in the case of combination of Clodronate and Ciprofloxacin in vitro and in vivo. While, Polyvinyl Alcohol and especially Chitosan modify the kinetic of the bioactivity in vivo. Concerning the hydroxyapatite, we tried to explore its detoxifying effect in rats receiving nickel chloride. Our results showed that nickel induces an oxidative stress in the liver, kidney, spleen and red cell pellet. Physiological disorders were observed in rats exposed to nickel. However, implantation of hydroxyapatite protects rats intoxicated by nickel against its toxic effects by decreasing the stress status. The used biomaterial is effective to correct ferric phosphate balance, protect kidney and liver function, reduce level of bone nickel and correct anemia.

Controlled release of drugs to the lungs is an interesting and evolving field of research. The influence of physicochemical properties of nanoparticles on the controlled release of ciprofloxacin and in-vivo pharmacokinetics following pulmonary administration was evaluated. The physicochemical properties had an effect on encapsulation efficiency and surface charge, but no significant effect on particle size. The in-vitro release profiles of ciprofloxacin in phosphate buffered saline showed small differences over the range of physicochemical properties evaluated. The physicochemical properties of ciprofloxacin nanoparticles resulted in variable and unreliable nebulizer output using a vibrating mesh nebulizer whereas the impact on the aerosol properties of a jet nebulizer was negligible. Addition of mucoadhesive polymers in the nanoparticles had a three-fold increase in apparent half-life in rats by releasing ciprofloxacin over an extended release period on the surfaces of the lungs.

In evolution alternative genetic trajectories can potentially lead to similar phenotypic outcomes. However, certain trajectories are preferred over others. These preferences bias the genomes of living organisms and the underlying processes can be observed in ongoing evolution. We have studied a variety of biases that can be found in bacterial chromosomes and determined the selective causes and functional consequences for the cell. We have quantified codon usage bias in highly expressed genes and shown that it is selected to optimise translational speed. We further demonstrated that the resulting differences in decoding speed can be used to regulate gene expression, and that the use of ‘non-optimal’ codons can be detrimental to reading frame maintenance. Biased gene location on the chromosome favours recombination between genes within gene families and leads to co-evolution. We have shown that such recombinational events can protect these gene families from inactivation by mobile genetic elements, and that chromosome organization can be selectively maintained because inversions can lead to the formation of unstable hybrid operons. We have used the development of antibiotic resistance to study how different bacterial lifestyles influence evolutionary trajectories. For this we used two distinct pairs of antibiotics and disease-causing bacteria, namely (i) Mycobacterium tuberculosis that is treated with rifampicin and (ii) Escherichia coli that is treated with ciprofloxacin. We have shown that in the slow-growing Mycobacterium tuberculosis, resistance mutations are selected for high-level resistance. Fitness is initially less important, and over time fitness costs can be ameliorated by compensatory mutations. The need for rapid growth causes the selection of ciprofloxacin resistance in Escherichia coli not only to be selected on the basis of high-level resistance but also on high fitness. Compensatory evolution is therefore not required and is not observed. Taken together, our results show that the evolution of a phenotype is the product of multiple steps and that many factors influence which trajectory is the most likely to occur and be most beneficial. Over time, selection will favour this particular trajectory and lead to biased evolution, affecting genome sequence and organization.

Biofilmes são comunidades bacterianas complexas encapsuladas em matrizes poliméricas autoproduzidas e podem se desenvolver em superfícies inertes ou tecidos vivos. A formação do biofilme é um importante fator de virulência, pois permite à bactéria resistir às respostas do hospedeiro e à terapia antimicrobiana. Devido a essa elevada resistência aos antimicrobianos, é difícil estabelecer uma estratégia eficaz para o tratamento de infecções com formação de biofilmes, levando a falhas na erradicação das mesmas. Nesse contexto, o objetivo do presente estudo é desenvolver um modelo farmacocinético/farmacodinâmico (PK/PD) para descrever o efeito do ciprofloxacino (CIP) na presença de biofilmes de Pseudomonas aeruginosa (ATCC 27853), visto que a modelagem PK/PD de antimicrobianos é uma ferramenta útil na escolha de regimes posológicos que atinjam o efeito bactericida máximo, minimizando o desenvolvimento de resistência. Para atingir esse objetivo, inicialmente um método analítico por CLAE/fluorescência foi desenvolvido para quantificar o CIP em amostras de plasma e microdialisado. O método desenvolvido foi simples, rápido e com sensibilidade adequada para corretamente caracterizar a farmacocinética plasmática e pulmonar do CIP. Posteriormente, um modelo animal de infecção pulmonar crônica foi adaptado da literatura e padronizado, permitindo a investigação da distribuição pulmonar do CIP em ratos Wistar sadios e infectados. Para tal, bactérias foram imobilizadas em beads de alginato a fim de manter a infecção por até 14 dias com cargas bacterianas superiores à 108 UFC/pulmão. Estudo de microdiálise foi então conduzido para avaliar as concentrações livres de CIP após administração intravenosa de 20 mg/kg. A análise não-compartimental (NCA) e a modelagem farmacocinética populacional (PopPK) dos dados foram realizadas nos softwares Phoenix® e NONMEM®, respectivamente. Diferenças significativas foram observadas no clearance plasmático (1,59 ± 0,41 L/h/kg e 0,89 ± 0,44 L/h/kg) e na constante de eliminação (0,23 ± 0,04 h-1 e 0,14 ± 0,08 h-1) para ratos sadios e infectados, resultando em uma exposição plasmática maior nos animais infectados (ASC0-∞ = 27,3 ± 12,1 μg·h/mL) quando comparados com os animais sadios (ASC0-∞ = 13,3 ± 3,5 μg·h/mL) ( = 0,05). Apesar da maior exposição plasmática, quando comparados com os animais saudáveis (fT = 1,69), animais infectados apresentaram uma penetração pulmonar quatro vezes menor (fT = 0,44). Diferenças na constante de eliminação pulmonar não foram observadas. Dados plasmáticos e pulmonares foram simultaneamente descritos por modelo PopPK constituído de compartimentos venoso e arterial, dois compartimentos representativos de duas regiões pulmonares distintas e dois compartimentos periféricos, representando outros tecidos que não os pulmões. Um clearance pulmonar foi adicionado ao modelo apenas para os dados de microdiálise dos animais infectados (CLlung = 0,643 L/h/kg) afim de explicar a exposição tecidual diminuída. O modelo desenvolvido descreveu, com sucesso, os dados plasmáticos e teciduais de animais sadios e infectados, permitindo a correta caracterização das alterações observadas na disposição plasmática e pulmonar do CIP decorrentes da infecção com biofilme. Para os estudos de farmacodinâmica, o efeito bactericida do CIP frente a biofilmes e células planctônicas de P. aeruginosa foi simultaneamente avaliado através do uso de curvas de morte bacteriana. Para a construção destas curvas, biofilmes de P. aeruginosa foram formados na superfície de blocos de acrílico e sua formação foi confirmada pelo ensaio cristal violeta e por microscopia eletrônica de varredura. Os blocos foram expostos a concentrações constantes de CIP (de 0,0625 a 10 μg/mL) e, em tempos pré-determinados, células planctônicas e de biofilmes eram amostradas para quantificação. Um modelo semi-mecanístico que incorpora um modelo Emax sigmoidal foi utilizado para descrever o efeito do CIP frente a ambos estilos de vida bacteriano. Uma subpopulação pré-existente com menor suscetibilidade ao CIP foi incluída no modelo e o efeito do CIP nesta subpopulação também foi descrito pelo modelo Emax sigmoidal. A comparação dos parâmetros estimados pelo modelo demonstrou que o efeito in vitro do CIP é maior para as células planctônicas (EC50 = 0,259 mg/L e 0,123 mg/L e Emax = 2,25 h-1 e 5,59 h-1 para biofilmes e planctônicas, respectivamente). A potência estimada do CIP para a subpopulação resistente foi muito menor para ambos estilos de vida bacteriano (EC50 = 2,71 mg/L e 1,15 mg/L para biofilmes e planctônicas, respectivamente). Os modelos desenvolvidos podem ser utilizados para a simulação de cenários não testados e servir como uma ferramenta para guiar a escolha dos regimes posológicos adequados, contribuindo para o sucesso terapêutico no tratamento de infecções associadas à biofilmes. / Biofilms are complex bacterial communities enclosed in self-produced polymeric matrices that can develop in inert surfaces or living tissues. Biofilm formation is an important virulence factor that allows bacteria to resist host responses and antibacterial agents. Due to this high resistance to antibiotics, it is difficult to establish an efficacious strategy for treatment of infections with biofilm formation leading to failure in infection eradication. In this context, the goal of this study was to develop a pharmacokinetic/pharmacodynamic (PK/PD) model to describe the antimicrobial effect of ciprofloxacin (CIP) in the presence of biofilms of Pseudomonas aeruginosa (ATCC 27853), since PK/PD modeling for antibacterial agents can be a useful tool to choose dosing regimens and to achieve the maximum bactericidal effect, minimizing the development of resistance. To reach this goal, firstly an analytical method based on HPLC/fluorescence was developed in order to quantify CIP in plasma and lung microdialysate. The developed method was simple, fast and with enough sensibility to proper characterize CIP plasma and lung pharmacokinetics. Secondly, an animal model of chronic lung infection was adapted from literature and standardized, allowing the analysis of CIP lung distribution in infected and healthy Wistar rats. Bacteria were immobilized in alginate beads prior to inoculation to Wistar rats in order to sustain the pneumonia for 14 days, maintaining a bacterial load superior to 108 CFU/lung. A microdialysis study was then conducted to evaluate free CIP concentrations after an intravenous administration of 20 mg/kg. Non-compartimental analysis (NCA) and populational PK modeling (PopPK) of the data were performed in Phoenix® and NONMEM®, respectively. Statistical differences were observed in the plasma clearance (1.59 ± 0.41 L/h/kg and 0.89 ± 0.44 L/h/kg) and elimination rate constant (0.23 ± 0.04 h-1and 0.14 ± 0.08 h-1) for healthy and infected rats, respectively, resulting in a significantly higher CIP plasma exposure in infected rats (AUC0-∞ = 27.3 ± 12.1 μg·h/mL) compare to healthy animals (AUC0-∞ = 13.3 ± 3.5 μg·h/mL) ( = 0.05). Besides the plasma exposure, a four times lower pulmonary penetration was observed in infected rat’s lungs (fT = 0.44) in comparison to healthy animals (fT = 1.69), with no significant differences in the lung elimination rate constant. Plasma and lung data were simultaneously fitted using a PopPK model consisting of an arterial and a venous compartment, two compartments representing different regions of the lungs and two peripheral distribution compartments, representing tissues other than lungs. A lung clearance was added to the model for infected animals (CLlung = 0.643 L/h/kg) to explain the lower tissue exposure. The model successfully described the plasma and microdialysis data from both, healthy and infected rats and allowed to correctly describe the changes in CIP plasma and lung disposition in biofilm infections. For the pharmacodynamic studies, CIP bactericidal effect against Pseudomonas aeruginosa biofilms and planktonic shedding cells were simultaneously evaluated using the time-kill curves approach. For the time-kill curves construction, P. aeruginosa biofilms were formed in acrylic blocks, which was confirmed by the crystal violet assay and scanning electron microscopy. The blocks were placed in flasks containing Mueller-Hinton growth medium and exposed to constant CIP concentrations (ranging from 0.0625 to 10 μg/mL). At pre-determined time points, biofilm and planktonic cells were sampled for bacterial counting. A mechanism-based model which incorporates a sigmoidal Emax model was used to describe the CIP effect against P.aeruginosa in both llifestyles, biofilm and planktonic. The presence of a pre-existing resistant subpopulation was included in the model and also modeled with a sigmoidal Emax model to describe CIP effect in this subpopulation. Comparison of the parameter estimates showed that the in vitro effect of CIP is higher for planktonic cells (EC50 = 0.259 mg/L and 0.123 mg/L and Emax = 2.25 h-1 and 5.59 h-1 for biofilm and planktonic cells, respectively). CIP potency was much lower for the resistant subpopulation, for both bacteria lifestyles (EC50 = 2.71 mg/L and 1.15 mg/L for biofilm and planktonic, respectively). The developed models can be used to simulate untested scenarios and serve as a tool to guide dosing regimen selection, contributing for the therapeutic success of treatments of biofilm-associated infections.

Instead of planktonic growth in nature, many species of bacteria form biofilm to survive in harsh conditions. Although many chronic bacterial infections are caused by bacterial species in a biofilm lifestyle, previous research has focused on studying antibiotic resistance in planktonic growth. Here we used a modified MBEC assay, i.e. biofilm growth on pegs, to determine Escherichia coli biofilm inhibitory concentrations (BIC) of ciprofloxacin, streptomycin and rifampicin and to study the minimal selective concentration (MSC) for ciprofloxacin in E. coli biofilm. We could observe high inhibitory concentrations for all antibiotics in the biofilm pre-formed in media without antibiotics compared to the biofilm formed in antibiotics. We also show preliminary result indicating that sublethal concentrations of ciprofloxacin lead to the selection of ciprofloxacin resistant mutants in biofilm and that the selection level is lower than what was observed in planktonic growing E. coli. With more knowledge in how the biofilm formation precedes in different antibiotic settings, the treatment for chronic biofilm infections used today could be evaluated and changed so that the infections could be eradicated.

Using a semi-PBPK modeling/quantitative meta-analysis approach, this project investigated what factors affect pulmonary and systemic exposures of Budesonide (BUD), Tobramycin (TOB), and Ciprofloxacin (CIP) after inhalation: Three structurally different pulmonary disposition models were developed for each drug, including pulmonary absorption (all three), excretion (TOB and CIP) and sequestration (TOB) in a peripheral and central lung compartment. Systemic disposition parameters were estimated using available human mean plasma (cp(t)) and sputum (cs(t)) concentration profiles after IV administration, and GI absorption parameters were estimated from these profiles after oral administration. Pulmonary disposition parameters were estimated from cp(t) and cs(t) profiles after inhalation using various devices along with their published pulmonary deposition characteristics. Appropriate covariate models accounted for effects of Cystic Fibrosis on the systemic disposition/GI absorption for TOB and CIP. Monte Carlo Simulations (MCS) were used to optimize parameters and validate the final models and parameter spaces against published data. Despite limited available data, especially cs(t) for BUD and CIP (after IV administration), the point estimates for the final model parameters were mechanistically plausible for all three drugs and consistent with their known differences in physicochemical and ADME properties. Model predictions adequately described the observed cp(t) and cs(t) profiles as well as exposure metrics across studies. As the most lipophilic drug, BUD showed the fastest pulmonary absorption rates and highest Fpul (83%). TOB, a very hydrophilic drug, exhibited (intracellular) pulmonary sequestration, resulting in slow pulmonary absorption and excretion and low Fpul (10%). CIP - as zwitterion - showed relatively slow pulmonary absorption and excretion, leading to low Fpul (8%); pulmonary excretion accounted for 27% of CIP overall elimination. Results of a formal parameter sensitivity analysis demonstrated that, for all three drugs, after inhalation, (1) their systemic exposures (cp(t)) depend primarily on CLtot along with Fpul/sequestration combined with Foral; (2) increasing pulmonary exposures (cs(t)) can be accomplished by slowing down pulmonary absorption rates (kca) and/or slowing down mucociliary clearance from the lungs into the GI tract (kcm) – affirming the overall hypothesis guiding the project.

La stabilité génomique des organelles de plantes suscite un grand intérêt dans le domaine de la biologie végétale. En effet, plusieurs études récentes suggèrent que ce type d’instabilité génomique pourrait mener à l’isolation de traits intéressants en l’agronomie. Plusieurs protéines sont d’ailleurs déjà été identifiés comme étant impliqués dans le maintien de la stabilité de ces génomes, tels que MSH1, la famille des POLI, OSB1, les protéines Whirly et les Recombinases A (RECA). Le génome nucléaire d’Arabidopsis thaliana encode trois protéines s’apparentant à la Recombinase A bactérienne et qui sont ciblées à la mitochondrie et/ou au chloroplaste, soit RECA1, RECA2 et RECA3. Globalement, ces gènes partagent une similarité de séquence de 61% avec leur homologue bactérien chez Escherichia coli. Chez les bactéries ces protéines jouent un rôle essentiel dans la recombinaison homologue et sont impliquées dans la réparation de l’ADN. Chez Arabidopsis, il a été démontré que RECA2 et RECA3 sont nécessaires au maintien de l’intégrité du génome mitochondriale. Toutefois leur contribution à la stabilité du génome chloroplastique ainsi que le rôle de RECA1 restent obscures. Le but de ce projet est donc de déterminer la contribution éventuelle des protéines RECA d’Arabidopsis dans la réparation de l’ADN chloroplastique et plus précisément le rôle du gène RECA1. Nous énonçons l’hypothèse que les RECA de plantes se comportent effectivement comme leurs orthologues bactériens en étant impliqués dans la recombinaison homologue. Dans le cadre de ce projet, nous avons tenté d’isoler des lignées mutantes pour chacun des gènes RECA d’Arabidopsis. En somme, nous avons pu obtenir des lignées convenables pour notre étude que dans le cas du gène RECA1. Ces lignées ont été utilisées pour évaluer la contribution de ce gène à la stabilité du génome du chloroplaste. Ensuite, pour étudier la relation épistatique des gènes RECA1, WHY1 et WHY3, un croisement des différentes lignées mutantes pour ces gènes a été réalisé. Nous avons ensuite étudié la sensibilité de toutes ces lignées mutantes à la ciprofloxacine, un agent causant des bris double brin exclusivement dans les organelles de plantes. Finalement, iii nous avons testé la présence de réarrangements dans le génome du chloroplaste en condition normal ou en présence de stress génotoxique. Nos résultats démontrent que les protéines Whirly et RECA1 sont impliquées dans deux voies de réparation de l’ADN différentes et que les Whirly sont suffisantes pour s’occuper des bris d’ADN double brin en l’absence de RECA1. Nous démontrons également que l’absence de Whirly et RECA1 entraine une forte augmentation de la quantité de réarrangements dans le génome du chloroplaste. De plus nous proposons que la polymérase POLIB est impliquée dans la même voie de réparation que RECA1. Finalement nous proposons un modèle pour expliquer nos résultats et impliquons RECA1 dans un mécanisme de réparation d’ADN et aussi un rôle potentiel dans la réplication. / The stability of plant organelles genomes elicits a great interest in the domain of plant biology. In fact, numerous studies suggest that genomic instability can lead to the isolation of interesting traits in the field of agronomy. Some factors such as MSH1, the POLI family, OSB1, the Whirly proteins and the Recombinase A (RECA), have already been identified has being implicated in the maintenance of genome stability. The nuclear genome of Arabidopsis thaliana encodes three proteins, RECA1, RECA2 and RECA3, that shares a high resemblance with bacterial Recombinase A. They are targeted to the mitochondria and/or to the chloroplast. Globally, these genes share a similarity of sequence of 61% with their bacterial homologue in Escherichia coli. In bacteria these proteins play an essential part in homologous recombination and are implicated in DNA repair. In Arabidopsis, RECA2 and RECA3 have been shown as being essential to maintain the integrity of the mitochondrial genome but their contribution to the stability of the chloroplast as well as the role of RECA1 remains obscure. The goal of this project is to establish the eventual contribution of the Arabidopsis RECA proteins in the repair of chloroplast DNA and more precisely the role of the RECA1 gene. We propose the hypothesis that plants RECA act in the same fashion as their bacterial orthologues by being implicated in homologous recombination. Within the framework of this project, we have attempted to isolate mutant lines for each RECA gene of Arabidopsis. In the end, we were able to obtain appropriate lines for our study only for the RECA1 gene. These lines were then used to evaluate the contribution of the gene to chloroplast genome stability. Afterwards, in order to study the epistatic relationship between the RECA1, WHY1 and WHY3 genes, a cross between different mutant lines of these genes was realised. We then studied the sensitivity of all of those mutant lines to ciprofloxacine, an agent causing double stranded breaks exclusively in plant organelles. Finally, we evaluated the presence of rearrangements in the chloroplast genome under normal conditions and under the presence of a genotoxic stress. Our v results show that the Whirly and RECA1 proteins are implicated in two separate pathways of DNA reparation and that the Whirly proteins are sufficient to take in charge DNA double strand breaks generated by the absence of RECA1. We also demonstrate that the absence of Whirly and RECA1 causes an increasein the quantity of rearrangements in the chloroplast genome. Furthermore, we propose that the polymerase POLIB is implicated in the same repair pathway as RECA1. Finally we propose a model to explain our results and implicate RECA1 in a DNA repair mechanism and propose a role for RECA1 in DNA replication.