Rising Antimicrobial Resistance is a threat faced all over the world. Bacterial infections that were treatable with antibiotics only a few years ago can now lead to life-threatening conditions. This thesis is part of the work of a large platform, PLATINEA, trying to reduce the rate of new resistances occurring in Sweden by preventing non optimal treatment. Due to shortages of the right antibiotics, suboptimal antibiotics are prescribed, which has shown to be accelerating the resistances among the bacterial populations. This study proposes an information exchange database and a central storage model for critical antibiotics to circumvent stock outs and inconveniences resulting from shortages of medically valuable antibiotics. Through interviewing prominent actors in the Swedish pharmaceutical supply chain an inside into the procurement of antibiotic in Sweden and what concerns are faced by the organs involved was created. Literature studies on occurred shortages of antibiotics in Sweden and the world were examined and possible reasons for these were identified. Examination of governmental efforts and assignments created the context in which gaps were identified that this thesis work could fill. A focus on Benzylpenicillin and Rifampicin were kept throughout the study. The collected data led to the implementation recommendation of two models by this study. An information platform suggested to allow better, faster and more accurate information exchange between all involved actors of the supply chain as well as a centralized storage model for the storage of antibiotics with medically high value in Sweden.  Through the implementation of the model systems shortages of critical antibiotics can be circumvented and better availability of information leads to quicker reactions ability to stock outs of other antibiotics.

<p>Ribosomes are the universal ribonucleoprotein organelles that translate the genetic message from mRNA to protein. In prokaryotes, the ribosomal subunits are 30S and 50S subunit, which bind together during the translation process forming 70S ribosome. The ribosome is a highly dynamic structure, and acts as a working platform for the different factors involved in the process of converting the genetic information into protein.</p><p>Cryo-electron tomography (cryo-ET) is an emerging imaging technology that combines the potential of three-dimensional (3D) reconstruction at molecular resolution with a close-to-native preservation of the specimen. Here, we have applied this method to reconstruct rifampicin-treated <i>Escherichia coli</i> individual 30S subunits in vitro and in situ, and individual 50S subunits in situ. In the 30S subunit, the head, the platform and the body show large conformational movements relative to each other. The particles are grouped into three conformational groups according to the width/height ratios. Also, an S15 fusion protein derivative has been used as a physical reporter to localize S15 in the 30S subunit. In the 50S subunit, the L1 stalk, the L7/L12 stalk, the central protuberance (CP), and the peptidyl transferase center (PTC) cleft are the most dynamic and flexible parts in the reconstructed structures with clear movements indicated. Different locations of the tunnel in the central cross-sections through the in situ 50S subunits indicate a flexible pathway inside the large subunit. In addition, gross morphological changes were also been observed in our reconstructions. Our results demonstrate a considerable conformational flexibility among individual ribosomal subunits, both in vitro and in situ.</p><p>Translation is an essential process for all cells and organisms. Translation initiation is the rate-limiting step and the most highly regulated phase of translation process. Several regions along the mRNA have been reported to influence translation initiation. The Shine-Dalgarno (SD) sequence located 5-9 bases upstream of the initiation codon supports translation initiation by complementary binding to the Anti-Shine-Dalgarno (ASD) sequence on the 16S rRNA.</p><p>We have here compared how an SD⁺ sequence influences gene expression, if located upstream or downstream of an initiation codon. The positive effect of an upstream SD⁺ is confirmed. A downstream SD⁺ gives decreased gene expression. If an SD⁺ is placed between two potential initiation codons, initiation takes place predominantly at the second start site. The first start site is activated if the distance between this site and the downstream SD⁺ is enlarged and/or if the second start site is weakened. Upstream initiation is eliminated if a stable stem-loop structure is placed between this SD⁺ and the upstream start site. The results suggest that the two start sites compete for ribosomes that bind to an SD⁺ located between them. A minor positive contribution to upstream initiation resulting from 3’ to 5’ ribosomal diffusion along the mRNA is suggested. Since the location of SD⁺or SD-like sequences can strongly influence gene expression, this should be of significant evolutionary importance.</p>

This study firstly reports the development and characterization of PVP-AgNPs, PANSA and PVPAgNPs/ PANSA nanocomposite on gold. AFM and TEM analyses revealed highly electroactive nanocomposites whose morphogy and properties were essential for the immobilization of CYP2E1. Secondly, the development and characterization of Au/PVPAgNPs/ PANSA/CYP2E1, Au/PVP-AgNPs/PANSA/SA-CYP2E1 and Au/PVPAgNPs/ PANSA/EG-CYP2E1 nanobiosensors are reported. AFM studies displayed globular morphologies with large roughness for the enzyme modified electrodes as opposed to those electrodes without enzymes. Finally, the biotransformation of standard solutions of TB drugs (isoniazid, ethambutol, pyrazinamide and rifampicin) in pH 7.4, 0.1 M phosphate buffer solution is reported. The biotransformations of the TB drugs were successfully studied using cyclic voltammetry (CV), square wave voltammetry (SWV), differential voltammetry (DPV) and steady state amperometry under aerobic conditions. Very good detection limits were obtained for the standard solutions of TB drugs and were found to be in the micromolar range. The detection limit values for the individual TB drugs were 0.55 μM (isoniazid), 0.7 μM (ethambutol), 0.054 μM (pyrazinamide) and 0.05 μM (rifampicin). The detection limit results showed that the nanobiosensors were more sensitive and suitable for the determination of the respective drugs in plasma and serum.

Ribosomes are the universal ribonucleoprotein organelles that translate the genetic message from mRNA to protein. In prokaryotes, the ribosomal subunits are 30S and 50S subunit, which bind together during the translation process forming 70S ribosome. The ribosome is a highly dynamic structure, and acts as a working platform for the different factors involved in the process of converting the genetic information into protein. Cryo-electron tomography (cryo-ET) is an emerging imaging technology that combines the potential of three-dimensional (3D) reconstruction at molecular resolution with a close-to-native preservation of the specimen. Here, we have applied this method to reconstruct rifampicin-treated Escherichia coli individual 30S subunits in vitro and in situ, and individual 50S subunits in situ. In the 30S subunit, the head, the platform and the body show large conformational movements relative to each other. The particles are grouped into three conformational groups according to the width/height ratios. Also, an S15 fusion protein derivative has been used as a physical reporter to localize S15 in the 30S subunit. In the 50S subunit, the L1 stalk, the L7/L12 stalk, the central protuberance (CP), and the peptidyl transferase center (PTC) cleft are the most dynamic and flexible parts in the reconstructed structures with clear movements indicated. Different locations of the tunnel in the central cross-sections through the in situ 50S subunits indicate a flexible pathway inside the large subunit. In addition, gross morphological changes were also been observed in our reconstructions. Our results demonstrate a considerable conformational flexibility among individual ribosomal subunits, both in vitro and in situ. Translation is an essential process for all cells and organisms. Translation initiation is the rate-limiting step and the most highly regulated phase of translation process. Several regions along the mRNA have been reported to influence translation initiation. The Shine-Dalgarno (SD) sequence located 5-9 bases upstream of the initiation codon supports translation initiation by complementary binding to the Anti-Shine-Dalgarno (ASD) sequence on the 16S rRNA. We have here compared how an SD+ sequence influences gene expression, if located upstream or downstream of an initiation codon. The positive effect of an upstream SD+ is confirmed. A downstream SD+ gives decreased gene expression. If an SD+ is placed between two potential initiation codons, initiation takes place predominantly at the second start site. The first start site is activated if the distance between this site and the downstream SD+ is enlarged and/or if the second start site is weakened. Upstream initiation is eliminated if a stable stem-loop structure is placed between this SD+ and the upstream start site. The results suggest that the two start sites compete for ribosomes that bind to an SD+ located between them. A minor positive contribution to upstream initiation resulting from 3’ to 5’ ribosomal diffusion along the mRNA is suggested. Since the location of SD+ or SD-like sequences can strongly influence gene expression, this should be of significant evolutionary importance.

No description available.

This study firstly reports the development and characterization of PVP-AgNPs, PANSA and PVPAgNPs/ PANSA nanocomposite on gold. AFM and TEM analyses revealed highly electroactive nanocomposites whose morphogy and properties were essential for the immobilization of CYP2E1. Secondly, the development and characterization of Au/PVPAgNPs/ PANSA/CYP2E1, Au/PVP-AgNPs/PANSA/SA-CYP2E1 and Au/PVPAgNPs/ PANSA/EG-CYP2E1 nanobiosensors are reported. AFM studies displayed globular morphologies with large roughness for the enzyme modified electrodes as opposed to those electrodes without enzymes. Finally, the biotransformation of standard solutions of TB drugs (isoniazid, ethambutol, pyrazinamide and rifampicin) in pH 7.4, 0.1 M phosphate buffer solution is reported. The biotransformations of the TB drugs were successfully studied using cyclic voltammetry (CV), square wave voltammetry (SWV), differential voltammetry (DPV) and steady state amperometry under aerobic conditions. Very good detection limits were obtained for the standard solutions of TB drugs and were found to be in the micromolar range. The detection limit values for the individual TB drugs were 0.55 μM (isoniazid), 0.7 μM (ethambutol), 0.054 μM (pyrazinamide) and 0.05 μM (rifampicin). The detection limit results showed that the nanobiosensors were more sensitive and suitable for the determination of the respective drugs in plasma and serum.

Philosophiae Doctor - PhD / This study firstly reports the development and characterization of PVP-AgNPs, PANSA and PVPAgNPs/ PANSA nanocomposite on gold. AFM and TEM analyses revealed highly electroactive nanocomposites whose morphogy and properties were essential for the immobilization of CYP2E1. Secondly, the development and characterization of Au/PVPAgNPs/ PANSA/CYP2E1, Au/PVP-AgNPs/PANSA/SA-CYP2E1 and Au/PVPAgNPs/ PANSA/EG-CYP2E1 nanobiosensors are reported. AFM studies displayed globular morphologies with large roughness for the enzyme modified electrodes as opposed to those electrodes without enzymes. Finally, the biotransformation of standard solutions of TB drugs (isoniazid, ethambutol, pyrazinamide and rifampicin) in pH 7.4, 0.1 M phosphate buffer solution is reported. The biotransformations of the TB drugs were successfully studied using cyclic voltammetry (CV), square wave voltammetry (SWV), differential voltammetry (DPV) and steady state amperometry under aerobic conditions. Very good detection limits were obtained for the standard solutions of TB drugs and were found to be in the micromolar range. The detection limit values for the individual TB drugs were 0.55 μM (isoniazid), 0.7 μM (ethambutol), 0.054 μM (pyrazinamide) and 0.05 μM (rifampicin). The detection limit results showed that the nanobiosensors were more sensitive and suitable for the determination of the respective drugs in plasma and serum. / South Africa

A permeabilidade através do epitélio intestinal tem se tornado um importante aspecto a ser determinado nas avaliações biofarmacotécnicas envolvendo fármacos e medicamentos. A técnica mais empregada para essa determinação in vitro é aquela que utiliza a cultura de células Caco-2. Entretanto, ainda são discutíveis as condições para a realização desses experimentos, uma vez que a padronização das mesmas é fator fundamental para a confiabilidade dos resultados. Nesta tese, foram avaliadas as condições para realização dos estudos de permeabilidade através de membranas de células Caco-2 para a rifampicina, principal fármaco utilizado no tratamento da tuberculose. Para tanto, foram investigados fatores tais como a citotoxicidade da rifampicina em diferentes concentrações, a influência da concentração do fármaco sobre a permeabilidade, do pH de realização dos experimentos e da presença de proteínas do muco intestinal, além da influência de proteínas plasmáticas. Foi também investigado o potencial indutor da rifampicina sobre a expressão da glicoproteína-P (Pgp) e seu impacto na permeabilidade da própria rifampicina. Os estudos foram desenvolvidos utilizando membranas de células Caco-2 provenientes da American Type Culture Collection (ATCC) cultivadas em placas Transwel®, a quantificação da fração permeada foi por cromatografia líquida de alta eficiência com métodos validados. A análise da indução da expressão da Pgp foi realizada por PCR-RT. Demonstrou-se que as concentrações da rifampicina (10,0; 25,0 e 50,0 &#181;g/mL) não ocasionaram danos às células Caco-2 no estudo de citotoxicidade pela técnica que emprega o sal do brometo de 3-(4,5-dimetil-2-tiazoli)-2,5-difenil-2H-tetrazólio (MTT). As concentrações de rifampicina (5,0; 10,0 e 25,0 &#181;g/mL) não resultaram em valores estatisticamente diferentes de permeabilidade aparente (Papp) em células Caco-2 nas condições do estudo. A rifampicina apresentou valor de Papp significativamente maior em pH 6,8 dentre os valores de pH avaliados (5,8 ; 6,8; 7,4). A presença de muco simulado e de soro fetal bovino não resultou em valores de permeabilidade significativamente distintos do resultado obtido sem a sua adição ao experimento. A expressão da Pgp em células Caco-2 é induzida pela adição da rifampicina (10&#181;g/mL), ocasionando diminuição da sua permeabilidade por mecanismo de efluxo. Pelos resultados de permeabilidade obtidos em todas as condições avaliadas, a rifampicina pode ser considerada um fármaco de alta permeabilidade de acordo com o Sistema de Classificação Biofarmacêutica. / The permeability through the intestinal epithelium has become an important aspect to be determined in evaluations involving drugs and pharmaceutical products. The most common technique for this determination in vitro is one that uses the culture of Caco-2 cells. Nevertheless, the conditions for carrying out such experiments are still questionable, since the standardization of them is essential to the reliability of the results. In this thesis, we evaluate the conditions for the studies of permeability of rifampicin through membranes of Caco-2 cells, the main drug used in the treatment of tuberculosis. To this end, we examined factors such as cytotoxicity of rifampicin at different concentrations, the influence of drug concentration on the permeability, as well as the pH of the experiments, the presence of proteins of intestinal mucus, and the influence of plasma proteins. It was also investigated the potential of rifampicin on the expression of P-glycoprotein (Pgp) and its impact on the permeability of rifampicin itself. The studies were developed using membranes of Caco-2 cells from American Type Culture Collection (ATCC) grown on plates Transwel®, and the quantification of the fraction of drug permeated was obtained by high performance liquid chromatography with validated methods. The analysis of induction of expression of Pgp was performed by RT-PCR. It was demonstrated that the concentrations of rifampicin (10,0; 25,0 and 50,0 &#181;g/mL) did not cause damage to Caco-2 cells in the study of the cytotoxicity technique that uses a bromide salt of 3 - (4,5-dimethyl-2 - thiazol) -2,5-diphenyl-2H-tetrazolium (MTT). The concentrations of rifampicin (5,0; 10,0 and 25,0 &#181g/mL) did not result in statistically different values of apparent permeability (Papp) in Caco-2 cells under the conditions of the study. Rifampicin showed a value of Papp significantly higher at pH 6.8 in comparison with other measured pH values (5,8 and 7,4). The presence of mucus simulated and fetal calf serum did not result in permeability values significantly different from the result obtained without its addition to the experiment. The expression of P-gp in Caco-2 cells is induced by the addition of rifampicin (10 &#181;g/ml), decreasing its permeability by efflux mechanism. Taking into account the results of permeability obtained in all conditions, the rifampicin can be considered a high permeability drug according to the biopharmaceutical classification system.

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No. of bitstreams: 1 adrianaferreirafaria.pdf: 20849316 bytes, checksum: 511836cab839ebb39105bd682c987241 (MD5) Previous issue date: 2010-08-13 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O objetivo principal da tese em questão foi o desenvolvimento, otimização e validação de metodologias analíticas para análise de formulações farmacêuticas utilizadas no tratamento da tuberculose, as quais contêm como princípio ativo etambutol (ETB), isoniazida (ISO), rifampicina (RIF) e pirazinamida (PIR), isolados ou em associação. Inicialmente, duas metodologias analíticas para análise de ETB em comprimidos foram desenvolvidas: a primeira permitiu a análise simultânea de ETB e da impureza 2-amino-1-butanol por eletroforese capilar de zona (CZE) utilizando um eletrólito de corrida contendo 60,0 mmol L-1 de tampão ácido acético/acetato de sódio e 5,0 mmol L-1 de Cu2+, polaridade normal (+25 kV) e detecção UV em 262 nm. A segunda foi realizada por espectrofotometria com diluição dos padrões e amostras em 5,0 mmol L-1 de tampão ácido acético/acetato de sódio e 0,5 mmol L-1 de Cu2+ e detecção UV em 262 nm. A formação do complexo CuETB foi necessária em ambas as metodologias desenvolvidas, uma vez que ETB apresenta baixa absortividade molar. Algumas figuras de mérito, tais como, linearidade, repetitividade, exatidão, limite de detecção e limite de quantificação foram avaliadas para as duas metodologias. Os dois métodos foram comparados e não apresentaram diferenças significativas no intervalo de 95% usando o teste t não pareado com variância agrupada. Em um segundo momento, um novo método para análise simultânea de dose fixa combinada (DFC), contendo ETB, ISO, RIF e PIR por CZE com detecção UV foi desenvolvido, otimizado e validado. A condição experimental consistiu em um eletrólito contendo 50,0 mmol L-1 de tampão ácido acético/acetato de sódio e 12,5 mmol L-1 de Cu2+ e polaridade normal (+22 kV). Essa metodologia foi aplicada com sucesso na análise de 2-DFC (ISO e PIR) em comprimidos e 4-DFC (ETB, ISO, RIF e PIR) em sache. Finalmente, uma metodologia por CZE utilizando detecção UV para a análise simultânea de ISO, suas impurezas e produtos de degradação, como o ácido isonicotínico, isonicotinato de etila, 4-cianopiridina e isonicotinamida foi otimizada. A condição experimental consistiu em um eletrólito contendo 50,0 mmol L-1 de tampão ácido acético/acetato de sódio e 12,5 mmol L-1 de Cu2+, polaridade normal (+20 kV) e detecção UV em 270 nm. É importante ressaltar que planejamentos de experimentos, tais como, planejamento fatorial completo 32 e Box-Behnken 33 foram utilizados como ferramenta auxiliar no desenvolvimento e otimização das metodologias analíticas (CZE e espectofotométrica) e na avaliação da robustez para a análise de 4-DFC. / The main focus of this thesis was the development, optimization and validation of analytical methodologies for analysis of pharmaceutical preparations used for tuberculosis treatment, which contain as active ingredients, ethambutol (ETB), isoniazid (ISO), rifampicin (RIF) and pyrazinamide (PYR) isolated or in association. Two analytical methodologies for ETB analysis in tablets were developed initially: the first one took into account the capillary zone electrophoresis (CZE) approach for simultaneous analysis of ETB and its impurity 2-amino-1-butanol using an electrolyte consisting of 60.0 mmol L-1 of acetic acid/acetate buffer, 5.0 mmol L-1 of Cu2+, under normal polarity (+25 kV) and UV detection at 262 nm. The second one was performed by spectrophotometry using 5.0 mmol L-1 of acetic acid/acetate buffer and 0.5 mmol L-1 of Cu2+ for standards and sample dilutions under UV detection at 262 nm. The CuETB complex was necessary for the two methodologies, since ETB presents low molar absorptivity. Some merit figures such as linearity, repeatability, accuracy, limit of detection and limit of quantification were evaluated for both methodologies. These methodologies were compared and they did not present significant differences at the 95% confidence level using the parametric independent sample t test. In a second phase a novel method for the simultaneous analysis of fixed dose combination (FDC) containing ETB, ISO, RIF and PYR by CZE under UV detection was developed, optimized and validated. The experimental condition optimized consisted of an electrolyte containing 50.0 mmol L-1 of acetic acid/acetate buffer and 12.5 mmol L-1 of Cu2+ under normal polarity (+22 kV). This methodology was successfully applied to the analysis of 2-FDC (ISO and PYR) in tablet samples and 4-FDC (ETB, ISO, RIF and PYR) in a sachet sample. Finally, a CZE methodology using UV detection for simultaneous analysis of ISO, its impurities and degradation products such as isonicotinic acid, ethyl isonicotinate, 4-cyanopyridine and isonicotinamide was ptimized. The optimized experimental condition consisted of an electrolyte containing 50.0 mmol L-1 of acetic acid/acetate buffer and 12.5 mmol L-1 of Cu2+ under normal polarity (+20 kV) and UV detection at 270 nm. It is important to stress that design of experiment such as 32 full factorial design and 33 Box-Behnken design were used as auxiliary tools in the development and optimization of the analytical methodologies (CZE and spectrophotemetric) and robustness evaluation for 4-FDC analysis.

Antibiotic resistance in bacteria is acquired through spontaneous chromosomal mutations or horizontal gene transfer. In the absence of antibiotics, resistant mutants generally show reduced fitness due to compromised growth rate, competitive ability and virulence compared to their antibiotic-sensitive ancestors. The focus of my research is to dissect the molecular underpinnings of the variations in the fitness cost of chromosomal antibiotic resistance using a systems-level approach. From an evolutionary perspective, my research aims are to understand how the fitness cost influences adaptation in resistant populations in an antibiotic-free environment. Using rifampicin resistance in Pseudomonas aeruginosa as a model, my work shows that most of the variation in the fitness cost of rifampicin resistance can be attributed to the direct effect of rifampicin resistance mutations on transcriptional efficiency. Through RNA-Seq transcriptome profiling, I demonstrate that global changes in gene expression levels associated with resistance mutations are surprisingly subtle, suggesting that the transcriptional regulatory network of P. aeruginosa is robust against compromised transcriptional efficiency. Using experimental evolution and whole-genome sequencing, my work reveals a systematic difference in the genetic basis of adaptation in mutants that were propagated in the absence of antibiotics. During compensatory adaptation, resistant mutants can recover the fitness cost of resistance by fixing second-site mutations that directly offset the deleterious effects of resistance mutations. Amongst resistant mutant populations with low fitness costs, general adaptation limits compensatory adaptation, which is most likely to be due to the rarity of compensatory mutations and clonal interference. Far from being the most ubiquitous mechanism in the evolution of resistance, compensatory adaptation is the exception that is more likely to be observed in resistant mutants with high fitness costs. In addition, I applied key elements of the integrative experimental approach developed in this work to dissect the molecular basis of the fitness cost associated with carriage of the pNUK73 small plasmid in P. aeruginosa, which carries the rep gene encoding a plasmid replication protein. My results confirmed that rep expression generates a significant fitness cost in P. aeruginosa and demonstrate how the molecular origins of the fitness cost of resistance can be dissected in a different biological context.