Le travail réalisé dans cette thèse concerne la synthèse de nouvelles structures macromoléculaires aromatiques et hétérocycliques. La synthèse de ces polymères a été envisagée par des procédés de polycondensation non conventionnels. A la différence des réactions classiques utilisées en polycondensation, des réactions de condensation « multi-composants » faisant intervenir trois ou quatre fonctions réactives ont été considérées. Les réactions de Debus-Radziszewski, Hantzsch, et Chichibabin, permettant la formation directe de structures aromatiques et ou hétérocycliques ont été plus particulièrement choisies. Ces polymérisations ont été réalisées à la fois par voie thermique classique et sous irradiation micro-ondes. Trois types de familles de polymères ont été synthétisés avec succès (PIM/PTAI, PPP, P-CNTP). Les résultats obtenus montrent que l’irradiation micro-ondes est bénéfique pour la synthèse de certaines structures, mais cet effet n’est pas systématique. En revanche, la technique d’irradiation sous micro-ondes s’impose comme outil très performant pour le développement de nouvelles structures macromoléculaires de par la réduction significative des temps de polymérisation. L’ensemble de ce travail souligne l’intérêt de la polycondensation par réaction multi-composant et ouvre de nouvelles perspectives pour le développement de nouveaux matériaux polymères aromatiques / hétérocycliques. / In this thesis, the synthesis of new aromatic and heterocyclic macromolecular structures is reported. These polymers have been synthetized by unconventional polycondensation processes. Unlike classic reactions used in polycondensation, "multicomponent" condensation involving three or four reactive functions were here described. More particularly, the reactions of Debus-Radziszewski, Hantzsch, and Chichibabin, allowing the direct formation of aromatic and heterocyclic structures have been chosen. These polymerizations were carried out both by conventional thermal method and under microwave irradiation. Three types of polymer families have been synthesized successfully (PIM / PTAI, PPP, P-CNTP). The results show that microwave irradiation is beneficial for the synthesis of some structures, but this effect is not systematic. On the other hand, microwave irradiation is a powerful tool to develop new macromolecular structures by significantly reducing the time of polymerization. This work underlines the interest of polycondensation by multicomponent reaction and opens perspectives for the development of new aromatic / heterocyclic polymeric materials.

No description available.

Polymyxins are potent antibiotics that bind to the outer membrane of Gram-negative bacteria, entering the cell and disrupting the inner membrane, resulting in cell death. They were traditionally used as antibiotics of last resort, but the recent surge of multidrug resistant pathogens has renewed interest in these antibiotics. The emergence of polymyxin resistance determinants such as the recently discovered plasmid-mediated phosphoethanolamine transferase MCR-1 may put a strain on the future effectiveness of this antibiotic. One method to combat the rise in antibiotic resistant bacteria is through the identification and development of antibiotic adjuvants. These are small molecules that are able to inhibit the resistance mechanism, allowing previously ineffective antibiotics to once again become effective at treating bacterial infections. In this work, a high throughput cell-based screen was conducted using an in-house library of Actinomycete-derived crude cell extracts in order to search for a natural product inhibitor of an E. coli strain expressing mcr-1. In addition, the development of a new enzyme assay was attempted using purified MCR-1 C-terminal catalytic domain and a chromogenic substrate to test enzymatic activity in vitro, in hopes of establishing a simple means of studying inhibition of MCR-1. The structure-function relationship of MCR-1 was also explored by generating amino acid substitutions and studying their effect on the ability of the enzyme to confer resistance to colistin, as well as the generation of MCR-1 transmembrane truncation mutants to determine if it was possible to generate a shorter variant of MCR-1 that retained its enzymatic activity. This work furthers our understanding of the biochemistry and enzymology of MCR-1, and outlines attempts to identify inhibitors of MCR-1 in order to re-sensitize resistant bacteria to polymyxins. / Thesis / Master of Science (MSc) / Polymyxins are potent antibiotics that are threatened by the spread of multi-drug resistant bacteria. Resistance to these antibiotics is relatively rare, although the recent discovery of a mobile polymyxin resistance enzyme, MCR-1, threatens the future use of this antibiotic for treating infections, as it can readily transfer to other bacteria. The goal of this work was to search for a natural product inhibitor of MCR-1 in order to reverse its ability to confer resistance to polymyxins. A color-changing assay was conducted with MCR-1 in hopes of establishing a method to study the inhibition of MCR-1 in vitro. Additionally, amino acid substitutions were generated in MCR-1 to better understand how key amino acids affect enzyme function, as well as transmembrane domain truncations to determine if it was possible to create a shorter functioning variant of MCR-1.

The primary focus of my work is the application of informatics methods to the fields of materials science and analytical chemistry. The statistical analysis of data has become increasingly important in understanding the properties of materials and analytes. Statistical methods like principal component analysis (PCA) and multivariate curve resolution (MCR) are widely used for analysis in chemistry and other fields given their ability to categorize spectra in an unsupervised way. PCA is relatively easy to apply and has appealing mathematical properties. However, the results can be challenging to interpret, even for experienced users. In contrast, MCR results can be more interpretable, because the factors resemble real spectra and do not have negative scores or loadings. Nevertheless, the useful orthogonality properties of the scores and loadings in PCA are sacrificed in doing so. Other statistical analysis methods like cluster analysis and partial least squares regression (PLS-R) present their own challenges. Pattern recognition entropy (PRE) is a novel application of Shannon’s information theory for understanding the underlying complexity in spectra. Unlike PCA and MCR, PRE is a summary statistic that adopts the mathematical quantification of information and applies it for chemometric analysis. PRE values reflect the shape and complexity of spectra. Chapter 1 contains a description of the analytical methods/instruments that provided the data I analyzed by PRE and other informatics tools, including (i) X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) and (ii) liquid chromatography-mass spectrometry (LC-MS) and capillary electrophoresis (CE), (iii) a discussion of some of the commonly used statistical analysis tools like PCA, MCR, cluster analysis and PLS-R, and (iv) a description of PRE. Chapter 2 describes in much greater detail the theory associated with the statistical tools I used and PRE. Chapter 3 describes the PRE and informatics analysis of depth profiles through thin films by XPS and ToF-SIMS. Chapter 4 introduces the concept of the ‘reordered spectrum’ as an intuitive, visual representation of spectra to address the abstraction associated with PRE result. Total ion current chromatograms (TICCs) generated using LC-MS are often extremely complex and ‘noisy’. Chapter 5 describes the application of PRE as a variable reduction method for producing higher quality TICCs. Chapter 6 discusses the limitations associated with the application of PRE to TICCs and presents a new method using cross-correlation (CC) in conjunction with a PRE analysis. Chapter 7 discusses a new methodology that uses CE and PRE to detect autologous blood doping (ABD). Chapter 8 presents my conclusions of this present work and discusses the scope of future work on PRE. The thesis also contains several appendices. Appendix 1 introduces polyallylamine (PAAm) as a simple, easy-to-apply adhesion promoter for the widely used photoresist SU-8. Appendices 2, 3 and 4 contain articles I wrote that relate to trends in modern XPS instrumentation and 5-8 contain supplemental information relating to Chapters 3, 4, 5, and 7 respectively.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Em diversos estados do Brasil, foram relatadas epidemias de infecções causadas por micobactérias de crescimento rápido (MCR) desde o ano 2000. A maioria dos casos foi principalmente associada ao clone BRA100 de Mycobacterium massiliense, recentemente renomeada para Mycobacterium abscessus subsp. bolletii, isolado de pacientes submetidos a procedimentos invasivos nos quais os instrumentos médicos não foram adequadamente esterilizados e/ou desinfetados. Sendo as quinolonas uma opção no tratamento de infecções por MCR e sugerida para esquemas terapêuticos para esses surtos, foram avaliadas nesse trabalho as atividades in vitro de quatro gerações de quinolonas para cepas clinicas e de referência de MCR através da microdiluição em caldo. Também foram analisadas as sequências peptídicas das regiões determinantes da resistência a quinolonas (RDRQ) das subunidades A e B da DNA gyrase (GyrA e GyrB) após o seqüenciamento de DNA seguido pela tradução da sequência de aminoácidos. Cinquenta e quatro cepas de M. abscessus subsp bolletii, incluindo o clone BRA100, isoladas em diferentes estados do Brasil, e 19 cepas de referência de MCR foram caracterizadas. Todas as 54 cepas clínicas de M. abscessus subsp. bolletii foram resistentes a todas as gerações de quinolonas e mostraram o mesmo resíduo nas RDRQ, incluindo Ala-83 em GyrA, Arg-447 e Asp-464 em GyrB, descritos como sendo responsáveis por gerar um baixo nível de resistência a quinolonas em micobactérias. Porém, outras espécies de MCR apresentaram diferentes susceptibilidade e padrões de mutações contrários aos classicamente já definidos, sugerindo que outros mecanismos de resistência, diferentes de mutações em gyrA e gyrB também possam estar envolvidos na alta resistência a quinolonas. / Several outbreaks of infections caused by rapidly growing mycobacteria (RGM) have been reported in many Brazilian states since 2000. Most of the cases were mainly associated to Mycobacterium massiliense, recently renamed as Mycobacterium abscessus subsp. bolletii, BRA100 clone recovered from patients who had undergone invasive procedures, in which medical instruments have not been properly sterilized and / or disinfected. Since quinolones have represented an option for the treatment of general RGM infections and suggested for therapeutic schemes for these outbreaks, we evaluated the in vitro activities of four generations of quinolones for clinical and reference RGM by broth microdilution, and analysis of peptide sequences of the quinolone resistance determining regions (QRDR) of GyrA and GyrB after DNA sequencing followed by amino acid translation. Fifty four isolates of M. abscessus subsp bolletii, including clone BRA100, recovered in different states of Brazil, and 19 reference strains of RGM species were characterized. All 54 M. abscessus subsp. bolletii isolates were resistant to all generations of quinolones and showed the same amino acids in the QRDR including the Ala-83 in GyrA, Arg-447 and Asp-464 in GyrB, described as responsible for an intrinsic low level of resistance to quinolones in mycobacteria. But other RGM species presented distinct susceptibilities to this class of antimicrobials and patterns of mutations contrary to what has been traditionally defined, suggesting that other mechanisms of resistance, different from gyrA or gyrB mutations, may also be involved in resistance to high levels of quinolones.

Parameter estimation techniques have been successfully and extensively applied to deterministic models based on ordinary differential equations but are in early development for stochastic models. In this thesis, we first investigate using parameter estimation techniques for a deterministic model to approximate parameters in a corresponding stochastic model. The basis behind this approach lies in the Kurtz limit theorem which implies that for large populations, the realizations of the stochastic model converge to the deterministic model. We show for two example models that this approach often fails to estimate parameters well when the population size is small. We then develop a new method, the MCR method, which is unique to stochastic models and provides significantly better estimates and smaller confidence intervals for parameter values. Initial analysis of the new MCR method indicates that this method might be a viable method for parameter estimation for continuous time Markov chain models.

L’objectif de ce travail a consisté en le développement de nouveaux processus multi-composant radicalaires et leur application en synthèse organique. Des carbo-alcénylation d'oléfines ont ainsi été réalisées avec de nouveaux précurseurs de radicaux, des oléfines diverses, en présence de Z-diphénylsulfonyléthylène comme accepteur terminal. Les conditions de la réaction ont été optimisées, en introduisant notamment la diphénylsulfonylhydrazine comme amorceur de radicaux sous irradiation UV, et substitut au couteux DTBHN. Des conditions sans étain ont également été étudiées avec l’objectif de remplacer le réactif (Bu3Sn)2 par des radicaux silylés. Le tris (triméthylsilyl)silylthiopropene a ainsi été testé avec succès en tant qu'agent de propagation des chaînes radicalaires. A l’issue de ce travail méthodologique, nous avons développé une stratégie de synthèse de l'Eucophylline, un alcaloïde isolé de Leuconotis griffithii, dont le squelette tétracyclique a été élaboré sur la base d’une réaction de carbo-oximation radicalaire d’oléfine. Ce processus multicomposant, suivi d’une réduction de la fonction oxime et d’une lactamisation offre une voie d’accès rapide au motif bicyclo[3.3.1]lactame, intermédiaire-clé de la synthèse. Une réaction de type Friedländer entre ce lactame et un ortho-aminobenzonitrile a permis d’accéder au squelette tetrahydrobenzo[1,8]naphthyridine de l'Eucophylline. La synthèse du composé modèle a enfin été complétée par l’introduction du substituant vinylique par un couplage de Heck. / The aim of this work was to develop new radical multi-component processes and their application in organic synthesis. Carbo-alkenylation processes were thus performed with new radical precursors, different olefins, in the presence of Z-diphenylsulfonylethylene as a terminal acceptor. Reaction conditions have also been optimized, including the diphenylsulfonylhydrazine as a radical initiator under U.V. irradiation, and substitute to the costly DTBHN. Tin-free conditions were also screened with the goal of replacing (Bu3Sn)2 with silyl radicals. Tris(trimethylsilyl)silylthiopropene was tested with success as a radical chain carrier. After this methodology studies, we developed a strategy toward the synthesis of Eucophylline, an alcaloid isolated from Leuconotis griffithii, which tetracyclic skeleton was elaborated based on a carbo-oximation of olefin. This multicomponent process, followed by a reduction of the oxime function and a lactamization offered a fast access to the bicyclo[3.3.1]lactam, a key-intermediate in the synthesis. A Friedländer-type reaction between this lactam and an ortho-aminobenzonitrile allowed an access to the Eucophylline tetrahydrobenzo[1,8]naphthyridine skeleton. The synthesis of the model compound was finally completed with the introduction of the vinylic substituent through a Heck coupling.

This thesis documents the development and application of a unique database orientated software package, BugsCEP, for environmental and climatic reconstruction from fossil beetle (Coleoptera) assemblages. The software tools are described, and the incorporated statistical methods discussed and evaluated with respect to both published modern and fossil data, as well as the author’s own investigations. BugsCEP consists of a reference database of ecology and distribution data for over 5 800 taxa, and includes temperature tolerance data for 436 species. It also contains abundance and summary data for almost 700 sites - the majority of the known Quaternary fossil coleopteran record of Europe. Sample based dating evidence is stored for a large number of these sites, and the data are supported by a bibliography of over 3 300 sources. Through the use of built in statistical methods, employing a specially developed habitat classification system (Bugs EcoCodes), semi-quantitative environmental reconstructions can be undertaken, and output graphically, to aid in the interpretation of sites. A number of built in searching and reporting functions also increase the efficiency with which analyses can be undertaken, including the facility to list the fossil record of species found by searching the ecology and distribution data. The existing Mutual Climatic Range (MCR) climate reconstruction method is implemented and improved upon in BugsCEP, as BugsMCR, which includes predictive modelling and the output of graphs and climate space maps. The evaluation of the software demonstrates good performance when compared to existing interpretations. The standardization method employed in habitat reconstructions, designed to enable the inter-comparison of samples and sites without the interference of differing numbers of species and individuals, also appears to be robust and effective. Quantitative climate reconstructions can be easily undertaken from within the software, as well as an amount of predictive modelling. The use of jackknifing variants as an aid to the interpretation of climate reconstructions is discussed, and suggested as a potential indicator of reliability. The combination of the BugStats statistical system with an enhanced MCR facility could be extremely useful in increasing our understanding of not only past environmental and climate change, but also the biogeography and ecology of insect populations in general. BugsCEP is the only available software package integrating modern and fossil coleopteran data, and the included reconstruction and analysis tools provide a powerful resource for research and teaching in palaeo-environmental science. The use of modern reference data also makes the package potentially useful in the study of present day insect faunas, and the effects of climate and environmental change on their distributions. The reconstruction methods could thus be inverted, and used as predictive tools in the study of biodiversity and the implications of sustainable development policies on present day habitats. BugsCEP can be downloaded from http://www.bugscep.com

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Em diversos estados do Brasil, foram relatadas epidemias de infecções causadas por micobactérias de crescimento rápido (MCR) desde o ano 2000. A maioria dos casos foi principalmente associada ao clone BRA100 de Mycobacterium massiliense, recentemente renomeada para Mycobacterium abscessus subsp. bolletii, isolado de pacientes submetidos a procedimentos invasivos nos quais os instrumentos médicos não foram adequadamente esterilizados e/ou desinfetados. Sendo as quinolonas uma opção no tratamento de infecções por MCR e sugerida para esquemas terapêuticos para esses surtos, foram avaliadas nesse trabalho as atividades in vitro de quatro gerações de quinolonas para cepas clinicas e de referência de MCR através da microdiluição em caldo. Também foram analisadas as sequências peptídicas das regiões determinantes da resistência a quinolonas (RDRQ) das subunidades A e B da DNA gyrase (GyrA e GyrB) após o seqüenciamento de DNA seguido pela tradução da sequência de aminoácidos. Cinquenta e quatro cepas de M. abscessus subsp bolletii, incluindo o clone BRA100, isoladas em diferentes estados do Brasil, e 19 cepas de referência de MCR foram caracterizadas. Todas as 54 cepas clínicas de M. abscessus subsp. bolletii foram resistentes a todas as gerações de quinolonas e mostraram o mesmo resíduo nas RDRQ, incluindo Ala-83 em GyrA, Arg-447 e Asp-464 em GyrB, descritos como sendo responsáveis por gerar um baixo nível de resistência a quinolonas em micobactérias. Porém, outras espécies de MCR apresentaram diferentes susceptibilidade e padrões de mutações contrários aos classicamente já definidos, sugerindo que outros mecanismos de resistência, diferentes de mutações em gyrA e gyrB também possam estar envolvidos na alta resistência a quinolonas. / Several outbreaks of infections caused by rapidly growing mycobacteria (RGM) have been reported in many Brazilian states since 2000. Most of the cases were mainly associated to Mycobacterium massiliense, recently renamed as Mycobacterium abscessus subsp. bolletii, BRA100 clone recovered from patients who had undergone invasive procedures, in which medical instruments have not been properly sterilized and / or disinfected. Since quinolones have represented an option for the treatment of general RGM infections and suggested for therapeutic schemes for these outbreaks, we evaluated the in vitro activities of four generations of quinolones for clinical and reference RGM by broth microdilution, and analysis of peptide sequences of the quinolone resistance determining regions (QRDR) of GyrA and GyrB after DNA sequencing followed by amino acid translation. Fifty four isolates of M. abscessus subsp bolletii, including clone BRA100, recovered in different states of Brazil, and 19 reference strains of RGM species were characterized. All 54 M. abscessus subsp. bolletii isolates were resistant to all generations of quinolones and showed the same amino acids in the QRDR including the Ala-83 in GyrA, Arg-447 and Asp-464 in GyrB, described as responsible for an intrinsic low level of resistance to quinolones in mycobacteria. But other RGM species presented distinct susceptibilities to this class of antimicrobials and patterns of mutations contrary to what has been traditionally defined, suggesting that other mechanisms of resistance, different from gyrA or gyrB mutations, may also be involved in resistance to high levels of quinolones.

La fitorremediación es una técnica de descontaminación de ecosistemas que aprovecha la capacidad de las plantas para acumular sustancias tóxicas en su interior sin que afecten severamente a su ciclo vital. Dicha técnica presenta un bajo impacto medioambiental, convirtiéndose en una alternativa a los métodos clásicos, más agresivos y costosos. En lo referente a metales pesados, las plantas inducen la síntesis intracelular de fitoquelatinas (PC), ligandos tiólicos que complejan los metales y los almacenan en orgánulos celulares de bajo metabolismo como las vacuolas. A pesar de las investigaciones realizadas hasta la fecha, el mecanismo de actuación de las fitoquelatinas no está totalmente establecido, incluida la secuencia de formación y la estequiometria final de los complejos PC-M. Por esta razón, resulta de gran interés estudiar estos procesos de complejación, pues sus conclusiones pueden ayudar a entender la fitorremediación y a optimizar su aplicación. Las investigaciones recogidas en esta tesis se sustentan -como metodología básica- en el análisis quimiométrico mediante MCR-ALS de los datos obtenidos de valoraciones complexométricas registradas por técnicas electroanalíticas, concluyendo con la proposición de modelos de complejación para el sistema en estudio. La elección del plomo como metal complejante se debe a su alta toxicidad y dispersión en el medio ambiente, así como por suponer un paso más en el uso de dicha metodología, pues el estudio de los sistemas PC/Pb(II) presentan problemas que la dificultan. Estos problemas son, principalmente, el desplazamiento lateral de las señales voltamperométricas que produce un decrecimiento en la linealidad de los datos obtenidos, y la presencia de señales anódicas que favorece un fuerte solapamiento entre los picos de las diferentes especies químicas; ambos problemas comprometen la aplicación del método MCR-ALS y el correcto examen de los resultados. El objetivo de esta tesis adquiere así una doble vertiente. Por un lado, para solucionar dichos problemas y, de alguna forma, ampliar la aplicabilidad de MCR-ALS a eventuales sistemas más complejos, se estudian nuevas adaptaciones metodológicas (análisis MCR-ALS de matrices espectro-voltamperométricas), herramientas (programa shiftfit, que corrige el desplazamiento de potencial de las señales voltamperométricas) y metodologías experimentales (uso de electrodos alternativos al de mercurio). Por otro lado, se procura la consecución de resultados para los propios sistemas PC/Pb(II) estudiados, es decir, la determinación de modelos de complejación lo bastante completos y sólidos para servir de apoyo a los resultados de los estudios in vivo o in vitro. Los trabajos publicados y la explicación de los resultados están organizados en tres bloques: • El primer bloque (artículo 11.1) recoge la aproximación inicial al estudio de la complejación de fitoquelatinas y ligandos relacionados con plomo utilizando la metodología básica. Los resultados ponen de relieve la relativa solvencia del procedimiento, así como el verdadero alcance de los problemas que se describen en el capítulo 5. • El segundo bloque recopila los resultados de la aplicación de las nuevas metodologías y herramientas propuestas para solucionar las insuficiencias o ambigüedades de los modelos de complejación obtenidos en el artículo anterior. Estas metodologías son el análisis quimiométrico conjunto de valoraciones registradas por polarografía y dicroísmo circular (11.2), la formulación del programa shiftfit que corrige el movimiento lateral de señales polarográficas, es decir, la falta de un valor fijo del potencial de pico (11.3) y, finalmente, el uso del electrodo de película de bismuto (BiFE) con la intención de minimizar el solapamiento que producen las señales anódicas (11.4). • Tras la aplicación de estas metodologías a sistemas sencillos, en el tercer bloque se aplican a sistemas con plomo (11.5 y 11.6), incluyendo la comparación de los diferentes modelos de complejación obtenidos en los artículos 11.1 y 11.5 para el sistema PC3/Pb(II). / Phytoremediation is a decontamination technique that takes profit by the plants ability to accumulate toxic substances without affecting severely their vital cycles. This technique presents the advantatges of being cheap and non-destructive to ecological systems. Regarding heavy metals, plants induce the intracellular synthesis of phytochelatins (PC), Cys-rich polypeptides that complex metals and storage them in cellular organelles of limited metabolism as vacuoles. Despite the research achieved to date, the mechanism of actuation of phytochelatins is not entirely established, including the sequence of formation and the final stoichiometry of the PC-M complexes. By this reason, it is of great interest to study these complexation processes, reaching conclusions that would be able to help the optimization of phytoremediation. The investigations collected in this doctoral thesis are held -as basic methodology- in the chemometric analysis through MCR-ALS of the data obtained from complexometric titrations carried out by voltammetric techniques. This methodology concludes with the proposition of complexation models for the systems under study, but when lead is used as complexing metal, PC/Pb(II) systems present problems that make it more difficult. Mainly, these problems are the lateral movement of the voltammetric signals (producing a decrease in the linearity of the data), and the presence of anodic signals that propitiate a strong overlapping between peaks of different chemical species; both troubles compromise the MCR-ALS application and the correct investigation of the results. To solve the aforementioned problems -and that way to increase the applicability of MCR-ALS to more complex systems-, some new tools have been applied for the first time: • Methodologic adaptations as the MCR-ALS simultaneous analysis of spectro- and electrochemical data (row-wise CD-DPP augmented matrices) to differenciate real chemical species from physicochemical or kinetic phenomena of the diffusion layer. • Chemometric programs as shiftfit that corrects the potential shift of the polarographic signals to obtain a matrix of corrected voltammograms with an increased linearity. • The use of the bismuth film electrode (BiFE) for complexation studies, to minimize the overlapping produced by the anodic signals.