This thesis explores the surface assembly of mechanically interlocked molecular architectures at gold surfaces for potential applications in molecular switches, anion sensing and stimuli (redox and optical) responsive molecular films. <b>Chapter One</b> introduces the field of mechanically interlocked molecules focusing on rotaxane and catenane surface assemblies in the form of single molecule thick self-assembled monolayers. A review of the surface-attached characteristics of mechanically interlocked molecules is given before exploring specific anion template directed strategies for their construction. The potential to incorporate both redox-active and optically-active functional groups within these mechanically interlocked molecules is also discussed. <b>Chapter Two</b> provides the experimental details and procedures employed in this thesis to characterise the molecular systems under investigation. <b>Chapter Three</b> introduces several surface characterisation techniques such as; ellipsometry, contact angle, X-ray reflectivity and X-ray photoelectron spectroscopy, with a particular focus of applying these tools to probe the surface co-conformation of switchable and interlocked molecules at surfaces. Electroanalytical techniques such as cyclic voltammetry, chronoamperometry and electrical impedance spectroscopy are also introduced. <b>Chapter Four</b> details the surface assembly of a series of ferrocene containing anion templated catenane self-assembled monolayers on gold. Detailed electrochemical and angle resolved X- ray photoelectron spectroscopy characterisation elucidates the co-conformation upon surface attachment. <b>Chapter Five</b> details the anion templated surface assembly of a redox-active rotaxane self- assembled monolayer on gold. Subsequent electroanalysis and X-ray photoelectron spectroscopy characterisation confirms the structural integrity of the film and a possible co- conformation at the surface is discussed. <b>Chapter Six</b> describes efforts towards constructing optically responsive hybrid d-f lanthanide containing mechanically interlocked molecules. Initial work focuses on switching characteristics of a redox switchable antennae and its ability to modulate the luminescence of a series of lanthanide complexes in solution. Subsequent surface attachment of the lanthanide complexes in the form of emissive self-assembled monolayers is also investigated.

L'étude des interactions non-covalentes et des relations structure-fonction est à la base de la compréhension des systèmes biologiques. La MS supramoléculaire est une technique de choix pour l’étude des interactions protéine/protéine ou protéine/ligand. Dans le cadre d'études qualitatives ou quantitatives, pour chaque système étudié, les conditions expérimentales et les paramètres instrumentaux ont été optimisés pour conserver le complexe en phase gazeuse (1). L'objectif principal de ce travail est de caractériser le site nucléotidique de hPEBP1 et de contribuer à la découverte de molécules anti-métastases. Sur le plan fonctionnel, une activité enzymatique de hPEBP1 n'a pas pu être mise en évidence. Pour ce projet, une méthode MS de détermination de KD de complexes à faible affinité, plus précise et ne nécessitant par l'utilisation d'un ligand de référence a été développée (2). Une recherche des déterminants structuraux d'un ligand optimal de hPEBP1 a été réalisée par criblage de composés issus d’une synthèse raisonnée basée sur la structure des nucléotides FMN et GTP et par la détermination de leur KD (3). Les criblages ont montré que les critères structuraux indispensables pour la liaison sont la présence d’un groupement chargé ou donneur d’électrons, d’une structure apparentée à une base azotée et d’un cycle additionnel. Une part importante de l’affinité est liée au caractère hydrophobe du ligand. Certains ligands de synthèse ont montré une activité inhibitrice de l’invasion des lignées tumorales. / The study of noncovalent interactions and structure-function relationships provides the basis for the understanding of biological systems. Supramolecular MS is a favored technique to dissect protein/protein or protein/ligand interactions. In the context of qualitative or quantitative studies, experimental conditions and instrumental parameters have been optimized for each system to preserve the noncovalent complex in the gas-phase (1). The main objective of this work is to characterize the nucleotide site of hPEBP1 and to contribute to the discovery of antimetastatic molecules. Functionally, a catalytic activity for hPEBP1 could not be detected. For this project, an original MS method to more accurately determine KD for low-affinity complexes without a reference ligand was developed (2). Structural features of an optimal hPEBP1 ligand were determined by screening compounds based on FMN and GTP nucleotides in the context of a rational design approach, using KD determination to rank affinities (3). Screening highlighted that the essential structural requirements for binding hPEBP1 consist in a charged group or an electron donor, a structure related to a cyclic nitrogenous base and an additional cycle. A significant part of the affinity depends on the hydrophobic nature of the ligand. Some of the synthesized nucleotide analogs are active as inhibitors of invasion in tumor cell lines.

Les différents agents pathogènes ont développé de multiples stratégies pour contourner ou modifier les mécanismes de défense de l'hôte. La bactérie intracellulaire Brucella n'est pas une exception à la règle, car elle a développé des mécanismes qui lui permettent d'échapper à la surveillance immunitaire, persister pendant de longues périodes dans l'hôte et établir une infection chronique. En effet, Brucella responsable de la brucellose ou fièvre de Malte. La brucellose est une zoonose en réémergence ; dans cette maladie l'homme infecté représente une impasse épidémiologique. Il est indispensable de mieux connaître l'immunité développée contre Brucella qui est un excellent modèle d'étude d'autres maladies chroniques bactériennes. Le projet de thèse a été centré sur le développement et la modulation des réponses immunes par Brucella et les molécules bactériennes. Dans la première partie de cette thèse, nous avons analysé les réponses immunitaires innées et adaptatives lors de l'infection avec Brucella. D'une part, nous avons étudié l'influence des neutrophiles dans la réponse immunitaire lors de l'infection, en étudiant le cours de brucellose dans les modèles de souris neutropéniques. D'autre part, nous avons identifié et caractérisé in vivo une population des cellules CD4+ cytotoxiques au cours des infections avec Brucella. Dans la deuxième partie, nous nous sommes intéressés dans les modèles murins et humains aux propriétés immunomodulatrices des différentes molécules bactériennes telles que les glucans cycliques et des lipopolysaccharides (LPS). / Various successful pathogens have evolved multiple mechanisms to overcome or alter many normally very effective host defense mechanisms, including both innate and acquired immunity. The intracellular pathogen Brucella is not an exception to the rule as it displays mechanisms that allow it to evade immune surveillance and that are required to establish persistent infections in mammals. In this work, we studied the induction and modulation of immune responses by the intracellular bacteria Brucella and bacterial components. In the first part of this thesis, we have performed a systemic analysis of the innate and adaptive immune responses upon Brucella infection. On the one hand, we investigated the influence of polymorphonuclear neutrophils (PMNs) in the immune response during Brucella infection by exploring the course of brucellosis in antibody neutropenic mouse models. On the other hand, we identified and characterized in vivo a cytotoxic CD4+ T cell population upon Brucella abortus and Salmonella thyphimurium infections. In the second part, we focused on the immunomodulatory properties of various bacterial components such as cyclic glucans and lipopolysaccharides (LPS) both in mouse and human models.

Doctor of Philosophy / Department of Biology / Rollie J. Clem / Apoptosis is an extremely conserved process among metazoans. This dissertation will describe apoptotic regulation in two orders of insects, Lepidoptera and Diptera. In the lepidopteran host Trichoplusia ni, we describe phenotypes of infection with the baculovirus AcMNPV lacking the caspase inhibitor gene P35. In the lepidopteran host Spodoptera frugiperda, infection with this mutant virus results in apoptosis, which dramatically hinders spread of the virus in the host. In T. ni, however, infection with this mutant virus is similar to wild-type with normal spread, but the end result of liquefaction does not occur. Experiments indicated that infection of T. ni cells with the P35 mutant virus (P35Δ) resulted in caspase activation, and the P35Δ virus lacked the ability to inhibit these active caspases. With the P35Δ virus a slower entry phenotype was observed, but when the P35Δ virus was grown in the presence of a caspase inhibitor the entry phenotype was rescued. This indicated that caspases have detrimental effects on budded virions, and illustrated that P35 is needed to make robust virions. With regards to Diptera, apoptosis-regulatory genes were annotated in the yellow fever mosquito, Aedes aegypti. The genes annotated included multiple caspases and caspase regulators. Phylogenetic relationships were determined among the caspases from Anopheles gambiae, Ae. aegypti and Drosophila melanogaster, expression patterns were determined for all the annotated genes in Ae. aegypti, and one of the genes, an IAP antagonist named IMP, was functionally characterized. Further characterization of the phylogenetic relationships of caspases from fifteen dipteran species was performed by obtaining gene models for caspases of recently sequenced genomes for twelve Drosophila species and three mosquito species. Furthermore, several Drosophila and mosquito species were found to contain caspase genes with substitutions in critical active site residues. These genes were proposed to encode caspase-like decoy molecules. While these have been found in humans and nematodes, this is the first report for these molecules in insects. One of the caspase-like decoy molecules was found to increase the activity of its paralog caspase.

Abstract Charge density studies have been conducted on ten CB1 cannabinoid receptor antagonists via high resolution x-ray crystallography. Bond critical point values and various other properties derived from these studies including the electrostatic potential were analyzed in correlation to the affinity of each compound with the CB1 receptor. Correlation/anti-correlation was found between several properties and Ki. The data was also interpreted by principal component analysis with three principal components accounting for 85% of the data variation. Data mining was limit due to the low sample count and the requirements set for the inclusion of correlated/anti-correlated variables left fewer variables to analyze. The model presented is left for future interpretation.

Beaucoup d’expériences et d’applications utilisant des molécules froides nécessitent d’avoir un échantillon de molécules froides à la fois en translation, en vibration et en rotation. Cette thèse se situe dans la même thématique, elle a pour objectif la généralisation de la méthode du pompage optique qui a permis de refroidir la vibration des molécules de Césium par un laser large bande dont les fréquences correspondantes aux transitions partant du niveau vibrationnel fondamental ont été supprimées. Nous avons, par exemple, réalisé un transfert de la population moléculaire dans un niveau vibrationnel pré-sélectionné. Nous avons ensuite démontré que le refroidissement vibrationnel est aussi efficace avec une source de lumière non cohérente. Enfin, une technique de conversion électronique a été démontrée et qui a permis de transférer les molécules formées dans l’état électronique métastable a3Σu+ vers l’état électronique fondamental X1Σg+. Finalement, l’application de cette méthode sur la rotation a été étudié, les résultats préliminaires montrent que le processus marche efficacement ce qui ouvre des perspectives sur le refroidissement lasers des molécules. / Many experiments and applications using cold molecules need to have a sample of molecules cold in all degrees of freedom. My activity in the cold molecule experiment considered several extensions and generalizations of the vibrational cooling technique using a shaped broadband laser. The first extension realized was the transfer of the molecular population to any pre-selected vibrational level. Another extension was the realization of vibrational cooling and molecular population transfer with the use of a broadband, non-coherent, diode light source, instead of a femtosecond laser. Finally, we demonstrate an efficient technique which allows us to convert molecules initially formed in the triplet state (a3Σu+) into the ground electronic state (X1Σg+). The generalization of the vibrational cooling technique to include rotation has also been studied. Preliminary experiments considered for rotational cooling as well as more detail theoretical treatment has been performed. This open the way for more general laser technique apply to molecules.

A análise química do extrato bruto de esponja marinha é um método clássico de descoberta de novas drogas. Metabólitos secundários e peptídeos são geralmente os resultados neste tipo de pesquisa, utilizando diferentes e consecutivos protocolos de purificação. Neste estudo de uma amostra de extrato aquoso esponja separada numa coluna Sephadex®-G25 foi purificado por HPLC, numa tentativa de isolar uma única molécula. Com uma base de dados de RNA e a análise in silico espera-se que o RNAm pode ser relacionado com a molécula precursora do composto bioativo ou mesmo o seu gene. A dissociação de células a partir da matriz da esponja é um método importante para a extração de RNA optimizado em quantidade e qualidade. Frações extrato bruto do organismo e dados de RNAm a partir de células isoladas da esponja podem ser comparados por uma abordagem de comparação dos dados. Ensaios de MTS foram utilizados para analisar a bioatividade e microscopia confocal foi a principal ferramenta para examinar os danos em células tumorais (T47D). / The chemical analysis of sea sponge crude extract is a classic method in drug discovery. Secondary metabolites and peptides are usually the results in this type of research using different and consecutives purification protocols. In this study a sample of sponge aqueous extract separated in a sephadex-G25 column was purified by HPLC in an attempt to isolate a single molecule. With a RNA databank and in silico analysis is expected that the mRNA may be related with the precursor molecule of the bioactive compound or even its gene. The dissociation of cells from the sponge matrix was an important method to the optimized RNA extraction in quantity and quality. Crude extract fractions of the organism and mRNA data from sponge-isolated cells were obtained to a next step cross-data approach. MTS assays were used to analyze the bioactivity and confocal microscopy was the main tool to scan the damage in tumor cells (T47D).

Venenos de aranhas podem ser boas fontes de moléculas com potencial terapêutico e biotecnológico. Sendo assim, esse estudo teve como objetivo analisar moléculas bioativas do veneno de Avicularia juruensis, com foco em PAMs e enzimas. O veneno foi extraído por estimulação elétrica e, através de CLAE-FR, ensaio de inibição do crescimento microbiano e LC-MS/MS, foram identificados e caracterizados 7 PAMs. Todos possuem o motivo nó de cistina do tipo ICK e têm similaridade com neurotoxinas de venenos de outras aranhas. O perfil eletroforético do veneno de A. juruensis indicou que ele possui moléculas com massa entre 130 e abaixo de 10 kDa. Utilizando LC-MS/MS e análise transcriptômica foi possível identificar 6 metaloproteinases. Elas possuem domínios conservados de proteínas do tipo ADAMs, MMPs e metalopeptidases astacina-like. A presença destas enzimas é, provavelmente, importante para a digestão extracorpórea, visto que esta aranha geralmente consome pequenas aves. O estudo de venenos de aranhas terafosídeas é essencial, visto que este é um grupo pouco estudado. / Spider venoms can be good sources of molecules with therapeutic and biotechnological potential. Thus, this study aimed to analyze bioactive molecules from venom of Avicularia juruensis, focusing on AMPs and enzymes. The venom was extracted by electrical stimulation. By RP-HPLC, liquid growth inhibition assay and LC-MS/MS, seven AMPs were identified and characterized. All these peptides have inhibitory cystine knot motif and they showed similarity with venom neurotoxins from others spiders. The electrophoretic profile of A. juruensis venom shows that it has molecules with molecular masses between 130 kDa and below 10 kDa. By LC-MS/MS and transcriptomic analysis yielded the identification of six metalloproteinases, which possess typical conserved domains from ADAMs, MMPs and astacin-like metallopeptidases. These metalloproteinases may be involved in a key role during preoral digestion. The study of Theraphosidae spider venom is essential, since this group is poorly studied.

Carcinoma da mama com apresentação bilateral é uma doença pouco avaliada na literatura, com raros trabalhos científicos que comparam os aspectos moleculares de ambos os tumores. No presente estudo, analisamos os tumores de 45 pacientes portadoras de carcinoma ductal invasivo bilateral em relação às expressões de claudinas-4 e 7, de E-caderina e de -catenina por meio de imunoistoquímica em TMA. Além desses marcadores, analisamos o estado dos receptores de estrógeno e de progesterona, bem como diversas características histopatológicas (grau histológico, nuclear, mitose, infiltrado, desmoplasia e necrose). A amostra foi caracterizado por média de idade de 52,4 anos e os tumores foram divididos em mama primário (MP) e mama secundário (MS). Não houve diferenças entre os dois grupos (MP e MS) nos marcadores testados, sendo que a expressão foi coincidente nas seguintes proporções: claudina-4 (83,8%, p=0,61), claudina-7 (82,2%, p=0,29), E-caderina (81%, p=0,48), -catenina (89,7%, p=0,48), receptor de estrogeno (66%, p=0.75) e receptor de progesterona (55%, p=0.99). Em relação aos aspectos morfológicos, grau histológico (SBR) II, infiltrado inflamatório discreto, necrose, desmoplasia moderada e índice mitótico (<10fm/10cga) foram coincidentes em 57,8%, 60%, 55,6%, 63,6% e 55,6%, respectivamente. Os presentes resultados nos permitem inferir que os tumores de apresentação bilateral são, em sua maioria, similares do ponto de vista morfológico e da expressão dos marcadores testados / Forty-five patients with invasive ductal carcinoma were evaluated for the expression of claudin-4, claudin-7, E-cadherin, and -catenin through tissue microarray (TMA) and immunohistochemistry (IHC) analysis. Besides these markers, estrogen (ER) and progesterone receptor (PR) status was analyzed, in addition to histopathologic characteristics, i.e., histologic grade, nuclear, mitoses, infiltrate, desmoplasia, and necrosis. Tumors were divided into primary breast (PB) and secondary breast (SB). The expression of claudin-4 and -7 was coincident in PB and SB in 83.78% and 82.22% respectively. The expression of -catenin and E-cadherin in PB and SB was coincident in 89.74% and 80.95% respectively. Estrogen receptor status was (+) in both breasts in 66%, while progesterone receptor status (+) was in 55%. The histological grade using the Nottingham-modified Scarff-Bloom-Richardson grading system (MSBR) showed mild infiltrate, necrosis (+), moderate desmoplasia and mitotic index (<10) was coincident in 57.77%, 60.00%, 55.55%, 63.63% and 55.55% respectively. The degree of agreement showed claudin-4 (p=0.61), claudin-7 (p=0.29), E-cadherin (p=0.48), and -catenin (p=0.48). The expression of claudin-4 and -7, E-cadherin and -catenin present a strong agreement between tumors, showing that bilateral tumors are not different. Histopathologic characteristics showed a lesser agreement between tumors

Neste trabalho apresentamos a construção de um novo sistema experimental para aprisionamento de átomos e moléculas. Trata-se de uma armadilha de dipolo cruzada totalmente óptica, formada por um laser de fibra com 40 W de potência com comprimento de onda em 1064 nm. Nesse sistema foi demonstrado o aprisionamento de átomos Rb e K e moléculas Rb2. Realizamos dois experimentos distintos neste se novo sistema: No primeiro, estudamos a evolução temporal de amostras dos isótopos 85Rb e 87Rb na armadilha de dipolo cruzada. Pudemos medir pela primeira vez o processo de mudança de estrutura hiperfina em átomos sem a presença de luz ressonante, e observamos a fotoassociação dos átomos pelo laser da armadilha de dipolo. E no segundo, desenvolvemos uma técnica que permite o estudo rápido e direto do decaimento no número de moléculas de Rb2 na armadilha. Com essa técnica, observamos também o comportamento dessas moléculas na presença de átomos preparados em um determinado estado hiperfino do estado fundamental. Estes resultados juntamente com um desenvolvimento teórico, nos sugerem novas perspectivas rumo a produção de um sistema que possa produzir e aprisionar moléculas KRb no estado fundamental 1&Sigma;+ (v = 0). / In this work, we present the construction of a new experimental system for trapping atoms and molecules. It is an all optical crossed dipole trap, formed by a fiber laser with 40 W of power at 1064 nm. In this system, we have trapped K and Rb atoms as well as Rb2 molecules. We have carried out two experiments in this new system. In the first, we studied the temporal evolution of atomic samples of different isotopes, 85Rb and 87Rb, in the crossed trap dipole. We were able to measure for the first time the hyperfine-changing collisions of atoms in the absence of resonant light, and we have observed photoassociation of atoms by the dipole trap laser beam. In the other experiment, we have developed a technique that allows us to study the trapped molecule population decay in the trap. It was also observed the molecule population decay in the presence of atoms prepared in a given hyperfine state of the ground state. These results together with a theoretical development may suggest us new perspectives towards the production of a system that can produce and trap KRb molecules in the ground state 1&Sigma;+ (v = 0).