Aspergillus fumigatus is a ubiquitous fungus associated with several airway complications and diseases including asthma, allergies, cystic fibrosis, and most commonly invasive aspergillosis. The airway epithelium, a protective barrier, is the first anatomical site to interact with A. fumigatus. Although this host-fungal interaction is often asymptomatic for immunocompetent individuals, for immunocompromised persons, due to a weakened competence of the immune system, they have an increased likelihood of fungal infection. This dissertation aims to investigate the effect of A. fumigatus on the transcriptional response of human airway epithelial cells, focusing on the relationship between innate immunity and iron regulation from the host perspective. The trace element iron is needed by both the fungus and the host for cellular maintenance and survival, but tightly controlled iron regulation in the host is required to prevent oxidative stress and cell death. The research methods in this dissertation employ a systems biology approach, by incorporating mathematical modeling, RNA-seq analysis, and experimental biology techniques to assess the role of airway epithelial cells in the host-fungal interaction. Both the quantitative and qualitative research design allows for characterization of airway epithelial cells and the downstream changes in iron importer genes. This study addresses literature gaps through analysis of the host transcriptome using multiple time points, by performing an extensive evaluation of the effect of cytokines on iron importer genes, and conceptualization of a comprehensive mathematical model of the airway epithelial cell. The major findings suggest the following: 1) airway epithelial cells avidly respond to A. fumigatus through modification of the expression of immune response related genes at different infection stages, 2) during A. fumigatus co-incubation with airway epithelial cells, the iron importers genes respond in strikingly different ways, and 3) cytokines have a significant effect on the increase in expression of an iron importer gene. We illuminated the role of airway epithelial cells in fungal recognition and activation of the immune response in signaling cascades that consequently modify iron importer genes and hope to use this information as a platform to discover potential therapeutic targets. / Ph. D.

Lipid bilayers are key components of biomembranes; they are self-assembled two-dimensional structures, primarily serving as barriers to the leakage of cell's contents. Lipid bilayers are typically charged in aqueous solution and may electrostatically interact with each other and with their environment. In this work, we investigate electrostatics of charged lipid bilayers with the main focus on the binding and bending of the bilayers. We first present a theoretical approach to charge-correlation attractions between like-charged lipid bilayers with neutralizing counterions assumed to be localized to the bilayer surface. In particular, we study the effect of nonzero ionic sizes on the attraction by treating the bilayer charges (both backbone charges and localized counterions) as forming a two-dimensional ionic fluid of hard spheres of the same diameter <i>D</i>. Using a two-dimensional Debye-H??ckel approach to this system, we examine how ion sizes influence the attraction. We find that the attraction gets stronger as surface charge densities or counterion valency increase, consistent with long-standing observations. Our results also indicate non-trivial dependence of the attraction on separations <i>h</i>: The attraction is enhanced by ion sizes for <i>h</i> ranges of physical interest, while it crosses over to the known <i>D</i>-independent universal behavior as <i>h</i> &rarr; &infin;; it remains finite as <i>h</i> &rarr; 0, as expected for a system of finite-sized ions. We also study the preferred curvature of an asymmetrically charged bilayer, in which the inner leaflet is negatively charged, while the outer one is neutral. In particular, we calculate the relaxed area difference &Delta; <i>A</i>₀ and the spontaneous curvature <i>C</i>₀ of the bilayer. We find &Delta; <i>A</i>₀ and <i>C</i>₀ are determined by the balance of a few distinct contributions: net charge repulsions, charge correlations, and the entropy associated with counterion release from the bilayer. The entropic effect is dominant for weakly charged surfaces in the presence of monovalent counterions only and tends to expand the inner leaflet, leading to negative &Delta; <i>A</i>₀ and <i>C</i>₀. In the presence of even a small concentration of divalent counterions, however, charge correlations counterbalance the entropic effect and shrink the inner leaflet, leading to positive &Delta; <i>A</i>₀ and <i>C</i>₀. We outline biological implications of our results.

The swelling-activated chloride current, commonly referred to as ICl,swell, is an outwardly-rectifying anion current that plays an important role in cell volume regulation, among other capacities. Despite several decades of research, the molecular identity of the channel responsible for this chloride current remains controversial. Recent indications that key endogenous sulfhydryl groups are capable of modifying the current led us to assess the effects of several divalent cations, including zinc, on ICl,swell. Zinc is known to tightly associate with sulfhydryl groups such as in zinc finger proteins. We found that extracellular zinc irreversibly inhibited ICl,swell at a site downstream in the signaling cascade. Moreover, zinc blocking kinetics were voltage dependent, suggesting interaction with a site within the electric field, across the pore of the channel responsible for ICl,swell. The importance of sulfhydryl groups was confirmed by demonstrating irreversible block by N-ethylmaleimide, a sulfhydryl alkylating reagent. In contrast, nickel failed to block ICl,swell, and as noted in previous studies, cadmium preferentially blocked the time-dependent component of ICl,swell. These data confirm the importance of sulfhydryl groups in the function of ICl,swell. Moreover, by demonstrating the voltage-dependence of block, the data strongly suggest the critical sulfhydryl group is within the channel pore. These biophysical characteristics of native ICl,swell are markers that should be recapitulated in expressed proteins claimed to be responsible for ICl,swell.

La construction de complexes polymétalliques de lanthanides préprogrammés et sophistiqués, de taille nanométrique, pour le développement de matériaux luminescents présentant des propriétés photophysiques nouvelles ou améliorées (double émission, transfert d'énergie intermétallique, etc.) est un des sujets de la chimie supramoléculaire des lanthanides suscitant énormément d'intérêt. La compréhension, le contrôle et la programmation de l'auto-assemblage de complexes de lanthanides est un défi majeur en raison de la difficulté à contrôler l'environnement de coordination de ces ions qui se caractérise par des nombres de coordinations importants et variables et peu de préférences stéréochimiques. Ainsi, la plupart des complexes polynucléaires de lanthanides décrits dans la littérature sont formés de façon fortuite plutôt que par conception rationnelle. Afin d'inclure les ions lanthanides dans des architectures polymétalliques de haute nucléarité tout en améliorant leurs propriétés photophysiques, nous nous sommes concentrés sur des études de complexation de ligands dissymétriques (tridentates anioniques, tétradentates chiraux) permettant de promouvoir la formation des assemblages. Nous avons par ailleurs commencé à explorer le potentiel d'une méthode synthétique originale de clusters oxo par réactivité redox de complexes divalents de lanthanides. Nous présentons ici la synthèse et les propriétés photophysiques de complexes stables émettant dans le proche infrarouge basés sur des ligands anioniques hydroxyquinoléine fonctionnalisé par des groupes carboxylates ou tétrazolates. En outre, nous pouvons montrer que l'utilisation de ligands chiraux possédant un groupement oxazoline favorise l'auto-assemblage diastéréosélectif de complexes de lanthanides homo- et hétéro-polymétalliques énantiopures émettant dans le visible et le proche infrarouge. Un complexe trinucléaire d'europium énantiopure a été caractérisé par cristallographie, celui-ci présentant une forte activité en polarisation circulaire de luminescence (CPL). Le ligand chiral oxazoline a permis d'obtenir une roue heptanucléaire d'europiums, le plus important assemblage polymétallique énantiopure. Enfin, nous avons pu préparer et caractériser des complexes de lanthanides divalents hautement réactifs basés sur un ligand tripode neutre possédant des groupements pyridine (tpa). Des résultats préliminaires montrent que ces complexes peuvent être des précurseurs très utiles pour isoler des clusters oxo polymétalliques. En particulier, la réaction d'un complexe de néodyme hautement réactif a conduit à isoler un cluster oxo volumineux et très intéressant par clivage de THF en présence de tpa. / The construction of preprogrammed, sophisticated and nanoscopic polymetallic lanthanide complexes for the development of luminescent materials that possess new or improved photophysical properties (dual emission, intermetallic energy transfer, etc.) is one of the hot topics in the lanthanide supramolecular chemistry. Understanding, controlling and programming self assembly of lanthanide complexes is a key challenge due to the difficulty in controlling the coordination environment of these ions which display high and variable coordination numbers with little stereochemical preferences. As a result of this, most of the polynuclear lanthanide complexes reported in literature are formed by serendipity rather than rational design. In order to include lanthanide ions in discrete high nuclearity polymetallic architectures with improved photophysical properties we have concentrated on complexation studies with dissymmetric chelating ligands (tridentate anionic ligands, tetradentate chiral ligand) with possibility of promoting assembly formation, and we started to investigate the potential of an original synthetic method using the redox reactivity of divalent lanthanides complexes for the synthesis of oxo clusters. Here we present the synthesis and photophysical properties of NIR emissive stable complexes obtained with hydroxyquinoline based tridentate dianionic ligands functionalised with carboxylic acid and tetrazole groups. Moreover we show that the use of a chiral tetradentate ligand possessing oxazoline ring promotes the diastereoselective self assembly of enantiopure homo- and hetero-polymetallic lanthanide complexes emitting in the visible and NIR range. An original enantiopure trinuclear europium complex was crystallographically characterised and we found that it displays a high circularly polarized luminescence (CPL) activity. The chiral oxazoline based ligand also led to the synthesis of the largest enantiopure polymetallic assembly of europium, a heptanuclear wheel. Finally we were able to prepare and characterize highly reactive complexes of divalent lanthanides with a neutral tripodal pyridine based ligand and very preliminary results show that these complexes can be useful precursors for the isolation of polymetallic oxoclusters. Notably, the reaction of the highly reactive neodymium complex led to the isolation of a very interesting large neodymium oxo cluster by cleavage of THF in the presence of the ligand tpa.

La chimie organométallique des lanthanides a été longtemps dominée par des ligands à base de cyclopentadiényle tandis que des ligands contenant du phosphore n'ont suscité de l'attention que récemment. Dans ce travail nous montrons l'influence de ligands organophosphorés sur la synthèse et la réactivité de composés organométalliques de lanthanides dans trois domaines différents. La première partie est dédiée à la synthèse de complexes divalents de lanthanides employant des ligands à base de cyclopentadiényle et de phospholyle. Une nouvelle méthode de synthèse – l'approche par réduction – est développée, qui permet la synthèse de thulocènes divalents ainsi que les premiers complexes divalents de dysprosium et de néodyme. L'activation de petites molécules montre la! nature fortement réductrice de ces complexes divalents et révèle quelques différences entre les composés à base de cyclopentadiényle et de phospholyle. La deuxième partie décrit la synthèse de premiers complexes monophospholyles bis(o-dimethylaminobenzyles) de lanthanides par métathèse. De plus, un phosphole 1H stable est utilisé pour la première fois comme précurseur dans une réaction de type acide base. L'application de ces composés dans la polymérisation du styrène est rapportée. La troisième partie s'intéresse à la synthèse et la réactivité de nouveaux complexes mono et bis(carbénique) de lanthanides utilisant le dianion 1,1-dilithio-bis(diphénylthiophosphinoyl)méthane comme précurseur carbénique. Une discussion sur la nature de la liaison Ln-C multiple par des analyses structurales ! et réactionnelles est incluse.

<p>RNase P is an essential ribonuclease responsible for removal of the 5’ leader of tRNA precursors. Bacterial RNase P consists of an RNA subunit and a small basic protein. The catalytic activity is associated with the RNA subunit, i.e. bacterial RNase P RNA is a ribozyme. The protein subunit is, however, essential for activity in vivo. RNase P RNA, as well as the holoenzyme, requires the presence of divalent metal ions for activity. The aim of this thesis was to increase our understanding of the catalytic mechanism of RNase P RNA mediated cleavage. The importance of the nucleotides close to the cleavage site and the roles of divalent metal ions in RNase P RNA-catalyzed reaction were investigated. Escherichia coli RNase P RNA (M1 RNA) was used as a model system.</p><p>It was shown that different metal ions have differential effects on cleavage site recognition. Cleavage activity was rescued by mixing metal ions that do not promote cleavage activity by themselves. This suggests that efficient and correct cleavage is the result of metal ion cooperativity in the RNase P RNA-mediated cleavage reaction. The results suggested that one of the metal ions involved in this cooperativity is positioned in the vicinity of a well-known interaction between RNase P RNA and its substrate. Based on my studies on how different metal ions bind to RNA and influence its activity we raise the interesting possibility that the activity of biocatalysts that depend on RNA for activity are up- or downregulated depending on the intracellular concentrations of the bulk biological metal ions Mg²⁺ and Ca²⁺.</p><p>The nucleotides upstream of the cleavage site in the substrate were found to influence the cleavage efficiency. This was not exclusively due to intermolecular base pairing within the substrate but also dependent on the identities of the nucleotides at position –2 and –1. The strength of the base pair at position –1/+73 was demonstrated to affect cleavage efficiency. These observations are in keeping with previous suggestion that the nucleotides close to the cleavage site are important for RNase P cleavage. We conclude that the residue at -1 is a positive determinant for cleavage by RNase P. Hence, my studies extend our understanding of the RNase P cleavage site recognition process.</p>

RNase P is an essential ribonuclease responsible for removal of the 5’ leader of tRNA precursors. Bacterial RNase P consists of an RNA subunit and a small basic protein. The catalytic activity is associated with the RNA subunit, i.e. bacterial RNase P RNA is a ribozyme. The protein subunit is, however, essential for activity in vivo. RNase P RNA, as well as the holoenzyme, requires the presence of divalent metal ions for activity. The aim of this thesis was to increase our understanding of the catalytic mechanism of RNase P RNA mediated cleavage. The importance of the nucleotides close to the cleavage site and the roles of divalent metal ions in RNase P RNA-catalyzed reaction were investigated. Escherichia coli RNase P RNA (M1 RNA) was used as a model system. It was shown that different metal ions have differential effects on cleavage site recognition. Cleavage activity was rescued by mixing metal ions that do not promote cleavage activity by themselves. This suggests that efficient and correct cleavage is the result of metal ion cooperativity in the RNase P RNA-mediated cleavage reaction. The results suggested that one of the metal ions involved in this cooperativity is positioned in the vicinity of a well-known interaction between RNase P RNA and its substrate. Based on my studies on how different metal ions bind to RNA and influence its activity we raise the interesting possibility that the activity of biocatalysts that depend on RNA for activity are up- or downregulated depending on the intracellular concentrations of the bulk biological metal ions Mg2+ and Ca2+. The nucleotides upstream of the cleavage site in the substrate were found to influence the cleavage efficiency. This was not exclusively due to intermolecular base pairing within the substrate but also dependent on the identities of the nucleotides at position –2 and –1. The strength of the base pair at position –1/+73 was demonstrated to affect cleavage efficiency. These observations are in keeping with previous suggestion that the nucleotides close to the cleavage site are important for RNase P cleavage. We conclude that the residue at -1 is a positive determinant for cleavage by RNase P. Hence, my studies extend our understanding of the RNase P cleavage site recognition process.

This thesis describes the use of chiral counter-ions for the enantiomeric separation of amines in non-aqueous capillary electrophoresis. The investigations have been concentrated on studies of the influence, of the chiral counter-ion, the solvent, the electrolyte and the analyte, on the enantioselective separation. Modified divalent dipeptides have been introduced in capillary electrophoresis for the separation of amino alcohols and chiral resolution of amines. Association constants for the ion-pair between dipeptide and amino alcohol could be utilized for development of separation systems with higher amino alcohol selectivity. Chiral discrimination (ion-pair formation) between the dipeptides and amines are preferably generated in non-aqueous background electrolytes (BGEs). The amount of triethylamine in the BGE determined the dipeptide charge and a divalent dipeptide promoted higher enantioselectivity than a monovalent dipeptide. An N-terminal-end blocking group and glutamic acid at the C-terminal-end of the dipeptide was important for chiral separation of the amines. Chemometric and univariate methods have been employed for evaluation of suitable solvent compositions in the BGE. An experimental design including a single solvent as well as binary, ternary and quaternary mixtures of polar organic solvents, showed that optimal enantioresolution was obtained with an ethanol:methanol 80:20 mixture in the BGE.  Furthermore, water was found to have an adverse influence on enantioselectivity and no enantioresolution was obtained with BGEs containing more than 30 % water. An alkali metal hydroxide added to the BGE affected the chiral separation by competing ion-pair formation with the selector. The electroosmosis was reduced in order of decreasing alkali metal ion solvated radius and became anodic using K, Rb or Cs in ethanolic BGEs. The correlation between the amino alcohol structure and the enantioselectivity was investigated using chemometrics. The obtained models showed that enantioselectivity for the amino alcohols was promoted by e.g. degree of substitution and substituent size on the nitrogen.

Lipid bilayers are key components of biomembranes; they are self-assembled two-dimensional structures, primarily serving as barriers to the leakage of cell's contents. Lipid bilayers are typically charged in aqueous solution and may electrostatically interact with each other and with their environment. In this work, we investigate electrostatics of charged lipid bilayers with the main focus on the binding and bending of the bilayers. We first present a theoretical approach to charge-correlation attractions between like-charged lipid bilayers with neutralizing counterions assumed to be localized to the bilayer surface. In particular, we study the effect of nonzero ionic sizes on the attraction by treating the bilayer charges (both backbone charges and localized counterions) as forming a two-dimensional ionic fluid of hard spheres of the same diameter <i>D</i>. Using a two-dimensional Debye-Hückel approach to this system, we examine how ion sizes influence the attraction. We find that the attraction gets stronger as surface charge densities or counterion valency increase, consistent with long-standing observations. Our results also indicate non-trivial dependence of the attraction on separations <i>h</i>: The attraction is enhanced by ion sizes for <i>h</i> ranges of physical interest, while it crosses over to the known <i>D</i>-independent universal behavior as <i>h</i> &rarr; &infin;; it remains finite as <i>h</i> &rarr; 0, as expected for a system of finite-sized ions. We also study the preferred curvature of an asymmetrically charged bilayer, in which the inner leaflet is negatively charged, while the outer one is neutral. In particular, we calculate the relaxed area difference &Delta; <i>A</i>₀ and the spontaneous curvature <i>C</i>₀ of the bilayer. We find &Delta; <i>A</i>₀ and <i>C</i>₀ are determined by the balance of a few distinct contributions: net charge repulsions, charge correlations, and the entropy associated with counterion release from the bilayer. The entropic effect is dominant for weakly charged surfaces in the presence of monovalent counterions only and tends to expand the inner leaflet, leading to negative &Delta; <i>A</i>₀ and <i>C</i>₀. In the presence of even a small concentration of divalent counterions, however, charge correlations counterbalance the entropic effect and shrink the inner leaflet, leading to positive &Delta; <i>A</i>₀ and <i>C</i>₀. We outline biological implications of our results.

Made available in DSpace on 2014-12-17T15:01:56Z (GMT). No. of bitstreams: 1 ShirlleKSN_TESE_PARCIAL.pdf: 1534638 bytes, checksum: ca047a7bd2b85b3f98d9d4d116c8a5d1 (MD5) Previous issue date: 2013-07-19 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / The petroleum production is associated to the produced water, which has dispersed and dissolved materials that damage not only the environment, but also the petroleum processing units. This study aims at the treatment of produced water focusing mainly on the removal of metals and oil and using this treated water as raw material for the production of sodium carbonate. Initially, it was addressed the removal of the following divalent metals: calcium, magnesium, barium, zinc, copper, iron, and cadmium. For this purpose, surfactants derived from vegetable oils, such as coconut oil, soybean oil, and sunflower oil, were used. The investigation showed that there is a stoichiometric relationship between the metals removed from the produced water and the surfactants used in the process of metals removal. It was also developed a model that correlates the hydrolysis constant of saponified coconut oil with the metal distribution between the resulting stages of the proposed process, flocs and aqueous phases, and relating the results with the pH of the medium. The correlation coefficient obtained was 0.963. Next, the process of producing washing soda (prefiro soda ahs ou sodium carbonate) started. The resulting water from the various treatment approaches from petroleum production water was used. During this stage of the research, it was observed that the surfactant assisted in the produced water treatment, by removing some metals and the dispersed oil entirety. The yield of sodium carbonate production was approximately 80%, and its purity was around 95%. It was also assessed, in the production of sodium carbonate, the influence of the type of reactor, using a continuous reactor and a batch reactor. These tests showed that the process with continuous reactor was not as efficient as the batch process. In general, it can be concluded that the production of sodium carbonate from water of oil production is a feasible process, rendering an effluent that causes a great environmental impact a raw material with large scale industrial use / A produ??o do petr?leo ? associada ? ?gua produzida, que apresenta materiais dispersos e dissolvidos que prejudicam n?o s? o meio ambiente, mas tamb?m, as unidades de processamento de petr?leo. Este trabalho objetiva o tratamento da ?gua de produ??o enfocando, principalmente, a remo??o de ?leo e de metais e a utiliza??o desta ?gua tratada como mat?ria-prima para produ??o de barrilha. Inicialmente, verificou-se a remo??o dos seguintes metais bivalentes: c?lcio, magn?sio, b?rio, zinco, cobre, ferro e o c?dmio. Utilizou-se para este fim tensoativos derivados de ?leos vegetais, tais como: ?leo de coco, ?leo de soja e ?leo de girassol. Verificou-se que existe uma rela??o estequiom?trica entre os metais removidos da ?gua de produ??o e os tensoativos utilizados no processo. Tamb?m, desenvolveu-se um modelo que relaciona a constante de hidr?lise do ?leo de coco saponificado com a distribui??o do metal entre as fases resultantes do processo proposto, fases floco e aquosa, relacionando os resultados com o pH do meio. Obteve-se um coeficiente de correla??o na ordem de 0,963. Em seguida, iniciou-se o processo de obten??o da barrilha. Utilizou-se a ?gua resultante das diversas correntes de tratamento da ?gua produzida. Nesta etapa do trabalho, observou-se que o tensoativo auxiliava no tratamento da ?gua de produ??o, removendo parte dos metais e a totalidade do petr?leo disperso. O rendimento da produ??o da barrilha foi da ordem de 80% e sua pureza ficou em torno de 95%. Avaliou-se, ainda, no processo de produ??o da barrilha, a influ?ncia do tipo de reator, utilizando-se um reator cont?nuo e um reator em batelada. Estes ensaios mostraram que o processo cont?nuo n?o foi t?o eficiente quanto o processo em batelada. De forma geral, pode-se concluir que a produ??o de barrilha a partir da ?gua de produ??o de petr?leo ? um processo vi?vel, transformando um efluente que causa grande impacto ambiental em mat?ria-prima de larga utiliza??o industrial / 2020-01-01