Polycyclic aromatic hydrocarbons (PAHs) are produced via the incomplete combustion of organic matter. They are ubiquitously present in the environment, and human exposures typically involve complex PAH mixtures in complex matrices (e.g., soil, urban air). Many PAHs are genotoxic carcinogens; exposures can augment cancer risk and reliable risk assessment of PAH mixtures is a regulatory concern. There is a paucity of in vivo genotoxicity information for most PAHs and PAH mixtures. Risk assessment of PAH mixtures assumes dose addition (i.e., additive, incremental contributions from each PAH); however, there is a lack of evidence to support this assumption. This thesis assessed the in vivo genotoxicity of 9 PAHs and 6 PAH mixtures following sub-chronic oral exposure of transgenic Muta™Mouse (i.e., adduct and lacZ mutant frequency across 5 tissues). The results revealed that PAHs and PAH mixtures induce significant levels of genetic damage; the mixtures induced very high levels of damage and mutations. Differences in the nature and magnitude of the effects in individual tissues appear to be related to the processes that govern PAH metabolism and the processing of genetic damage (e.g., repair and translesion synthesis). Scrutiny of the dose addition assumption revealed more-than-additive effects in tissues proximal to the exposure route (i.e., intestine, liver), but less-than-additive effects in distal tissues (i.e., bone marrow); however, discrepancies between the experimentally-observed and predicted responses were typically small (i.e., within 5-fold). Comparisons of cross-tissue patterns in adduct and mutant frequencies revealed that the frequency of the former is generally inversely related to that of the latter. This appears to be related to the experimental design, and the influence of repair and replication on adduct and mutant frequency. The BMD approach was employed to estimate genotoxic (i.e., adduct) potency and mutagenic (i.e., lacZ mutant) potency for all agent-tissue combinations. The results demonstrate that the mutagenic potency of PAHs and PAH mixtures is empirically related to genotoxic potency; moreover, that there is cross-tissue and cross-compound congruence in the processing of PAH-induced damage. The results obtained significantly advance existing knowledge regarding the genotoxic hazards of PAHs and PAH mixtures; moreover, the empirical relationships between genetic toxicity endpoints.

L'asthme allergique est caractérisé par une réponse prédominante de typeTh2, mais d'autres profils tels que Th17 et Th22 sont aussi observés dans l'asthme plus sévère. La pollution atmosphérique et notamment les hydrocarbures aromatiques polycycliques (HAP) contenus dans les particules d'échappement diesel (DEP) contribuent à l'augmentation de la prévalence de l'asthme et jouent un rôle adjuvant dans le développement et l'exacerbation de l'inflammation allergique en orientant la réponse immune vers un profil Th2Dans la première partie de la thèse, nous avons évalué les effets des HAP sur la polarisation Th17/Th22 de PBMC de sujets allergiques asthmatiques et sujets non-allergiques. Les PBMC de patients asthmatiques présentent une augmentation des profils Th17/Th22 par rapport aux sujets non-allergiques. La stimulation par DEP-HAP et le benzo [a] pyrène (B[a]P) induit une augmentation de l’IL-22 mais de façon étonnante diminue la production d'IL-17A dans les deux groupes. Les facteurs de transcription associés aux cellules Th17: RORA et RORC, sont diminués, alors que le gène cible d’AhR, CYP1A1, est augmenté dans les deux groupes. Notch est diminué uniquement chez les patients asthmatiques. La production d'IL-22 induite par les HAP provient principalement de cellules Th22. L'antagoniste d’AhR reverse presque complètement les effets des DEP, mais seulement partiellement les effets de B[a]P, sur la regulation réciproque entre IL-22/IL-17. Les kinases PI3K, JNK et ERK participent à l’augmentation de l’IL-22 induite par le B[a]P, alors que la p38 MAP kinase a un effet inhibiteur. La deuxième partie de la thèse a évalué l'effet combiné des PRRs et des allergènes sur l’activation et leur capacité à induire une polarisation Th17/Th22 chez des sujets sains et des sujets allergiques asthmatiques. Les DCs stimulées par les allergènes de chien induisent une faible production d'IL-22 par les cellules T. L’activation supplémentaire par les ligands de TLR3, TLR9 et NOD2 conduit à une augmentation de la production augmentée de chimiokines pro-Th2 uniquement par les DCs de patients asthmatiques allergiques aux chiens. 7 A l’inverse, un rôle adjuvant est observé sur la maturation et la production de cytokines pro-Th17/Th22 par les DCs de sujets asthmatiques et de sujets non-allergiques. Parmi les cellules T co-cultivées avec des DC stimulées par l'allergène de chien et les ligands de PRR, nous observons un mélange de cellules de type Th2/Th17 et Th22 chez les patients asthmatiques et un profil Th1/Th22 chez les sujets non-allergiques. L’IL-22 est principalement produite par les Th22 dans les deux groupes avec plus de cellules Th22 observés chez les sujets asthmatiques. L’IL-17 et l’IL-22 sont régulées différemment entre les sujets asthmatiques et les sujets sains, le TGF-β ayant un rôle pro-Th17 tandis que l'IL-23 a un rôle pro-Th22. In vivo, un modèle d'asthme chronique induite par l’allergène de chien a été développé et conduit à une augmentation de la résistance des voies aériennes, une production de chimiokines Th2 et de cytokines Th2/Th17/Th22 ainsi qu’au recrutement de neutrophiles mais peu d’éosinophiles dans le poumon. L'expression du gène de l'IL-22 intervient de façon précoce alors que la protéine apparait plus tard. Le ligand de NOD2 induit une augmentation de la résistance des voies aériennes, ainsi que de la production de protéines et l'expression des gènes induits par l'allergène de chien, mais réduit le recrutement des éosinophiles dans les poumons. Ces résultats montrent que chez l'homme, les productions d’IL-22 et d'IL-17 sont régulées différemment entre les sujets asthmatiques allergiques et les sujets sains. Au total, la pollution et certaines infections bactériennes ou virales pourraient participer chez les patients asthmatiques à sévérité de la maladie et la progression du remodelage des voies aériennes. La modèle in vivo développée permettra de mieux disséquer les mécanismes qui participent à la sévérité de l'asthme. / Allergic asthma is characterized by a predominant Th2 response, but additional profiles such as Th17 and Th22 are observed in more severe asthma. Components of the air pollution such as polycyclic aromatic hydrocarbons (PAH) contained in diesel exhausts particles (DEP) contributes to increased prevalence of asthma and play an adjuvant role in the development and exacerbation of allergic inflammation through the skewing of the immune response towards a Th2 profile. In the first part of the thesis, we evaluated the effects of PAH on the Th17/Th22 polarization of PBMCs from healthy and allergic asthmatic subjects, PBMCs from athmatic patients exhibited an increased Th17/Th22 profile compared with non-allergic subjects. DEP-PAH and Benzo[a]Pyrene (B[a]P) stimulation further increased IL-22 but surprisingly decreased IL-17A production in both groups. Th17 transcription factors RORA and RORC were down regulated, whereas AhR target gene CYP1A1 was up-regulated in both groups. Notch was decreased only in asthmatic patients. PAH-induced IL-22 production originated mainly from Th22 cells. The AhR antagonist reversed almost completely the effects of DEP-PAH, but only partially the effects of B[a]P, on IL-22/IL-17 reciprocal regulation. The kinases PI3K, JNK and ERK participated to the enhancing effect of B[a]P on IL-22 production, whereas p38 MAP kinase had an inhibitory effect.The second part of the thesis evaluated the co-stimulatory effect of combined PRR- and allergen-activated DCs on Th17/Th22 polarization in healthy and asthmatic subjects. Dog allergen stimulated DCs induced a small production of IL-22 in T cells. Additional activation by TLR3, TLR9 and NOD2 ligands led to increased production of pro-Th2 chemokines by DCs only from asthmatic patients allergic to dogs. In contrast, an adjuvant role was observed on the maturation and pro-Th17/Th22 cytokines production by DCs from both asthmatic and non-allergic subjects. In T cells co-cultured with DCs stimulated by dog allergen and PRR ligands, we found a mixed Th2/Th17/Th22 profile in asthmatic patients and a Th1/Th22 profile in non-allergic subjects. IL-22 producing cells were mainly Th22 in both groups with more Th22 cells were observed in asthmatic subjects. IL-17 and IL-22 production was9differently regulated between asthmatic subjects and non-allergic subjects, TGF-β having a pro-Th17 role while IL-23 having a pro-Th22 role.In vivo, a model of chronic dog-induced asthma was developed leading increased airway resistance, Th2 chemokine and Th2/Th17/Th22 cytokine production as well as neutrophil but little eosinophil recruitment in the lung. Gene expression of IL-22 was observed at early time points whereas IL-22 protein appeared later on. NOD2 ligand further increased airway resistance, protein production and gene expression induced by dog allergen challenge but inhibited the small eosinophil recruitment in the lung.These results show that in humans, IL-17 and IL-22 productions are regulated differently between allergic asthmatic and non-allergic subjects. Altogether, pollution and some bacterial or viral infections may contribute in asthmatic patients to the severity of the disease and to progression of airway remodeling. The developed in vivo model will allow dissecting the mechanisms participating to the severity of asthma.

For decades the opioid receptors have been an attractive therapeutic target for the treatment of pain. Since the first discovery of enkephalin, approximately a dozen endogenous opioid peptides have been known to produce opioid activity and analgesia, but their therapeutics have been limited mainly due to low blood brain barrier penetration and poor resistance to proteolytic degradation. One versatile approach to overcome these drawbacks is the cyclization of linear peptides to cyclic peptides with constrained topographical structure. Compared to their linear parents, cyclic analogs exhibit better metabolic stability, lower offtarget toxicity, and improved bioavailability. Extensive structure-activity relationship studies have uncovered promising compounds for the treatment of pain as well as further elucidate structural elements required for selective opioid receptor activity. The benefits that come with employing cyclization can be further enhanced through the generation of polycyclic derivatives. Opioid ligands generally have a short peptide chain and thus the realm of polycyclic peptides has yet to be explored. In this review, a brief history of designing ligands for the opioid receptors, including classic linear and cyclic ligands, is discussed along with recent approaches and successes of cyclic peptide ligands for the receptors. Various scaffolds and approaches to improve bioavailability are elaborated and concluded with a discourse towards polycyclic peptides.

Orientador: Lucia Regina Durrant, Matthew James Grossman / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-22T02:43:16Z (GMT). No. of bitstreams: 1 Santos_LigiaGibinidos_M.pdf: 3848321 bytes, checksum: 46f91a01a783f6fd7d5153ba73c6e8a0 (MD5) Previous issue date: 2013 / Resumo: Dentre os contaminantes ambientais mais abundantes, destacam-se os Hidrocarbonetos aromáticos policíclicos (HAPs), que apresentam elevado potencial tóxico, sendo imprescindível sua remoção do ambiente. O objetivo deste trabalho foi analisar, em microcosmos, a biodegradação de HAPs por um consórcio bacteriano e identificar fatores que influenciam nesta degradação e na análise dos dados. A degradação dos HAPs no solo sem histórico de contaminação foi muito semelhante em todos os microcosmos, apresentando uma porcentagem de aproximadamente 85%. Para analisar a toxicidade do solo antes e depois da biorremediação, realizou-se um testes de germinação de sementes de Lactuca sativa (alface). O teste mostrou baixa toxicidade do solo após 80 dias da contaminação, com ou sem a adição do consórcio. Durante estudos de remediação biológica, é necessário utilizar um marcador interno para minimizar a dispersão e extração irregulares dos contaminantes. Neste estudo foi utilizado o hexaclorobenzeno, que mostrou excelente, uma vez que não sofreu nenhum tipo de degradação. Análises moleculares mostram que a adição de HAPs alterou significativamente a comunidade microbiana, favorecendo os membros degradadores de tais poluentes. O consórcio adicionado inibiu o crescimento de alguns micro-organismos autóctones. Além disso, não houveram evidências de que os micro-organismos degradadores de HAPs adicionados persistiram, sugerindo que eles podem não competir eficientemente com a população microbiana autóctone. Não houve efeito claramente identificado do hexaclorobenzeno sobre o crescimento de micro-organismos, com exceção de um aumento no número de organismos pertencentes da classe Alphaproteobacteria / Abstract: Polycyclic aromatic hydrocarbons (PAHs) stand out as among the most abundant and toxic of environmental contaminants, and their removal from contaminated sites is indispensable for a healthy environment. The objective of this study was to analyze, in soil microcosms, the biodegradation of PAHs by a bacterial PAH degrading consortium and identify factors that influence this degradation and data analysis. Degradation of PAHs in soil with no history of contamination was very similar in microcosms with or without bioaugmentation, with the extent of PAH removal of about 85% in all cases. The germination of Lactuca sativa (lettuce) in soils taken from the microcosms was used to examine the toxicity of the soil before and after bioremediation. The test showed a low toxicity of the soil 80 days after PAH contamination, with or without the addition of the consortium. During studies of biological remediation it is necessary to use an internal non-biodegradable marker to minimize the effect of uneven dispersion and irregular extraction of pollutants. This study used hexachlorobenzene as the nonbiodegradable marker and it proved to be an excellent marker as it did not suffer any significant degradation in the soil microcosms. Molecular analyzes showed that the addition of PAHs significantly altered the microbial community by encouraging the growth of PAH degraders. In addition, the added microbial consortium was found to inhibit the growth of some of the indigenous microorganisms. Furthermore, there was no evidence that the added PAH degraders persisted, suggesting that they might not compete effectively with the native microbial population. There was little effect of hexachlorobenzene on the microbial community or on the removal of the PAH contaminants, with the exception of an increase in the number of organisms belonging to the class Alphaproteobacteria / Mestrado / Ciência de Alimentos / Mestra em Ciência de Alimentos

Routine monitoring of environmental pollution demands simplicity and speed without sacrificing sensitivity or accuracy. The development and application of sensitive, fast and easy to implement analytical methodologies for detecting emerging and traditional water and airborne contaminants in South Florida is presented. A novel method was developed for quantification of the herbicide glyphosate based on lyophilization followed by derivatization and simultaneous detection by fluorescence and mass spectrometry. Samples were analyzed from water canals that will hydrate estuarine wetlands of Biscayne National Park, detecting inputs of glyphosate from both aquatic usage and agricultural runoff from farms. A second study describes a set of fast, automated LC-MS/MS protocols for the analysis of dioctyl sulfosuccinate (DOSS) and 2-butoxyethanol, two components of Corexit®. Around 1.8 million gallons of those dispersant formulations were used in the response efforts for the Gulf of Mexico oil spill in 2010. The methods presented here allow the trace-level detection of these compounds in seawater, crude oil and commercial dispersants formulations. In addition, two methodologies were developed for the analysis of well-known pollutants, namely Polycyclic Aromatic Hydrocarbons (PAHs) and airborne particulate matter (APM). PAHs are ubiquitous environmental contaminants and some are potent carcinogens. Traditional GC-MS analysis is labor-intensive and consumes large amounts of toxic solvents. My study provides an alternative automated SPE-LC-APPI-MS/MS analysis with minimal sample preparation and a lower solvent consumption. The system can inject, extract, clean, separate and detect 28 PAHs and 15 families of alkylated PAHs in 28 minutes. The methodology was tested with environmental samples from Miami. Airborne Particulate Matter is a mixture of particles of chemical and biological origin. Assessment of its elemental composition is critical for the protection of sensitive ecosystems and public health. The APM collected from Port Everglades between 2005 and 2010 was analyzed by ICP-MS after acid digestion of filters. The most abundant elements were Fe and Al, followed by Cu, V and Zn. Enrichment factors show that hazardous elements (Cd, Pb, As, Co, Ni and Cr) are introduced by anthropogenic activities. Data suggest that the major sources of APM were an electricity plant, road dust, industrial emissions and marine vessels.

Several different mechanisms leading to the formation of (substituted) naphthalene and azanaphthalenes were examined using theoretical quantum chemical calculations. As a result, a series of novel synthetic routes to Polycyclic Aromatic Hydrocarbons (PAHs) and Nitrogen Containing Polycyclic Aromatic Compounds (N-PACs) have been proposed. On Earth, these aromatic compounds originate from incomplete combustion and are released into our environment, where they are known to be major pollutants, often with carcinogenic properties. In the atmosphere of a Saturn’s moon Titan, these PAH and N-PACs are believed to play a critical role in organic haze formation, as well as acting as chemical precursors to biologically relevant molecules. The theoretical calculations were performed by employing the ab initio G3(MP2,CC)/B3LYP/6-311G** method to effectively probe the Potential Energy Surfaces (PES) relevant to the PAH and N-PAC formation. Following the construction of the PES, Rice-Ramsperger-Kassel-Markus (RRKM) theory was used to evaluate all unimolecular rate constants as a function of collision energy under single-collision conditions. Branching ratios were then evaluated by solving phenomenological rate expressions for the various product concentrations. The most viable pathways to PAH and N-PAC formation were found to be those where the initial attack by the ethynyl (C2H) or cyano (CN) radical toward a unsaturated hydrocarbon molecule led to the formation of an intermediate which could not effectively lose a hydrogen atom. It is not until ring cyclization has occurred, that hydrogen elimination leads to a closed shell product. By quenching the possibility of the initial hydrogen atom elimination, one of the most competitive processes preventing the PAH or N-PAC formation was avoided, and the PAH or N-PAC formation was allowed to proceed. It is concluded that these considerations should be taken into account when attempting to explore any other potential routes towards aromatic compounds in cold environments, such as on Titan or in the interstellar medium.

A novel route for the synthesis of the polycyclic aromatic hydrocarbon peropyrene (Pp) is reported along with the efforts to synthesize derivatives of Pp, 2,2′- and 5,5′-linked tetracene dimers as candidates for study as singlet fission materials in photovoltaic devices. Peropyrene was synthesized by the McMurry coupling conditions from phenalenone and low-valent titanium species. The crystal structure of Pp is formed by π-stacked molecular pairs in a herringbone arrangement. The direct functionalization of Pp was studied, and several indirect methods for the functionalization of Pp via phenalenone derivatives are reported. Nucleophilicly dependent, regioselective Michael addition pathways for phenalenone are described. Phenalenone forms a nucleophilic complex with bispinacolatodiboron and yields chiral 3,3′-linked phenalenone dimers and a bicyclo[3.2.1]octane derivative product of an unusual 3,4 addition. An active complex product of phenalenone and (dimethylphenylsilyl)boronic acid pinacolic ester forms Pp directly. The synthesis of 2,2′- and 5,5′-linked tetracene dimers led to the study of the reduction of 1-arylprop-2-yn-1-ol derivatives via TFA-catalyzed hydride transfer from triethylsilane. Substrates with terminal and TMS-protected alkynes showed silane exchange upon reduction. A TMS-protected, terminal alkyne became triethylsilyl-protected by about 50% whereas only triethylsilyl-protected, terminal alkyne was observed from the reduction of an unprotected, terminal alkyne. A new conformational polymorph of 1,4-bis(triisopropylsilyl)buta-1,3-diyne is reported. Five other rotamers are studied by density functional theory as possible candidates of conformational polymorphism by the analysis of torsional strain energies. The relative stabilities and interconversion equilibria of the seven conformational isomers are studied.

Nonbenzenoid carbocyclic rings are postulated to serve as important structural elements toward tuning the chemical and electronic properties of extended polycyclic aromatic hydrocarbons (PAHs, or namely nanographenes), necessitating a rational and atomically precise synthetic approach toward their fabrication. Here, using a combined bottom-up in-solution and on-surface synthetic approach, we report the synthesis of nonbenzenoid open-shell nanographenes containing two pairs of embedded pentagonal and heptagonal rings. Extensive characterization of the resultant nanographene in solution shows a low optical gap, and an open-shell singlet ground state with a low singlet–triplet gap. Employing ultra-high-resolution scanning tunneling microscopy and spectroscopy, we conduct atomic-scale structural and electronic studies on a cyclopenta-fused derivative on a Au(111) surface. The resultant five to seven rings embedded nanographene displays an extremely narrow energy gap of 0.27 eV and exhibits a pronounced open-shell biradical character close to 1 (y0 = 0.92). Our experimental results are supported by mean-field and multiconfigurational quantum chemical calculations. Access to large nanographenes with a combination of nonbenzenoid topologies and open-shell character should have wide implications in harnessing new functionalities toward the realization of future organic electronic and spintronic devices.

The combustion of petroleum-based fuels leads to the formation of several pollutants. Among them, soot particles are particularly harmful due to their severe consequences on human health. Over the past decades, strict regulations have been placed on automotive and aircraft engines to limit these particulate matter emissions. This work is primarily focused on understanding the fundamental behaviour of soot particles and their formation. Though the focus of this work is on soot formation and growth pathways, the study of the gas-phase combustion process was also an integral part to validate the mechanism. A reduced mechanism is developed with retaining the larger PAH species till coronene from KAUST-ARAMCO mechanism. Counterflow diffusion flames had emphasized the simulation of canonical configuration where the reduced mechanism is validated and the soot growth pathways are evaluated. The importance of the significant contribution of larger PAH species on the soot growth pathways in both SF and SFO flames is evident in this analysis. The sensitivity of these flames with respect to strain rates, dilution, and at higher pressures are analysed. Direct Numerical Simulation (DNS) of two-dimensional counterflow diffusion flames is conducted to understand the impact of vortex interactions on soot characteristics. The results indicate that the larger PAH species contributes to the soot formation in the air-side perturbation regimes, whereas the soot formation is dominated by the soot transport in fuel-side perturbation. The study is extended to simulate and compare coflow laminar flame using different statistical moment methods MOMIC, HMOM and CQMOM.

This dissertation summarizes my research in the Nuckolls group on two projects, with a central theme of achieving control of electronic coupling in various nanoscale systems. The two studies of interest aim at the study of emerging properties from alkali-doping of polyaromatic hydrocarbons (PAH), and the synthesis of novel metal chalcogen molecular clusters. Chapter 1 is divided into two parts. Part one provides a brief history of the forces we associate with bond formation. We will learn that although defining a “chemical bond” is helpful, it is limited to our incomplete understanding of what forces contribute to its existence. The behavior of an electron in externally applied magnetic fields will be discussed, where the collective behavior of electrons in a material can be measured, showing a myriad of emerging properties. The known superconducting alkali-doped PAHs are introduced, followed by the unresolved problems of reproducibility and lack of structural data to accompany superconducting samples. Finally, the proximity of AFM to superconductivity is discussed, which could give us insights on further exploration of hight temperature organic superconductors. Part two introduces atomically precise clusters of atoms, also knows as superatoms. Various synthetic approaches to create metal chalcogenide superatoms are introduced. Next, a closer look into the cobalt selenide core, [Co6Se8], is presented. The ability to selectively substitute the ligands on this superatom, achieves dimensional control. The subunit can be seen as a 0-dimensional subunit, where it readily gives away its electrons. Furthermore, assembly of the clusters into 1-, 2-, and 3-dimensional structures is described. Chapter 2 introduces a novel approach to acquire phase pure alkali-doped PAHs, p-terphenyl specifically. Previous reports of solution-processed doping of PAH have inspired highly reliable synthesis of these salts, by employing a chelating agent to stabilize the alkali metal. The first half of chapter 2 analyzes one such crystal in detail, describing emerging AFM fluctuations. The AFM coupling between nearest neighboring p-terphenyls occurs in all three crystallographic directions. Interestingly, this coupling can be seen as an unconventional bond between two terphenyl units along the hard axis, and resembles resonance structures seen in polyacetylene. The second half of the chapter further investigates the novel method, obtaining a library of alkali-doped p-terphenyls. This approach allows for selective variation of either the alkali-metal, the chelating agent, or the electronic structure of p-terphenyl. Obtaining nearly a dozen structures allows for a study of trends of doping level and accompanied magnetic properties. Lastly, Chapter 3 proves a new mechanism for ligand substitution of cobalt selenide superatomic clusters, using an easily removable carbene as the ligand. This approach grants access to new surface ligands and core shapes to expand the properties of these superatoms. Through this approach, larger atomically precise materials can be targeted, giving rise to new types of electronic properties.