My thesis examines nonlinearity between catch and effort. I use a meta-analysis of published literature and generalized linear mixed-effects models (GLMM) on both fixed and mobile gear fisheries of Atlantic Canada. The meta-analysis examines the proportionality of catch to effort using the slope of the reduced major axis (RMA) log-log regression, which accounts for “errors-in-variables”. The GLMMs explored proportionality while accounting for variation among fishing vessels. Both analyses found evidence for disproportionality between catch and effort. Catch that increases disproportionally to effort could result from either facilitation or recruitment of effort into the fishery. Catch increases that are less than proportional are expected from competitive interactions among fishers or gear saturation. The GLMM also revealed that the level of aggregation (by set, trip, monthly, or annually) can affect the apparent proportionality between catch and effort. In general, catch and effort should not be considered to be proportional. / May 2016

This dissertation thesis focuses on the removability of algal organic matter (AOM) by coagulation during water treatment and also on the influence of AOM on the coagulation of other substances present in source water. Special emphasis is put on the description of coagulation mechanisms. The effectiveness of AOM removal by coagulation was investigated by coagulation tests performed with optimized doses of coagulants (aluminium or ferric sulphate) under different pH values. Peptides and proteins contained in cellular organic matter of cyanobacterium Microcystis aeruginosa were used in the experiments since they have been previously reported to disturb the coagulation process. Moreover, peptides and proteins underwent coagulation experiments together with kaolin particles, representing clay particles in turbid waters, in both the presence and absence of coagulants to investigate the effect of AOM on the coagulation of turbid waters. To enable the description of coagulation mechanisms, AOM were characterised in terms of charge, functional groups, molecular weight and ability to form dissolved complexes with coagulant metals. The experimental results demonstrated that the removability of peptides and proteins is greatly dependent on pH value and on the properties of the involved particles or molecules....

Les protéines amyloïdes sont impliquées dans de nombreux processus pathologiques de maladies qui restent souvent incurables. Ces protéines solubles dans leur forme native, s’auto- assemblent pour former des oligomères, des fibrilles, des fibres et enfin des agrégats riches en feuillets β. C’est ce processus délétère qui est le point commun entre ces maladies amyloïdes. La protéine amyloïde la plus décrite est le peptide Aβ suspecté de jouer un rôle primordial dans la maladie d’Alzheimer. Récemment, les petits oligomères du peptide Aβ1-42 formés lors des étapes précoces de ce processus ont été décrit comme étant les plus toxiques.Au cours de cette thèse, nous avons donc développé deux méthodes pour pouvoir évaluer l’activité des composés synthétisés sur les étapes précoces de l’oligomérisation et une pour étudier l’affinité du peptide Aβ1-42 pour son ligand. Nous avons également conçu et synthétisé des peptidomimétiques comme ligands du peptide Aβ1-42 capables ainsi de perturber les interactions protéine-protéine du processus d’agrégation du peptide Aβ1-42. L’évaluation de ces composés ainsi que de différents ligands synthétisés au laboratoire a permis une intéressante étude sur la relation entre la structure des composés évalués et leurs activités sur les étapes cruciales du processus d’oligomérisation du peptide Aβ1-42. Des études de viabilité cellulaire, de RMN et de Docking sont en cours pour améliorer notre compréhension du mode d’action de ces composés et du processus d’oligomérisation du peptide Aβ1-42. / Amyloid proteins are involved in many pathological processes of diseases that are often incurable. These soluble proteins in their native form self-assemble to form oligomers, fibrils, fibers and finally aggregates rich in β-sheets. It is this deleterious process which is the common point between these amyloid diseases. The most described amyloid protein is the Aß peptide suspected of playing a key role in Alzheimer's disease. Recently, small peptide Aβ1-42 oligomers formed during the early stages of this process have appeared to be the most toxic species.In this thesis, we have developed two methods to evaluate the activity of different synthesized compounds on the early steps of oligomerization and one method to study the affinity of Aβ1-42 peptide for its ligand. We have also designed and synthesized peptidomimetics as ligands of Aβ1-42 peptide which are able to disrupt protein-protein interactions involved in the aggregation process of Aβ1-42 peptide. Evaluation of these compounds as well as other ligands synthesized in the laboratory allowed an interesting study on the relationship between the structure of the tested compounds and their activities on the critical steps of the oligomerization process of Aβ1-42 peptide. Cell viability studies, NMR and docking are underway to improve our understanding of the mode of action of these compounds and of the oligomerization process of Aβ1-42 peptide.

No labirinto dos gotejadores ocorrem diferentes interações entre as partículas de argila e as características do escoamento, sendo que essas interações interferem no potencial de obstrução dos mesmos. Considerando que os principais fatores que interferem no processo de obstrução causado por partículas de argila estão relacionados à natureza das argilas, ao regime de escoamento, à força iônica e ao pH da solução, e à concentração de partículas em suspensão. Esta pesquisa apresentou como objetivo identificar como esses fatores podem influenciar o desempenho dos gotejadores. Além disso, visando a caracterização do processo de obstrução causado por partículas desta natureza, buscou-se: relacionar o potencial de agregação das partículas com o desempenho dos gotejadores; e, analisar o comportamento da deposição de partículas no interior dos labirintos dos gotejadores. Para isso, além da realização dos ensaios em bancada utilizando diferentes dispersões de argila, foram realizadas análises sobre o potencial de agregação das partículas, e, utilizando um dispositivo milifluidico, foi realizada uma análise de deposição de partículas. Durante a pesquisa foram utilizados dois tipos de argilas, caulinita e montmorilonita. A força iônica da solução e a natureza dos materiais de argila apresentaram efeito sobre o desempenho dos gotejadores, enquanto que a caulinita em solução salina de sódio proporcionou incremento máximo de vazão de 5%, a montmorilonita causou redução máxima de vazão de 15%. No geral, as partículas de argila começaram a causar redução de vazão significativas com concentrações iguais ou superiores a 1000 mg L-1. Observou-se que as partículas de argila estão sujeitas ao fenômeno de autolimpeza que ocorre no interior dos labirintos após o acionamento do sistema. Não foi possível encontrar uma relação entre o potencial de agregação das partículas de argila e o desempenho dos gotejadores. Possivelmente, o índice de agregação utilizado pela teoria DLVO clássica não seja o mais adequado para obter esta relação. Em relação a deposição de partículas, as regiões que apresentaram maiores deposições de partículas coincidem com aquelas que apresentam menores valores de intensidade de turbulência e energia cinética turbulenta. A deposição de partícula ocorre principalmente nas regiões de vórtices e estagnação, localizadas nos dois primeiros defletores dos labirintos. Não foi observado acúmulo de partículas na região do fluxo principal. Por isso, sugere-se que partículas de argila, como agente isolado de obstrução, não apresentam potencial para causar obstrução completa dos gotejadores. / In the drippers labyrinth different interactions occur between the clay particles and the flow characteristics, and these interactions interfere in the clogging potential of the particles. Considering the main factors that affect the process of clogging caused by clay particles are related to the type of the clays, the flow regime, the ionic strength and pH of the solution, and the concentration of suspended particles. This research aims to identify how these factors can influence the performance of drippers. In addition, aiming to characterize the clogging process caused by particles of clay, it was sought to relate the potential of particles aggregation with the performance of drippers; and, to analyze the behavior of particles deposition inside the labyrinths of drippers. For this, in addition to performing bench tests using different clay dispersions, analyzes were carried out on the particle aggregation potential, and a particle deposition analysis was performed using a microfluidic device. During the research two types of clays were used, kaolinite and montmorillonite. The ionic strength of the solution and the type of the clay materials had an effect on the drippers performance. Whereas the kaolinite in sodium saline provided a maximum flow rate increase of 5%, the montmorillonite caused a maximum flow rate reduction of 15%. In general, clay particles began to cause significant flow rate reduction with concentrations equal to or greater than 1000 mg L-1. It was observed that clay particles are subject to the phenomenon of self-cleaning which occurs inside the labyrinths after turn on the system. It was not possible to find a relation between the potential of clay particles aggregation and the drippers performance. Possibly, the aggregation index used by the classical DLVO theory is not the most adequate to obtain this relation. In relation to the particles deposition, the regions of greatest deposition coincide with those that present lower values of turbulence intensity and turbulent kinetic energy. Particles deposition occurs mainly in the vortex and stagnation regions, located in the first two baffles of the labyrinths. In addition, no particle accumulation occurs in the main stream region, it suggested that clay particles, as an isolated clogging agent, do not have the potential to cause total clogging of drippers.

A L- asparaginase é uma enzima aplicada no tratamento de Leucemia Linfoide Aguda, que atua na hidrólise da L- asparagina, privando a célula tumoral de um aminoácido essencial para o seu crescimento. A L- asparaginase, como outros biofármacos, deve ser estável, manter sua atividade específica e formar poucos agregados. A fim de manter a integridade do biofármaco, são utilizados adjuvantes nas formulações farmacêuticas, e dentre os mais importantes estão os osmólitos. Essas moléculas protegem a estrutura nativa da proteína, sendo capazes de interferir na formação de agregados e garantir a estabilidade proteica. O presente trabalho teve o objetivo de estudar o efeito dos osmólitos sacarose, sorbitol, arginina e glicina na atividade específica, estabilidade, cinética e caracterização de agregados na solução de L- asparaginase II de Erwinia chrysanthemi. Os resultados mostraram que a maioria dos osmólitos testados aumentou a atividade específica e a estabilidade da enzima, o que pode estar relacionado com o aumento da velocidade máxima e do kcat observados no ensaio cinético realizado com sacarose e sorbitol. Um perfil diferente de agregados foi encontrado para cada tipo de osmólito. A presença de sacarose ou sorbitol resultou na menor quantidade de agregados na faixa de, respectivamente, 100 a 200 e 200 a 300 nm em relação a enzima sem osmólito. Por outro lado, aumento no número total de agregados e presença de moléculas de alto peso molecular (300 a 500 nm) foram observados nas soluções enzimáticas contendo, respectivamente, glicina e arginina. Dessa forma, os resultados obtidos neste trabalho poderão auxiliar na produção e escolha da formulação de biofármacos, e, consequentemente, melhorar o tratamento medicamentoso de pacientes. / L L-Asparaginase is an enzyme applied in the treatment of Acute Lymphoblastic Leukemia, which acts on the hydrolysis of L- asparagine, depriving the tumor cell of an essential amino acid for its growth. L-asparaginase, as other biopharmaceuticals, must be stable, maintain its specific activity and form few aggregates. In order to maintain the integrity of the biopharmaceutical, adjuvants are used in the pharmaceutical formulations, and among the most importants adjuvants are the osmolytes. These molecules protect the native structure of the protein, being able of interfering in the formation of aggregates and guarantee protein stability. The present work had the objective of studying the effect of the osmolytes sucrose, sorbitol, arginine and glycine in the specific activity, stability, kinetic and aggregates characterization, in L- asparaginase II solution of Erwinia chrysanthemi. The results showed that the majority of the tested osmolytes increased the specific activity of the enzyme and its stability, which may be related to the augment of maximum velocity and kcat observed in the kinetic assay performed with sucrose and sorbitol. A different profile of aggregates was found for each type of osmolyte. The presence of sucrose or sorbitol resulted in the least amount of aggregates in the range of, respectively, 100-200 and 200-300nm in relation to the enzyme without osmolyte. On the other hand, increase in the total number of aggregates and the presence of high molecular weight molecules (300 to 500 nm) were observed in the enzymatic solutions containing, respectively, glycine and arginine. Thus, the results obtained in this work may help in the production and choice of the formulation of biopharmaceuticals and, consequently, improve the drug treatment of patients.

Proteína dissulfeto isomerase (PDI) é uma ditiol-dissulfeto óxido redutase ubíqua que é responsável por uma série de funções celulares, inclusive na sinalização celular e nas respostas a eventos que causam dano celular. Entretanto, a PDI pode se tornar disfuncional através das modificações pós-traducionais, incluindo as promovidas por oxidantes biológicos. Estes oxidantes são provavelmente os responsáveis pelas modificações oxidativas pós-traducionais da PDI que foram detectadas em várias condições associadas ao estresse oxidativo, levando à disfunção da proteína. Devido a falta de estudos cinéticos com a PDI nativa e a falta de caracterização dos produtos dessas reações, investigamos se a diminuição da fluorescência da PDI nativa pode ser empregada para estudos da cinética de oxidação com peróxido de hidrogênio. Posteriormente, investigamos a cinética e os produtos da reação entre PDI e peroxinitrito. Nossos experimentos mostraram que a oxidação por excesso de peróxido de hidrogênio levava a uma diminuição da fluorescência de forma dependente do tempo e da concentração do oxidante, permitindo a determinação da constante de velocidade de segunda ordem (k = (17,3±1,3) M-1 s-1, pH 7,4, 25 ºC). Relevantemente, mostramos que o processo era totalmente revertido por DDT, mostrando que o peróxido de hidrogênio oxida quase que exclusivamente os grupos ditióis da PDI (Cys53 e Cys56 e Cys397 e Cys400). Utilizando a mesma abordagem para estudar a oxidação da PDI por peroxinitrito, notamos que o decréscimo da fluorescência intrínseca da PDI nativa e a velocidade só era proporcional à concentrações sub-estequiométricas ou estequiométricas do oxidante em relação aos tióis reativos da PDI. Somente nessas condições o processo se mostrava reversível por DDT, indicando que os ditióis da PDI eram o alvo preferencial do peroxinitrito mas que a oxidação de outros resíduos também ocorria. A reação dos tióis reativos da PDI com peroxinitrito foi considerada relativamente rápida (6,9 ± 0,6 × 104 M-1 s-1, pH 7,4, 25 °C), e os resíduos de Cys reativos dos domínios a e a\' aparentam reagir com constantes de velocidade similares. Experimentos de proteólise limitada, simulações cinética e análises de MS e MS/MS confirmaram que o peroxinitrito oxida preferencialmente os tióis redox ativos da PDI para os ácidos sulfênicos correspondentes, que, subsequentemente, reagem com os tióis vizinhos, produzindo dissulfetos (Cys53- Cys56 e Cys397- Cys400). Entretanto, uma fração de peroxinitrito decai para radicais levando à hidroxilação e nitração de outros resíduos próximos ao sítio redox ativo (Trp52 Trp396 e Tyr393). Assim, investigamos também a oxidação da PDI por excesso de peroxinitrito em relação aos grupos tióis reativos por diferentes metodologias. Experimentos de SDS-PAGE, western-blot e atividade redutase mostraram que o peroxinitrito promove inativação, nitração e agregação da PDI de forma dependente da concentração de peroxinitrito. Análises de MS e MS/MS mostraram que, em excesso, o peroxinitrito promove nitração (Tyr43, Tyr49, Tyr196, Tyr393, Trp52, Trp396) e hidroxilação (Trp52, Trp396) da PDI. Em síntese, nossos estudos contribuem para melhor compreensão da oxidação da PDI por peroxinitrito e de suas possíveis consequências biológicas. / Protein disulfide isomerase (PDI) is a ubiquitous dithiol-disulfide oxidoreductase that performs an array of cellular functions, including in cellular signaling and responses to cell-damaging events. Nevertheless, PDI can become dysfunctional by post-translational modifications, including those promoted by biological oxidants. These oxidants are likely responsible for the oxidative post-translational modifications of PDI, which have detected under various conditions associated with oxidative stress, leading to protein dysfunction. However, the kinetics of the reactions of PDI with biological oxidants received limited studies and the products of these reactions were not characterized. Here, we examined whether the decrease in PDI fluorescence can be employed to follow the kinetics of the reaction of the full-length protein with biological oxidants. Also, we investigated the kinetics and products of the reaction between PDI and peroxynitrite. Our experiments showed that oxidation by excess hydrogen peroxide led to a decrease of PDI intrinsic fluorescence in a time- and concentration-dependent manner , permitting the determination of the second-order rate constant of the reaction (k = (17.3 ± 1.3 ) M1 s-1, pH 7.4, 25 ° C). The oxidation was reversed by DDT, indicating that hydrogen peroxide oxidizes mainly PDI dithiols (Cys53 and Cys56 and Cys397 and Cys400). Using the same approach to study PDI oxidation by peroxynitrite we noted that the decrease of the native PDI fluorescence was proportional to sub-stoichiometric or stoichiometric concentrations of the oxidant relative to that of PDI reactive thiols. Only under these conditions, PDI oxidation was reversed by DDT, indicating that PDI dithiols were the preferred target of peroxynitrite but that oxidation of other residues also occurred. The reaction of the active redox thiols of the PDI with peroxynitrite can be considered relatively fast (6.9 ± 0.6 × 104 M-1 s-1, pH 7.4, 25 ° C), and the reactive Cys residues of domains a and a\' were kinetically indistinguishable. Limited proteolysis experiments, kinetic simulations, and MS and MS/MS analyses confirmed that peroxynitrite preferentially oxidizes the redox-active Cys residues of PDI to the corresponding sulfenic acids, which subsequently react with the resolving thiols to produce disulfides (Cys53-Cys56 and Cys397-Cys400). However, a fraction of peroxynitrite decays to radicals leading to hydroxylation and nitration to other residues located close to the active site (Trp52 Trp396 and Tyr393). SDS-PAGE, western blotting and inhibition of the reductase activity experiments confirmed that excess peroxynitrite promotes further PDI oxidation, nitration, inactivation and aggregation in a concentration-dependent manner. MS and MS/MS analyzes showed that peroxynitrite in a ten times excess relative to PDI reactive thiols promote PDI nitration (Tyr43, Tyr49, Tyr196, Tyr393, Trp52, Trp396) and hydroxylation (Trp52, Trp396). In conclusion, our studies contribute to a better understanding of PDI oxidation by peroxynitrite and its possible biological consequences

INTRODUÇÃO: Os Inibidores de Bombas de Prótons (IBP´s) são comumente prescritos a pacientes em uso de dupla antiagregação plaquetária (DAP) com ácido acetilsalicílico (AAS) e clopidogrel. Entretanto, esta classe de medicamentos, especialmente o omeprazol, tem sido associada à redução da potência antiplaquetária do clopidogrel, levando em muitos casos ao uso de ranitidina como alternativa. MÉTODOS: Foram analisados pacientes com doença arterial coronária (DAC) estável em uso de AAS 100 mg uma vez ao dia. A agregabilidade plaquetária foi medida no momento basal e após uma semana de terapia com clopidogrel na dose de 75 mg uma vez ao dia. Após essa fase inicial, os participantes foram randomizados de modo duplo-cego e duplo-mascarado para omeprazol 20 mg duas vezes dia ou ranitidina 150 mg duas vezes ao dia, sendo os testes de agregação plaquetária novamente repetidos após uma semana. A agregabilidade foi avaliada com a utilização dos seguintes métodos: VerifyNow P2Y12® (Accumetrics - San Diego, CA, EUA, meta principal do estudo), utilizando-se Unidades de Reatividade ao P2Y12 (\"P2Y12 Reactivity Units\" - PRU) e Inibição Percentual da Agregabilidade (IPA) na descrição da agregabilidade; agregometria de sangue total (AST) por bioimpedância utilizando os reagentes ADP e colágeno, sendo a agregabilidade medida em Ohms; \"Platelet Function Analyser\" 100® (Siemens Healthcare Diagnostics®, Newark, Delaware, EUA) utilizando o cartucho de colágeno/ADP, com a agregabilidade avaliada pelo tempo de fechamento do orifício em segundos. Além disso, foi feita dosagem de tromboxano B2 (TXB2) sérico na última visita a fim de se avaliar o efeito do AAS. RESULTADOS: Oitenta e cinco pacientes foram incluídos na análise final, sendo 41 no grupo omeprazol e 44 no grupo ranitidina. Houve redução significativa da IPA após o acréscimo de omeprazol (de 26,3 ± 32,9% para 17,4 ± 33,1%; P = 0,025), enquanto o grupo ranitidina não demonstrou modificação significativa (de 32,6 ± 28,9% para 30,1 ± 31,3%; P = 0,310). Levando-se em conta o valor em PRU, houve um aumento numérico porém não significativo estatisticamente no grupo omeprazol (de 159,73 ± 83,06 para 173,54 ± 72,29; P = 0,116) enquanto no grupo ranitidina houve uma diferença muito pequena (de 153,61 ± 70,12 to 158,77 ± 76,37; P = 0,440). Em relação aos demais testes de agregabilidade e à dosagem de TXB2 sérico, não houve alterações significativas em qualquer um dos grupos. CONCLUSÃO: A ranitidina não influenciou o efeito antiplaquetário do clopidogrel, ao contrário do omeprazol, que reduziu a atividade antiplaquetária do medicamento. Esses achados podem ter um importante impacto na tomada de decisão quanto ao protetor gástrico a ser utilizado em pacientes submetidos a DAP com AAS e clopidogrel. / BACKGROUND: Proton-pump inhibitors (PPIs) are often prescribed to patients taking dual antiplatelet therapy (DAPT) with acetylsalicylic acid (ASA) and clopidogrel. However, this class of medication, especially omeprazole, has been associated with a reduction of clopidogrel efficacy, leading many to substitute omeprazole with ranitidine. METHODS: The present study analyzed patients with stable coronary artery disease (CAD) in use of ASA 100 mg daily. Platelet aggregability was measured at baseline and after one week of clopidogrel 75 mg daily. Then, the subjects were randomized, in a double-blinded, doubledummy fashion, to omeprazole 20 mg twice a day or ranitidine 150 mg twice a day. After one more week, aggregability tests were repeated. Platelet aggregability was evaluated by the following methods: VerifyNow P2Y12TM (Accumetrics - San Diego, California, USA, main endpoint of the study), with aggregability depicted as percent Inhibition of Platelet Aggregation (IPA) and as P2Y12 Reactivity Units (PRU); whole blood aggregometry by bioimpendance using ADP and collagen with aggregability measured in Ohms; and Platelet Function Analyser 100TM (Siemens Healthcare Diagnostics, Newark, Delaware, USA) using collagen/ADP cartridge with aggregability measured in time to closure in seconds. Besides that, serum thromboxane B2 dosage was done on the last visit to evaluate ASA effect. RESULTS: Eighty-five patients were included in final analysis (41 in the omeprazole group and 44 in the ranitidine group). IPA was significantly decreased after addition of omeprazole (from 26.3% ± 32.9 to 17.4% ± 33,1; P = 0.025), with no significant changes being observed in the ranitidine group (from 32.6% ± 28.9 to 30.1% ± 31.3; P = 0.310). When taking into account PRU values, there was a numerical, but statistically non-significant increase in the omeprazole group (from 159.73 ± 83.06 to 173.54 ± 72.29; P = 0.116), with a very slight difference in the ranitidine group (from 153.61 ± 70.12 to 158.77 ± 76.37; P = 0.44). There were no significant changes taking into account other aggregability tests and serum thromboxane B2 dosage. CONCLUSION: In patients with stable CAD, ranitidine did not influence clopidogrel antiplatelet activity, in contrast to omeprazole, which reduced antiplatelet drug effect. These findings may have a great impact in clinical decision making regarding gastrointestinal prophylaxis choice in patients taking DAPT with ASA and clopidogrel

No description available.

Mass spectrometry is a versatile analytical tool for chemical and biomolecule identification, quantitation, and structural analysis. Tandem mass spectrometry further expands the applications of mass spectrometry, making it more than a mere detector. With tandem mass spectrometry, the mass spectrometer is capable of probing reaction mechanisms, monitoring reaction processes, and performing fast analysis on complex samples. In tandem mass spectrometry, after activation the precursor ions fragment into small fragment ions through one or more pathways, which are affected by the ion’s inherit property, the ion type, and the activation method. To obtain complementary information, one can alter the fragmentation pathway by changing the ion via ion charge manipulation and covalent modification to the ion. Gas-phase ion/ion reactions provide an easy approach to changing ion type and facile modification to the analyte ions. It has been extensively used for spectrum simplification and analyte structural studies. In this dissertation, ion/ion reaction facilitated mass spectrometry methods are studied, and explorations into the method development involving front-end mass spectrometer are discussed.<br>The first work demonstrates a special rearrangement reaction for gas-phase Schiff-base-modified peptides. Gas-phase Schiff-base modification of peptides has been applied to facilitate the primary structural characterization via tandem mass spectrometry. A major or minor fragment pathway related to the novel rearrangement reaction was observed upon in-trap collisional activation of the gas-phase Schiff-base-modified peptides. The rearrangement reaction involves the imine of the Schiff base and a nucleophile present in the polypeptide. The occurrence of the rearrangement reaction is affected by several factors, such as ion polarity, identity of the nucleophile in the peptide (e.g., side chains of lysine, histidine, and arginine), and the position of the nucleophile relative to the imine. The rearrangement reaction does not affect the amount of structural information that can be obtained by collisional activation of the Schiff-base-modified peptide, but when the rearrangement reaction is dominant, it can siphon away signal from the structurally diagnostic processes.<br>Efforts have also been put into the method development of peptide and protein aggregation detection via electrospray ionization mass spectrometry (ESI-MS). People have studied peptide and protein aggregation processes to understand the mechanism of amyloid-related diseases and to control the quality of the peptide and protein pharmaceuticals. ESI-MS is suitable for solution aggregation studies because of its compatibility with solution samples and the straightforward result of the analyte’s oligomeric state on the mass spectrum. However, peak overlap issue and nonspecific aggregation in the ESI process can obscure the result. Here, the application of proton transfer ion/ion reaction to the analyte has been found useful to reduce or eliminate the peak overlap issue. A statistical model based on Poisson statistics has been proposed to deal with the ESI-induced nonspecific aggregation in the droplet and to differentiate the solution-phase aggregation from the droplet-induced aggregation. Factors that affect the accuracy of the statistical model have been discussed with MATLAB simulations.<br>In the era of biological system studies, sample complexity is a challenge every analytical chemist has to face. The analysis of complex sample can be facilitated by the combination of separation techniques outside the mass spectrometer (such as differential mobility spectrometry (DMS)) and ion structure probing techniques inside the mass spectrometer (such as tandem mass spectrometry and gas-phase ion/ion reactions). Here the coupling method between DMS and ion/ion reaction is developed and tested with model peptide systems to demonstrate its possible application in complex sample characterization such as isomer identification.<br>

Beta-Amyloid (1-40) (Aβ40) is an aggregation prone protein, which undergoes a nucleation-dependent aggregation process causing the pathological neurodegeneration by amyloid plaque formation implicated in Alzheimer’s disease. In this thesis, we investigated the effects of small molecule modulators extracted from the marine invertebrate Pseudopterogorgia elisabethae on the Aβ40 amyloidogenic process using in- vitro ThT fluorescence assay and atomic force microscopy. We also investigated the effects of neutral and anionic phospholipid liposomes on Aβ40 aggregation. Our results show that a marine natural product Pseudopterosin-A and its derivatives can suppress and modulate the Aβ40 aggregation process. Furthermore, our results demonstrate that a neutral phospholipid liposome inhibits Aβ40 fibril formation, whereas the anionic liposomes promote it. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2015 / FAU Electronic Theses and Dissertations Collection