Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (leaves 246-276).

Orientador: Valber de Albuquerque Pedrosa / Resumo: O desenvolvimento de novos dispositivos para monitorar o metabolismo celular e o diagnóstico de doenças expandiu as pesquisas com biossensores, que aliados à nanotecnologia possibilitaram a criação de novos elementos com alta sensibilidade de detecção, especificidade e capacidade de multiplexação, mostrando grande potencial para sua aplicabilidade no diagnóstico clínico. O trabalho foi desenvolvido em duas etapas. A primeira, referiu-se no desenvolvimento de uma metodologia para acoplar o aptâmero conjugado com as nanopartículas de ouro sobre o sensor da Ressonância Plasmônica de Superfície (SPR). Foi utilizado MUA para formação das monocamadas auto-organizadas; ativação dos grupos carboxílicos utilizando solução de EDC/NHS e a imobilização do aptâmero conjugado. Após este processo, foram realizadas as injeções de Mucina Epitelial Polimórfica tipo 1 (MUC1). A segunda etapa, consistiu na mesma metodologia de acoplamento do aptâmero, porém substituindo a MUC1 por sobrenadante da linhagem celular LNCaP (células prostáticas tumorais). Desse modo, foi desenvolvida uma metodologia analítica utilizando aptâmeros e biomarcadores para diagnosticar o Câncer de Próstata (PCa) através da SPR. / Mestre

abstract: Plasmon resonance in nanoscale metallic structures has shown its ability to concentrate electromagnetic energy into sub-wavelength volumes. Metal nanostructures exhibit a high extinction coefficient in the visible and near infrared spectrum due to their large absorption and scattering cross sections corresponding to their surface plasmon resonance. Hence, they can serve as an attractive candidate for solar energy conversion. Recent papers have showed that dielectric core/metallic shell nanoparticles yielded a plasmon resonance wavelength tunable from visible to infrared by changing the ratio of core radius to the total radius. Therefore it is interesting to develop a dispersion of core-shell multifunctional nanoparticles capable of dynamically changing their volume ratio and thus their spectral radiative properties. Nanoparticle suspensions (nanofluids) are known to offer a variety of benefits for thermal transport and energy conversion. Nanofluids have been proven to increase the efficiency of the photo-thermal energy conversion process in direct solar absorption collectors (DAC). Combining these two cutting-edge technologies enables the use of core-shell nanoparticles to control the spectral and radiative properties of plasmonic nanofluids in order to efficiently harvest and convert solar energy. Plasmonic nanofluids that have strong energy concentrating capacity and spectral selectivity can be used in many high-temperature energy systems where radiative heat transport is essential. In this thesis，the surface plasmon resonance effect and the wavelength tuning ranges for different metallic shell nanoparticles are investigated, the solar-weighted efficiencies of corresponding core-shell nanoparticle suspensions are explored, and a quantitative study of core-shell nanoparticle suspensions in a DAC system is provided. Using core-shell nanoparticle dispersions, it is possible to create efficient spectral solar absorption fluids and design materials for applications which require variable spectral absorption or scattering. / Dissertation/Thesis / M.S. Mechanical Engineering 2012

Les cyanobactéries sont des micro-organismes qui préoccupent les autorités de santé publique dans le monde entier, en raison de la toxicité des cyanotoxines qu'elles produisent. Certaines cyanotoxines dont les microcystines (MC) sont des hépatotoxines inhibitrices de protéines phosphatases à sérine/thréonine. Aujourd'hui, plus de 200 variants de MCs ont été identifiés. Il s'agit d'heptapeptides monocycliques synthétisés par voie non-ribosomale dont la MC-LR (cyclo- (D-Ala-L-Leu-D-érythro-β-méthylAsp-L-Arg-ADDA-D-Glu-N-méthyl-hydro-Ala) est le variant le plus étudié en raison de sa fréquence et de sa forte toxicité. L’objectif de cette étude est le développement d'une méthode d'immunoanalyse rapide, sensible et fiable pour détecter les MCs. Le projet vise donc à développer un outil alternatif de détection de la MC-LR, qui serait mieux adapté aux analyses sur le terrain que les méthodes analytiques, biologiques ou les méthodes d'inhibition d'activité enzymatique actuellement disponibles. L'originalité de ce projet réside dans l'utilisation de deux approches différentes pour sélectionner de nouveaux anticorps spécifiques de la MC-LR. La première repose sur l'immunisation d'animaux de laboratoire, la technologie d'hybridation cellulaire et la sélection d'hybridomes sécréteurs d'anticorps monoclonaux. Si la méthodologie mise en œuvre a effectivement permis d'obtenir des immun-sérums spécifiques, la sélection des hybridomes d'intérêt reste à optimiser. La seconde stratégie mise en œuvre est basée sur la technologie du phage display pour sélectionner des fragments d'anticorps spécifiques de MC-LR à partir d'une banque de taille d’environ 109 phages, exprimant en surface des anticorps sous un format scFv (Shahsavarian et al., 2014). Plusieurs méthodes de criblage ont été développées et trois scFv ont été sélectionnés et étudiés, parallèlement à un quatrième scFv identifié dans une étude précédente (McElhiney et al., 2002), tous spécifiques à la MC-LR. Ces scFv ont été produits sous forme libre, soluble et leur spécificité à la MC-LR a été évaluée par ELISA et résonance plasmonique de surface. Les résultats obtenus montrent que les scFv sélectionnés sont tous capables de reconnaître la MC-LR. Néanmoins, ces résultats sont peu reproductibles et remettent en question le protocole de renaturation utilisé. Un travail de fond sur l’optimisation du protocole de renaturation s’avèrerait nécessaire pour les scFv ici sélectionnés, afin d’identifier les paramètres précis aboutissant à la perte ou au gain de leur fonctionnalité. / Cyanobacteria are ubiquitous microorganisms that present a worldwide concern to public health authorities because of the toxicity of the cyanotoxins they produce. Some cyanotoxins are hepatotoxins such as microcystins (MCs). At least 200 variants of MCs have been identified till today. In our study, we focus on MC-LR, a monocyclic heptapeptide (cyclo-(D-Ala-L-Leu-D-erythro-β-methylAsp-L-Arg-ADDA-D-Glu-N-methyldehydro-Ala), since it is the most frequently detected and one of the most toxic. In our study, we are interested in developing a fast, sensitive and reliable method to detect MCs. The project aims to develop an alternative pollution detection method that would be better suited to field measurements than the physicochemical methods currently available. The originality of this project lies in the use of two different approaches to select a panel of antibodies suitable for the development of immunodetection tests. The first one is based on the hybridoma technology for the production of monoclonal antibodies. The second one is based on phage display technique to select antibody fragments that are specific to MC-LR from a library of approximately 109 phages, expressing on the surface scFv fragments (Shahsavarian et al., 2014). Two monoclonal antibodies were selected using the first approach, and their specificity was evaluated using ELISA technique. Along with three scFvs selected from phage display approach. An additional scFv was added to this list: 3A8, selected from a previous study (McElhiney et al., 2002) and also specific to MC-LR. The scFvs were cloned into an expression vector in order to get each clone in its scFv soluble form. Then, their specificity to MC-LR was evaluated using ELISA technique and Surface plasmon resonance. The results show a potential specificity to MC-LR. Nevertheless, these results are not very reproducible and call into question the refolding protocol used. A thorough work on this protocol optimization would be necessary, in order to find the key parameters that control the loss or gain of their functionality

abstract: Signal transduction networks comprising protein-protein interactions (PPIs) mediate homeostatic, diseased, and therapeutic cellular responses. Mapping these networks has primarily focused on identifying interactors, but less is known about the interaction affinity, rates of interaction or their regulation. To better understand the extent of the annotated human interactome, I first examined > 2500 protein interactions within the B cell receptor (BCR) signaling pathway using a current, cutting-edge bioluminescence-based platform called “NanoBRET” that is capable of analyzing transient and stable interactions in high throughput. Eighty-three percent (83%) of the detected interactions have not been previously reported, indicating that much of the BCR pathway is still unexplored. Unfortunately, NanoBRET, as with all other high throughput methods, cannot determine binding kinetics or affinities. To address this shortcoming, I developed a hybrid platform that characterizes > 400 PPIs quantitatively and simultaneously in < 1 hour by combining the high throughput and flexible nature of nucleic programmable protein arrays (NAPPA) with the quantitative abilities of surface plasmon resonance imaging (SPRi). NAPPA-SPRi was then used to study the kinetics and affinities of > 12,000 PPIs in the BCR signaling pathway, revealing unique kinetic mechanisms that are employed by proteins, phosphorylation and activation states to regulate PPIs. In one example, activation of the GTPase RAC1 with nonhydrolyzable GTP-γS minimally affected its binding affinities with phosphorylated proteins but increased, on average, its on- and off-rates by 4 orders of magnitude for one-third of its interactions. In contrast, this phenomenon occurred with virtually all unphosphorylated proteins. The majority of the interactions (85%) were novel, sharing 40% of the same interactions as NanoBRET as well as detecting 55% more interactions than NanoBRET. In addition, I further validated four novel interactions identified by NAPPA-SPRi using SDS-PAGE migration and Western blot analyses. In one case, we have the first evidence of a direct enzyme-substrate interaction between two well-known proto-oncogenes that are abnormally regulated in > 30% of cancers, PI3K and MYC. Herein, PI3K is demonstrated to phosphorylate MYC at serine 62, a phosphosite that increases the stability of MYC. This study provides valuable insight into how PPIs, phosphorylation, and GTPase activation regulate the BCR signal transduction pathway. In addition, these methods could be applied toward understanding other signaling pathways, pathogen-host interactions, and the effect of protein mutations on protein interactions. / Dissertation/Thesis / Doctoral Dissertation Biological Design 2018

Submitted by VANESSA MORAIS BRAITE null (vbraite@fmb.unesp.br) on 2017-09-27T13:56:27Z No. of bitstreams: 1 Dissertação Final.pdf: 994807 bytes, checksum: 8a4fd4046da2b6f8872103545cdfc8c4 (MD5) / Approved for entry into archive by Monique Sasaki (sayumi_sasaki@hotmail.com) on 2017-09-28T14:19:51Z (GMT) No. of bitstreams: 1 braite_vm_me_bot.pdf: 994807 bytes, checksum: 8a4fd4046da2b6f8872103545cdfc8c4 (MD5) / Made available in DSpace on 2017-09-28T14:19:51Z (GMT). No. of bitstreams: 1 braite_vm_me_bot.pdf: 994807 bytes, checksum: 8a4fd4046da2b6f8872103545cdfc8c4 (MD5) Previous issue date: 2017-09-01 / O desenvolvimento de novos dispositivos para monitorar o metabolismo celular e o diagnóstico de doenças expandiu as pesquisas com biossensores, que aliados à nanotecnologia possibilitaram a criação de novos elementos com alta sensibilidade de detecção, especificidade e capacidade de multiplexação, mostrando grande potencial para sua aplicabilidade no diagnóstico clínico. O trabalho foi desenvolvido em duas etapas. A primeira, referiu-se no desenvolvimento de uma metodologia para acoplar o aptâmero conjugado com as nanopartículas de ouro sobre o sensor da Ressonância Plasmônica de Superfície (SPR). Foi utilizado MUA para formação das monocamadas auto-organizadas; ativação dos grupos carboxílicos utilizando solução de EDC/NHS e a imobilização do aptâmero conjugado. Após este processo, foram realizadas as injeções de Mucina Epitelial Polimórfica tipo 1 (MUC1). A segunda etapa, consistiu na mesma metodologia de acoplamento do aptâmero, porém substituindo a MUC1 por sobrenadante da linhagem celular LNCaP (células prostáticas tumorais). Desse modo, foi desenvolvida uma metodologia analítica utilizando aptâmeros e biomarcadores para diagnosticar o Câncer de Próstata (PCa) através da SPR. / The development of new devices to monitor cell metabolism and the diagnosis of diseases has expanded research with biosensors, which together with nanotechnology enable the creation of new elements with high detection sensitivity, specificity and multiplexing capacity. The work has developed in two stages. First, concerning the development of a methodology for the coupling or the conjugate with the gold nanoparticles on the Surface Plasmon Resonance (SPR) sensor. MUA has used for the formation of self-organized monolayers; activation of social media groups, EDC / NHS solution, and a conjugate fit immobilization. After this process, they have performed as injections of Polimorphic Epithelial Mucin type 1 (MUC1). The second step consisted of the same aptamer coupling methodology, but replacing a MUC1 with supernatant of the LNCaP cell line (prostatic tumor cells). Thus, an analytical methodology has developed, using aptamers and biomarkers for the diagnosis of Prostate Cancer (PCa) through the SPR.

abstract: Surface plasmon resonance (SPR) has emerged as a popular technique for elucidating subtle signals from biological events in a label-free, high throughput environment. The efficacy of conventional SPR sensors, whose signals are mass-sensitive, diminishes rapidly with the size of the observed target molecules. The following work advances the current SPR sensor paradigm for the purpose of small molecule detection. The detection limits of two orthogonal components of SPR measurement are targeted: speed and sensitivity. In the context of this report, speed refers to the dynamic range of measured kinetic rate constants, while sensitivity refers to the target molecule mass limitation of conventional SPR measurement. A simple device for high-speed microfluidic delivery of liquid samples to a sensor surface is presented to address the temporal limitations of conventional SPR measurement. The time scale of buffer/sample switching is on the order of milliseconds, thereby minimizing the opportunity for sample plug dispersion. The high rates of mass transport to and from the central microfluidic sensing region allow for SPR-based kinetic analysis of binding events with dissociation rate constants (kd) up to 130 s-1. The required sample volume is only 1 &#956;L, allowing for minimal sample consumption during high-speed kinetic binding measurement. Charge-based detection of small molecules is demonstrated by plasmonic-based electrochemical impedance microscopy (P-EIM). The dependence of surface plasmon resonance (SPR) on surface charge density is used to detect small molecules (60-120 Da) printed on a dextran-modified sensor surface. The SPR response to an applied ac potential is a function of the surface charge density. This optical signal is comprised of a dc and an ac component, and is measured with high spatial resolution. The amplitude and phase of local surface impedance is provided by the ac component. The phase signal of the small molecules is a function of their charge status, which is manipulated by the pH of a solution. This technique is used to detect and distinguish small molecules based on their charge status, thereby circumventing the mass limitation (~100 Da) of conventional SPR measurement. / Dissertation/Thesis / Ph.D. Electrical Engineering 2013

abstract: The bleomycins are a family of glycopeptide-derived antibiotics isolated from various Streptomyces species and have been the subject of much attention from the scientific community as a consequence of their antitumor activity. Bleomycin clinically and is an integral part of a number of combination chemotherapy regimens. It has previously been shown that bleomycin has the ability to selectively target tumor cells over their non-malignant counterparts. Pyrimidoblamic acid, the N-terminal metal ion binding domain of bleomycin is known to be the moiety that is responsible for O2 activation and the subsequent chemistry leading to DNA strand scission and overall antitumor activity. Chapter 1 describes bleomycin and related DNA targeting antitumor agents as well as the specific structural domains of bleomycin. Various structural analogues of pyrimidoblamic acid were synthesized and subsequently incorporated into their corresponding full deglycoBLM A6 derivatives by utilizing a solid support. Their activity was measured using a pSP64 DNA plasmid relaxation assay and is summarized in Chapter 2. The specifics of bleomycin&mdash;DNA interaction and kinetics were studied via surface plasmon resonance and are presented in Chapter 3. By utilizing carefully selected 64-nucleotide DNA hairpins with variable 16-mer regions whose sequences showed strong binding in past selection studies, a kinetic profile was obtained for several BLMs for the first time since bleomycin was discovered in 1966. The disaccharide moiety of bleomycin has been previously shown to be a specific tumor cell targeting element comprised of L-gulose-D-mannose, especially between MCF-7 (breast cancer cells) and MCF-10A ("normal" breast cells). This phenomenon was further investigated via fluorescence microscopy using multiple cancerous cell lines with matched "normal" counterparts and is fully described in Chapter 4. / Dissertation/Thesis / Ph.D. Chemistry 2013

Submitted by Irene Nascimento (irene.kessia@ufpe.br) on 2017-02-01T18:32:19Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) DM Henrique Patriota Alves.pdf: 2961953 bytes, checksum: cd856b581753170ffb1c56ff445144f8 (MD5) / Made available in DSpace on 2017-02-01T18:32:19Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) DM Henrique Patriota Alves.pdf: 2961953 bytes, checksum: cd856b581753170ffb1c56ff445144f8 (MD5) Previous issue date: 2016-07-22 / CNPQ / Esta dissertação apresenta uma modelagem computacional da dinâmica de rugosidade de superfície gerada durante o processo de corrosão de um elemento transdutor metálico do sensor à fibra óptica. Tal modelagem é implementada num software dedicado de simulação multifísica que faz uso do Método dos Elementos Finitos. Considerando que a rugosidade de superfície pode ser definida por geometria fractal, que pode ser complexa, é proposta nesta dissertação uma forma alternativa e simples para modelar a superfície rugosa e a sua dinâmica sob corrosão. Para a modelagem computacional, é definida uma função periódica, chamada de função rugosidade, onde seus parâmetros são ajustados com dados experimentais do processo de corrosão. Os resultados da simulação computacional são comparados com um modelo analítico, que faz uso das equações de Fresnel. Nos resultados da simulação, é observado o acoplamento do sinal óptico na superfície rugosa do filme metálico. Esse acoplamento observado é explicado pelo fenômeno de Ressonância de Plásmon de Superfície. A modelagem proposta nesta dissertação apresenta excelente ajuste aos resultados experimentais. / This dissertation presents a computer modeling of the surface roughness dynamics generated during the corrosion process of a metallic element transducer of the fiber-optic sensor. This modeling is implemented in dedicated software that uses the Finite Element Method. Since the surface roughness can be defined by the fractal geometry, which can be complex, it is proposed in this dissertation an alternative and simple way to model the surface roughness and its dynamics under corrosion. The proposed modeling uses a roughness function that is defined by a periodic function, where their parameters are obtained from experimental data of the corrosion process. The computer simulation results are compared to an analytical model, which uses the Fresnel’s equations. In the simulation results, it is observed the optical signal coupling with the rough surface of the metallic film. This observed coupling is explained by the phenomenon of Surface Plasmon Resonance. The proposed modeling and simulations presents excellent fitting to the experimental results.

Orientador: Lauro Tatsuo Kubota / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-07T10:16:36Z (GMT). No. of bitstreams: 1 Damos_FlavioSantos_D.pdf: 8044516 bytes, checksum: a3443f4130ad6150c52dfa20c571bb04 (MD5) Previous issue date: 2006 / Resumo: O presente trabalho descreve as aplicações da ressonância de plásmon de superfície (surface plasmon resonance-SPR) e da microbalança de cristal de quartzo (quartz crystal microbalance-QCM) na investigação de processos interfaciais, visando o melhor entendimento e aplicação dos sistemas investigados bem como o estabelecimento das aplicações da técnica SPR aliada à eletroquímica. Neste sentido são apresentadas investigações do comportamento óptico-eletroquímico da molécula de azul de metileno (sistema 1), polímeros condutores (sistema 2) e monocamadas auto-organizadas (sistema 3). A escolha de tais sistemas, embora distintos, tem a finalidade de exploração ampla da técnica SPR na investigação de processos superficiais e interfaciais. O uso da técnica SPR na investigação do sistema 1 mostra a sua aplicabilidade no monitoramento do intumescimento de filmes em dimensões nanométricas e a investigação de processos adsortivos e difusionais com elevada sensibilidade. Assim sendo, a técnica SPR foi aplicada na investigação de processos de formação de filmes finos de polímeros condutores, bem como os processos de dopagem destes filmes. Neste sentido, foi investigada a eletropolimerização do pirrol e da polianilina bem como o efeito de dopantes aniônicos sobre as propriedades ópticas e eletroquímicas destes materiais. As medidas ópticas obtidas foram correlacionadas aos processos de dopagem e desdopagem dos filmes confeccionados mediante um estudo comparativo destes processos por QCM tendo em vista a consolidação da mesma na investigação de tais processos. Por fim, com o propósito de explorar a sensibilidade da técnica SPR a sistemas de dimensões sub-nanométricas, foram investigadas monocamadas auto-organizadas de ácido 11-mercapto-undecanóico e mono(6-deoxi-6-mercapto)-b-ciclodextrina. Neste sentido, foram determinadas a espessura e a constante dielétrica destes filmes, assim como a cinética de adsorção destes empregando um modelo de adsorção fundamentado na adsorção, desorção e re-arranjo molecular / Abstract: The present work describes the applications of surface plasmon resonance (SPR) and quartz crystal microbalance (QCM) in the investigation of interface processes in the attempt to improve the understanding and application of the investigated systems as well as the establishment of the applications of the SPR allied with electrochemical techniques. In this sense, are presented the investigation of the electrochemical behavior of the methylene blue molecule (system 1), conducting polymers (system 2) and self-assembled monolayers (system 3). The selection of these systems, although distinct, has a focus on the exploration of the SPR technique in the investigation of surface and interface processes. The use of SPR technique in the investigation of the system 1 shows its applicability in the monitoring of swelling of films in nanometric size as well as the investigation of adsorptive and diffusional processes with high sensitivity. Thus, SPR was applied in the investigation of construction of thin conducting polymer films as well as its doping processes. In this sense, were investigated pyrrole and aniline electropolymerization as well as the effects of anionic dopants on its optical and electrochemical properties. The optical measurements were correlated with the doping and dedoping processes of the films by means of a comparative study of these processes by QCM due to the better establishment of this technique in the investigation of these processes. Finally, with the purpose of explore the sensitivity of the SPR technique in sub-nanometric size systems, the SPR technique was applied in the investigation of selfassembled monolayers of 11-mercapto-undecanoic acid and mono(6-deoxy-6-mercapto)-b- cyclodextrin. In this sense, were determined the thickness and dielectric constant of these films as well as the adsorption kinetic by using a kinetic model based on adsorption, desorption and re-arrangement of molecules / Doutorado / Físico-Química / Mestre em Química