This thesis investigates the use of engineered DNA to program fusion and aggregation behaviors of artificial cells, mimicking biological cells and their important functions. To achieve this goal, we construct synthetic cells from engineered lipids and DNA to recognize and process intercellular signals.<div><br></div><div>Cell fusion is regulated by snap receptor (SNARE) proteins in mammalian cells. The zippering of SNARE proteins exerts forces to the adjacent cell membrane and induces membrane fusion. The hybridization of membrane anchored DNA can induce fusion in a similar way. The advantage of using DNA as a fusion signal is that oligonucleotides are much easier to engineer and control. In this study, we construct two types of small vesicles decorated with DNA oligonucleotides and demonstrate their fusion using programmable DNA base-pairing. Fluorescent probes are used to measure fusion events. The experiment advances our understanding of the dynamic vesicle fusion behavior.<br></div><div><br></div><div>Cell aggregation is a complex behavior that is closely associated to the differentiation, migration, and viability of biological cells. An effort to create synthetic analogs could lead to considerable advances in cell physiology and biophysics. Rendering and modulating such a dynamic artificial cell system require mechanisms for receiving, transducing, and transmitting intercellular signals, yet effective tools are limited at present. Here we construct synthetic cells and show their programmable aggregation behaviors using DNA oligonucleotides as a signaling molecule. The synthetic cells have transmembrane DNA origami that are used to recognize and process intercellular signals. We demonstrate that multiple small vesicles aggregate onto a giant vesicle after a transduction of external DNA signals by an intracellular enzyme, and that the small vesicles dissociate when receiving ‘release’ signals.<br></div><div><br></div><div>We envision that this thesis will provide a new platform for building programmable synthetic protocells capable of chemical communication and coordination. <br></div>

Thesis (Ph. D.)--Rutgers University, 2010. / "Graduate Program in Chemistry and Chemical Biology." Includes bibliographical references (p. 153-165).

Red blood cells (RBCs) are the most abundant cells in human blood, representing 40 to 45% of the blood volume (hematocrit). These cells have the particular ability to deform and bridge together to form aggregates under very low shear rates. The theory and mechanics behind aggregation are, however, not yet completely understood. The purpose of this work is to provide a novel method to analyze, understand and mimic blood behaviour in microcirculation. The main objective is to develop a methodology to quantify and characterize RBC aggregates and hence enhance the current understanding of the non-Newtonian behaviour of blood at the microscale. For this purpose, suspensions of porcine blood and human blood are tested in vitro in a Poly-di-methylsiloxane (PDMS) microchannel to characterize RBC aggregates within these two types of blood. These microchannels are fabricated using standard photolithography methods. Experiments are performed using a micro Particle Image Velocimetry ( PIV) system for shear rate measurements coupled with a high speed camera for the flow visualization. Corresponding numerical simulations are conducted using a research Computational Fluid Dynamic (CFD) solver, Nek5000, based on the spectral element method solution to the incompressible non-Newtonian Navier-Stokes equations. RBC aggregate sizes are quantified in controlled and measurable shear rate environments for 5, 10 and 15% hematocrit. Aggregate sizes are determined using image processing techniques. Velocity fields of the blood flow are measured experimentally and compared to numerical simulations using simple non-Newtonian models (Power law and Carreau models). This work establishes for the first time a relationship between RBC aggregate sizes and corresponding shear rates in a microfluidic environment as well as one between RBC aggregate sizes and apparent blood viscosity at body temperature in a microfluidic controlled environment. The results of the investigation can be used to help develop new numerical models for non-Newtonian blood flow, provide a better understanding of the mechanics of RBC aggregation and help determine aggregate behaviour in clinical settings such as for degenerative diseases like diabetes and heart disease.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第18267号 / 工博第3859号 / 新制||工||1592(附属図書館) / 31125 / 京都大学大学院工学研究科機械理工学専攻 / (主査)教授 富田 直秀, 教授 安達 泰治, 教授 井手 亜里 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

Plant derived natural products represent some of the most effective anti-cancer and anti-infectious disease pharmaceuticals available today. However, uncertainty regarding the feasibility of commercial supply due to the limited availability of many plants in nature has resulted in a dramatic reduction in the use of natural products as leads in modern drug discovery. Plant cell suspension culture, consisting of dedifferentiated plant cells grown in vitro and amenable to large scale industrial biotechnology processes, is a production alternative which promises renewable and economical supply of these important drugs. The widespread application of this technology is limited by low product yields, slow growth rates, challenges in scale-up, and above all, variability in these properties, which is poorly understood. Plant cells grow as aggregates in suspension cultures ranging from two to thousands of cells (less than 100 micron to well over 2 mm). Aggregates have long been identified as an important feature of plant cell culture systems, as they create microenvironments for individual cells with respect to nutrient limitations, cell-cell signaling, and applied shear in the in vitro environment. Despite its purported significance, a rigorous engineering analysis of aggregation has remained elusive. In this thesis, aggregation was characterized, analyzed, and modeled in Taxus suspension cultures, which produce the anti-cancer drug paclitaxel. A technique was developed to reliably and routinely measure aggregate size using a Coulter counter. The analysis of aggregate size as a process variable was then used to evaluate the effect of aggregation on process performance, and the analysis of single cells isolated from different sized aggregates was used to understand the effect of aggregation on cellular metabolism and heterogeneity. Process characterization studies indicated that aggregate size changed over a batch cycle as well as from batch to batch, so a population balance equation model was developed to describe and predict these changes in the aggregate size distribution. This multi-scale engineering approach towards understanding plant cell aggregation serves as an important step in the development of rational strategies aimed at controlling the process variability which has heretofore limited the application of plant cell culture technology.

Orientador: Alessandra Alves de Souza / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-12T18:36:53Z (GMT). No. of bitstreams: 1 Caserta_Raquel_M.pdf: 8932792 bytes, checksum: 642a7e654340f17e79b37b6fa4a560cc (MD5) Previous issue date: 2008 / Resumo: É inquestionável a importância da participação da citricultura na economia brasileira. O Brasil é o maior exportador de suco concentrado do mundo. Em 2007 as exportações brasileiras quase alcançaram 400 milhões de caixas de laranja, retrato de uma cultura que gera uma diversidade enorme de empregos diretos e indiretos, movimentando também a indústria de insumos. O estado de São Paulo tem maior destaque nessa produção e no final dos anos 80 foi severamente prejudicado pela Clorose Variegada dos Citros (CVC), uma doença que acarreta danos da ordem de milhões de dólares por diminuir o tamanho dos frutos e, por conseqüência, a quantidade de suco produzido. Foi comprovado que a bactéria causadora da CVC é a Xylella fastidiosa, um fitopatógeno de crescimento limitado ao xilema. Devido a importância da citricultura para o estado de São Paulo, a X. fastidiosa teve seu genoma completo seqüenciado e foram encontrados diversos genes relacionados a adesão, muitos deles similares a patógenos de humanos e animais. Isso sugeriu que a adesão e a formação do biofilme fossem fatores essenciais para a sobrevivência da bactéria na planta. Essa hipótese é reforçada pelo fato de plantas sintomáticas apresentarem colônias de bactérias aderidas nas paredes dos vasos do xilema. Trabalhos posteriores comprovaram que sua colonização se dá pela formação de um biofilme que ocasiona o bloqueio dos vasos, dificultando a eficiência do transporte de água e seiva pela planta. Nesse contexto, o estudo da participação de proteínas de adesão, sejam elas fimbriais ou afimbriais, é fundamental para o entendimento da formação e estrutura do biofilme. Por apresentarem funções distintas, adesinas fimbriais e afimbriais são expressas em momentos diferentes durante a formação do biofilme. Diante do exposto acima, o objetivo desse trabalho foi monitorar a expressão de duas adesinas fimbriais e duas adesinas afimbriais de X. fastidiosa envolvidas com a formação do biofilme in vitro. Para tal, foram realizados Western blot e microscopia de fluorescência utilizando anticorpos desenvolvidos contra as proteínas alvo. Os resultados revelaram que adesinas fimbriais se expressam preferencialmente nas fases iniciais do bioflme, enquanto que adesinas afimbriais estão expressas nas fases mais tardias, quando o biofilme já apresenta traços de agregação celular. Esse padrão de expressão sugere que a adesão inicial da bactéria ao substrato seja mediada por proteínas fimbriais e a adesão célula a célula seja função de proteínas afimbriais. Além disso, uma maior ou menor quantidade de cada proteína se encontra expressa em todas as fases o biofilme, sugerindo haver uma regulação de expressão que resulta em interação biológica entre elas, a fim de manter a estabilidade e estruturação do biofilme. Com o objetivo de monitorar a expressão dessas adesinas in vivo, foram analisadas também secções ultrafinas de pecíolos de vinca, hibisco e citros infectados e apresentando sintomas da doença. Em todas as análises foi possível detectar a presença das proteínas alvo, comprovando que elas são necessárias para o processo de infecção da planta pela bactéria. Os resultados aqui apresentados demonstram que proteínas fimbriais e afimbriais, assim como em patógenos de humanos, são necessárias para a formação do biofilme de X. fastidiosa. Este é o único fitopatógeno cujo mecanismo de patogenicidade é a formação de um biofilme. Neste sentido, os resultados aqui apresentados são importantes no auxílio de possíveis controles de doenças formadas por biofilmes, uma vez que o tempo de expressão de cada adesina foi determinado, elas poderiam ser neutralizadas antes de desempenharem suas funções, quebrando a estabilidade do biofilme através da interrupção da interação entre as proteínas / Abstract: The importance of citriculture in Brazilian's economy is unquestionable. Brazil is the major exporter of concentrate juice in the world. In 2007, Brazilian exportations of orange almost reached 400 million boxes, reflecting the importance of a product that generates an enormous diversity of direct and indirect jobs, even helping the insums industry. In Brazil, São Paulo state has a great prominence in orange production. In the 80's, the citrus fields were severely harmed by Citrus Variegated Chlorosis (CVC), a disease that causes losses of million dollars since it affects the fruit size and, consequently, juice production. It was proved that the Xylella fastidiosa, a phytopathogen that grows limited to the xylem vessels, is the causal agent of CVC. Due to the importance of citriculture in the São Paulo state, the genome of X. fastidiosa was sequenced and there were found many genes related to adhesion, some of them similar to human and animal pathogens. This fact suggested that adhesion and biofilm formation were essential for the survey of the bacteria within the plant. This hypothesis is supported by the fact that symptomatic plants have colonies of bacteria adhered to the walls in xylem vessels. Subsequent works demonstrated that the colonization occurs through the formation of a biofilm that blocks the vessels, reducing the efficiency of water and sap transportation. In this context, the study of the role of the fimbrial or afimbrial adhesion proteins is fundamental to the elucidation of the biofilm structure and formation. These adhesins show different functions, and because of that they are not expressed at the same time during biofilm formation. In face of what was shown above, the aim of this work was to monitor the expression of two fimbrial and two non fimbrial adhesins involved in biofilm formation in vitro. Western blot and fluorescence microscopy using polyclonal antibodies developed against the target proteins were performed, and the results revealed that fimbrial adhesins are expressed preferentially at the initial phases of biofilm formation, while non fimbrial adhesins are expressed at the late phases, when the biofilm already presents cellular aggregation traits. This expression pattern suggests that the initial adhesion of the bacteria to the substrate is mediated by fimbrial adhesins and that the function of cell to cell adhesion is performed by non fimbrial adhesins. Besides, each protein studied is found more or less to be expressed during all stages of biofilm development, suggesting the existence of a regulatory mechanism that results in a biological interaction between these proteins, in order to keep the stability and structure of the biofilm. In order to accompany the expression of these adhesins in vivo, ultra thin sections of petioles of periwinkle, hibiscus and citrus infected by X. fastidiosa and presenting symptoms were prepared. All the sections showed the presence of the target proteins, suggesting that they are necessary to the infectious process of the plants. The results demonstrated that fimbrial and non fimbrial proteins, as well as in human pathogens, are necessary for the biofilm formation by X. fastidiosa. This is the only phytopathogen which requires the formation of a biofilm to cause the disease. In this way, the results obtained in this work may contribute with the development of possible approaches to control diseases caused by biofilm formation, once the expression profile of each adhesin was determined. In a possible attempt to prevent the symptoms, the interaction between these adhesins could be blocked, breaking the stability of biofilm / Mestrado / Genetica de Microorganismos / Mestre em Genética e Biologia Molecular

A hallmark feature of Dictyostelium development is the establishment and maintenance of precise cell-type proportions. In the case of D. discoideum, roughly 20% of the cells that aggregate form the stalk while the remaining 80% form the spores. In order to identify genes involved in cell-type proportioning Jaiswal et al. (2006) carried out random insertional mutagenesis (REMI) of the D. discoideum genome. This led to the identification of a novel gene, which was named trishanku (triA). A knock-out of triA did not show any defects during growth and early development but multiple defects later during development. To understand the reasons for the multiple developmental defects in the absence of triA, I looked at the genomic organization and the pattern of expression of the triA gene. In silico analysis points to the presence of more than one consensus D. discoideum promoter sequence upstream to exons1 and 2, raising the possibility that the triA gene could code for more than one transcript. Northern blot analysis confirms this prediction and provides evidence for the presence of two transcripts: triA1-2-3 (~ 2.9 kb, containing exons 1+2+3) and triA2-3 (~ 2 kb, containing exons 2+3). Both transcripts have exons 2 and 3 in common. In triA- cells, the REMI cassette is inserted in exon 2, which is common to both transcripts; thus, the absence of triA results in the lack of both. The transcripts are absent in vegetative cells but expressed during development. triA2-3 is expressed earlier, by 3h, while triA1-2-3 is expressed later, by 9h, and both remain till the end of development. triA2-3 and triA1-2-3 are differentially regulated by different aspects of the extracellular environment which include mode of development of cells (solid substratum versus shaken suspension), the presence of a high level of extracellular cAMP and formation of stable cell-cell contacts. The expression of triA2-3 and triA1-2-3 in triA- cells, one at a time under a constitutive promoter (Actin15 promoter), suggests that the two transcripts have both specific as well as overlapping functions in the cell. The triA2-3 transcript can specifically restore spore forming efficiency and stalk thickness, while the triA1-2-3 transcript can rescue the stream break up defect. Both the transcripts can rescue the sub-terminal position of the sorus, spore shape and spore viability. To address the question of stream break-up during mid to late aggregation in triA- cells, I have looked at the cell adhesion profile of triA- cells and compared it with the wild type (Ax2). triA- cells show transient disaggregation in buffer and a 2h delay in agglutination in presence of buffer with 10mM EDTA. This aberrant cell adhesion profile seen in triA- cells is in accordance with the expression pattern of genes encoding known cell adhesion molecules. triA- cells also overproduce an extracellular factor which significantly decreases the aggregate size of both Ax2 and triA-. The nature of the extracellular factor overproduced by in triA- cells is currently unknown, but it is not the same as cell-counting factor which is overproduced by smlA null cells. To look at the mis-expression of cell type-specific genes, I have monitored the movement of prestalk cells into the prespore region and vice versa in both Ax2 and triA- slugs. My studies show that there is extensive movement of prestalk cells into the prespore region and of prespore cells into the prestalk region in triA- slugs, which is absent in Ax2 slugs. Also, cells that move into the ‘wrong’ region show a change their cell fate (transdifferentiate) appropriate to the new location; whether transdifferentiation precedes or succeeds cell movement is not yet clear. Transdifferentiation is observed to a certain extent in Ax2 slugs, but only after prolonged migration; triA- slugs show enhanced transdifferentiation even in the absence of migration. To find out the possible reason(s) for the formation of a sub-terminal spore mass in the absence of triA, I have checked whether the defect lies in the ability of the prespore cells to rise up the stalk or in the ability of the upper cup (cells present above the spore mass contributed by a subset of prestalk cells and anterior like-cells) to pull the spore mass to the top. To see which of the two reasons could be responsible for the formation of a sub-terminal spore mass in triA-, I carried out transplantation experiments where the anterior one-fourth region of an Ax2 or triA- slug is grafted to the posterior four-fifth region of a triA- or Ax2 slug and the morphology of the fruiting body is observed. My studies show that the sub-terminal position of the spore mass in triA- is not due to an inability of the prespore cells to rise to the top but to a defect in the upper cup. The upper cup in triA- remains motile but is unable to remain attached to the prespore mass during culmination. It detaches, rises up the stalk and is present at the tip of the stalk. Mixing a minority of triA- cells (20%) with an excess of Ax2 (80%) results in an upper up formed by Ax2 alone. In this situation, the wild type upper cup is able to lift the triA- prespore mass to the top. Thus, the presence of triA (a prespore-specific gene) is essential for the proper functioning of the upper cup cells (which belong to the prestalk class) in order to enable prespore cells to ascend to the top of the stalk.

L'athérosclérose est une maladie cardiovasculaire complexe affectant la paroi artérielle où le développement et la progression de la plaque sont fortement favorisés par une inflammation chronique. L'instabilité de la plaque carotidienne peut conduire à de potentiels évènements ischémiques majeurs tels que l'accident vasculaire cérébral (AVC) dont le caractère imprévisible rend la prévention primaire très compliquée. Ainsi, il n'existe pas à l'heure actuelle de biomarqueurs prédictifs efficaces de la rupture de plaque. Néanmoins, il est maintenant clairement établi que l'hémorragie intraplaque (IPH), la néovascularisation et l'accumulation excessive de macrophages sont les principaux facteurs d'instabilité de la plaque. Sur la base de travaux précédents, l'objectif de cette thèse était d'évaluer de manière indépendante les effets de l'activité physique (AP) et de la sédentarité, premièrement sur les paramètres histologiques d'instabilité de plaque, et deuxièmement, sur les facteurs de risque secondaires de l'athérosclérose, que sont l'inflammation, le stress oxydant et le profil hémorhéologique de patients asymptomatiques à risque d'AVC traités chirurgicalement. La 1ère étude a montré que l'AP régulière était associée à une prévalence d'IPH diminuée, et était l'unique facteur protecteur de l'IPH. Cette étude a également suggéré un effet bénéfique de l'AP sur le stress oxydant, ainsi que sur l'accumulation de macrophages. Dans une 2ème étude, nous avons caractérisé l'état fonctionnel de protéines potentiellement impliquées dans les dysfonctions du système immunitaire, et l'implication des cellules inflammatoires dans ces mécanismes. Nous avons alors identifié une cytokine pro-inflammatoire jouant un rôle déterminant dans les processus inflammatoires de déstabilisation de plaque. L'étude 3 nous a permis de caractériser l'effet du niveau d'AP sur la réponse monocytaire chez des patients avec plaque d'athérosclérose, et d'identifier une chimiokine qui pourrait avoir un rôle dans la modulation de la réponse monocytaire par l'AP. Enfin, la 4ème étude démontre l'altération de paramètres hémorhéologiques chez des patients atteints de maladie carotidienne sévère, et comment l'AP permet de limiter cette altération via la diminution de l'agrégation érythrocytaire. Ce travail de thèse apporte des informations quant à la pratique de l'AP dans la prévention primaire de l'athérosclérose. Des études complémentaires seront toutefois nécessaires afin de confirmer ces résultats, en proposant notamment une approche interventionnelle en activité physique / Atherosclerosis is a complex cardiovascular disease that affects the arterial wall where plaque development and progression are severely promoted by chronic inflammation. Carotid plaque destabilization could lead to potential major ischemic events such stroke which is still unpredictable, making primary prevention very complex. Thus, there is still currently no suitable predictive biomarker of plaque rupture. Nevertheless, it is now clearly established that intraplaque hemorrhage (IPH), neovascularization and excessive macrophage accumulation are the three main risk factors of plaque instability. Based on previous studies, the aim of this work was to evaluate independently the impact of physical activity (PA) and sedentary behavior, first on histological parameters of plaque instability, and secondly on secondary risk factors of atherosclerosis, such as inflammation, oxidative stress and hemorheological profile of asymptomatic patients at high-risk of stroke who underwent endarterectomy surgery. The first study shows that regular PA was associated to a decreased occurrence of IPH, and was the only protective factor for IPH. This study also suggested a beneficial effect of PA on macrophage accumulation as well as on oxidative stress. Then, in the 2nd study, we have characterized the functional state of proteins potentially implicated in immune system dysfunctions, and the implication of inflammatory cells in these mechanisms. We have identified a pro-inflammatory cytokine as a key driver of disrupting inflammatory process of plaque. In the same way, we have characterized in the 3rd study, the effect of PA on the monocytic response in atherosclerosis patients, and identified a chemokine associated that could explain the modulation of this monocytic response by PA. Finally, the 4th study demonstrates the hemorheological parameters alteration in carotid artery disease patients, and how PA could limit this alteration via red blood cell aggregation. This PhD thesis provided information regarding regular PA in primary prevention of atherosclerosis. However, additional studies are required to confirm these results, using in particular PA interventional approach

Nous avons étudié les marqueurs hémorhéologiques, hématologiques et biochimiques chez des sujets drépanocytaires homozygotes SS (HbS/HbS) et hétérozygotes composites SC (HbS/HbC) dans deux cohortes, pédiatriques et adultes, de patients drépanocytaires, et ce, à travers 7 complications récurrentes de la drépanocytose : 2 appartenant au profil hémolytique (l’ulcère de jambes et la glomérulopathie) et 5 appartenant au phénotype visqueux/vaso-occlusif (l’hypertension artérielle, le syndrome thoracique aigu (STA), la crise vaso-occlusive (CVO), la rétinopathie et l’ostéonécrose). Nous avons montré que : 1) une viscosité sanguine et une déformabilité érythrocytaire élevées sont des facteurs de risques de CVO chez les enfants homozygotes ; 2) Une viscosité sanguine élevée est associée à une hypertension artérielle systémique relative chez des adultes SS ; 3) les enfants SC présente une fonction vasculaire mieux préservée que les enfants SS pour faire face à une augmentation de la viscosité sanguine ; 4) les patients adultes SS avec une ostéonécrose présentent une déformabilité érythrocytaire plus élevée que les patients sans ostéonécrose ; 5) une viscosité sanguine élevée est associée à la présence d’une rétinopathie chez les adultes SC mais pas chez les SS ; 6) les patients adultes SS présentant une glomérulopathie ont un taux d’hémolyse élevé, une déformabilité érythrocytaire réduite et des agrégats érythrocytaires très robustes ; 7) les patients adultes SS avec des ulcères de jambes récurrents ont un taux d’hémolyse accru et une déformabilité érythrocytaire réduite. De plus, nos travaux confirment que l’-thalassémie module les propriétés de déformabilité érythrocytaire, mais montrent pour la première fois qu’elle module aussi les propriétés d’agrégation érythrocytaire, et notamment la force des agrégats érythrocytaires. En conclusion, ces travaux permettent de préciser le rôle de la rhéologie sanguine dans un certain nombre de complications de la drépanocytose et d’enrichir le modèle préexistant divisant les complications de la drépanocytose selon 2 phénotypes : hémolytique versus visqueux/vaso-occlusif. Nous montrons pour la première fois que le phénotype hémolytique est caractérisé aussi par des anomalies de la rhéologie du globule rouge : rigidité accrue et agrégats érythrocytaire robustes. / Hemorheological, hemathological, and biochemical marquers of patients with sickle cell anemia (SS) and patients with sickle cell SC disease (SC) were studied in 2 cohorts: children and adults. We focused on 7 recurrent complications: 5 belonging to the viscosity/vaso-occlusion phenotype (systemic hypertension, acute chest syndrome (ACS), vaso-occlusive crisis (VOC), retinopathy and osteonecrosis) and 2 belonging to the hemolytic phenotype (leg ulcer and glomerulopathy). Our results show that 1) high viscosity is associated with increased risk for VOC in SS children; 2) blood viscosity is increased in SS adults with systemic relative hypertension; 3) SC children have preserved vascular function compared to SS children; 4) SS adults with osteonecrosis are characterized by higher red blood cell (RBC) deformability than SS adults without osteonecrosis; 5) high blood viscosity is associated with retinopathy in SC adults but not in SS adults; 6) SS adults affected by glomerulopathy have high hemolytic rate, low RBC deformability and increased RBC aggregates strenght; 7) SS adults with recurrent leg ulcers have high hemolytic rate and reduced RBC deformability. Moreover, our studies shows that alpha-thalassemia modulate RBC deformability and RBC aggregation properties. In conclusion, this work shows for the first time that the hemolytic phenotype is characterized by an abnormal RBC rheology which may play a role in several sickle cell complications.

Alzheimer's disease (AD) is characterised by a series of biomolecular aggregation events, which include the formation of neurotoxic protein structures composed of the β-amyloid (Aβ) peptide. In this thesis, fluorescence self-quenching (FSQ) between fluorescently-labelled peptides is introduced as a strategy for detecting and characterizing Aβ aggregates in solution, and for overcoming limitations associated with conventional methods. Using a combination of steady-state, picosecond time-resolved fluorescence and transmission electron microscopy, the fluorescence response of HiLyte Fluor 555-labelled Aβ peptides is characterised to demonstrate that Aβ self-assembly organizes the covalently attached probes in close proximity to trigger the self-quenching sensing process over a broad range of conditions. Importantly, N-terminal tagging of β-amyloid peptides is shown to not alter the self-assembly kinetics or the resulting aggregated structures. When performed in Förster resonance energy transfer (FRET) format, this method becomes a ratiometric platform to gain insights into amyloid structure and for standardizing in vitro studies of amyloid self-assembly. The ability of FSQ-based methods to monitor the inhibition of Aβ aggregation by model test compounds including the small heat shock protein (Hsp), the amyloid-binding alcohol dehydrogenase protein (ABAD) and bovine serum albumin (BSA) is also demonstrated. Given that Aβ is formed within the cell membrane and is known to induce its disruption, sophisticated single-molecule fluorescence spectroscopy methods were developed to quantify membrane dynamics induced by the presence of disrupting agents, such as Aβ and detergents. The solubilisation dynamics of single liposomes induced by the non-ionic surfactant Triton-X 100 (TX-100) were studied in real-time. Using this approach, the swelling and permeabilization steps of the solubilisation process were unambiguously separated within single FRET trajectories, and their kinetic details as a function of Triton-X 100 and presence of cholesterol within the membrane structure were examined. Finally, single-molecule stepwise-photobleaching techniques were employed to study the effect of Aβ oligomers interacting with supported-lipid bilayers, establishing a platform from which to investigate how the presence of a membrane layer affects Aβ oligomerization at the level of individual molecules. Overall, the fluorescence-based strategies for amyloid- and liposome-sensing presented in this work bridges the gap between current morphology-specific techniques and highly-specialized single-molecule methods to provide a biophysical toolbox to investigate the changes in structure, size and molecular interactions accompanying the amyloid aggregation pathway and for the screening of novel therapeutic and diagnostic agents.