The self-assembly of amyloidogenic proteins to form cytotoxic species that give rise to brain deterioration underlies numerous neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. Increasing evidence indicates that it is the rare, low-molecular-weight species (oligomers) rather than the more abundant high-molecular-weight fibrils of certain proteins that are the most cytotoxic in several neurodegenerative diseases. However, these species have proven difficult to study using traditional methods due to their transient nature and the heterogeneity of aggregation mixtures. In this thesis, I describe my work to develop advanced methods where I combine single-molecule and ensemble fluorescence techniques with microfluidic strategies to enable the study of protein aggregation, spanning small, transient oligomers to large, insoluble aggregates. In Chapter 1 I give an overview of the biological context and relevance of this work, including the background of neurodegenerative disease, amyloidogenic aggregation and key proteins involved. I then briefly review fluorescence microscopy techniques and the field of microfluidics. In Chapter 2 I describe how complex microfluidics can be integrated with single-molecule confocal techniques to provide a highly sensitive method to continuously probe protein aggregation in vitro. I show, for the first time, that the dilution of aggregating mixtures may be automated, by up to five orders of magnitude, down to the picomolar concentrations suitable for single-molecule measurements. By incorporating this microfluidic dilution device I greatly improve the temporal resolution of the technique and facilitate the observation of more transient species through the ability to rapidly dilute and take fluorescence measurements of samples. In Chapter 3 I overcome the need for in situ labels to monitor amyloidogenic aggregation using single-molecule confocal microscopy. I describe my work to adapt the single-molecule confocal technique to achieve the ultrasensitive detection of individual aggregate species under flow without covalently-attached labels. I have demonstrated the ability of this new method to monitor the aggregation of label-free amyloidogenic proteins using extrinsic labels ex-aggregation, opening the way for biological samples to be probed in a high-throughput manner. In Chapter 4 I describe my work to combine the high precision of confocal microscopy with a microfluidic device developed to directly characterise the sizes and interactions of biomolecules in the continuous phase. By monitoring the spatial and temporal mass transport on the micron scale, the diffusion coefficient, and thus hydrodynamic radius, of species may be determined. The technique delivers much greater sensitivity for size quantification, allowing scarce and other challenging samples to be characterised, and provides significant steps towards accurate sizing for single-molecule aggregation experiments under flow. In Chapter 5 I describe my work to determine the microscopic driving force for the spatial propagation of amyloid-beta. The epifluorescence instrument I built has enabled the proliferation of aggregate species to be monitored over a macro distance on a timescale of minutes. This has greatly improved the scope of the experimental data attained, which will be used in conjunction with Monte Carlo simulations to deliver a model for the propagation of amyloid-beta in vitro. Together this thesis represents my work developing the above novel fluorescence techniques to improve their temporal and size resolution, sensitivity and adaptability to study highly complex and fundamental protein aggregation linked to neurodegenerative disease.

Quantitative three dimensional maps of cellular structure, activity and function provide the key to answering many prevalent questions in modern biological research. Fluorescence microscopy has emerged as an indispensable tool in generating such maps, but common techniques are limited by fundamental physical constraints which render them incapable of simultaneously achieving high spatial and temporal resolution. This thesis will describe the development of novel microscopy techniques and complementary computational tools capable of addressing some of the aforementioned limitations of fluorescence microscopy and further outline their application in providing novel biological insights. The first section details the design of a light sheet microscope capable of high-throughput imaging of cleared, macroscopic samples with cellular resolution. In light sheet microscopy, the combination of spatially confined illumination with widefield detection enables multi-megapixel acquisition in a single camera exposure. The corresponding increase in acquisition speed enables systems level biological studies to be performed. The ability of this microscope to perform rapid, high-resolution imaging of intact samples is demonstrated by its application in a project which established a niche and hierarchy for stem cells in the adult nervous system. Light sheet microscopy achieves fast volumetric imaging rates, but the two dimensional nature of each measurement results in an inevitable lag between acquisition of the initial and final planes. The second section of this thesis describes the development and optimization of a light field microscope which captures volumetric information in a snapshot. Light field microscopy is a computational technique and images are reconstructed from raw data. Both the fidelity of computed volumes and the efficiency of the algorithms are strongly dependent on the quality of the rectification. A highly accurate, automated procedure is presented in this section. Light field reconstruction techniques are investigated and compared and the results are used to inform the re-design of the microscope. The new optical configuration is demonstrated to minimize the long-object problem. In the final section of the thesis, the spatial resolution limits of light field microscopy are explored using a combination of simulations and experiments. It is shown that light field microscopy is capable of localizing point sources over a large depth of field with high axial and lateral precision. Notably, this work paves the way towards frame rate limited super resolution localization microscopy with a depth of field larger than the thickness of a typical mammalian cell.

The aim of the work described in this thesis is to improve the understanding, implementation, and overall capabilities of structured illumination microscopy (SIM). SIM is a superresolution technique that excels in gentle live-cell volumetric imaging tasks. Many modalities of SIM were developed over the last decade that tailored SIM into the versatile and powerful technique that it is today. Nevertheless, the field of SIM continues to evolve and there is plenty of room for novel concepts. Specifically, in this thesis, a generalised framework for a theoretical description of SIM variants is introduced, the constraints of optical components for a flexible SIM system are discussed and the set-up is realised, the important aspect of deconvolution in SIM is highlighted and further developed, and finally novel SIM modalities introduced that improve its time-resolution, gentleness, and volumetric imaging capabilities. Based on the generalised theory, the computational steps for the extraction of superresolution information from SIM raw data are outlined and the essential concept of spatial frequency un-mixing explained for standard SIM as well as for multifocal SIM. Multifocal SIM hereby acts as a parallelised confocal as well as widefield technique and thus serves as link between the two modalities. Using this novel scheme deconvolution methods for SIM are then further developed to allow a holistic reconstruction procedure. Deconvolution is of great important in the SIM reconstruction process, and hence rigorous derivations of advanced deconvolution methods are provided and further developed to enable generalised ‘multi-image’ Richardson-Lucy deconvolution in SIM, called joint Richardson-Lucy deconvolution (jRL). This approach is demonstrated to robustly produce optically sectioned multifocal SIM images and, through the incorporation of a 3D imaging model, also volumetric standard SIM images within the jRL framework. For standard SIM this approach enabled acquisition speed doubling, because the recovery of superresolved images from a reduced number of raw frames through constrained jRL was made possible. The method is validated in silico and in vitro. For the study of yet faster moving samples deconvolution microscopy is found to be the method of choice. To enable optical sectioning, a key feature of SIM, in deconvolution microscopy, a new modality of optical sectioning microscopy is introduced that can be implemented as a single-shot technique. Via polarised excitation and detection in orthogonal directions in conjunction with structured illumination the theoretical framework is rigorously derived and validated.

Fluorescence based microscopy techniques have been extensively used in biological sciences. The most common approach is the steady-state fluorescence microscopy. Although the said approach is powerful, it often lacks sensitivity to detect several biochemical processes that may indicate relevant conditions of biological tissues. The fluorescence dynamics analysis not only brings intrinsic information about the tissue, but is also less sensitive to the medium scattering and absorption, and sometimes capable of distinguishing between fluorescent structures with indistinguishable spectra. The intrinsic fluorescence lifetime of biological tissues is usually affected by some clinical conditions, especially when those conditions cause or are correlated with metabolic modifications. Time-resolved spectroscopy techniques can be used to detect those modifications and may be used as a tool to improve the detection and diagnosis rate of such conditions. Fluorescence Lifetime Imaging Microscopy (FLIM) combines the temporal resolution and the microscopy concept, so fluorescence lifetime images can be generated. This technique has a great potential for clinical applications since it may be able to detected lesions and delineate its borders. However, FLIM usually demands a more sophisticated instrumentation than most techniques based on the steady-state approach, what creates a difficulty for moving such a system to a clinical setting. We report the assembly, characterization, validation, and clinical application of a multispectral FLIM system featuring a handheld probe composed of a laser scanning rigid endoscope. The assembled system uses a 355 nm short pulsed laser as excitation and has three spectral channels, targeting the emission of collagen, NADH, and FAD, which are important endogenous fluorophores. The system acquires images of 8.65 x 8.65 mm2 areas in ~ 2.4 s. MATLAB codes were written to process the images using a biexponential model and a modified phasor approach. In vivo validation measurements of tumors induced in mice were performed. The system was also validated with in vivo imaging of skin of healthy volunteers. The assembled FLIM system was moved to Hospital Amaral Carvalho, where we performed a pilot clinical study, in which different types of skin lesions were imaged in vivo in a clinical setting. A significant contrast was achieved on seborrheic keratosis, Bowen´s disease, and sclerodermiform basal cell carcinoma tumors. These results indicate the potential of this technique for clinical imaging of skin lesions. / Técnicas de microscopia baseadas em fluorescência têm sido extensamente utilizadas em ciências biológicas. A abordagem mais comum se baseia na microscopia de fluorescência de estado estacionário. Apesar de poderosa, essa abordagem frequentemente não apresenta sensibilidade suficiente para detectar diversos processos bioquímicos que podem ser indicadores de relevantes problemas em tecidos biológicos. A análise da dinâmica da fluorescência não apenas trás informações intrínsecas sobre o tecido, mas também é menos sensível a espalhamento e absorção pelo meio, além de ser capaz de distinguir entre estruturas fluorescentes com espectros indistinguíveis em alguns casos. O tempo de vida intrínseco de tecidos biológicos é normalmente afetado por condições clínicas, especialmente quando estas condições causam ou são relacionadas a modificações metabólicas. As técnicas de espectroscopia resolvidas no tempo podem detectar essas modificações e podem ser utilizadas como uma ferramenta para melhorar a detecção e o diagnóstico dessas condições. A Microscopia de Tempo de Vida de Fluorescência (FLIM) combina a resolução temporal ao conceito de microscopia, de forma que imagens de tempos de vida de fluorescência podem ser gerados. Essa técnica tem um grande potencial para aplicações clínicas uma vez que ela pode ser capaz de detectar lesões e delinear suas bordas. No entanto, FLIM requer uma instrumentação muito mais sofisticada do que a maior parte das técnicas baseadas no estado estacionário, o que cria uma dificuldade para que tais sistemas possam ser levados a ambientes clínicos. Nós reportamos a montagem, caracterização, validação e aplicação clínica de um sistema FLIM multiespectral com uma sonda manual composta de um endoscópio rígido de varredura laser. O sistema montado utiliza um laser pulsado de 355 nm como fonte de excitação e conta com três canais espectrais, visando a emissão do colágeno, do NADH e do FAD, três importantes fluoróforos endógenos. O sistema é capaz de adquirir imagens de áreas de 8,65 x 8,65 mm2 em ~ 2,4 s. Códigos em MATLAB foram escritos para processar as imagens usando um modelo biexponencial e uma abordagem modificada dos fasores. Medidas in vivo de tumores induzidos em camundongos foram realizadas para validação do sistema. O sistema também foi validado com a realização de medidas in vivo da pele de voluntários sadios. O sistema montado foi levado ao Hospital Amaral Carvalho, onde realizamos um teste clínico piloto no qual diferentes tipos de lesões de pele foram imageados in vivo em um ambiente clínico. Um contraste significante foi alcançado em tumores de queratose seborreica, doença de Bowen e carcinoma basocelular esclerodermiforme. Esses resultados indicam o potencial desta técnica para o imageamento clínico de lesões de pele.

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The morphology, composition, and distribution of elements within nanocrystals are critical parameters which dictate the material's properties and performance in a diverse array of emerging applications. The (scanning) transmission electron microscope ((S)TEM) represents a powerful tool for probing the structure and chemistry of materials on the nanoscale. Understanding of the mechanisms by which nanocrystals grow, transform, and degrade is vital if we are to develop rational synthesis routes and hence control the properties of the resulting materials. Electron microscopy represents a key tool in developing such an understanding. In situ techniques, where the material of interest is subjected to stimuli such as heat or a chemically reactive environment in the microscope, allow direct observation of dynamic transformations. Ex situ approaches, where multiple samples are prepared in the lab with the reaction parameters systematically altered, can also give important mechanistic insights. This thesis explores the use of both in situ and ex situ (S)TEM to gain insights into the growth and transformation of nanocrystals. Ex situ TEM is used to assess the structure of PbS nanocrystals in a polymer matrix, revealing new methods of morphological control through reaction temperature, precursor structures (appendix 4), and the processing of the polymer matrix (appendix 5). In situ techniques are used to observe the solution phase growth and shelling of nanocrystals (appendix 1) as well as the transformations of nanocrystals during heating in vacuum (appendices 2 and 3). The subjects of my in situ investigations are systems with heterogeneous distributions of elements. Historically, in situ electron microscope has been largely limited to imaging. However, to understand many dynamic transformations knowledge of changing elemental distributions is vital. For this reason, I have focused on the use of energy dispersive X-ray (EDX) spectroscopy to reveal changes in composition and elemental distributions during in situ experiments (appendices 1-3). This type of in situ elemental mapping is especially challenging for liquid-cell experiments, and my results represent the first report of EDX spectrum imaging for nanomaterials in liquid (appendix 1).

The aim of this work was to investigate the precipitation and stability of nm-sized Ti oxides in vanadium-based alloys, a prime candidate material for future nuclear fusion reactors based on the magnetic confinement of the plasma. Fusion energy reproduces the nuclear reactions occurring in stars. It can potentially produce more energy than current nuclear fission power plants, and it is meant to be a solution to the clash of today's increasing energy demand with the continuous decrease of fossil-based energy sources, whose use is harmful for the environment. The operating conditions in a fusion reactor will be unprecedented in terms of ultra-high temperatures, stresses, radiation fields and very corrosive media. Only a limited number of materials may be able to withstand such combination of harsh environmental conditions, and vanadium-based alloys are among them. Recent research efforts have identified V-4Cr-4Ti as the most promising vanadium-based alloy for application in the first wall of future fusion nuclear reactors such as DEMO and beyond. The presence of TiO-type precipitates, containing relatively small amounts of C and N, strongly influences the final mechanical properties and radiation resistance of the alloy. Therefore, a thorough understanding of the precipitate structure and evolution at both relatively high temperatures and radiation dose levels is primordial to predict and optimise the final performance of the structural component in the fusion reactor. This thesis is written in alternative format and collects one article already published in Scripta Materialia, and two additional articles to be submitted to peer-review scientific journals. Atomic resolution imaging of the precipitates, coupled with chemical analysis, constitutes the main body of the first article: a novel intergrowth of the fcc Ti oxide in the bcc V matrix is revealed at the precipitate/matrix interface. The evolution of the vacancies present in the TiO precipitates above 400°C, together with the recovery of dislocations in the matrix and the formation of extra precipitates, is studied in the second article by positron annihilation spectroscopy and micro-hardness measurements. The formation of additional precipitates below 400°C induced by radiation is assessed in the third article using proton irradiation as a surrogate of neutron damage. The structure of those additional precipitates and of the dislocation loops induced by the proton bombardment is characterized by advanced analytical electron microscopy.

La peau joue le rôle de barrière, participe à l'homéostasie générale de l'organisme et à la régulation de la perte d'eau trans-épidermique grâce à un échafaudage de couches de cellules. Avec le temps et l'exposition à des agressions extérieures chroniques telles que le tabac, la pollution et les UV, la peau se détériore. On parle de vieillissement cutané chronologique, extrinsèque et de photovieillissement. Le photovieillissement contribue à l'accélération du vieillissement chronologique et à l'induction de cancers cutanés. Les UVA et les UVB sont responsables de la production d'espèces réactives de l'oxygène qui sont impliquées dans la création de dommages à l'ADN et de modifications morphologiques de la peau. Afin de protéger l'organisme de ces altérations, les industriels cherchent à créer de nouveaux produits protecteurs. Pour répondre à cette problématique, il est nécessaire de développer de nouveaux outils et des modèles cutanés d'évaluation avant de tester sur volontaires ou pour éviter les tests sur animaux. Dans cet objectif, ces travaux de thèse se proposent dans un premier temps de caractériser un modèle cutané, l'explant de peau humaine, grâce à une nouvelle méthodologie d'imagerie couplant transparisation et microscopie à feuille de lumière (LSFM). Nos résultats montrent qu'il est possible d'imager des biopsies entières en 3D par sectionnement optique, rapidement et avec une bonne résolution. Il est également possible d'observer les composants majeurs de la peau et de ses annexes, pour étudier des pathologies ou les effets d'agressions extérieures comme les UV. Dans un second temps, nous avons choisi de mettre en place un modèle cutané permettant d'étudier les effets des UVA dans le photovieillissement et de tester l'effet de nouvelles molécules protectrices. Nos résultats montrent qu'une irradiation répétée d'UVA sur un explant de peau provoque l'apparition de cellules apoptotiques et des cassures de l'ADN. L'épaisseur de l'épiderme est diminuée et des immunomarquages in situ observés par LSFM montrent une modification de la localisation de deux protéines impliquées dans la différenciation tardive de l'épiderme. L'analyse de l'ultrastructure du derme montre une altération des principales fibres de la matrice extracellulaire. L'utilisation d'une protection solaire SPF30 a permis de valider la réponse du modèle à un traitement et de tester ainsi une librairie de molécules protectrices. En conclusion, Nos travaux ont permis d'observer pour la première fois la peau par LSFM et démontrer les multiples applications de cette méthodologie en dermatologie. Le modèle " explant UVA ", mimant le photovieillissement, permet d'identifier de nouveaux protecteurs solaires et actifs anti-UVA. / Skin plays the role of a barrier, contributing to the general homeostasis of the body and regulating transepidermal water loss thanks to many cell layers. Over time and with chronic external aggressions such as the tobacco, the pollution and the UV, skin deteriorates. The terms chronological, extrinsic skin aging and photoaging are used. Photoaging is involved in particular in the acceleration of chronological aging and in the induction of skin cancer. UVA and UVB are responsible for producing reactive oxygen species that are involved in DNA damages and morphological modifications of skin. To protect the body against these changes, industrials are working to create new protective products. To further this pursuit, it is necessary to develop new tools and cutaneous models before testing on volunteers or animals. To this end, this thesis first aim to characterize a cutaneous model, the human skin explant, thanks to new imaging methodology coupling clearing and light sheet fluorescence microscopy (LSFM). These results show that it was possible to observe, by optical section, entire 3D biopsies, quickly and with a good resolution. It is thus possible to visualize the major components of skin and these appendages, to study pathologies and external aggressions effect such as UV. Subsequently, we choose to create a cutaneous model making it possible to study the effects of UVA in photoaging and to test the protective effect of new molecules. These results show that repeated UVA irradiation of a skin explant cause apoptotic cells and DNA strand breaks. The thickness of the epidermis decreased and LSFM In situ immunolabeling reveal the modified location of two proteins involved in late differentiation of the epidermis. Analysis of dermis ultrastructure shows a change in the main fibers of the extracellular matrix. The use of SPF30 sunscreen allowed us to validate the model's response to treatment and to test protective molecules. In conclusion, own research has made it possible, for the first, to observe skin by LSFM and to demonstrate the many applications of this methodology in dermatology. The "UVA explant" model, miming photoaging, allows researchers to identify new sunscreens and anti-UVA actives.

Finally, we have systematically investigated the SAMs of four specially designed anthracene-based thiols. These molecules include 9-mercaptoanthracene (MA), (4-mercaptophenyl) (9-anthryl) acetylene (MPAA), (4-mercaptophenyl) (10-nitro-9-anthryl) acetylene (MPNAA), and (4-mercaptophenyl) (10-carboxyl-9-anthryl) acetylene (MPCAA) adsorbed on Au(111). For all SAMs, the parallel-displaced pi-pi stacking interactions and adsorbate-substrate interactions are dominant, which leads to a common wave-like row structure along the pi-pi interaction direction. Compared to MA, the phenyl-acetylene group of MPAA acts as space, which enhances the molecular flexibility and improves the long-range ordering. The repulsive dipole-dipole interactions of MPCAA cause a slight enlargement of the unit cell. For MPCAA, a structure similar to that of MPNAA is formed first. Then with an extended growth time, hydrogen bonding drives the pairing of adjacent inter-row molecules in the expenses of compromising intea-row parallel-displaced pi-pi interaction. / Fourth, we studied the growth of CF3 CH2SH on Au(111). We found that the adsorbed molecules mainly form low coverage phases even after a long time growth in solution. This is attributed to the strong dipole-dipole repulsion between the molecules. However, due to the special short molecular geometry, the molecules can pack with a denser packing arrangement in comparison to the long-chain fluorinated thiols. A "liquid phase" is present in all the samples studied, which solidifies quickly at elevated temperatures. Annealing causes both the growth of stable phases and desorption of weakly adsorbed molecules. Six different stripe phases with the configuration of p x 3 and p x 2a are observed on the surface. The inter-molecular interactions are either van der Waals in nature or the Columbic attraction between the slightly negatively charged F atoms and the slightly positively charged H atoms of the CH 2 group. / Second, we have observed several dash-line structures on HOPG with STM. We suggest that the structures are formed by the gliding of some top surface layers of carbon atoms. The arrest of the gliding action causes the formation of a ridge of carbon atoms and the relaxation of the ridge at room temperature leads to the formation of amorphous carbon clusters queuing along the ridge. As such, the dash-line structures are formed. They are defect structures of HOPG. / Several adsorption systems have been studied by atomic force microscopy (AFM) and scanning tunneling microscopy (STM) in this thesis. / The first system is Fe deposited on 3 x 3 -Al on Si(111). We found by STM that at a low coverage of less than 0.1ML and room temperature; most Fe atoms are incorporated to the 3 x 3 -Al adatom lattice. When the Fe coverage increases further, clustering of Fe atoms into three-dimensional islands occurs. These clusters draw neighboring silicon surface or sub-surface atoms and the formation of Fe-Si bonds is evident. Samples with Fe deposited at or above 400°C show Fe-Si with the CsCl crystalline structure and a top surface lattice of 2 x 2 Si (111) in nature. The crystalline island has a triangular shape and a preferred location along the step edges of the Si(111) surface. / Third, STM has been used successfully in determining the molecular morphology of some novel dendrimers. The morphology of dispersed individual molecule can be identified. In this study, we found that AFM is not applicable because of considerable tip-molecule interactions which distort the morphology of the probed molecule. / Xi Luan = SPM对表面吸附分子的研究 / 席峦. / "June 2005." / Adviser: Lau Woon Ming Leo. / Source: Dissertation Abstracts International, Volume: 67-01, Section: B, page: 0491. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (p. 109-117). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Text in English; abstracts in English and Chinese. / School code: 1307. / Xi Luan = SPM dui biao mian xi fu fen zi de yan jiu / Xi Luan.