Complete resection is correlated to better patient outcome in aggressive cancers such as glioblastoma. Optical biopsy refers to a family of techniques utilizing optical properties of living targets to make diagnoses where a biopsy would conventionally be used. Such a technology can potentially guide neurosurgeons in removing glioblastomas. Diffuse reflectance (DR) and Time-resolved fluorescence (TRF) have previously been investigated for their ability to measure biomarkers indicative of cancer. One of the difficulties faced in using TRF as a diagnostic tool is that multiple endogenous fluorophores will simultaneously contribute to the signal. This makes it difficult to attribute fluorescence lifetimes or spectral changes to one type of molecule in the tissue. This thesis focuses on the challenge of separating the components in a TRF measurement and their fractional contributions. A DR-TRF instrument was designed and built and characterized using fluorescent dyes. An orthonormal basis deconvolution method combined with a Fourier-domain method were tested for their ability to unmix fluorescent components in a hyperspectral TRF measurement. This method was tested on dye mixtures and retrieved fluorescence lifetimes of 4.6±0.4 ns and 2.7±0.2 ns in a mixture of Fluorescein and Coumarin-6 at concentrations of 5 μM each. It was also tested on an ex-vivo brain tissue where the fluorescence was approximated as a sum of 2 components. / Thesis / Master of Applied Science (MASc)

Protein-protein interactions are important for biological processes. Therefore, many small molecules target a specific protein or interaction in the cell to have biological consequence. While we can measure some protein-protein interactions in a test tube, many proteins cannot be purified making it difficult to properly test that a drug is “on target”. An alternative is to measure these interactions in live cells. We express the proteins of interest fused to fluorophores allowing the use of fluorescence techniques. Förster Resonance Energy Transfer (FRET) provides a molecular level ruler to measure the distance, within a few nanometers, between two proteins. FRET indicates binding. The gold standard for measuring FRET in live cells is by quantifying changes in fluorescence lifetime using Fluorescence lifetime imaging microscopy (FLIM). The change in fluorescence lifetime is inversely proportional to the ratio of bound to non-bound proteins. Tradition FLIM-FRET microscopy is too slow for screening applications. Our aim was to develop a highly multiplexed confocal system for rapid FLIM-FRET acquisition. We present the development of multiple prototypes for confocal multiplexing. In this work, our final design includes 32×32 multiplexed excitation points which scan the sample using refractive window scanners. We coupled this excitation scheme to a 64×32 time-gated single-photon avalanche photodiode (SPAD) sparse array detector. This multiplexed setup allows the use of the sparse array with high frame rate and sub-nanosecond time-gating to achieve high throughput FLIM acquisition. Using our multiplexed FLIM prototype we measured Bcl-2 family protein-protein interactions in live cells (310×310 μm FOV) with two-channel confocal FLIM in 1.5 s. Protein binding affinities were estimated by measuring the changes in FRET as a function of acceptor to donor ratio. The resulting speed of this system meets requirements for implementation in screening applications. / Thesis / Candidate in Philosophy / Inside a cell, proteins are the “workers” and they interact with each other, doing that work. Many of these interactions are important for the cell to live. Pharmaceutical companies may design drugs that can interfere with a specific interaction in order to cause an effect in the cell. Scientists are interested in measuring these interactions and we can do this by “taking a picture” of the interaction using a specialized microscope. One of the major issues with these microscopes is that it takes scientists a long time to collect pictures of these interactions. This means only a few drugs can be tested in a day. To speed up the drug discovery and testing we want to design faster microscopes that can test hundreds of drugs in a day. In my thesis I contributed to building a state-of-the-art super fast microscope. We made progress in steps, and by the third attempt we successfully measured interactions in cells in seconds! Our new microscope is ~400x faster than current technologies. We hope that this research will be useful to speed up drug discovery in the future.

I have analyzed the interactions between SR proteins and splicing components that are bound at the 5’ or 3’ splice site using fluorescence resonance energy transfer (FRET) microscopy. The SR proteins interact with the U1 snRNP-associated 70 kDa protein (U170K) at the 5’splice site and with the small subunit of the U2 snRNP auxiliary factor (U2AF35) at the 3’ splice site. These interactions have been extensively characterized biochemically in the past, and are proposed to play roles in both intron and exon definition. We employed FRET acceptor photobleaching and fluorescence lifetime imaging microscopy (FLIM) to identify and spatially localise sites of direct interactions of SF2/ASF, and other SR proteins, with U2AF35 and U1-70K in live cell nuclei. These interactions were shown to occur more strongly in interchromatin granule clusters (IGCs). They also occur in the presence of the RNA polymerase II inhibitor, DRB, demonstrating that they are not exclusively co-transcriptional. FLIM data have also revealed a novel interaction between HCC1, a factor highly related to the large subunit of the U2AF splicing factor, with both subunits of U2AF that occur in discrete domains within the nucleoplasm but not within IGCs. These data demonstrate that the interactions defining intron and exon definition do occur in living cells in a transcription-independent manner.

Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique to non-invasively map the physical and chemical environment within microfluidic devices. In this work FLIM has been used in conjunction with a variety of other techniques to provide a greater insight into flow behaviour and fluid properties at the microscale. The pH-sensitive fluorescent dyes, fluorescein and C-SNARF 1, have been used to generate pH maps of microfluidic devices with a time-gated camera and a time-and-space-correlated single photon counting (TSCSPC) detector, respectively. Using time-gated detection and fluorescein, the fluorescence lifetime images allow for direct reading of the pH. The relative contribution to fluorescence of the acid and basic forms of C-SNARF 1 was spatially resolved on the basis of pre-exponential factors, giving quantitative mapping of the pH in the microfluidic device. Three dimensional maps of solvent composition have been generated using 2-photon excitation FLIM (2PE-FLIM) in order to observe the importance of gravitational effects in microfluidic devices. Two fluidic systems have been studied: glycerol concentration in the microfluidic device was measured using Kiton red; water concentration in a methanolic solution was measured using ANS. The density mismatch between two solutions of different composition induced a rotation of the interface between two streams travelling side by side in a microchannel. The experiment has provided evidence of non-negligible gravitational effects in microflows. 2PE-FLIM has superior capability than methods used previously to assess similar phenomena. FLIM and micro-particle imaging velocimetry (μ-PIV) have been implemented on a custom-built open frame microscope and used simultaneously for multimodal mapping of fluid properties and flow characteristics. It has been shown that viscosity mismatch between two streams induces a non-constant advective transport across the channel and results in a flow profile that deviates from the usual Poiseuille profile, characteristic of pressure driven flow in microfluidic devices.

The fluorescence spectroscopy and lifetime analysis in biological tissues has been presented as a technique of great potential for tissue characterization for diagnostic purposes. This potential is due to the main advantages of optical techniques based on fluorescence for diagnosis, which includes the possibility of evaluating the tissue metabolism in situ, without removal and processing of the biological sample, through a fast and non-invasive response. Skin lesions were the target interrogated tissue in the present study. They can be clinically classified into two major groups: pigmented and non-pigmented lesions. In each group, the clinical discrimination of benign and malignant lesions may be a complex task, especially for non-experienced clinicians. When these lesions have clinically similar features, the choice of the treatment modality becomes difficult. In this context, auxiliary diagnostic techniques are very important to improve the diagnostic resolution as well as treatment planning and success. Gold standard for skin diagnosis is obtained with the biopsy and further histological analysis. The information about these features is invasive and time consuming. When using a non-invasive procedure such as fluorescence lifetime measurements, the main interrogated fluorophores are NADH (nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide), biomolecules involved in cellular respiration that may provide information on the metabolism of the cells. To differentiate each skin lesion, it is necessary to take into account the contribution of endogenous fluorophores emission such as collagen and elastin, and the absorption of chromophores such as melanin and hemoglobin. In addition to fluorescence decay analysis considering the contribution of fluorophores and chromophores, a stable and portable system is desired for clinical measurements and interrogation of biological tissue in vivo. In this study, we have assembled, calibrated, and characterized one of the worlds first portable time-resolved fluorescence spectroscopy system for single-point measurements. This system was designed to be robust and user-friendly for clinical applications. The system was calibrated and characterized in vitro before the clinical application. It was used for evaluation of the photoaging process in sun-exposed and non-exposed skin and for discrimination of clinically similar skin lesions. Significant statistical differences were observed for 10 parameters when comparing normal and photoaged skin (students t-test, p < 0.001), and for all combinations of non-pigmented and pigmented lesions when using tri-exponential decay parameters (Wilcoxon rank sum test, p<0.05). Both in vivo measurements showed promising results and have potential for many applications in dermatology, oncology and aesthetics. Next steps include multivariate data analysis and the determination of the diagnostic resolution of fluorescence lifetime spectroscopy. Further investigation of optical processes related to fluorescence decay changes is necessary, since fluorescence lifetime values in biological tissues reported on the literature are very scarce and heterogeneous and not completely understood. / A análise da espectroscopia e do tempo de vida da fluorescência em tecidos biológicos vem sendo apresentada como uma técnica com grande potencial para a caracterização tecidual com finalidade diagnóstica. Esse potencial é devido às principais vantagens das técnicas ópticas de diagnóstico baseadas em fluorescência, que possibilitam avaliar o metabolismo in situ, sem a necessidade de remoção e processamento da amostra biológica, com uma resposta rápida e não-invasiva. Lesões de pele foram os tecidos investigados no presente estudo. Elas podem ser clinicamente classificadas em dois grandes grupos: pigmentadas e não pigmentadas. Em cada grupo, a discriminação clínica de lesões benignas e malignas pode ser uma tarefa complexa, principalmente para médicos com pouca experiência. Quando essas lesões apresentam características clínicas semelhantes, a escolha do tipo de tratamento torna-se difícil. Nesse contexto, técnicas auxiliares de diagnóstico são de grande relevância para melhorar a resolução de diagnóstico, assim como o planejamento e o sucesso do tratamento. O padrão ouro para o diagnóstico do câncer de pele é obtido por meio da biópsia e posterior análise histopatológica. A obtenção de informações sobre essas características é invasiva e consome bastante tempo. Ao utilizar procedimentos não-invasivos como medidas de tempo de vida de fluorescência, os fluoróforos de mais investigados são o NADH (nicotinamida adenina dinucleotídeo) e o FAD (flavina adenina dinucleotídeo), biomoléculas envolvidas na respiração celular que podem fornecer informação sobre o metabolismo das células. Para diferenciar cada tipo de lesão de pele, é necessário levar em conta a contribuição da emissão de fluoróforos endógenos como o colágeno, elastina e da absorção de cromóforos como melanina e hemoglobina. Além da análise do decaimento de fluorescência considerando a contribuição de fluoróforos e cromóforos, um sistema estável e portátil é desejado para medidas clínicas e investigação de tecidos biológicos in vivo. Nesse estudo, nós montamos, calibramos e caracterizamos um dos primeiros sistemas portáteis do mundo para espectroscopia de fluorescência resolvida no tempo para medidas pontuais. Esse sistema foi projetado para ser robusto e amigável ao usuário em aplicações clínicas. O sistema foi calibrado e caracterizado in vitro antes das aplicações clínicas. Ele foi utilizado para avaliação do processo de fotoenvelhecimento em pele exposta e não-exposta ao sol e para a discriminação de lesões de pele clinicamente semelhantes. Diferenças estatísticas significativas foram observadas para 10 parâmetros na comparação entre pele normal e fotoenvelhecida (teste t-student, p<0.001) e para todas as combinações de lesões pigmentadas e não-pigmentadas ao utilizar parâmetros do decaimento triexponencial (teste Wilcoxon rank sum, p<0.05). Ambas medidas in vivo mostraram resultados promissores e um potencial para muitas aplicações em dermatologia, oncologia e estética. As próximas etapas incluem análise multivariada de dados e determinação da resolução de diagnóstico da espectroscopia de tempo de vida de fluorescência. Uma maior investigação dos processos ópticos relacionados a mudanças nos decaimentos de fluorescência é necessária, pois o número de valores de tempo de vida de fluorescência em tecidos biológicos reportados na literatura é escasso e os valores são heterogêneos e não completamente compreendidos.

FLIM is branch of microscopy mainly used in biology which is quickly improving thanks to a rapid enhancement of instrumentation and techniques enabled by new sensors. In FLIM, the most precise method of measuring fluorescent decays is called TCSPC. High voltage PMT detection devices together with costly and bulky optical setups which scan the sample are usually required in TCSPC instrumentation. SPADs have enabled a big improvement in TCSPC measurement setup, providing a CMOS compatible device which can be designed in wide arrays format. However, sensors providing in-pixel TCSPC do not scale in size and in large array like the time-gated SPAD pixel sensors do. Time-gated pixels offer a less precise lifetime estimation, discarding any photon information outside a given time window, but this loss in photon-efficiency is offset by gains in pixel size. This work is aimed at the development of a wide field TCSPC sensor with a pixel size and fill factor able to reduce the cost of such devices and to obtain a high resolution time-resolved fluorescence image in the shortest time possible. The study focuses on SPAD and pixel design required to maximise the fill factor in sub 10 μm pixel pitch. Multiple pixel designs are proposed in order to reduce pixel area and so enable affordable wide array TCSPC systems. The first proposed pixel performs the CMM lifetime estimation in order to reduce the frame rate needed to stream the data out of the SPAD array. This pixel is designed in a 10 μm pitch and attains with the most aggressive design a fill factor of 10:17 %. A second design proposes an analogue TCSPC which consists in a S/H TAC circuitry. This simpler pixel can achieve a higher fill factor of 19:63% as well as smaller pitch of 8 μm thanks to the adoption of SPAD n-well and electronics area sharing. This last design is implemented in a 320 x 256 SPAD array in which is included part of a novel ADC aimed at reduction of the processing time required to build a TCSPC histogram. A more conventional analogue readout is used to evaluate the pixel performance as well as a more fine TCSPC histogram. The device was used to measure the fluorescence lifetime of green micro-spheres while the 2b flash ADC is used to demonstrate rapid resolution and separation of two different fluorescence decays.

Time-resolved fluorescence spectroscopy (TRFS) is a powerful analytical tool for quantifying the biochemical composition of organic and inorganic materials. The potentials of TRFS as nondestructive clinical tool for tissue diagnosis have been recently demonstrated. To facilitate the translation of TRFS technology to the clinical arena, algorithms for online TRFS data analysis are of great need. A fast model-free TRFS deconvolution algorithm based on the Laguerre expansion method has been previously introduced, demonstrating faster performance than standard multiexponential methods, and the ability to estimate complex fluorescence decay without any a-priori assumption of its functional form. One limitation of this method, however, was the need to select, a priori, the Laguerre parameter a and the expansion order, which are crucial for accurate estimation of the fluorescence decay. In this thesis, a new implementation of the Laguerre deconvolution method is introduced, in which a nonlinear least-square optimization of the Laguerre parameter is performed, and the selection of optimal expansion order is attained based on a Minimum Description Length (MDL) criterion. In addition, estimation of the zero-time delay between the recorded instrument response and fluorescence decay is also performed based on a normalized means square error criterion. The method was fully validated on fluorescence lifetime, endogenous tissue fluorophores, and human tissue. The automated Laguerre deconvolution method is expected to facilitate online applications of TRFS, such as clinical real-time tissue diagnosis.

The pH of tumors and surrounding tissues is a key biophysical property of the tumor microenvironment that affects how a tumor survives and how it invades the surrounding space of normal tissue. Research into tumorigenesis and tumor treatment is greatly dependent on accurate, precise, and reproducible measurements. Optical imaging is generally regarded as the best choice for non-invasive and high spatial resolution measurements. Ratiometric fluorescence imaging and fluorescence lifetime imaging microscopy (FLIM) are two primary ways for measuring tumor pH.pH measurements in a window chamber animal model using a ratiometric fluorescence imaging technique is demonstrated in this dissertation. The experimental setup, imaging protocols, and results are presented. A significantly varying bias was consistently observed in the measured pH. A comprehensive analysis on the possible error sources accounting for this bias is carried out. The result of analysis reveals that accuracy of ratiometric method is most likely limited by biological and physiological factors.FLIM is a promising alternative because the fluorescence lifetime is insensitive to the biological and physiological factors. Photon noise is the predominant error source of FLIM. The Fisher information matrix and the Cram&eacute;r-Rao lower bound are used to calculate the lowest possible variance of estimated lifetime for time-domain (TD) FLIM. A statistical analysis of frequency-domain (FD) FLIM using homodyne lock-in detection is also performed and the probability density function of the estimated lifetime is derived. The results allow the derivation of the optimum experimental parameters, which yields the lowest variance of the estimated lifetime in a given period of imaging time. The analyses of both TD and FD-FLIM agree with results of corresponding Monte Carlo simulations.

Many biosurfactants show antimicrobial activity and some are found to be superior for isolating membrane proteins. This study was aimed towards a general understanding of the interactions of biosurfactants with lipid membranes on a molecular level. To this end, a new, fluorescence lifetime-based membrane leakage assay has been established that does not only quantify membrane permeabilization more precisely but reveals also the leakage mechanism. This mechanism, referred to as graded or all-or-none leakage, is crucial for interpreting potential biological activities and modes of action. Lipopeptides of the surfactin, fengycin, and iturin families as produced by Bacillus subtilis were studied along with synthetic surfactants. Their membrane permeabilizing activity and selectivity mirrored, to some extent, the active concentrations and fungicidal selectivity of the compounds in vivo. Furthermore, the effects of co-surfactants and co-solvents (glycerol, urea, DMSO) have been investigated to better understand and predict means of improving the performance of fungicidal products as well as conditions for membrane protein solubilization.

Many biosurfactants show antimicrobial activity and some are found to be superior for isolating membrane proteins. This study was aimed towards a general understanding of the interactions of biosurfactants with lipid membranes on a molecular level. To this end, a new, fluorescence lifetime-based membrane leakage assay has been established that does not only quantify membrane permeabilization more precisely but reveals also the leakage mechanism. This mechanism, referred to as graded or all-or-none leakage, is crucial for interpreting potential biological activities and modes of action. Lipopeptides of the surfactin, fengycin, and iturin families as produced by Bacillus subtilis were studied along with synthetic surfactants. Their membrane permeabilizing activity and selectivity mirrored, to some extent, the active concentrations and fungicidal selectivity of the compounds in vivo. Furthermore, the effects of co-surfactants and co-solvents (glycerol, urea, DMSO) have been investigated to better understand and predict means of improving the performance of fungicidal products as well as conditions for membrane protein solubilization.