La polyprotéine Gag du VIH-1 qui contient quatre principaux domaines (Matrix (MA), capside (CA), nucléocapside (NC), et P6) est l’orchestrateur privilégié de l'assemblage du virus HIV-1, assemblage qui a lieu pendant la phase tardive de la réplication. Il est bien connu que Gag interagit avec les lipides de la membrane plasmique de la cellule hôte et s’auto-assemble sur le feuillet interne de cette dernière afin de générer de nouvelles particules virales. Le bourgeonnement de ces particules virales hors de la cellule hôte est décrit comme étant dépendant de la machinerie cellulaire ESCRT. Différentes études structurales, fonctionnelles ainsi que des simulations de dynamique gros grain ont montré que la liaison de Gag à la membrane est médiée par une interaction duale. Une spécifique de nature éléctrostatique, qui associe une région hautement basique (HBR) du domaine MA de Gag au lipide acide,phosphatidyl inositol biphosphate (PI(4,5)P2) du feuillet interne de la membrane plasmique. Une de type hydrophobe, qui consiste en l’insertion du myristate de Gag dans la membrane plasmique. Savoir si Gag reconnait spécifiquement des domaines lipidiques pré-existants de type « rafts » ou si, au contraire, Gag tri ses lipides et les réorganise latéralement afin d’optimiser sa multimérisation et son bourgeonnement est une question à la fois fondamentale et d’actualité en virologie.Durant ma thèse, j’ai vérifié l’existence de la seconde hypothèse en utilisant des membranes modèles contenant du PI (4,5) P2 marqué de façon fluorescente et différent mutants et produits de la protéine Gag non-myristoylée. Ces expériences ont montré de fortes affinités de ces protéines pour les membranes contenant du PI (4,5) P2. S’appuyant sur les propriétés d’auto-extinction de fluorescence du marqueur choisit et à l’aide des différents variants de la protéine Gag, j'ai pu montré que la multimérisation de Gag génère l’existence de nanodomaines contenant du PI (4, 5) P2 et du cholestérol, la sphingomyéline étant au contraire exclue de ces domaines. En marquant la protéine Gag par un autre fluorophore, j’ai pu montrer par microscopie optique sur des vésicules lipidiques géantes (GUVs) que la protéine Gag partitionnait préférablement dans des microdomaines lipidiques de type liquide désordonnés (Ld). Par la suite, j’ai testé la capacité de la protéine Gag d’induire la formation de vésicules sur des membranes modèles (Bicouches supportés et GUVs) contenant du PI(4,5) P2 et de la phosphatidyl sérine (PS). En utilisant une microbalance à cristal de quartz (QCM-D) et des techniques de microscopie de fluorescence, j’ai suivi l'auto-assemblage de Gag dans le temps et ai montré que la protéine Gag était suffisante pour générer une courbure de la membrane et libérer des vésicules lipidiques. Grâce à différents produits de maturation de cette protéine, j’ai montré que la présence des domaines MA et CA est suffisante pour produire ces vésicules.L’ensemble de ces résultats suggèrent que la liaison et la multimérisation de la protéine Gag ne se produit pas dans des domaines lipidiques préexistants de type « raft », mais, au contraire, que la liaison et multimérisation de la protéine Gag génère l’existence de domaines lipidiques enrichis en PI (4,5) P2 et en cholestérol. La générescence de ces domaines lipidiques pourrait participer à la courbure de la membrane plasmique nécessaire au bourgeonnement du virus. / Gag polyprotein of HIV-1 is made of four main domains Matrix (MA), Capsid (CA), Nucleocapsid (NC), and P6 and is the prime orchestrator of virus assembly that occurs during the late phase of replication. It is well known that Gag interacts with host cell lipids and self-assemble along the inner-leaflet of the plasma membrane in order to generate virus like particles (VLPs). Budding of these VLPs out of the living cell is described to be ESCRT dependent. Structural, functional and simulation based studies has shown that Gag membrane binding is mediated by a bipartite interaction. One specific electrostatic interaction, between the highly basic region (HBR) of its MA domain and the host cell acidic lipid phosphatidyl inositol bisphophate (PI(4,5)P2), plus a hydrophobic interaction through Gag’s myristate insertion in the plasma membrane. It is still an opened question whether Gag would specifically recognize pre-existing lipid domains such as rafts to optimize its multimerization or, on the contrary, would reorganize lipids during its multimerization. During my Ph.D. I explored the second hypothesis using purified myr(-) Gag protein and model membranes containing fluorescently labelled PI(4,5)P2.Bonding experiments have shown strong affinities of these purified proteins towards PI(4,5)P2 containing lipid bilayers. Using PI(4,5)P2 fluorescence self-quenching properties, I found that multimerization Gag generates PI(4,5)P2/Cholesterol enriched nanoclusters. On the opposite, sphingomyelin was excluded from these nanoclusters. In addition to this, using a fluorescently labelled myr(-) Gag, I have observed its preferable partitioning into lipid disordered (Ld) phases of giant unilamellar vesicles (GUVs). Further, possibility of whether HIV-1 Gag alone, as a minimal system, can induce the formation of vesicles on PI(4,5)P2/PS containing supported lipid bilayers (SLBs) & GUVs was tested. Using quartz crystal microbalance (QCM-D) and fluorescence microscopy techniques, I monitored the self-assembly of HIV-1 Gag with time and found that Gag was sufficient to generate membrane curvature and vesicle release. Moreover, using mutants of this protein, I found that having MA and CA domain is enough for Gag to produce vesicle like structures. Taken together, these results suggest that binding and multimerization of Gag protein does not occur in pre-existing lipid domains (such as “rafts”) but this multimerization is more likely to induce PI(4,5)P2/Cholesterol nanoclusters. This nanophase separation could locally play a role in the membrane curvature needed for the budding of the virus.

The majority of colours in the natural world are produced via the wavelength selective absorption of light by pigmentation. Some species of both flora and fauna, however, are particularly eye-catching and visually remarkable as a result of the sub-micron, light-manipulating architecture of their outer-integument material. This thesis describes detailed investigations of a range of previously unstudied photonic structures that underpin the creation of the interesting visual appearances of several such species of flora and fauna. These structures were examined using a variety of methods, including optical microscopy, scanning and transmission electron microscopy, focused ion-beam milling and atomic force microscopy. This enabled detailed characterisation of the species’ photonic systems. The degree of order discerned in the species’ photonic structures ranged from: ‘ordered’ systems, where multiple layers of two materials produces metallic and often mirror-like reflections; to ‘quasi-ordered’ systems, where an average periodicity of the structure in all directions gives rise to diffuse, coloured scatter; to disordered systems, where no discernible order is observed, which results in a diffuse, broad-band, white appearance. In addition to this, the range of systems also encompassed: periodicities in one-dimension in the form of multilayering; ‘quasi-two-dimensional’ structures in the form of aligned fibres; and three-dimensional structures formed from arrangements of spherical particles. Alongside this experimental characterisation, an in-depth series of supporting theoretical analyses were undertaken. For the one-dimensional systems studied here, the models’ theoretical reflectance was calculated using analytical methods. For other systems, with more complex structural-geometries, theoretical simulations of their electromagnetic response to incident radiation were carried out using finite-difference-time-domain and finite-element-method numerical modelling approaches. Theoretical modelling results were compared to experimental measurements of each sample's optical properties. These were primarily reflectance measurements, which were taken using a range of techniques appropriate for each specific investigation. In addition to this, a synthetic sample, mimicking the white-appearance and remarkable polarisation-dependant reflectance of one insect’s photonic structure, was created using polymer electrospinning. Using these experimental measurements and theoretical simulation predictions, the structural colour production mechanisms adopted by several species of flora and fauna were elucidated.

Quantitative phase imaging (QPI) is a label-free technique providing both morphology and quantitative biophysical information in biomedicine. However, applying such a powerful technique to in vivo pathological diagnosis remains challenging. Multi-core fiber bundles (MCFs) enable ultra-thin probes for in vivo imaging, but current MCF imaging techniques are limited to amplitude imaging modalities. We demonstrate a computational lensless microendoscope that uses an ultra-thin bare MCF to perform quantitative phase imaging with microscale lateral resolution and nanoscale axial sensitivity of the optical path length. The incident complex light field at the measurement side is precisely reconstructed from the far-field speckle pattern at the detection side, enabling digital refocusing in a multi-layer sample without any mechanical movement. The accuracy of the quantitative phase reconstruction is validated by imaging the phase target and hydrogel beads through the MCF. With the proposed imaging modality, three-dimensional imaging of human cancer cells is achieved through the ultra-thin fiber endoscope, promising widespread clinical applications.

“Lab on a Chip” technologies have revolutionized the field of bio-chemical analytics. The crucial role of optical techniques in this revolution resulted in the emergence of a field by itself, which is popularly termed as “optofluidics”. The miniaturization and integration of the optical parts in the majority of optofluidic devices however still remains a technical challenge. The works described in this thesis focuses on developing integration methods to combine various optical techniques with microfluidics in an alignment-free geometry, which could lead to the development of portable analytical devices, suitable for field applications. The integration approach was applied to implement an alignment-free optofluidic chip for optical chromatography; a passive optical fractionation technique fractionation for cells or colloids. This system was realized by embedding large mode area photonic crystal fiber into a microfluidic chip to achieve on-chip laser beam delivery. Another study on passive sorting envisages an optofluidic device for passive sorting of cells using an optical potential energy landscape, generated using an acousto-optic deflector based optical trapping system. On the analytical side, an optofluidic chip with fiber based microfluidic Raman spectroscopy was realized for bio-chemical analysis. A completely alignment-free optofluidic device was realized for rapid bio-chemical analysis in the first generation by embedding a novel split Raman probe into a microfluidic chip. The second generation development of this approach enabled further miniaturization into true microfluidic dimensions through a technique, termed Waveguide Confined Raman Spectroscopy (WCRS). The abilities of WCRS for online process monitoring in a microreactor and for probing microdroplets were explored. Further enhanced detection sensitivity of WCRS with the implementation of wavelength modulation based fluorescent suppression technique was demonstrated. WCRS based microfluidic devices can be an optofluidic analogue to fiber Raman probes when it comes to bio-chemical analysis. This allows faster chemical analysis with reduced required sample volume, without any special sample preparation stage which was demonstrated by analyzing and classifying various brands of Scotch whiskies using this device. The results from this study also show that, along with Raman spectroscopic information, WCRS picks up the fluorescence information as well, which might enhance the classification efficiency. A novel microfabrication method for fabricating polymer microlensed fibers is also discussed. The microlensed fiber, fabricated with this technique, was combined with a microfluidic gene delivery system to achieve an integrated system for optical transfection with localized gene delivery.

In recent years, the study of stimulated emission from and by biological systems has gained wide spread attention as a promising technology platform for novel biointegrated laser. However, the photonic properties and the associated physics of many biological laser systems are not yet fully understood and many promising resonator architectures and laser classes have not yet transitioned into the biological world. In this thesis, we investigate the fundamental photonic properties of lasers based on single biological cells and explore the potential of distributed feedback (DFB) gratings as novel biointegrated laser resonators. We show how the easy and flexible fabrication of DFB resonators helps to realize optofluidic and solid-state biological lasers. Lasing characteristics, such as tunable and single mode emission, are investigated and different applications are explored. Fourier-space emission studies on different biological lasers give insight in to the photonic dispersion relation of the system and the fundamental creation of lasing modes and their confinement in living systems. The first purely water based optofluidic DFB laser is demonstrated and novel sensing applications are suggested. This device shows low threshold lasing due to an optimized mode shape, which is achieved by a low refractive index substrate and the use of a mixed-order grating. Next, by integrating a high refractive index interlayer on a DFB resonator, a laser device incorporating the novel solid-state biological gain material green fluorescent protein (GFP) is realized. Lastly, we show how the thickness of organic polymer lasers can be reduced to its fundamental limit (< 500 nm) and the resulting membrane like laser devices can be applied to and operated on various body parts to potentially complement biometric identification.

Two examples of our biophotonic research utilizing nanoparticles are presented, namely laser-based fluoroimmuno analysis and in-vivo optical oxygen monitoring. Results of the work include significantly enhanced sensitivity of a homogeneous fluorescence immunoassay and markedly improved spatial resolution of oxygen gradients in root nodules of a legume species.

Moving towards label-free technologies is essential for many clinical and research applications. Raman spectroscopy is a powerful tool in the field of biomedicine for label-free cell characterisation and disease diagnosis, owing to its high chemical specificity. However, Raman scattering is a relatively weak process and can require long acquisition times, thus hampering its integration to clinical technologies. Multimodal analysis is currently pushing the boundaries in biomedicine, obtaining more information than would be possible using a single mode and overcoming any limitations specific to a single technique. Digital holographic microscopy (DHM) is a rapid and label-free quantitative phase imaging modality, providing complementary information to Raman spectroscopy, and is thus an ideal candidate for combination in a multimodal system. Firstly, this thesis explores the use of wavelength modulated Raman spectroscopy (WMRS), for the classification of immune cell subsets. Following this a multimodal approach, combining Raman spectroscopy and DHM, is demonstrated, where each technique is considered individually and in combination. The complementary modalities provide a wealth of information (both chemical and morphological) for cell characterisation, which is a step towards achieving a label-free technology for the identification of human immune cells. The suitability of WMRS to discriminate between closely related neuronal cell types is also explored. Furthermore optical spectroscopic techniques are useful for the analysis of food and beverages. The use of Raman and fluorescence spectroscopy to successfully discriminate between various whisky and extra-virgin olive oil brands is demonstrated, which may aid the detection of counterfeit or adulterated samples. The use of a compact Raman device is utilised, demonstrating the potential for in-field analysis. Finally, monodisperse and highly spherical nanoparticles are synthesised. A short study demonstrates the potential for these nanoparticles to benefit the techniques of surface enhanced Raman spectroscopy and optical trapping, by way of minimising variability.

In this work, we investigated the spectroscopic characteristics of Nd3+ and Yb3+ doped/co-doped materials for potential applications in photonic devices, particularly lasers emitting in the IR and visible (blue) and thermal sensing operating in the first and second biological windows. For such purposes, we used the fluorescence spectroscopy technique in steady state and time resolved. Initially we investigated the spectroscopic characteristics of the Yb3+ doped oxyfluoride glass, analyzing three important effects present in Yb3+ doped systems: Radiation Trapping (RT), Self-Quenching (SQ), and Cooperative Luminescence (CL). We show that the effects of RT and SQ affect substantially the line shape of Yb3+ emission spectrum, thereby inducing miscalculations of the emission cross section, overestimation of the laser level lifetime, as well as errors in non-radiative decay rates. On the other hand, we show that the strong presence of RT favors the CL effect between Yb3+ ions, which configures an advantageous feature for the generation of blue light via CL. In the thermal sensing context, we carried out a study on application of Nd3+ single doped materials for optical temperature sensors based on Fluorescence Intensity Ratio (FIR) using the 4F3/2, 4F5/2 and 4F7/2 Nd3+ energy levels, more precisely, Nd3+ doped Q-98 phosphate glass, where we showed that the investigated phosphate glass present good perspectives for applications in optical thermometer, being its thermal sensitivity and the maximum thermal range, strongly dependent on the considered energy levels. Following the studies on thermal sensing, we investigated the effects of structure core and core@shell of lanthanum fluoride nanocrystals (LaF3) doped/co-doped with Nd3+ and Yb3+ for temperature sensor based on energy transfer (ET). For this, LaF3 nanocrystals in structural configurations LaF3:Nd (only core), LaF3:Nd/Yb (only core), LaF3 :Nd@LaF3:Yb (Nd3+ in core and Yb3+ in shell), and LaF3:Yb@LaF3:Nd (Yb3+ in core and Nd3+ in shell) were synthesized. We evaluated the FIR of the emission from Yb3+ (2F5/2→2F7/2 at ~990 nm) and Nd3+ (4F3/2→4I13/2 at ~1060 nm) against the temperature and we concluded that their sensitivities are strongly dependent on the structural configurations, i.e., we get control the ET processes and their temperature dependence. In addition, we show that FIR, using 990 and 1330 nm emissions present thermal sensitivity at least one order of magnitude greater that the other FIR’s. / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Neste trabalho investigamos as características espectroscópicas de materiais dopados/co-dopados com os íons terras-raras Nd3+ e Yb3+ para potenciais aplicações em dispositivos fotônicos, particularmente lasers emissores no infravermelho e visível (azul) e sensoriamento térmico operando na primeira e segunda janelas biológicas. Para tais propósitos, usamos a técnica de espectroscopia de fluorescência no estado estacionário e resolvida no tempo. Inicialmente investigamos as características espectroscópicas do vidro oxifluoreto dopado com Yb3+, analisando três importantes efeitos presentes em sistemas dopados com Yb3+: Radiation Trapping (RT), Self- Quenching (SQ) e Luminescência Cooperativa (LC). Mostramos que os efeitos de RT e SQ afetam de forma substancial a forma de linha do espectro de emissão do Yb3+, induzindo, assim, cálculos errôneos na seção de choque de emissão, superestimação do valor do tempo de vida do nível laser emissor, bem como erros nas taxas de decaimentos não-radiativos. Por outro lado, mostramos que a forte presença dos efeitos de RT observados favorece o processo de LC entre íons Yb3+, o que de certa forma constitui uma característica vantajosa para a geração de luz azul via processo de LC do Yb-Yb. Já no âmbito de sensoriamento térmico, realizamos um estudo sobre a aplicação de materiais mono-dopados com Nd3+ em sensores ópticos de temperatura baseados na Razão de Intensidade de Fluorescência (RIF) dos níveis de energia 4F3/2, 4F5/2 e 4F7/2 do Nd3+, mais precisamente, vidro fosfato Q-98 dopado com Nd3+, onde mostramos que o vidro fosfato investigado apresenta boas perspectivas para aplicações em termômetro óptico, sendo sua sensibilidade térmica, bem como o intervalo de temperatura de máxima sensibilidade, fortemente dependente dos níveis de energia considerados. Continuando os estudos sobre sensoriamento térmico, investigamos os efeitos da estrutura core e core@shell de nanocristais de fluoreto de lantânio (LaF3) dopados/co-dopados com Nd3+ e Yb3+ para sensor térmico por Transferência de Energia (TE). Para tanto, nanocristais de LaF3 nas configurações estruturais de LaF3: Nd (somente core), no LaF3: Nd/Yb (somente core), LaF3: Nd@LaF3: Yb (com Nd3+ no core e Yb3+ no shell) e LaF:Yb@LaF3:Nd (com Yb3+ no core e Nd3+ no shell) foram sintetizados. Nós avaliamos as RIF das emissões do Yb3+ (2F5/2 → 2F7/2 em ~990 nm) e do Nd3+ (4F3/2→4I13/2 em ~1060 nm) com a temperatura e concluímos que suas sensibilidades são fortemente dependentes das configurações estruturais, ou seja, conseguimos controlar os processos de TE e a dependência destes com a temperatura. Adicionalmente, mostramos que o sensor de RIF, usando as emissões em 990 nm e 1330 nm, apresenta uma sensibilidade térmica de pelo menos uma ordem de grandeza maior que os demais RIF’s.

Les nano-antennes optiques permettent la manipulation, le confinement et l'exaltation des champs électromagnétiques dans des volumes sub-longueur d'onde. Les applications de ces nano-objetsconcernent des domaines variés tels que les nano-sources de lumière,la photovoltaïque, la microscopie, la spectroscopie... Les propriétés physiques de ces nano-antennes dépendant essentiellementde leur nature, leurs tailles et leurs géométries, lacaractérisation expérimentale de ces nano-objets est essentielle car elle permet d'en améliorer fortement le design et d'amplifier les réponses électromagnétiques.La problématique de ce travail de thèse concerne la caractérisation et l'exploitation des propriétés de nano-antennes optiques. Différentes techniques de caractérisation expérimentale de nano-antennes ont été développées au cours de cette thèse: spectroscopie de corrélation de fluorescence, suivi de dynamique temporelle de boîtes quantiques, spectroscopie sous saturation de fluorescence. Ces techniques ont été appliqués pour étudier différents types d'antennes optiques: microsphères diélectriques, nano-ouvertures simples et nano-ouvertures corruguées. Réciproquement, ces nano-antennes optiques ont été utilisées pour améliorer efficacement la détection de molécules fluorescentes en solution, avec des exaltations de fluorescence moléculaire supérieures à un facteur 100 et un contrôle de la directivité d'émission de fluorescence, ouvrant ainsi de nouvelles opportunités en biophotonique. / Optical nanoantennas allow manipulation, confinement and enhancement of light in sub-wavelength volumes. The applications of these nano-objects are related to various fields such as nano-lightsources, photovoltaic, microscopy, spectroscopy... The physical properties of these nanoantennas depending mainly on their nature,sizes and geometries, the experimental characterization of thesenano-objects is essential because it allows to improve significantly their design and amplify the electromagnetic responses.The focus of this work concerns the characterization and exploitationproperties of optical nanoantennas. Several experimental characterization techniques of nanoantennas have been developedduring this thesis: fluorescence correlation spectroscopy FCS,temporal dynamics monitoring of quantum dots, spectroscopy bysaturated excitation of fluorescence. These techniques were appliedto study different types of optical antennas: dielectricmicrospheres, bare nanoapertures and corrugated nanoapertures. Theseoptical antennas have been used to effectively improve the detectionof fluorescent molecules in solution, with fluorescence enhancementgreater than a factor of 100, together with a directivity control ofthe fluorescence emission, opening new opportunities inbiophotonics.

The quantitative measurement of structural alterations at the nanoscale level is important for understanding the physical states of weakly disordered optical mediums such as cells/tissues. Progress in certain diseases, such as cancer or abnormalities in the brain, is associated with the nanoscale structural alterations at basic building blocks of the cells/tissues. Elastic light scattering, especially at visible wavelengths range provides non-invasive ways to probe the cells/tissues up to nanoscale level. Therefore, a mesoscopic physics-based open light scattering technique with added finer focusing, partial wave spectroscopy (PWS), is developed to probe nanoscale changes. Then, molecular-specific light localization technique, a close scattering approach called inverse participation ratio (IPR) is proposed that is sensitive to nano to microstructural cell/tissue alterations. In this dissertation, we have introduced the further engineered PWS system with the finer focus for precise volume scattering and molecular-specific light localization IPR techniques. As an application of PWS, we first probe precise scattering volume in commercially available tissue microarrays (TMA) tissue samples to standardize the existing cancer diagnostic methods by distinguishing the cancer stages. We also apply the PWS technique to probe chemotherapy drug-treated metastasizing cancer patients by xenografting prostate cancer cells using a mouse model and identify drug-sensitive and drug-resistance treatment cases. On the other hand, as an illustration of another mesoscopic physics-based molecular specific light localization technique, Confocal-IPR, we study the effects of a probiotic on chronic alcoholic mice brains by targeting the molecular specific alteration in glial cells, astrocytes and microglia, and chromatin of the brain cells through staining with appropriate dyes/proteins. Using structural disorder of IPR as a biomarker, the results show that probiotics in the presence of alcohol are beneficial and help overall brain health. Finally, a TEM-IPR study was performed using nanoscale resolution TEM imaging to support the optical IPR method by studying the anti-cancerous drug effect in ovarian cancer cells. The result shows that we can quantitatively measure the effect of anti-cancerous drugs in cancer treatment and the level of tumorigenicity far below the diffraction limit, and it has a similar effect and supports the optical IPR method.