Lifetime estimation of moving vesicles in frequency-domain fluorescence lifetime imaging microscopy

International audienceWe propose a framework for correcting the effect of vesicles motion in frequency domain FLIM imaging. Estimation of movement and lifetime are decoupled and alternatively performed. Robust M-estimation is involved to improve the accuracy of our estimate. Our method has been evaluated with both simulated and real samples

Lifetime estimation on moving sub-cellular objects in frequency domain FLIM imaging

International audienceFluorescence lifetime is usually defined as the average nanosecond-scale delay between excitation and emission of fluorescence. It has been established that lifetime measurement yields numerous indications on cellular processes such as inter-protein and intra-protein mechanisms through fluorescent tagging and Förster resonance energy transfer (FRET). In this area, frequency domain fluorescence lifetime imaging microscopy (FD FLIM) is particularly well appropriate to probe a sample non-invasively and quantify these interactions in living cells. The aim is then to measure fluorescence lifetime in the sample at each location in space from fluorescence variations observed in a temporal sequence of images obtained by phase modulation of the detection signal. This leads to a sensitivity of lifetime determination to other sources of fluorescence variations such as intracellular motion. In this paper, we propose a robust statistical method for lifetime estimation on both background and small moving structures with a focus on intracellular vesicle trafficking

Lifetime MAP reconstruction in frequency-domain fluorescence lifetime imaging microscopy

International audienceWe propose a robust statistical framework for reconstructing lifetime map corrupted by vesicle motion in frequency domain FLIM imaging. Instrumental noise is taken into account to improve lifetime estimation. Robust M-estimators and MLestimators allow to jointly estimate motion and lifetime. Performances are demonstrated on simulated and real samples

NANOSCALE INVESTIGATION OF NUCLEAR STRUCTURES BY TIME-RESOLVED MICROSCOPY

The eukaryotic cell nucleus is composed by heterogeneous biological structures, such as the nuclear envelope (NE) and chromatin. At a morphological level, chromatin organization and its interactions with nuclear structures, such as nuclear lamina (NL) and nuclear pore complex (NPC), are suggested to play an essential role in the regulation of gene activity, which involves the packaging of the genome into transcriptionally active and inactive sites, bound to healthy cell proliferation and maintenance. However, the processes governing the relation between nuclear structures and gene regulation are still unclear. For this reason, the advanced microscopy methods represent a powerful tool for imaging nuclear structures at the nanometer level, which is essential to understand the effect of nuclear interactions on genome function. The nanometer information may be achieved either through the advanced imaging techniques in combination with fluorescence spectroscopy or with the help of super-resolution methods, increasing the spatial resolution of the conventional optical microscopy. In this thesis, I implemented a double strategy based on a novel FLIM-FRET assay and super resolution SPLIT-STED method for the investigation of the chromatin organization and nuclear envelope components (lamins and NPC) at the nanoscale, in combination with the phasor analysis. The phasor approach can be applied to several fluorescence microscopy techniques abled to provide an image with an additional information in a third channel. Phasor plot is a graphical representation, which decodes the fluorescence dynamics encoded in the image, revealing a powerful tool for the data analysis in time-resolved imaging. The Chapter 1 of the thesis is characterized by an Introduction, which provides an overview on the chromatin organization at the nanoscale and the description of the several advanced fluorescence microscopy techniques used for its investigation. They are broadly divided into two main categories: the advanced imaging techniques, such as Fluorescence Correlation Spectroscopy (FCS), single particle tracking (SPT) and Fluorescence Recovery After Photobleaching (FRAP), Forster Resonance Energy Transfer (FRET) and Fluorescence Lifetime Imaging Microscopy (FLIM) and the super-resolution techniques, which include Stimulated Emission Depletion (STED), Structured Illumination Microscopy (SIM) and single molecule localization microscopy (SMLM). Following, Chapter 2 focus on the capabilities of the phasor approach in time-resolved microscopy, as a powerful tool for the analysis of the experimental data. After a description of the principles of time-domain and frequency-domain measurements, in this section are explained the rules of the phasor analysis and its applications in different fluorescence microscopy techniques. In Chapter 3, I present a FRET assay, based on the staining of the nuclei with two DNA-binding dyes (e.g. Hoechst 33342 and Syto Green 13) by using frequency-domain detection of FLIM and the phasor analysis in live interphase nuclei. I show that the FRET level strongly depends on the relative concentration of the two fluorophores. I describe a method to correct the values of FRET efficiency and demonstrate that, with this correction, the FLIM-FRET assay can be used to quantify variations of nanoscale chromatin compaction in live cells. In Chapter 4, the phasor analysis is employed to the improvement of the resolving power of the super-resolution STED microscopy. I describe a novel method to investigate nuclear structures at the nanometer level, known as SPLIT (Separation of Photons by Lifetime Tuning), developed by my group in last years. By using the phasor approach, the SPLIT technique decodes the variations of spectroscopic parameters of fluorophores, such as lifetime and fluorescence intensity, due to the effect of the modulated depletion power of the STED technique, increasing the resolving power. In this chapter, I develop the concept of the SPLIT method modulating the excitation pattern during the image acquisition to overcome its limitation linked to the photobleaching effect and the signal-to-noise ratio

Impact of substrate topology, chemical stimuli and Janus nanoparticles on cellular properties

Cellular behavior is influenced by many biochemical but also physical factors in the direct cellular environment. Thereby, cells not only react to external cues, the interaction between cells and their environment is also dependent on the properties of the cell itself. The endocytosis of nanoparticles for example depends on the intermolecular forces between plasma membrane and particle as well as on the mechanical properties of the membrane. In the first part of this thesis I focus on the interaction between inorganic Janus nanoparticles, a new type of nanomaterials, which possess amphiphilic properties, and model membranes. In coarse grain simulations it has been demostrated that incubation of membranes with these particles lead either to pore formation in the lipid bilayer or to tubulation and vesiculation by long-range attractive interaction between particles bound to the membrane. Conducting surface plasmon resonance spectroscopy experiments I show that the binding energy of the used inorganic Janus particles to a solid supported monolayer could be sufficient to induce tubulation of tension-free membranes but is to small to provide the energy necessary to form a vesicle. This result is confirmed by fluorescence microscopic examination of giant unilamellar vesicles serving as a model system for the plasmamembrane, which were treated with Janus particles. Vesicles incubated with Janus particles show inwards directed membrane tubes, while incubation of vesicles with isotropic control particles had no effect on the membrane or could be attributed to an osmotic gradient. However, uptake experiments into living cells and cytotoxicity assays show no obvious difference between spherical particles and Janus particles, which hints for a negligible contribution of nanoparticle-induced tubulation or vesiculation to cellular uptake of nanoparticles and cytotoxicity. On the one hand mechanical properties of the cell influence the interaction between the cell and its environment. On the other hand, mechanical properties of cells change in response to environmental cues. Therefore, in the next part, atomic force microscopy-based microrheology is used to measure frequency-dependent mechanical properties of cells in different conditions. Fixation of cells with different chemical fixatives and transformation of epithelial cells to mesenchymal cells lead to more solid-like mechanical properties, while interaction with the actin cytoskeleton lead to more fluid-like properties. A comparison between malignant cells and non-malignant cells shows that malignant cells are more fluid-like compared to their non-malignant counterparts. Furthermore, the influence of substrate topology on cellular mechanics and cytoskeletal arrangement is examined. Changing physical properties of the substrate such as stiffness or topography has been shown to affect plenty of cellular processes like migration, proliferation, morphology or differentiation. Here, I investigate the impact of porous substrates on cellular morphology, cytoskeletal organization and elasticity in the context of confluent epithelial monolayers. I found that cells eventually self-organize to match the geometry of the pore pattern and remodel their actin cytoskeleton to reinforce their adhesion zone. Cells fluidize with increasing pore size up to 2 µm but eventually become stiffer if grown on very large pores up to 5 µm. The adhesion of cells to substrates is further researched by application of metal-induced energy transfer fluorescence lifetime imaging, which is used for the first time for this purpose. The fluorescence lifetime of a fluorophore in proximity to a metal layer is a function of the distance between fluorophore and metal layer. Applying a quantitative model of this interaction facilitates locating the fluorophore with nanometer precision in the axial direction up to 200 nm above the metal layer. By staining of the plasmamembrane I was able to image to basal membrane of three different cell lines and follow spreading of cells with high axial resolution. The introduced method is not restricted to measurement of cell/substrate distance and can be used for applications, which necessitate axial nanometer resolution in a range up to 200 nm

A study of SNARE-mediated autophagosome clearance using fluorescence lifetime microscopy

Cell survival requires the turnover of toxic cellular material and recycling of biomolecules in low nutrient conditions. An efficient degradation system is therefore essential for disease prevention and its dysfunction has been linked to both neurodegeneration and oncogenesis. Bulk degradation is accomplished through the collection of cytoplasmic material in a unique sequestration vesicle, which forms de novo and subsequently deposits cargo in the lysosome for degradation. This process, known as autophagy, therefore requires membrane fusion between the autophagosomal vesicle and the lysosome. SNARE proteins mediate membrane fusion events and therefore their careful regulation ensures the proper organisation of the membrane trafficking network. The SNARE proteins governing autophagosome clearance have been identified as syntaxin 17, SNAP29 and VAMP8 and SNARE assembly appears to be positively regulated by VPS33A. This well established model of SNARE-mediated autophagosome clearance has not, however, been demonstrated within the spatiotemporal framework of the cell and little is known about how VPS33A modulates SNARE function. The research presented in this thesis therefore aims to determine the applicability of the proposed SNARE model within the cellular environment and to investigate the regulatory mechanisms controlling syntaxin 17 function. To accomplish this, carefully validated fluorescence colocalisation and time-resolved fluorescence lifetime imaging techniques were primarily employed. The limitations of these techniques were also considered for data interpretation and a novel prototype SPAD array technology, designed for high-speed time-correlated single photon counting, was trialled for widefield FLIM-FRET. FLIM-FRET revealed that VAMP8 has been incorrectly assigned as the dominant autophagosomal R-SNARE and VPS33A studies evidence a multi-modal regulation of Stx17 that diverges from other studied syntaxin family modulation mechanisms. A new model of SNAREmediated autophagosome clearance is therefore proposed, where syntaxin 17 engages with SNAP29 and VAMP7 to drive membrane fusion with the endolysosome in a manner governed by VPS33A and dependent on the phosphorylation status of syntaxin 17

Optical imaging methods for the study of disease models from the nano to the mesoscale

The visualisation of disease phenotypes allows scientists to study fundamental mechanisms of disease. Optical imaging methods are useful not only to observe anatomical features of biological samples, but also to infer interactions between molecular species using fluorescence labelling. This thesis presents the development of imaging and analysis tools to study biological questions in three models of disease, with samples ranging from the sub-cellular to the organ scale. First, the role of the alpha-synuclein (a-syn) protein, whose dysfunction is a hallmark of Parkinson’s Disease, was studied with respect to vesicle trafficking at the synapse. Synaptic vesicles are ∼40 nm in diameter; imaging vesicles therefore requires methods with resolution below the diffraction limit. Single-molecule localisation microscopy (SMLM), which circumvents the diffraction limit by separating fluorophore emission in time to localise individual molecules in space with ∼20 nm precision, was thus implemented to study a-syn in purified synaptic boutons. A software package was developed to analyse the colocalisation of a-syn with internalised vesicles, and the clustering of a-syn under differing synaptic calcium levels. The colocalisation of a-syn and internalised vesicles was found to be temperature independent, suggesting that a-syn is involved in non-canonical trafficking mechanisms. Ground truth simulations from a synaptosome model were used to benchmark two cluster analysis methods. Both methods applied on the experimental data showed that a-syn becomes less clustered at low synaptic calcium levels. Second, the spatiotemporal association of ESCRT-II, a protein complex whose role in the budding of the human immunodeficiency virus (HIV) was previously considered dispensable, and the HIV polyprotein Gag was studied during viral egress using novel image analysis tools. A nearest-neighbour analysis showed the ESCRT-II protein EAP45 colocalises with Gag similarly to ALIX, a protein well known to be involved in HIV budding. However, upon deletion of EAP45’s N-terminus, its colocalisation with Gag was significantly impaired, highlighting the importance of this EAP45 domain in linking to Gag. Single particle tracking was used to trace the trajectories of EAP45 and Gag in live cells, and an algorithm was developed to visualise the simultaneous motion of two particles; these analyses revealed three types of potential dynamic interaction between EAP45 and Gag. Finally, an open-source instrument to visualise phenotypes from large organs in 3D was developed for the study of chronic obstructive pulmonary disease (COPD) models. The instrument implements Optical Projection Tomography, a technique which can reconstruct cross-sectional slices of a transparent object from its orthographic projections, using off-the- shelf components and novel ImageJ plugins for artefact correction and volume reconstructions. Excised and cleared mouse lungs were imaged in which high order airways can be discerned with 50 μm resolution. The raw lung data, instructions for building the instrument, the free ImageJ plugins, and a detailed software manual are available in an online repository to encourage the widespread use of OPT for imaging large samples.Gates Cambridg

Advanced Fluorescence Microscopy Techniques-FRAP, FLIP, FLAP, FRET and FLIM

Fluorescence microscopy provides an efficient and unique approach to study fixed and living cells because of its versatility, specificity, and high sensitivity. Fluorescence microscopes can both detect the fluorescence emitted from labeled molecules in biological samples as images or photometric data from which intensities and emission spectra can be deduced. By exploiting the characteristics of fluorescence, various techniques have been developed that enable the visualization and analysis of complex dynamic events in cells, organelles, and sub-organelle components within the biological specimen. The techniques described here are fluorescence recovery after photobleaching (FRAP), the related fluorescence loss in photobleaching (FLIP), fluorescence localization after photobleaching (FLAP), Forster or fluorescence resonance energy transfer (FRET) and the different ways how to measure FRET, such as acceptor bleaching, sensitized emission, polarization anisotropy, and fluorescence lifetime imaging microscopy (FLIM). First, a brief introduction into the mechanisms underlying fluorescence as a physical phenomenon and fluorescence, confocal, and multiphoton microscopy is given. Subsequently, these advanced microscopy techniques are introduced in more detail, with a description of how these techniques are performed, what needs to be considered, and what practical advantages they can bring to cell biological research

High-Resolution Imaging of Natural Killer Cell Immunological Synapses

The first observations of the immunological synapse have demonstrated that immune-cell signalling in situ does not simply depend on protein structures and signalling pathways but also on temporal and spatial coordinates. With the advent of new live-cell, three-dimensional fluorescence microscopy techniques our understanding of the relationship between the formation of the immunological synapse and the development of an immune response has been greatly improved. Using artificial activating substrates as surrogate target cells or antigen presenting cells in conventional microscopes has so far been the state-of-the-art to obtain high-resolution images of immunological synapses. However, such artificial substrates may not fully recapitulate the complexity of intercellular interactions. Newly developed super-resolution techniques are very promising, but they remain inadequate for live-cell imaging. Technical improvements are therefore crucially needed to address these bottlenecks and improve our understanding of immune-cell signalling. In this report we achieve high-speed high-resolution imaging of live intercellular immunological synapses by combining confocal microscopy with optical tweezers. We design, build and demonstrate the performance and flexibility of the instrument by imaging a variety of molecules at T cell and NK cell synapses. NKG2D is an important receptor that allows NK cells to recognise and kill tumour cells. Due to the lack of suitable imaging technology, NKG2D signalling at the synapse remains unclear. We specifically use our new instrument to gain further understanding of NKG2D signalling, signal integration, and NKG2D-mediated cytotoxicity. For the first time at live intercellular NK-cell immunological synapses, we describe the formation and the dynamics of NKG2D microclusters. We show that these microclusters actively signal and that they coalesce around a secretory domain through which lytic secretions are delivered. Importantly, these results suggest that the physical distribution of NKG2D at the immunological synapse may play an important role in directing lytic-secretion delivery at the NK cell synapse