Frequency domain lifetime and spectral imaging microscopy

How many photons are needed for FRET imaging?

Förster resonance energy transfer (FRET) imaging is an essential analytical method in biomedical research. The limited photon-budget experimentally available, however, imposes compromises between spatiotemporal and biochemical resolutions, photodamage and phototoxicity. The study of photon-statistics in biochemical imaging is thus important in guiding the efficient design of instrumentation and assays. Here, we show a comparative analysis of photon-statistics in FRET imaging demonstrating how the precision of FRET imaging varies vastly with imaging parameters. Therefore, we provide analytical and numerical tools for assay optimization. Fluorescence lifetime imaging microscopy (FLIM) is a very robust technique with excellent photon-efficiencies. However, we show that also intensity-based FRET imaging can reach high precision by utilizing information from both donor and acceptor fluorophores.

Large-scale 3-dimensional quantitative imaging of tissues: state-of-the-art and translational implications

Recent developments in automated optical sectioning microscope systems have enabled researchers to conduct high resolution, three-dimensional (3D) microscopy at the scale of millimeters in various types of tissues. This powerful technology allows the exploration of tissues at an unprecedented level of detail, while preserving the spatial context. By doing so, such technology will also enable researchers to explore cellular and molecular signatures within tissue and correlate with disease course. This will allow an improved understanding of pathophysiology and facilitate a precision medicine approach to assess the response to treatment. The ability to perform large-scale imaging in 3D cannot be realized without the widespread availability of accessible quantitative analysis. In this review, we will outline recent advances in large-scale 3D imaging and discuss the available methodologies to perform meaningful analysis and potential applications in translational research.

Autofluorescence lifetime variation in the cuticle of the bedbug Cimex lectularius

The decay time of the fluorescence of excited molecules, called fluorescence lifetime, can provide information about the cuticle composition additionally to widely used spectral characteristics. We compared autofluorescence lifetimes of different cuticle regions in the copulatory organ of females of the bedbug, Cimex lectularius. After two-photon excitation at 720 nm, regions recently characterised as being rich in resilin showed a longer bimodal distribution of the mean autofluorescence lifetime τ_m (tau-m) at 0.4 ns and 1.0-1.5 ns, while resilin-poor sites exhibited a unimodal pattern with a peak around 0.8 ns. The mean lifetime, and particularly its second component, can be useful to distinguish resilin-rich from resilin-poor parts of the cuticle. The few existing literature data suggest that chitin is unlikely responsible for the main autofluorescent component observed in the resilin-poor areas in our study and that melanin requires further scrutiny. Autofluorescence lifetime measurements can help to characterise properties of the arthropod cuticle, especially when coupled with multiphoton excitation to allow for deeper tissue penetration.

Ex vivo imaging of active caspase 3 by a FRET-based molecular probe demonstrates the cellular dynamics and localization of the protease in cerebellar granule cells and its regulation by the apoptosis-inhibiting protein survivin

Background

Apoptosis takes place in naturally occurring neuronal death, but also in aging, neurodegenerative disorders, and traumatic brain injuries. Caspase 3 (Casp3) is the most important effector protease in apoptosis: being inactive inside the cell, it undergoes enzymatic cleavage and - hence - activation once the apoptotic cascade is triggered. Immunological techniques with antibodies against cleaved Casp3 (cCasp3) or assays with colorimetric/fluorogenic substrates are commonly in use, but they do not allow to directly follow the dynamics of activation in alive neurons that may be committed to die.

Results

By combined biolistic transfection, confocal microscopy, and fluorescence resonance energy transfer (FRET), we have implemented a methodology to dynamically monitor Casp3 activation in organotypic cerebellar slices from postnatal mice. After transfection with pSCAT3 FRET probes, we measured the ratio of the emissions of the donor/acceptor pair (ECFP_em/Venus_em) in fixed or alive cultures. In so doing, we i. discriminated the cellular compartment(s) of enzyme activation (nucleus, perikaryon, neurites); ii. demonstrated that Casp3 was constitutively active in the granule cells; iii. followed the fluctuations of ECFP_em/Venus_em, and its response to 25 mM KCl depolarization, or to increased intracellular Ca⁺⁺ after NMDA (1 mM), kainic acid (1 mM), or A23187 (100–200 μM). The specificity of the active pSCAT3-DEVD probe was confirmed with RNA interference and after inhibition of Casp3 with Ac-DEVD-CMK (100 μM), as both sets of experiments brought ECFP_em/Venus_em to the values recorded with the control probe pSCAT3-DEVG. After double-transfection with pSCAT3-DEVD + pHcRed1-C1-survivin, we also showed a 44–56 % reduction of basal Casp3 activity in cells overexpressing survivin, a protein-member of the family of apoptosis inhibitors, with augmented survival (2.82 folds). Survivin-rescued cells were sensitive to 5 mM H₂O₂ oxidative stress but died without intervention of Casp3.

Conclusions

This ex vivo FRET-based methodology provides quantitative information on the functional and histological dynamics of Casp3 activation in individual neurons at a cell level resolution. Not only it can be combined with experimental manipulation of the apoptotic machinery inside the cell, but offers several advantages over existing protocols for monitoring apoptosis in live mammalian neurons, and has potential to be transferred in vivo. Due to the pivotal role of Casp3 in apoptosis, our approach is relevant for a better comprehension of molecular neurodegeneration in the normal and pathological brain.

Electronic supplementary material

The online version of this article (doi:10.1186/s13024-016-0101-8) contains supplementary material, which is available to authorized users.

Quantifying intracellular protein binding thermodynamics during mechanotransduction based on FRET spectroscopy

Mechanical force modulates myriad cellular functions including migration, alignment, proliferation, and gene transcription. Mechanotransduction, the transmission of mechanical forces and its translation into biochemical signals, may be mediated by force induced protein conformation changes, subsequently modulating protein signaling. For the paxillin and focal adhesion kinase interaction, we demonstrate that force-induced changes in protein complex conformation, dissociation constant, and binding Gibbs free energy can be quantified by lifetime-resolved fluorescence energy transfer microscopy combined with intensity imaging calibrated by fluorescence correlation spectroscopy. Comparison with in vitro data shows that this interaction is allosteric in vivo. Further, spatially resolved imaging and inhibitor assays show that this protein interaction and its mechano-sensitivity are equal in the cytosol and in the focal adhesions complexes indicating that the mechano-sensitivity of this interaction must be mediated by soluble factors but not based on protein tyrosine phosphorylation.

Total variation versus wavelet-based methods for image denoising in fluorescence lifetime imaging microscopy

We report the first application of wavelet-based denoising (noise removal) methods to time-domain box-car fluorescence lifetime imaging microscopy (FLIM) images and compare the results to novel total variation (TV) denoising methods. Methods were tested first on artificial images and then applied to low-light live-cell images. Relative to undenoised images, TV methods could improve lifetime precision up to 10-fold in artificial images, while preserving the overall accuracy of lifetime and amplitude values of a single-exponential decay model and improving local lifetime fitting in live-cell images. Wavelet-based methods were at least 4-fold faster than TV methods, but could introduce significant inaccuracies in recovered lifetime values. The denoising methods discussed can potentially enhance a variety of FLIM applications, including live-cell, in vivo animal, or endoscopic imaging studies, especially under challenging imaging conditions such as low-light or fast video-rate imaging.

Fluorescence lifetime imaging comes of age how to do it and how to interpret it

Fluorescence lifetime imaging (FLI) has been used widely for measuring biomedical samples. Practical guidelines on taking successful FLI data are provided to avoid common errors that arise during the measurement. Several methods for analyzing and interpreting FLI results are also introduced; e.g., a model-free data analysis method called the polar plot allows visualization and analysis of FLI data without iterative fitting, and an image denoising algorithm called variance-stabilizing-transform TI Haar helps to elucidate the information of a complex biomedical sample. The instrument considerations and data analysis of Spectral-FLI are also discussed.

Spectral resolution in conjunction with polar plots improves the accuracy and reliability of FLIM measurements and estimates of FRET efficiency

A spectrograph with continuous wavelength resolution has been integrated into a frequency-domain fluorescence lifetime-resolved imaging microscope (FLIM). The spectral information assists in the separation of multiple lifetime components, and helps resolve signal cross-talking that can interfere with an accurate analysis of multiple lifetime processes. This extends the number of different dyes that can be measured simultaneously in a FLIM measurement. Spectrally resolved FLIM (spectral-FLIM) also provides a means to measure more accurately the lifetime of a dim fluorescence component (as low as 2% of the total intensity) in the presence of another fluorescence component with a much higher intensity. A more reliable separation of the donor and acceptor fluorescence signals are possible for Förster resonance energy transfer (FRET) measurements; this allows more accurate determinations of both donor and acceptor lifetimes. By combining the polar plot analysis with spectral-FLIM data, the spectral dispersion of the acceptor signal can be used to derive the donor lifetime - and thereby the FRET efficiency - without iterative fitting. The lifetime relation between the donor and acceptor, in conjunction with spectral dispersion, is also used to separate the FRET pair signals from the donor alone signal. This method can be applied further to quantify the signals from separate FRET pairs, and provide information on the dynamics of the FRET pair between different states.

Precise fluorophore lifetime mapping in live-cell, multi-photon excitation microscopy

Fluorophore excited state lifetime is a useful indicator of micro-environment in cellular optical molecular imaging. For quantitative sensing, precise lifetime determination is important, yet is often difficult to accomplish when using the experimental conditions favored by live cells. Here we report the first application of temporal optimization and spatial denoising methods to two-photon time-correlated single photon counting (TCSPC) fluorescence lifetime imaging microscopy (FLIM) to improve lifetime precision in live-cell images. The results demonstrated a greater than five-fold improvement in lifetime precision. This approach minimizes the adverse effects of excitation light on live cells and should benefit FLIM applications to high content analysis and bioimage informatics.

A method to unmix multiple fluorophores in microscopy images with minimal a priori information

The ability to quantify the fluorescence signals from multiply labeled biological samples is highly desirable in the life sciences but often difficult, because of spectral overlap between fluorescent species and the presence of autofluorescence. Several so called unmixing algorithms have been developed to address this problem. Here, we present a novel algorithm that combines measurements of lifetime and spectrum to achieve unmixing without a priori information on the spectral properties of the fluorophore labels. The only assumption made is that the lifetimes of the fluorophores differ. Our method combines global analysis for a measurement of lifetime distributions with singular value decomposition to recover individual fluorescence spectra. We demonstrate the technique on simulated datasets and subsequently by an experiment on a biological sample. The method is computationally efficient and straightforward to implement. Applications range from histopathology of complex and multiply labelled samples to functional imaging in live cells.

Spectrally resolved fluorescent lifetime imaging

Placing an imaging spectrograph or related components capable of generating a spectrum between a microscope and the image intensifier of a conventional fluorescence lifetime imaging (FLIM) system creates a spectrally resolved FLIM (SFLIM). This arrangement provides a number of opportunities not readily available to conventional systems using bandpass filters. The examples include: simultaneous viewing of multiple fluorophores; tracking of both the donor and acceptor; and observation of a range of spectroscopic changes invisible to the conventional FLIM systems. In the frequency-domain implementation of the method, variation in the fractional contributions from different fluorophores along the wavelength dimension can behave as a surrogate for a frequency sweep or spatial variations while analysing fluorophore mixtures. This paper reviews the development of the SFLIM method, provides a theoretical and practical overview of frequency-domain SFLIM including: presentation of the data; manifestations of energy transfer; observation of multiple fluorophores; and the limits of single frequency methods.

Fluorescence lifetime imaging study of a thin protein layer on solid surfaces

Understanding the fundamental interactions between proteins and solid surfaces is essential in the area of implantable medical devices. Fluorescence methods offer the sensitivity required to study the formation of the initial thin protein layers that mediate biocompatibility of materials. Thin protein layers (bovine serum albumin labelled with 1-anilino-8-naphthalenesulfonate, BSA-ANS) deposited on several surfaces (glass, silicon, stainless steel, polystyrene, and silver island film) were studied using confocal frequency domain Fluorescence Lifetime Imaging Microscopy (FLIM) and single-point multifrequency lifetime analysis techniques. FLIM provides spatial information about both fluorophores located on the surface and physicochemical parameters of the surface microenvironment. The average fluorescence lifetimes (tau(av)) of the adsorbed BSA-ANS generated by the contact between a protein solution and the material surface were measured by the multifrequency modulation and phase shift. Results indicate that tau(av) values of the albumin complexes on the surfaces (approximately 12 ns) are, in general, shorter than tau(av) found in the bulk solution (approximately 14 ns). For some surfaces, like polystyrene and silver island film the differences in tau(av) of the adsorbed BSA-ANS were found to be much greater. The differences in fluorescence lifetimes may indicate structural changes in the BSA protein induced by contact with the surface.