Pitfalls and Their Remedies in Time-Resolved Fluorescence Spectroscopy and Microscopy

"Radical" differences between two FLIM microscopes affect interpretation of cell signaling dynamics

The outcome of cell signaling depends not only on signal strength but also on temporal progression. We use Fluorescence Lifetime Imaging of Resonance Energy Transfer (FLIM/FRET) biosensors to investigate intracellular signaling dynamics. We examined the β1 receptor-Gαs-cAMP signaling axis using both widefield frequency domain FLIM (fdFLIM) and fast confocal time-correlated single photon counting (TCSPC) setups. Unexpectedly, we observed that fdFLIM revealed transient cAMP responses in HeLa and Cos7 cells, contrasting with sustained responses as detected with TCSPC. Investigation revealed no light-induced effects on cAMP generation or breakdown. Rather, folic acid present in the imaging medium appeared to be the culprit, as its excitation with blue light sensitized degradation of β1 agonists. Our findings highlight the impact of subtle phototoxicity on experimental outcomes, advocating confocal TCSPC for reliable analysis of response kinetics and stressing the need for full disclosure of chemical formulations by scientific vendors.

Pyglotaran: a lego-like Python framework for global and target analysis of time-resolved spectra

The dynamics of molecular systems can be studied with time-resolved spectroscopy combined with model-based analysis. A Python framework for global and target analysis of time-resolved spectra is introduced with the help of three case studies. The first study, concerning broadband absorption of intersystem crossing in 4-thiothymidine, demonstrates the framework's ability to resolve vibrational wavepackets with a time resolution of ≈10 fs using damped oscillations and their associated spectra and phases. Thereby, a parametric description of the "coherent artifact" is crucial. The second study addresses multichromophoric systems composed of two perylene bisimide chromophores. Here, pyglotaran's guidance spectra and lego-like model composition enable the integration of spectral and kinetic properties of the parent chromophores, revealing a loss process, the undesired production of a radical pair, that reduces the light harvesting efficiency. In the third, time-resolved emission case study of whole photosynthetic cells, a megacomplex containing ≈500 chromophores of five different types is described by a combination of the kinetic models for its elements. As direct fitting of the data by theoretical simulation is unfeasible, our global and target analysis methodology provides a useful 'middle ground' where the theoretical description and the fit of the experimental data can meet. The pyglotaran framework enables the lego-like creation of kinetic models through its modular design and seamless integration with the rich Python ecosystem, particularly Jupyter notebooks. With extensive documentation and a robust validation framework, pyglotaran ensures accessibility and reliability for researchers, serving as an invaluable tool for understanding complex molecular systems.

Functional in vivo imaging using fluorescence lifetime light-sheet microscopy

Light-sheet microscopy has become an indispensable tool for fast, low phototoxicity volumetric imaging of biological samples, predominantly providing structural or analyte concentration data in its standard format. Fluorescence lifetime imaging microscopy (FLIM) provides functional contrast, but often at limited acquisition speeds and with complex implementation. Therefore, we incorporate a dedicated frequency domain CMOS FLIM camera and intensity-modulated laser into a light-sheet setup to add fluorescence lifetime imaging functionality, allowing the rapid acquisition of volumetric data with concentration independent contrast. We then apply the system to image live transgenic zebrafish, demonstrating the capacity to rapidly collect volumetric FLIM data from an in vivo sample.

Effect of the substitution position (2, 3 or 8) on the spectroscopic and photophysical properties of BODIPY dyes with a phenyl, styryl or phenylethynyl group

Understanding the spectroscopic properties of BODIPY dyes for a rational design of tailored fluorescent probes.

A high speed multifocal multiphoton fluorescence lifetime imaging microscope for live-cell FRET imaging

We demonstrate diffraction limited multiphoton imaging in a massively parallel, fully addressable time-resolved multi-beam multiphoton microscope capable of producing fluorescence lifetime images with sub-50ps temporal resolution. This imaging platform offers a significant improvement in acquisition speed over single-beam laser scanning FLIM by a factor of 64 without compromising in either the temporal or spatial resolutions of the system. We demonstrate FLIM acquisition at 500 ms with live cells expressing green fluorescent protein. The applicability of the technique to imaging protein-protein interactions in live cells is exemplified by observation of time-dependent FRET between the epidermal growth factor receptor (EGFR) and the adapter protein Grb2 following stimulation with the receptor ligand. Furthermore, ligand-dependent association of HER2-HER3 receptor tyrosine kinases was observed on a similar timescale and involved the internalisation and accumulation or receptor heterodimers within endosomes. These data demonstrate the broad applicability of this novel FLIM technique to the spatio-temporal dynamics of protein-protein interaction.

Unusual spectroscopic and photophysical properties of meso-tert-butylBODIPY in comparison to related alkylated BODIPY dyes

meso-t-Bu-BODIPY produces unusual spectroscopic and photophysical characteristics in comparison to those of related alkylated BODIPY dyes.

Time-resolved fluorescence methods (IUPAC Technical Report)

This IUPAC Technical Report describes and compares the currently applied methods for measuring and analyzing time-resolved fluorescence traces using phase-modulation fluorometry as well as pulse fluorometry (direct emission decay measurements, single-photon timing, streak camera measurements, fluorescence upconversion, and optical Kerr gating). The paper starts with a brief description of the basic principles for time and frequency domain fluorescence spectroscopy. The fundamental equations are given, and recommendations for adequate use are emphasized. The up-to-date, commonly employed excitation sources and photodetectors are described in detail. The analysis of time-resolved fluorescence data is discussed. Attention is paid to possible artifacts, and remedies are presented on how to avoid them or to account for them. Finally, fluorescence lifetime standards for the nanosecond and picosecond timescales are collected.

Time-resolved fluorescence anisotropy imaging

Fluorescence can be characterized by its intensity, position, wavelength, lifetime, and polarization. The more of these features are acquired in a single measurement, the more can be learned about the sample, i.e., the microenvironment of the fluorescence probe. Polarization-resolved fluorescence lifetime imaging-time-resolved fluorescence anisotropy imaging, TR-FAIM-allows mapping of viscosity or binding or of homo-FRET which can indicate dimerization or generally oligomerization.

In vivo imaging of cerebral energy metabolism with two-photon fluorescence lifetime microscopy of NADH

Minimally invasive, specific measurement of cellular energy metabolism is crucial for understanding cerebral pathophysiology. Here, we present high-resolution, in vivo observations of autofluorescence lifetime as a biomarker of cerebral energy metabolism in exposed rat cortices. We describe a customized two-photon imaging system with time correlated single photon counting detection and specialized software for modeling multiple-component fits of fluorescence decay and monitoring their transient behaviors. In vivo cerebral NADH fluorescence suggests the presence of four distinct components, which respond differently to brief periods of anoxia and likely indicate different enzymatic formulations. Individual components show potential as indicators of specific molecular pathways involved in oxidative metabolism.

Fluorescence anisotropy measurements in solution: Methods and reference materials (IUPAC Technical Report)

After recalling the basic relations relevant to both steady-state and time-resolved fluorescence polarization, it is shown how the values of steady-state polarized intensities recorded experimentally usually need to be corrected for systematic effects and errors, caused by instrumentation and sample properties. A list of selected reference values of steady-state fluorescence anisotropy and polarization is given. Attention is also paid to analysis of time-resolved fluorescence anisotropy data obtained by pulse fluorometry or phase and modulation fluorometry techniques. Recommendations for checking the accuracy of measurements are provided together with a list of selected time-resolved fluorescence anisotropy data as reported in the literature.

State-of-the art comparability of corrected emission spectra. 2. Field laboratory assessment of calibration performance using spectral fluorescence standards

In the second part of this two-part series on the state-of-the-art comparability of corrected emission spectra, we have extended this assessment to the broader community of fluorescence spectroscopists by involving 12 field laboratories that were randomly selected on the basis of their fluorescence measuring equipment. These laboratories performed a reference material (RM)-based fluorometer calibration with commercially available spectral fluorescence standards following a standard operating procedure that involved routine measurement conditions and the data evaluation software LINKCORR developed and provided by the Federal Institute for Materials Research and Testing (BAM). This instrument-specific emission correction curve was subsequently used for the determination of the corrected emission spectra of three test dyes, X, QS, and Y, revealing an average accuracy of 6.8% for the corrected emission spectra. This compares well with the relative standard uncertainties of 4.2% for physical standard-based spectral corrections demonstrated in the first part of this study (previous paper in this issue) involving an international group of four expert laboratories. The excellent comparability of the measurements of the field laboratories also demonstrates the effectiveness of RM-based correction procedures.

Fluorescence lifetime imaging of molecular rotors in living cells

Diffusion is often an important rate-determining step in chemical reactions or biological processes and plays a role in a wide range of intracellular events. Viscosity is one of the key parameters affecting the diffusion of molecules and proteins, and changes in viscosity have been linked to disease and malfunction at the cellular level.^1-3 While methods to measure the bulk viscosity are well developed, imaging microviscosity remains a challenge. Viscosity maps of microscopic objects, such as single cells, have until recently been hard to obtain. Mapping viscosity with fluorescence techniques is advantageous because, similar to other optical techniques, it is minimally invasive, non-destructive and can be applied to living cells and tissues.

Fluorescent molecular rotors exhibit fluorescence lifetimes and quantum yields which are a function of the viscosity of their microenvironment.^4,5 Intramolecular twisting or rotation leads to non-radiative decay from the excited state back to the ground state. A viscous environment slows this rotation or twisting, restricting access to this non-radiative decay pathway. This leads to an increase in the fluorescence quantum yield and the fluorescence lifetime. Fluorescence Lifetime Imaging (FLIM) of modified hydrophobic BODIPY dyes that act as fluorescent molecular rotors show that the fluorescence lifetime of these probes is a function of the microviscosity of their environment.^6-8 A logarithmic plot of the fluorescence lifetime versus the solvent viscosity yields a straight line that obeys the Förster Hoffman equation.⁹ This plot also serves as a calibration graph to convert fluorescence lifetime into viscosity.

Following incubation of living cells with the modified BODIPY fluorescent molecular rotor, a punctate dye distribution is observed in the fluorescence images. The viscosity value obtained in the puncta in live cells is around 100 times higher than that of water and of cellular cytoplasm.^6,7 Time-resolved fluorescence anisotropy measurements yield rotational correlation times in agreement with these large microviscosity values. Mapping the fluorescence lifetime is independent of the fluorescence intensity, and thus allows the separation of probe concentration and viscosity effects.

In summary, we have developed a practical and versatile approach to map the microviscosity in cells based on FLIM of fluorescent molecular rotors.

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.

Analysis of variance in spectroscopic imaging data from human tissues

The analysis of cell types and disease using Fourier transform infrared (FT-IR) spectroscopic imaging is promising. The approach lacks an appreciation of the limits of performance for the technology, however, which limits both researcher efforts in improving the approach and acceptance by practitioners. One factor limiting performance is the variance in data arising from biological diversity, measurement noise or from other sources. Here we identify the sources of variation by first employing a high throughout sampling platform of tissue microarrays (TMAs) to record a sufficiently large and diverse set data. Next, a comprehensive set of analysis of variance (ANOVA) models is employed to analyze the data. Estimating the portions of explained variation, we quantify the primary sources of variation, find the most discriminating spectral metrics, and recognize the aspects of the technology to improve. The study provides a framework for the development of protocols for clinical translation and provides guidelines to design statistically valid studies in the spectroscopic analysis of tissue.

Efficient isolation of Pseudomonas aeruginosa type III secretion translocators and assembly of heteromeric transmembrane pores in model membranes

Translocation of bacterial toxins or effectors into host cells using the type III secretion (T3S) system is a conserved mechanism shared by many Gram-negative pathogens. Pseudomonas aeruginosa injects different proteins across the plasma membrane of target cells, altering the normal metabolism of the host. Protein translocation presumably occurs through a proteinaceous transmembrane pore formed by two T3S secreted protein translocators, PopB and PopD. Unfolded translocators are secreted through the T3S needle prior to insertion into the target membrane. Purified PopB and PopD form pores in model membranes. However, their tendency to form heterogeneous aggregates in solution had hampered the analysis of how these proteins undergo the transition from a denatured state to a membrane-inserted state. Translocators were purified as stable complexes with the cognate chaperone PcrH and isolated from the chaperone using 6 M urea. We report here the assembly of stable transmembrane pores by dilution of urea-denatured translocators in the presence of membranes. PopB and PopD spontaneously bound liposomes containing anionic phospholipids and cholesterol in a pH-dependent manner as observed by two independent assays, time-resolved Förster resonance energy transfer and sucrose-step gradient ultracentrifugation. Using Bodipy-labeled proteins, we found that PopB interacts with PopD on the membrane surface as determined by excitation energy migration and fluorescence quenching. Stable transmembrane pores are more efficiently assembled at pH <5.0, suggesting that acidic residues might be involved in the initial membrane binding and/or insertion. Altogether, the experimental setup described here represents an efficient method for the reconstitution and analysis of membrane-inserted translocators.

Impact of collagen crosslinking on the second harmonic generation signal and the fluorescence lifetime of collagen autofluorescence

BACKGROUND/PURPOSE

Collagen is the major structural protein of the skin and its crosslinks are essential for its mechanical stability. In photodamaged skin, a decrease of the mature collagen crosslink histidinohydroxylysino-norleucine was reported. In this study, we investigated the consequences and measurability of the reduced crosslinking.

METHODS

In order to determine the consequences of reduced collagen crosslinking, in vitro models of reduced collagen crosslinking were established. The collagen synthesis and structure was analyzed using the signals second harmonic generation (SHG) and the fluorescence lifetime of the collagen autofluorescence by a multiphoton laser scanning microscope.

RESULTS

Reduced collagen crosslinking results in a posttranscriptionally diminished collagen synthesis, a modified structure of the collagen fibers and fibrils and a higher intensity of the SHG signal. The SHG signal might be influenced by the interspaces of the collagen molecules within one collagen fibril. Because of these findings, it can be speculated that reduced collagen crosslinking changes the interspace of single collagen molecules within the collagen fibril, resulting in an enhanced SHG signal. Alternative explanations are discussed. Furthermore, the fluorescence lifetime was reduced in the in vitro models of reduced collagen crosslinking. In the crosslink sites of the collagen molecules, the main ratio of fluorescence is found. As the fluorescence lifetime is determined not only by the fluorescent molecule itself but also by its microenvironment, the change in the fluorescence lifetime might be explained by reduced crosslinking at the crosslink site.

CONCLUSION

A reduction of collagen crosslinking (as seen in photodamaged skin) results in an increase of the SHG signal and a decrease of the fluorescence lifetime in vitro. In vivo measurements of the two parameters might reveal the status of collagen crosslinking and therefore help to identify the status of dermal photodamage or pathogenesis using collagen crosslinking determination.

Precise measurement of protein interacting fractions with fluorescence lifetime imaging microscopy

Precise quantification of endogenous protein-protein interactions across live cells would be a major boon to biology. Such precise measurement is theoretically possible with fluorescence lifetime imaging microscopy (FLIM) but requires first properly addressing multiple biological, instrumental, statistical, and photophysical challenges. We present a detailed investigation of the last three FLIM-specific challenges. Using an efficient, highly accurate analysis code for time-domain FLIM data that accounts for all significant instrumental artifacts (in part, through use of a parametrized model for the instrument response function) and is rigorously based on both conventional statistics (full lifetime histogram fitting by χ(2) minimization) and novel statistics (single pixel fitting of lifetime populations using "maximum fidelity"), we address multiple photophysical challenges, including the proper side-by-side statistical comparison of fluorophore monoexponentiality, the precise assessment of fluorophore lifetimes and lifetime photostability, and the determination of acceptor dark state fractions. Finally, we demonstrate the feasibility of precise measurement of the interacting fraction of a protein across live cells with FLIM.

Boron Dipyrromethene Analogs with Phenyl, Styryl, and Ethynylphenyl Substituents: Synthesis, Photophysics, Electrochemistry, and Quantum-Chemical Calculations

Seven fluorescent boradiazaindacene-based compounds with one or two phenyl, ethenylphenyl, and ethynylphenyl substituents at the 3- (or 3,5-) position(s) were synthesized via palladium-catalyzed coupling reactions with the appropriate 3,5-dichloroBODIPY derivative. The effect of the various substituents at the 3- (or 3,5-) position(s) on the spectroscopic and photophysical properties were studied as a function of solvent by means of UV/vis absorption, steady-state, and time-resolved fluorometry, and theoretical modeling. The emission maxima of the symmetrically 3,5-disubstituted dyes are shifted to longer wavelengths (by 30 to 60 nm) relative to the related asymmetrically 3,5-disubstituted ones. Introduction of styryl substituents causes the largest red shift in both the absorption and emission spectra. BODIPY derivatives with ethynylaryl groups also shift the spectral maxima to longer wavelengths compared to aryl-substituted ones but to a lesser degree than the styryl compounds. The quantum-chemical calculations confirm these trends and provide a rationale for the spectral shifts induced by substitution. The fluorescence quantum yields of the ethenylaryl and ethynylaryl analogs are significantly higher that those of the aryl-substituted dyes. The 3,5-diethynylaryl dye has the highest fluorescence quantum yield (approximately 1.0) and longest lifetime (around 6.5 ns) among the BODIPY dyes studied. The differences in the photophysical properties of the dyes are also reflected in their electrochemical properties where the symmetrically 3,5-disubstituted dyes display much lower oxidation potentials when compared to their asymmetric counterparts.

Fluorescence lifetime standards for time and frequency domain fluorescence spectroscopy

A series of fluorophores with single-exponential fluorescence decays in liquid solution at 20 degrees C were measured independently by nine laboratories using single-photon timing and multifrequency phase and modulation fluorometry instruments with lasers as excitation source. The dyes that can serve as fluorescence lifetime standards for time-domain and frequency-domain measurements are all commercially available, are photostable under the conditions of the measurements, and are soluble in solvents of spectroscopic quality (methanol, cyclohexane, water). These lifetime standards are anthracene, 9-cyanoanthracene, 9,10-diphenylanthracene, N-methylcarbazole, coumarin 153, erythrosin B, N-acetyl-l-tryptophanamide, 1,4-bis(5-phenyloxazol-2-yl)benzene, 2,5-diphenyloxazole, rhodamine B, rubrene, N-(3-sulfopropyl)acridinium, and 1,4-diphenylbenzene. At 20 degrees C, the fluorescence lifetimes vary from 89 ps to 31.2 ns, depending on fluorescent dye and solvent, which is a useful range for modern pico- and nanosecond time-domain or mega- to gigahertz frequency-domain instrumentation. The decay times are independent of the excitation and emission wavelengths. Dependent on the structure of the dye and the solvent, the excitation wavelengths used range from 284 to 575 nm, the emission from 330 to 630 nm. These lifetime standards may be used to either calibrate or test the resolution of time- and frequency-domain instrumentation or as reference compounds to eliminate the color effect in photomultiplier tubes. Statistical analyses by means of two-sample charts indicate that there is no laboratory bias in the lifetime determinations. Moreover, statistical tests show that there is an excellent correlation between the lifetimes estimated by the time-domain and frequency-domain fluorometries. Comprehensive tables compiling the results for 20 (fluorescence lifetime standard/solvent) combinations are given.

Photophysics of 3,5-diphenoxy substituted BODIPY dyes in solution

We have prepared two fluorescent dyes derived from 8-(4-tolyl)-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene with phenoxy and (o-bromo)phenoxy substituents at the 3,5-positions by a novel nucleophilic substitution reaction of the corresponding 3,5-dichloroBODIPY analogue. UV-vis absorption, steady-state and time-resolved fluorimetry have been used to investigate their solvent-dependent photophysical properties. The two BODIPY derivatives show narrow absorption and emission bands and display small Stokes shifts. The substituents at the 3,5-positions (phenoxy in 1 and o-bromophenoxy in 2) have a minor effect on the fluorescence quantum yields (0.16-0.40 for 1, 0.17-0.44 for 2) and lifetimes (1.09-2.51 ns for 1, 1.11-2.78 ns for 2). For both compounds, the fluorescence rate constant equals (1.5 +/- 0.1) x 10(8) s(-1).

Calibration of a wide-field frequency-domain fluorescence lifetime microscopy system using light emitting diodes as light sources

High brightness light emitting diodes are an inexpensive and versatile light source for wide-field frequency-domain fluorescence lifetime imaging microscopy. In this paper a full calibration of an LED based fluorescence lifetime imaging microscopy system is presented for the first time. A radio-frequency generator was used for simultaneous modulation of light emitting diode (LED) intensity and the gain of an intensified charge coupled device (CCD) camera. A homodyne detection scheme was employed to measure the demodulation and phase shift of the emitted fluorescence, from which phase and modulation lifetimes were determined at each image pixel. The system was characterized both in terms of its sensitivity to measure short lifetimes (500 ps to 4 ns), and its capability to distinguish image features with small lifetime differences. Calibration measurements were performed in quenched solutions containing Rhodamine 6G dye and the results compared to several independent measurements performed with other measurement methodologies, including time correlated single photon counting, time gated detection, and acousto optical modulator (AOM) based modulation of excitation sources. Results are presented from measurements and simulations. The effects of limited signal-to-noise ratios, baseline drifts and calibration errors are discussed in detail. The implications of limited modulation bandwidth of high brightness, large area LED devices ( approximately 40 MHz for devices used here) are presented. The results show that phase lifetime measurements are robust down to sub ns levels, whereas modulation lifetimes are prone to errors even at large signal-to-noise ratios. Strategies for optimizing measurement fidelity are discussed. Application of the fluorescence lifetime imaging microscopy system is illustrated with examples from studies of molecular mixing in microfluidic devices and targeted drug delivery research.