Wide-field fluorescence lifetime imaging of neuron spiking and subthreshold activity in vivo

High-throughput fluorescence lifetime imaging flow cytometry

Flow cytometry is a vital tool in biomedical research and laboratory medicine. However, its accuracy is often compromised by undesired fluctuations in fluorescence intensity. While fluorescence lifetime imaging microscopy (FLIM) bypasses this challenge as fluorescence lifetime remains unaffected by such fluctuations, the full integration of FLIM into flow cytometry has yet to be demonstrated due to speed limitations. Here we overcome the speed limitations in FLIM, thereby enabling high-throughput FLIM flow cytometry at a high rate of over 10,000 cells per second. This is made possible by using dual intensity-modulated continuous-wave beam arrays with complementary modulation frequency pairs for fluorophore excitation and acquiring fluorescence lifetime images of rapidly flowing cells. Moreover, our FLIM system distinguishes subpopulations in male rat glioma and captures dynamic changes in the cell nucleus induced by an anti-cancer drug. FLIM flow cytometry significantly enhances cellular analysis capabilities, providing detailed insights into cellular functions, interactions, and environments.

The promise and peril of comparing fluorescence lifetime in biology revealed by simulations

Signaling dynamics are crucial in biological systems, and biosensor-based real-time imaging has revolutionized their analysis. Fluorescence lifetime imaging microscopy (FLIM) excels over the widely used fluorescence intensity imaging by allowing the measurement of absolute signal levels, independent of sensor concentration. This capability enables the comparison of signaling dynamics across different animals, body regions, and timeframes. However, FLIM's advantage can be compromised by factors like autofluorescence in biological experiments. To address this, we introduce FLiSimBA, a flexible computational framework for realistic F luorescence Li fetime Sim ulation for B iological A pplications. Through simulations, we analyze the signal-to-noise ratios of fluorescence lifetime data, determining measurement uncertainty and providing necessary error bars for lifetime measurements. Furthermore, we challenge the belief that fluorescence lifetime is unaffected by sensor expression and establish quantitative limits to this insensitivity in biological applications. Additionally, we propose innovations, notably multiplexed dynamic imaging that combines fluorescence intensity and lifetime measurements. This innovation can transform the number of signals that can be simultaneously monitored, thereby enabling a systems approach in studying signaling dynamics. Thus, by incorporating diverse factors into our simulation framework, we uncover surprises, identify limitations, and propose advancements for fluorescence lifetime imaging in biology. This quantitative framework supports rigorous experimental design, facilitates accurate data interpretation, and paves the way for technological advancements in fluorescence lifetime imaging.

Advancements in fluorescence lifetime imaging microscopy Instrumentation: Towards high speed and 3D

Fluorescence lifetime imaging microscopy (FLIM) is a powerful imaging tool offering molecular specific insights into samples through the measurement of fluorescence decay time, with promising applications in diverse research fields. However, to acquire two-dimensional lifetime images, conventional FLIM relies on extensive scanning in both the spatial and temporal domain, resulting in much slower acquisition rates compared to intensity-based approaches. This problem is further magnified in three-dimensional imaging, as it necessitates additional scanning along the depth axis. Recent advancements have aimed to enhance the speed and three-dimensional imaging capabilities of FLIM. This review explores the progress made in addressing these challenges and discusses potential directions for future developments in FLIM instrumentation.

Single-sample image-fusion upsampling of fluorescence lifetime images

Fluorescence lifetime imaging microscopy (FLIM) provides detailed information about molecular interactions and biological processes. A major bottleneck for FLIM is image resolution at high acquisition speeds due to the engineering and signal-processing limitations of time-resolved imaging technology. Here, we present single-sample image-fusion upsampling, a data-fusion approach to computational FLIM super-resolution that combines measurements from a low-resolution time-resolved detector (that measures photon arrival time) and a high-resolution camera (that measures intensity only). To solve this otherwise ill-posed inverse retrieval problem, we introduce statistically informed priors that encode local and global correlations between the two "single-sample" measurements. This bypasses the risk of out-of-distribution hallucination as in traditional data-driven approaches and delivers enhanced images compared, for example, to standard bilinear interpolation. The general approach laid out by single-sample image-fusion upsampling can be applied to other image super-resolution problems where two different datasets are available.

Pioglitazone Phases and Metabolic Effects in Nanoparticle-Treated Cells Analyzed via Rapid Visualization of FLIM Images

Fluorescence lifetime imaging microscopy (FLIM) has proven to be a useful method for analyzing various aspects of material science and biology, like the supramolecular organization of (slightly) fluorescent compounds or the metabolic activity in non-labeled cells; in particular, FLIM phasor analysis (phasor-FLIM) has the potential for an intuitive representation of complex fluorescence decays and therefore of the analyzed properties. Here we present and make available tools to fully exploit this potential, in particular by coding via hue, saturation, and intensity the phasor positions and their weights both in the phasor plot and in the microscope image. We apply these tools to analyze FLIM data acquired via two-photon microscopy to visualize: (i) different phases of the drug pioglitazone (PGZ) in solutions and/or crystals, (ii) the position in the phasor plot of non-labelled poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs), and (iii) the effect of PGZ or PGZ-containing NPs on the metabolism of insulinoma (INS-1 E) model cells. PGZ is recognized for its efficacy in addressing insulin resistance and hyperglycemia in type 2 diabetes mellitus, and polymeric nanoparticles offer versatile platforms for drug delivery due to their biocompatibility and controlled release kinetics. This study lays the foundation for a better understanding via phasor-FLIM of the organization and effects of drugs, in particular, PGZ, within NPs, aiming at better control of encapsulation and pharmacokinetics, and potentially at novel anti-diabetics theragnostic nanotools.

A red-emitting carborhodamine for monitoring and measuring membrane potential

Biological membrane potentials, or voltages, are a central facet of cellular life. Optical methods to visualize cellular membrane voltages with fluorescent indicators are an attractive complement to traditional electrode-based approaches, since imaging methods can be high throughput, less invasive, and provide more spatial resolution than electrodes. Recently developed fluorescent indicators for voltage largely report changes in membrane voltage by monitoring voltage-dependent fluctuations in fluorescence intensity. However, it would be useful to be able to not only monitor changes but also measure values of membrane potentials. This study discloses a fluorescent indicator which can address both. We describe the synthesis of a sulfonated tetramethyl carborhodamine fluorophore. When this carborhodamine is conjugated with an electron-rich, methoxy (-OMe) containing phenylenevinylene molecular wire, the resulting molecule, CRhOMe, is a voltage-sensitive fluorophore with red/far-red fluorescence. Using CRhOMe, changes in cellular membrane potential can be read out using fluorescence intensity or lifetime. In fluorescence intensity mode, CRhOMe tracks fast-spiking neuronal action potentials (APs) with greater signal-to-noise than state-of-the-art BeRST 1 (another voltage-sensitive fluorophore). CRhOMe can also measure values of membrane potential. The fluorescence lifetime of CRhOMe follows a single exponential decay, substantially improving the quantification of membrane potential values using fluorescence lifetime imaging microscopy (FLIM). The combination of red-shifted excitation and emission, mono-exponential decay, and high voltage sensitivity enable fast FLIM recording of APs in cardiomyocytes. The ability to both monitor and measure membrane potentials with red light using CRhOMe makes it an important approach for studying biological voltages.

Chirality-Regulated Clusteroluminescence in Polypeptides

The low emission efficiency of clusteroluminogens restricts their practical applications in the fields of sensors and biological imaging. In this work, the clusteroluminescence of ordered/disordered polypeptides was observed, and the photoluminescence (PL) intensity of polypeptides can be modulated by the chirality of amino acid residues. Polyglutamates with different chiral compositions were synthesized, and the racemic polypeptides exhibited a significantly higher PL intensity than the enantiopure ones. This emission originates from the n-π* transition between C═O groups of polypeptides and is enhanced by clusterization of polypeptides. CD and Fourier transform infrared spectra demonstrated that the enantiopure and racemic polypeptides form α-helix and random coil structures, respectively. The disordered polypeptides can form more chain entanglements and interchain interactions because of their high flexibility, leading to more clusterizations and stronger PL intensity. The rigidity of ordered helical structures restrains the chain entanglements, and the formation of intrachain hydrogen bonds between amide groups of the backbone impairs the interchain interaction between polypeptides, resulting in lower PL intensity. The PL intensity of the polypeptides can also be manipulated by the addition of urea or trifluoroacetic acid. Our study not only elucidates the chirality/order-based structure-property relationship of clusteroluminescence in peptide-based polymers but also offers implications for the rational design of fluorescent peptides/proteins.

Optical Estimation of Membrane Potential Values Using Fluorescence Lifetime Imaging Microscopy and Hybrid Chemical-Genetic Voltage Indicators

Introduction

Membrane potential (Vm), the voltage across a cell membrane, is an important biophysical phenomenon, central to the physiology of cells, tissues, and organisms. Voltage-sensitive fluorescent indicators are a powerful method for interrogating membrane potential in living systems, but most indicators are best suited for detecting changes in membrane potential rather than measuring values of the membrane potential. One promising approach is to use fluorescence lifetime imaging microscopy (FLIM) in combination of chemically synthesized dyes to estimate a value of membrane potential. However, a drawback is that chemically synthesized dyes show poor specificity of staining.

Objectives

To address this problem, we applied a chemical-genetic voltage imaging approach to FLIM to enable optical estimation of membrane potential values from genetically defined cells.

Results

In this report, we detail the characterization and evaluation of two of these systems in mammalian cells. We further validate the use of a FLIM-based chemical genetic voltage indicator in mammalian neurons.

Conclusions

Finally, we discuss opportunities for future improvements to chemical-genetic FLIM-based voltage indicators.

Fast and slow: Recording neuromodulator dynamics across both transient and chronic time scales

Neuromodulators transform animal behaviors. Recent research has demonstrated the importance of both sustained and transient change in neuromodulators, likely due to tonic and phasic neuromodulator release. However, no method could simultaneously record both types of dynamics. Fluorescence lifetime of optical reporters could offer a solution because it allows high temporal resolution and is impervious to sensor expression differences across chronic periods. Nevertheless, no fluorescence lifetime change across the entire classes of neuromodulator sensors was previously known. Unexpectedly, we find that several intensity-based neuromodulator sensors also exhibit fluorescence lifetime responses. Furthermore, we show that lifetime measures in vivo neuromodulator dynamics both with high temporal resolution and with consistency across animals and time. Thus, we report a method that can simultaneously measure neuromodulator change over transient and chronic time scales, promising to reveal the roles of multi-time scale neuromodulator dynamics in diseases, in response to therapies, and across development and aging.

Nanocrystals for Deep-Tissue In Vivo Luminescence Imaging in the Near-Infrared Region

In vivo imaging technologies have emerged as a powerful tool for both fundamental research and clinical practice. In particular, luminescence imaging in the tissue-transparent near-infrared (NIR, 700-1700 nm) region offers tremendous potential for visualizing biological architectures and pathophysiological events in living subjects with deep tissue penetration and high imaging contrast owing to the reduced light-tissue interactions of absorption, scattering, and autofluorescence. The distinctive quantum effects of nanocrystals have been harnessed to achieve exceptional photophysical properties, establishing them as a promising category of luminescent probes. In this comprehensive review, the interactions between light and biological tissues, as well as the advantages of NIR light for in vivo luminescence imaging, are initially elaborated. Subsequently, we focus on achieving deep tissue penetration and improved imaging contrast by optimizing the performance of nanocrystal fluorophores. The ingenious design strategies of NIR nanocrystal probes are discussed, along with their respective biomedical applications in versatile in vivo luminescence imaging modalities. Finally, thought-provoking reflections on the challenges and prospects for future clinical translation of nanocrystal-based in vivo luminescence imaging in the NIR region are wisely provided.

Phasor identifier: A cloud-based analysis of phasor-FLIM data on Python notebooks

This paper introduces an innovative approach utilizing Google Colaboratory for the versatile analysis of phasor fluorescence lifetime imaging microscopy (FLIM) data collected from various samples (e.g., cuvette, cells, tissues) and in various input file formats. In fact, phasor-FLIM widespread adoption has been hampered by complex instrumentation and data analysis requirements. We mean to make advanced FLIM analysis more accessible to researchers through a cloud-based solution that 1) harnesses robust computational resources, 2) eliminates hardware limitations, and 3) supports both CPU and GPU processing. We envision a paradigm shift in FLIM data accessibility and potential, aligning with the evolving field of artificial intelligence-driven FLIM analysis. This approach simplifies FLIM data handling and opens doors for diverse applications, from studying cellular metabolism to investigating drug encapsulation, benefiting researchers across multiple domains. The comparative analysis of freely distributed FLIM tools highlights the unique advantages of this approach in terms of adaptability, scalability, and open-source nature.

A red-emitting carborhodamine for monitoring and measuring membrane potential

Biological membrane potentials, or voltages, are a central facet of cellular life. Optical methods to visualize cellular membrane voltages with fluorescent indicators are an attractive complement to traditional electrode-based approaches, since imaging methods can be high throughput, less invasive, and provide more spatial resolution than electrodes. Recently developed fluorescent indicators for voltage largely report changes in membrane voltage by monitoring voltage-dependent fluctuations in fluorescence intensity. However, it would be useful to be able to not only monitor changes, but also measure values of membrane potentials. This study discloses a new fluorescent indicator which can address both. We describe the synthesis of a new sulfonated tetramethyl carborhodamine fluorophore. When this carborhodamine is conjugated with an electron-rich, methoxy (-OMe) containing phenylenevinylene molecular wire, the resulting molecule, CRhOMe, is a voltage-sensitive fluorophore with red/far-red fluorescence. Using CRhOMe, changes in cellular membrane potential can be read out using fluorescence intensity or lifetime. In fluorescence intensity mode, CRhOMe tracks fast-spiking neuronal action potentials with greater signal-to-noise than state-of-the-art BeRST (another voltage-sensitive fluorophore). CRhOMe can also measure values of membrane potential. The fluorescence lifetime of CRhOMe follows a single exponential decay, substantially improving the quantification of membrane potential values using fluorescence lifetime imaging microscopy (FLIM). The combination of red-shifted excitation and emission, mono-exponential decay, and high voltage sensitivity enable fast FLIM recording of action potentials in cardiomyocytes. The ability to both monitor and measure membrane potentials with red light using CRhOMe makes it an important approach for studying biological voltages.

Open Questions about the Roles of DnaA, Related Proteins, and Hyperstructure Dynamics in the Cell Cycle

The DnaA protein has long been considered to play the key role in the initiation of chromosome replication in modern bacteria. Many questions about this role, however, remain unanswered. Here, we raise these questions within a framework based on the dynamics of hyperstructures, alias large assemblies of molecules and macromolecules that perform a function. In these dynamics, hyperstructures can (1) emit and receive signals or (2) fuse and separate from one another. We ask whether the DnaA-based initiation hyperstructure acts as a logic gate receiving information from the membrane, the chromosome, and metabolism to trigger replication; we try to phrase some of these questions in terms of DNA supercoiling, strand opening, glycolytic enzymes, SeqA, ribonucleotide reductase, the macromolecular synthesis operon, post-translational modifications, and metabolic pools. Finally, we ask whether, underpinning the regulation of the cell cycle, there is a physico-chemical clock inherited from the first protocells, and whether this clock emits a single signal that triggers both chromosome replication and cell division.