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The effects of photobleaching on electrochemiluminescence (ECL) was investigated for the first time. The plasma membrane of Chinese Hamster Ovary (CHO) cells was labeled with a [Ru(bpy)3 ]2+ derivative. Selected regions of the fixed cells were photobleached using the confocal mode with sequential stepwise illumination or cumulatively and they were imaged by both ECL and photoluminescence (PL). ECL was generated with a model sacrificial coreactant, tri-n-propylamine. ECL microscopy of the photobleached regions shows lower ECL emission. We demonstrate a linear correlation between the ECL decrease and the PL loss due to the photobleaching of the labels immobilized on the CHO membranes. The presented strategy provides valuable information on the fundamentals of the ECL excited state and opens new opportunities for exploring cellular membranes by combining ECL microscopy with photobleaching techniques such as fluorescence recovery after photobleaching (FRAP) or fluorescence loss in photobleaching (FLIP) methods.

International audience; By limiting protein exchange between the soma and the axon, the axon initial segment (AIS) enables the segregation of specific proteins and hence the differentiation of the somatodendritic compartment and the axonal compartment. Electron microscopy and super-resolution fluorescence imaging have provided important insights in the ultrastructure of the AIS. Yet, the full extent of its filtering properties is not fully delineated. In particular, it is unclear whether and how the AIS opposes the free exchange of soluble proteins. Here we describe a robust framework to combine whole-cell photobleaching and retrospective high-resolution imaging in developing neurons. With this assay, we found that cytoplasmic soluble proteins that are not excluded from the axon upon expression over tens of hours exhibit a strong mobility reduction at the AIS-i.e., are indeed compartmentalized-when monitored over tens of minutes. This form of compartmentalization is developmentally regulated, requires intact F-actin and may be correlated with the composition and ultrastructure of the submembranous spectrin cytoskeleton. Using computational modeling, we provide evidence that both neuronal morphology and the AIS regulate this compartmentalization but act on distinct time scales, with the AIS having a more pronounced effect on fast exchanges. Our results thus suggest that the rate of protein accumulation in the soma may impact to what extent and over which timescales freely moving molecules can be segregated from the axon. This in turn has important implications for our understanding of compartment-specific signaling in neurons.

Fluorescence loss in photobleaching (FLIP) is a modern microscopy method for visualization of transport processes in living cells. This paper presents the simulation of FLIP sequences based on a calibrated reaction–diffusion system defined on segmented cell images. By the use of a discontinuous Galerkin method, the computational complexity is drastically reduced compared to continuous Galerkin methods. Using this approach on green fluorescent protein (GFP), we can determine its intracellular diffusion constant, the strength of localized hindrance to diffusion as well as the permeability of the nuclear membrane for GFP passage, directly from the FLIP image series. Thus, we present for the first time, to our knowledge, a quantitative computational FLIP method for inferring several molecular transport parameters in parallel from FLIP image data acquired at commercial microscope systems.

The intraparticle diffusion of a fluorescent dye in single microparticles in an aqueous solution was analyzed using fluorescence recovery after photobleaching, with a confocal fluorescence microscope. The fluorescence depth profile of single microparticles, and the fluorescence recovery at the particle center, were measured; further, the intraparticle diffusion coefficient was determined through simulations of three-dimensional diffusion in the respective microparticles. The intraparticle diffusion of coumarin 102 in octadecylsilyl silica gel was limited by the surface diffusion.

BCL-XL, an anti-apoptotic BCL-2 family protein, potently inhibits BAK oligomerization and the formation of toxic mitochondrial pores in response to cellular stress. This report aims to explore which form of mitochondrial monomeric and oligomerized BAK can be retrotranslocated by BCL-XL. Fluorescence imaging of living cells co-expressing CFP-BCL-XL and YFP-BAK showed that BCL-XL markedly inhibited mitochondrial BAK oligomerization and resulted in partial cytosolic BAK distribution. Live-cell fluorescence resonance energy transfer (FRET) analyses showed that BAK auto-oligomerized on mitochondria and BCL-XL physically sequestrated monomeric BAK to prevent BAK oligomerization. Fluorescence loss in photobleaching (FLIP) analyses showed that BCL-XL retrotranslocated the monomeric BAK from mitochondria into cytosol, whereas monomeric BAK reduced the retrotranslocation rate of BCL-XL. Live-cell time-lapse imaging and FLIP experiments in living cells with BAK oligomers displayed that BCL-XL did not depolymerize or retrotranslocate the oligomerized BAK. Collectively, BCL-XL retrotranslocates monomeric instead of oligomerized BAK from mitochondria into cytosol.

The export of photosynthetically produced sugars from leaves depends on plasmodesmatal transport of sugar molecules from mesophyll to phloem. Traditionally, the density of plasmodesmata (PD) along this phloem loading pathway has been used as a defining feature of different phloem loading types, with species proposed to have either many or few PD between the phloem and surrounding cells of the leaf. However, quantitative determination of PD density has rarely been performed. Moreover, the structure of PD has not been considered, even though it could impact permeability, and functional data is only available for very few species. Here, a comparison of PD density, structure and function using data from transmission electron microscopy and live-cell microscopy was conducted for all relevant cell-cell interfaces in leaves of nine species. These species represent the three principal phloem loading types currently discussed in literature. Results show that relative PD density among the different cell-cell interfaces in one species, but not absolute PD density, is indicative of phloem loading type. PD density data of single interfaces, even combined with PD diameter and length data, did not correlate with the intercellular diffusion capacity measured by the fluorescence loss in photobleaching method. This means that PD substructure not visible on standard transmission electron micrographs may have a strong influence on permeability. Furthermore, the results support a proposed passive symplasmic loading mechanism in the tree species horse-chestnut (Aesculus hippocastanum), birch (Betula pubescens), apple (Malus domestica) and poplar (Populus x canescens) as functional cell coupling and PD structure differed from active symplasmic and apoplasmic phloem loading species.

Single-molecule fluorescence microscopy (SMFM) is a powerful technique in monitoring single molecular machine actions at ambient conditions. To improve the fluorescence intensity and photostability, one strategy is to attach multiple dyes to the same single molecular machine. However, it is unclear how the fluorescence property of the dyes will change when multiple dyes are compacted into the same molecule within a distance between them of ∼2 nm. In this study, we investigated the photophysics of two types of single molecular machines that are each equipped with two BODIPY dyes with different distances. We found that at the air–glass interface, single molecules attached with two dyes have a high tendency to show a single-step-like photobleaching, making them to appear like a single dye. We propose that the product of the first photobleaching event, possibly a superoxide anion radical, is involved in the destruction of the neighboring dye. In addition, the fluorescence intensity of the two-dye system does ...

Photoswitchable fluorophores are promising in single-molecule optical devices and super-resolution fluorescence imaging, especially in single-molecule photo-activated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM). However, the scarcity of current photoswitchable fluorophores stimulates researchers to develop complicated optical systems and processing software, in accordance with the limited photoswitchable fluorescent proteins and organic fluorophores. Previous efforts to develop synthetic photoswitchable fluorophores have exhibited their promising potential in super-resolution fluorescence imaging. Here, we have designed and synthesized a fluorescence molecular switch with reversible green emission, a napthalimide-hexaarylbiimidazole conjugate (NI-N-HABI), which exhibits strong fluorescence in the emissive state, with fast thermal fading of the photochromism and spontaneous fluorescence recovery after photobleaching (FRAP) induced by blue-light. The photoswitchable fluorophore enables the red-edge wavelength of the optical response to red-shift from the initial near-UV region at less than 400 nm, to 500 nm. The relatively fast fading speed of NI-N-HABI and its sensitivity to longer blue-light irradiation (400-500 nm) have allowed simplification of the optical microscopic system from a two-wavelength laser source to a single-wavelength laser. We applied NI-N-HABI in single-wavelength-controlled in situ dynamic super-resolution fluorescence imaging for the self-assembly and solvent annealing of amphiphilic block polymers, with 50 nm of optical resolution. Single-wavelength-controlled dynamic super-resolution fluorescence imaging facilitates nanoscale optical visualization for the dynamic physical and chemical fluctuation processes of stimuli-responsive nanostructures.

Photobleaching of fluorophores is one of the key problems in fluorescence microscopy. Overcoming the limitation of the maximum number of photons, which can be detected from a single emitter, would allow one to enhance the signal-to-noise ratio and thus the temporal and spatial resolution in fluorescence imaging. It would be a breakthrough for many applications of fluorescence spectroscopy, which are unachievable up to now. So far, the only approach for diminishing the effect of photobleaching has been to enhance the photostability of an emitter. Here, we present a fundamentally new solution for increasing the number of photons emitted by a fluorophore. We show that, by exposing a single SiO2 nanoparticle to UV illumination, one can create new luminescent centers within this particle. By analogy with nanodiamonds, SiO2 nanoparticles can possess luminescent defects in their regular SiO2 structure. However, due to the much weaker chemical bonds, it is possible to generate new defects in SiO2 nanostructures using UV light. This allows for the reactivation of the nanoparticle's fluorescence after its photobleaching.

The green fluorescent protein has gained interest in bioanalytical applications due to its visible fluorescence. As the usage of green fluorescent protein increases, more appropriate fluorescence instrumentation is required. Most fluorescence instrumentation uses ultraviolet light as the excitation source for the determination of green fluorescent protein. However, ultraviolet radiation may damage biological molecules and affect the quantitative analysis. In this study, the effects of the ultraviolet radiation period and the mass of green fluorescent protein on the fluorescence determination were characterized using gel imaging. The ultraviolet illumination period affected the green fluorescent protein fluorescence intensity. The fluorescence increased with the ultraviolet illumination time from 30–90 s. However, the fluorescence intensity decreased when the excitation period was longer, probably due to photobleaching. The photobleaching decreased when a higher concentration of enhanced green fluo...

Lee et al. show that the ER in the C. elegans embryo is continuous, but its membrane is compartmentalized, as found in budding yeast and mouse NSCs. This compartmentalization plays a potential role in the polarity of the early embryo., The one-cell Caenorhabditis elegans embryo is polarized to partition fate determinants between the cell lineages generated during its first division. Using fluorescence loss in photobleaching, we find that the endoplasmic reticulum (ER) of the C. elegans embryo is physically continuous throughout the cell, but its membrane is compartmentalized shortly before nuclear envelope breakdown into an anterior and a posterior domain, indicating that a diffusion barrier forms in the ER membrane between these two domains. Using mutants with disorganized ER, we show that ER compartmentalization is independent of the morphological transition that the ER undergoes in mitosis. In contrast, compartmentalization takes place at the position of the future cleavage plane in a par-3–dependent manner. Together, our data indicate that the ER membrane is compartmentalized in cells as diverse as budding yeast, mouse neural stem cells, and the early C. elegans embryo.

Cholesterol is an abundant and important lipid component of cellular membranes. Analysis of cholesterol transport and diffusion in living cells is hampered by the technical challenge of designing suitable cholesterol probes which can be detected for example by optical microscopy. One strategy is to use intrinsically fluorescent sterols, as dehydroergosterol (DHE), having minimal chemical alteration compared to cholesterol but giving low fluorescence signals in the UV region of the spectrum. Alternatively, one can use dye-tagged cholesterol analogs and in particular BODIPY-cholesterol (BChol), whose synthesis and initial characterization was pioneered by Robert Bittman. Here, we give a general overview of the properties and applications but also limitations of BODIPY-tagged cholesterol probes for analyzing intracellular cholesterol trafficking. We describe our own experiences and collaborative efforts with Bob Bittman for studying diffusion in the plasma membrane (PM) and uptake of BChol in a quantitative manner. For that purpose, we used a variety of fluorescence approaches including fluorescence correlation spectroscopy and its imaging variants, fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP). We also describe pulse-chase studies from the PM using BChol in direct comparison to DHE. Based on the gathered imaging data, we present a two-step kinetic model for sterol transport between PM and recycling endosomes. In addition, we highlight the suitability of BChol for determining transport of lipoprotein-derived sterol using electron microscopy (EM) and show that this approach ideally complements fluorescence studies.

Background Intracellular phase separation and aggregation of proteins with extended poly-glutamine (polyQ) stretches are hallmarks of various age-associated neurodegenerative diseases. Progress in our understanding of such processes heavily relies on quantitative fluorescence imaging of suitably tagged proteins. Fluorescence loss in photobleaching (FLIP) is particularly well-suited to study the dynamics of protein aggregation in cellular models of Chorea Huntington and other polyQ diseases, as FLIP gives access to the full spatio-temporal profile of intensity changes in the cell geometry. In contrast to other methods, also dim aggregates become visible during time evolution of fluorescence loss in cellular compartments. However, methods for computational analysis of FLIP data are sparse, and transport models for estimation of transport and diffusion parameters from experimental FLIP sequences are missing. Results In this paper, we present a computational method for analysis of FLIP imaging experiments of intracellular polyglutamine protein aggregates also called inclusion bodies (IBs). By this method, we can determine the diffusion constant and nuclear membrane transport coefficients of polyQ proteins as well as the exchange rates between aggregates and the cytoplasm. Our method is based on a reaction-diffusion multi-compartment model defined on a mesh obtained by segmentation of the cell images from the FLIP sequence. The discontinuous Galerkin (DG) method is used for numerical implementation of our model in FEniCS, which greatly reduces the computing time. The method is applied to representative experimental FLIP sequences, and consistent estimates of all transport parameters are obtained. Conclusions By directly estimating the transport parameters from live-cell image sequences using our new computational FLIP approach surprisingly fast exchange dynamics of mutant Huntingtin between cytoplasm and dim IBs could be revealed. This is likely relevant also for other polyQ diseases. Thus, our method allows for quantifying protein dynamics at different stages of the protein aggregation process in cellular models of neurodegeneration. Electronic supplementary material The online version of this article (10.1186/s13628-018-0046-0) contains supplementary material, which is available to authorized users.

Importin 13 (IPO13) is a key member of the importin β superfamily, which can transport cargoes both into and out of the nucleus to contribute to a variety of important cellular processes. IPO13 is known to undergo phosphorylation, but the impact of this on function has not been investigated. Here, we show for the first time that IPO13 is phosphorylated by cAMP-dependent protein kinase A specifically at serine 193. Results from fluorescence recovery after photobleaching and fluorescence loss in photobleaching approaches establish that negative charge at serine 193 through phosphorylation or point mutation both reduces IPO13 nuclear import and increases its nuclear export. Importantly, phosphorylation also appears to enhance cargo interaction on the part of IPO13, with significant impact on localization, as shown for the Pax6 homeobox-containing transcription partner. This is the first report that IPO13 can be phosphorylated at Ser193 and that this modification regulates IPO13 subcellular localization and nucleocytoplasmic transport function, with important implications for IPO13's role in development and other processes.

The fluorescence labeling technology has opened new horizons in chemistry and biosciences, by turning nonluminescent or weakly luminescent molecules into highly fluorescent products. Fluorescence labeling, that can be achieved by covalent labeling, noncovalent binding, enzymatic reactions, metal complexation and other particular reactions, is a powerful tool for the analysis of a number of biomolecules and other solutes with high sensitivity and selectivity. Most of the methods developed for fluorescence labeling are based on the use organic fluorophores, metal centered dyes, molecular beacons, fluorescent proteins, among others. Besides, a novel family of fluorophores comprising luminescent nanoparticles provides several advantages over conventional labels, such as high quantum yield and less susceptibility to bleaching. In this article, the basic principles of different fluorescent labeling techniques relevant to chemistry and biology, their advantaged and drawbacks, are discussed.

Luminescence lifetime is an important characteristic of fluorescent molecules. The radiative fluorescence lifetime τ r is related to the time the fluorophore remains on average in the excited state before emission takes place. Most of fluorophores display lifetimes from 1 to 10 ns. Lifetime measurements can reveal dynamic information on the nanosecond timescale, where some processes like rotational diffusion, resonance-energy transfer, or dynamic quenching occur. Therefore, they can be used not only in analytical methodologies to enhance selectivity and/or to perform multicomponent determinations, but also it is useful in fundamental studies of quenching and energy transfer. Time-resolved fluorescence measurements are performed in time and frequency domain. In time-domain or pulse-excitation fluorimetry, the fluorophore is excited with a short-duration pulse of light and resulting fluorescence emission decay signal after the excitation pulse is captured while in frequency-domain, phase-resolved, phase-modulation, or phase-sensitive lifetime, measurements are based on the use of a continuous, sinusoidally modulated excitation source and phase-sensitive detection. Time- and frequency-domain fluorescence methods have been used in different fields for several purposes, such as distinguishing sample constituents whose fluorescence spectra overlap one another, to distinguish the fluorescence of an analyte from background scattering or luminescence of other sample constituents, especially as a noninvasive technique for biology and biochemistry.

Large magnitudes of mechanical strain applied to tendon cells induce catabolic and inflammatory responses, whereas a moderate level of strain promotes anabolism. Gap junction intercellular communication (GJIC) plays an essential role in these responses, however direct regulation of GJIC by mechanical loading has not been characterised in detail. Here, we show that the GJIC between tenocytes are enhanced or inhibited depending on the magnitude of the tensile strain. The GJIC was analysed using fluorescence loss in photobleaching (FLIP), combined with a molecular diffusion model. Intercellular and intracellular transport of fluorescence tracer molecules, calcein, across multiple cells through the gap junctions was evaluated by determining the intercellular and intracellular diffusion coefficients of calcein. It was demonstrated that the intercellular diffusion coefficient was significantly higher when the cells were subjected to a physiological static tensile strain (4%) for 1 h, but significantly lower when subjected to a strain with non-physiological amplitude (8%). The intracellular diffusion coefficient was not altered by the application of static strain at any level. Connexin 43 proteins were localised within cytoplasm and at cell–cell boundaries in no strained state and were also localised near cell nuclei by the 4% strain, but the localisation was reduced by the 8% strain. The findings suggest that the increase in GJIC in response to 4% strain involves opening of gap junction pores via mechanotransduction events of tenocytes, whereas the inhibition in response to 8% strain involves mechanical disruption of the junctions.

Coupling to metal nanoparticles can increase the fluorescence intensity and photostability of fluorescent probes, and this plasmon-enhanced fluorescence is particularly promising for the dimmer fluorescent proteins common in biological imaging. Here, we measure the intensity distribution of single Cy3.5 dye molecules and mCherry fluorescent proteins one at a time as they adsorb on a conformal surface 4.8–61.0 nm thick over a gold nanorod (NR). The emission intensities for both types of fluorophores depend nonmonotonically on the spacer thickness, and an optimal spacer thickness of ∼10 nm is observed for both fluorophores using two different spacer layer materials. Emission from fluorophores coupled to metal nanoparticles is affected by two competing processes: an enhanced spontaneous decay rate and quenching via nonradiative antenna modes. After averaging over a conformal surface, the product of the simulated enhanced local electric field intensity and the quantum efficiency modification reproduces the ex...

Polymers, glass and fiber reinforced materials are increasingly being used in photophysical devices. The inherent fluorescence of devices made of these materials may itself become important during fluorescence detection. It may interfere with or even negate the low fluorescence signals emitted from fluorophores molecules of interest especially when the fluorophores exist in microvolume samples. Such effects are significant when tissue micro-sections placed on substrata of high background fluorescence. Using different excitation wavelengths, fluorescence spectral and imaging studies were carried out to examine the effect of background fluorescence of microslides made of various substrata such as glass, polycarbonate and aluminium on autofluorescence of tissue sections. With decreasing wavelength of excitation, all substrata showed increased autofluorescence. Glass showed least inherent fluorescence and aluminium showed more reflectance than autofluorescence. After continuous exposure to blue and UV light, all substrata showed irreversible decreased autofluorescence. During spectrofluorimetric studies, a definite blue shift was observed in the autofluorescence of tissue sections placed on microslides made of each of the materials. This suggests an interference of tissue autofluorescence by background fluorescence emitted by the substratum. This may lead to false positive or negative reporting of the fluorophores, particularly important while analyzing micro-sections of biological samples. Microscopic imaging did not show any background fluorescence for glass substratum with blue light. However, with UV light, glass also showed background fluorescence during imaging. Other substrata showed strong background fluorescence or reflectance with both blue and UV light. This study has the potential for accurate quantification of fluorescence spectral and decay and improved fluorescence imaging using the photobleaching effect.

Total internal reflection fluorescence (TIRF) microscopy is widely used in fluorescent imaging. Evanescent wave fields generated by the internal reflection are used to illuminate the sample, and only fluorophores within a thickness of 100 nm thick from the surface are activated, improving the signal-to-noise ratio (SNR) of the image. Sub-diffraction imaging with TIRF microscopy by stochastic photobleaching is studied. Each fluorophore can be localized from the recorded streaming followed by image subtraction. This method can yield contrast-enhanced images with a higher SNR and improve the lateral resolution to approximately 120 nm.

Baltimore has been the home of numerous biophysical studies using light to probe cells. One such study, quantitative measurement of lateral diffusion of rhodopsin, set the standard for experiments in which recovery after photobleaching is used to measure lateral diffusion. Development of this method from specialized microscopes to commercial scanning confocal microscopes has led to widespread use of the technique to measure lateral diffusion of membrane proteins and lipids, and as well diffusion and binding interactions in cell organelles and cytoplasm. Perturbation of equilibrium distributions by photobleaching has also been developed into a robust method to image molecular proximity in terms of fluorescence resonance energy transfer between donor and acceptor fluorophores.

The development of two-photon fluorophores remains an important issue. Dyes that possess both large two-photon excited fluorescence action cross-sections and cell membrane permeability are especially in demand to maximize the underlying virtue of two-photon microscopy for bioimaging. Herein, a novel two-photon excited fluorescence dye has been synthesized. This V-shaped dye exhibited large two-photon excited fluorescence action cross-sections and high plasma membrane permeability. Cell imaging experiments demonstrated that the dye could stain living cells with bright two-photon excited fluorescence. All the results have indicated the potential of the dye as a basic platform for the development of two-photon excited fluorescence probes.

We proposed a cell analysis system without optical filters using a filter-free fluorescence sensor which used wavelength dependent absorption depth in a silicon substrate. Excitation light and fluorescence from fluorescently labeled cells were separated and their light intensities were measured at the same time by applying the proposed parameter. This result shows the filter-free fluorescence sensor can be used to detect cell labeled with various fluorescence reagents. The measured fluorescence of cells was good agreement with fluorescence intensity observed by conventional fluorescence microscopy.

The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms. These proteins also move rapidly and continuously in the nuclei, and their movements are affected by ATP depletion. The U2AF65 proteins are splicing factors that interact with SF1 and U2AF35 proteins to promote U2snRNP for the recognition of the pre-mRNA 3′ splice site during early spliceosome assembly. We have determined the subcellular localization and movement of these proteins’ Arabidopsis homologs. It was found that Arabidopsis U2AF65 homologs, AtU2AF65a, and AtU2AF65b proteins interact with AtU2AF35a and AtU2AF35b, which are Arabidopsis U2AF35 homologs. We have examined the mobility of these proteins including AtSF1 using fluorescence recovery after photobleaching and fluorescence loss in photobleaching analyses. These proteins displayed dynamic movements in nuclei and their movements were affected by ATP depletion. We have also demonstrated that these proteins shuttle between nuclei and cytoplasms, suggesting that they may also function in cytoplasm. These results indicate that such splicing factors show very similar characteristics to their human counterparts, suggesting evolutionary conservation.

Site-specific fluorescent labeling of proteins inside live mammalian cells has been achieved by employing Streptolysin O, a bacterial toxin which forms temporary pores in the membrane and allows delivery of virtually any fluorescent probes, ranging from labeled IgG’s to small ligands, with high efficiency (>85% of cells). The whole process, including recovery, takes 30 min, and the cell is ready to be imaged immediately. A variety of cell viability tests were performed after treatment with SLO to ensure that the cells have intact membranes, are able to divide, respond normally to signaling molecules, and maintains healthy organelle morphology. When combined with Oxyrase, a cell-friendly photostabilizer, a ~20x improvement in fluorescence photostability is achieved. By adding in glutathione, fluorophores are made to blink, enabling super-resolution fluorescence with 20–30 nm resolution over a long time (~30 min) under continuous illumination. Example applications in conventional and super-resolution imaging of native and transfected cells include p65 signal transduction activation, single molecule tracking of kinesin, and specific labeling of a series of nuclear and cytoplasmic protein complexes. DOI: http://dx.doi.org/10.7554/eLife.20378.001

Coronaviruses (CoVs) generate specialized membrane compartments, which consist of double membrane vesicles connected to convoluted membranes, the so-called replicative structures, where viral RNA synthesis takes place. These sites harbor the CoV replication-transcription complexes (RTCs): multi-protein complexes consisting of 16 nonstructural proteins (nsps), the CoV nucleocapsid protein (N) and presumably host proteins. To successfully establish functional membrane-bound RTCs all of the viral and host constituents need to be correctly spatiotemporally organized during viral infection. Few studies, however, have investigated the dynamic processes involved in the formation and functioning of the (subunits of) CoV RTCs and the replicative structures in living cells. In this chapter we describe several protocols to perform time-lapse imaging of CoV-infected cells and to study the kinetics of (subunits of) the CoV replicative structures. The approaches described are not limited to CoV-infected cells; they can also be applied to other virus-infected or non-infected cells.

Flow cytometers are powerful high-throughput devices that capture spectroscopic information from individual particles or cells. These instruments provide a means of multi-parametric analyses for various cellular biomarkers or labeled organelles and cellular proteins. However, the spectral overlap of fluorophores limits the number of fluorophores that can be used simultaneously during experimentation. Time-resolved parameters enable the quantification of fluorescence decay kinetics, thus circumventing common issues associated with intensity-based measurements. This contribution introduces fluorescence lifetime excitation cytometry by kinetic dithering (FLECKD) as a method to capture multiple fluorescence lifetimes using a hybrid time-domain approach. The FLECKD approach excites fluorophores by delivering short pulses of light to cells or particles by rapid dithering and facilitates measurement of complex fluorescence decay kinetics by flow cytometry. Our simulations demonstrated a resolvable fluorescence lifetime value as low as 1.8 ns (±0.3 ns) with less than 20% absolute error. Using the FLECKD instrument, we measured the shortest average fluorescence lifetime value of 2.4 ns and found the system measurement error to be ±0.3 ns (SEM), from hundreds of monodisperse and chemically stable fluorescent microspheres. Additionally, we demonstrate the ability to detect two distinct excited state lifetimes from fluorophores in single cells using FLECKD. This approach presents a new ability to resolve multiple fluorescence lifetimes while retaining the fluidic throughput of a cytometry system. The ability to discriminate more than one average fluorescence lifetime expands the current capabilities of high-throughput and intensity-based cytometry assays as the need to tag one single cell with multiple fluorophores is now widespread.

Background: Little is known about the signaling dynamics of AMP-activated protein kinase. Results: We define the dynamics of yeast AMPK signaling under different glucose concentrations. Conclusion: The Snf1-Mig1 signaling system monitors glucose concentration changes and absolute glucose levels to adjust the metabolism to a wide range of conditions. Significance: This description of AMPK signaling dynamics will stimulate studies defining the integration of signaling and metabolism. Analysis of the time-dependent behavior of a signaling system can provide insight into its dynamic properties. We employed the nucleocytoplasmic shuttling of the transcriptional repressor Mig1 as readout to characterize Snf1-Mig1 dynamics in single yeast cells. Mig1 binds to promoters of target genes and mediates glucose repression. Mig1 is predominantly located in the nucleus when glucose is abundant. Upon glucose depletion, Mig1 is phosphorylated by the yeast AMP-activated kinase Snf1 and exported into the cytoplasm. We used a three-channel microfluidic device to establish a high degree of control over the glucose concentration exposed to cells. Following regimes of glucose up- and downshifts, we observed a very rapid response reaching a new steady state within less than 1 min, different glucose threshold concentrations depending on glucose up- or downshifts, a graded profile with increased cell-to-cell variation at threshold glucose concentrations, and biphasic behavior with a transient translocation of Mig1 upon the shift from high to intermediate glucose concentrations. Fluorescence loss in photobleaching and fluorescence recovery after photobleaching data demonstrate that Mig1 shuttles constantly between the nucleus and cytoplasm, although with different rates, depending on the presence of glucose. Taken together, our data suggest that the Snf1-Mig1 system has the ability to monitor glucose concentration changes as well as absolute glucose levels. The sensitivity over a wide range of glucose levels and different glucose concentration-dependent response profiles are likely determined by the close integration of signaling with the metabolism and may provide for a highly flexible and fast adaptation to an altered nutritional status.

A two-phase fluorescence dequenching was for the first time demonstrated in dye-loaded liposomes upon exposure to a prolonged duration of excitation. Liposomes encapsulating self-quenching concentrations (100 mM) of carboxyfluorescein were subjected to illumination under a 405 nm continuous-wave laser. Emission spectra collected over the span of exposure exhibited a peculiar behavior--two consecutive hikes in peak emission over time that were subsequently attributed to photobleaching induced dequenching. A mathematical model considering the effects of photobleaching on fluorescence quantum yield and absorption then accounted for the observed peaking. Specifically, the dequenching of dye in the outermost and bulk inner regions of the core, were ascribed to the first (fast, primary) and second (slow, secondary) peaking event, correspondingly. The occurrence of the latter was attributed to the combined effects of lower photobleaching rates and anomalous diffusion, stemming to a slower dequenching event. Results not only provided insight to future application of these liposomes in random lasing, but also highlight a potential method of optically tuning the extent of self-quenching.

We propose a single molecule localization method which takes advantage of stochastic photobleaching to improve the resolution of confocal fluorescence microscopy. By detecting the stochastic intensity loss of fluorophores, each fluorophore in the field can be localized. When all locations are known, a sub-diffraction image can be retrieved through single molecule localization algorithms. A confocal scheme is used to record the bleaching process of the sample. Each fluorophore can be localized from the recorded streaming followed by image subtraction. Compared with other single molecule localization concepts such as stochastic optical reconstruction microscopy (STORM) and photoactivated localization microscopy (PALM), this method does not require a laser cycling equipment and the pixel size is no longer limited by the size of CCD. This technique works well with common fluorescent dyes and does not require the use of engineered photoactivatable proteins or photoswitchable synthetic dye pairs.

Borna disease virus (BDV) is a nonsegmented, negative-stranded RNA virus characterized by noncytolytic persistent infection and replication in the nuclei of infected cells. To gain further insight on the intracellular trafficking of BDV components during infection, we sought to generate recombinant BDV (rBDV) encoding fluorescent fusion viral proteins. We successfully rescued a virus bearing a tetracysteine tag fused to BDV-P protein, which allowed assessment of the intracellular distribution and dynamics of BDV using real-time live imaging. In persistently infected cells, viral nuclear inclusions, representing viral factories tethered to chromatin, appeared to be extremely static and stable, contrasting with a very rapid and active trafficking of BDV components in the cytoplasm. Photobleaching (fluorescence recovery after photobleaching [FRAP] and fluorescence loss in photobleaching [FLIP]) imaging approaches revealed that BDV components were permanently and actively exchanged between cellular compartments, including within viral inclusions, albeit with a fraction of BDV-P protein not mobile in these structures, presumably due to its association with viral and/or cellular proteins. We also obtained evidence for transfer of viral material between persistently infected cells, with routing of the transferred components toward the cell nucleus. Finally, coculture experiments with noninfected cells allowed visualization of cell-to-cell BDV transmission and movement of the incoming viral material toward the nucleus. Our data demonstrate the potential of tetracysteine-tagged recombinant BDV for virus tracking during infection, which may provide novel information on the BDV life cycle and on the modalities of its interaction with the nuclear environment during viral persistence.

Fluorescence images present low signal-to-noise ratio (SNR), are corrupted by a type of multiplicative noise with Poisson distribution, and are affected by a time intensity decay due to photoblinking and photobleaching (PBPB) effects. The noise and the PBPB effects together make long-term biological observation very difficult. Here, a theoretical model based on the underlying quantum mechanic physics theory of the observation process associated with this type of image is presented and the common empirical weighted sum of two decaying exponentials is derived from the model. Improvement in the SNR obtained in denoising when the proposed method is used is particularly important in the last images of the sequence where temporal correlation is used to recover information that is sometimes faded and therefore useless from a visual inspection point of view. The proposed PBPB model is included in a Bayesian denoising algorithm previously proposed by the authors. Experiments with synthetic and real data are presented to validate the PBPB model and to illustrate the effectiveness of the model in denoising and reconstruction results.

With unique capability of biomedical diagnosis and chemical analysis, microfluidics has received worldwide applications in various fields. Multiple methods have been proposed to measure velocity profile of flow in microchannels, among which the laser induced fluorescence photobleaching anemometer (LIFPA) provides great performance with not only high spatial resolution but also superior temporal resolution compared with former systems. The measurement sensitivity and temporal resolution of LIFPA system is largely determined by the speed of fluorescence photobleaching effect, meaning that a half-life decay time as short as possible is required to achieve superior temporal resolution. In this paper, several experiments are done to investigate the influence over the half-life decay time by several factors, including incident laser power, dye concentration, buffer concentration and fluidic pH value. Based on the experimental results, a certain dye solution is specially designed, which demonstrates an extremely fast photobleaching effect with a half-life decay time of about 55 μs. Fluorescent dye solution with such a fast photobleaching effect is potentially applicable in the analysis of transient flows, such as the rise time of electroosmotic flow, where high temporal resolution is required.

Autofluorescence of aldehyde-fixed tissues greatly hinders fluorescence microscopy. In particular, lipofuscin, an autofluorescent component of aged brain tissue, complicates fluorescence imaging of tissue in neurodegenerative diseases. Background and lipofuscin fluorescence can be reduced by greater than 90% through photobleaching using white phosphor light emitting diode arrays prior to treatment with fluorescent probes. We compared the effect of photobleaching versus established chemical quenchers on the quality of fluorescent staining in formalin-fixed brain tissue of frontotemporal dementia with tau-positive inclusions. Unlike chemical quenchers, which reduced fluorescent probe signals as well as background, photobleaching treatment had no effect on probe fluorescence intensity while it effectively reduced background and lipofuscin fluorescence. The advantages and versatility of photobleaching over established methods are discussed.

In addition to reflectance confocal microscopy, multiwave confocal microscopes with different laser wavelengths in combination with exogenous fluorophores allow fluorescence mode confocal microscopy in vivo and ex vivo. Fluorescence mode confocal microscopy improves the contrast between the epithelium and the surrounding soft tissue and allows the depiction of certain structures, like epithelial tumors, nerves, and glands.

Summary We describe the theory and implementation of a frequency-domain fluorescence lifetime confocal microscope using switched diode laser illumination. Standard, communications-type, radio-frequency electronics are used to provide inexpensive modulation references and to perform phase-sensitive detection. This allows the rapid acquisition of fluorescence intensity and lifetime images and their display in real time. We show fluorescence lifetime images of bead objects and fluorescence lifetime images of biological specimens from a single confocal scan.

Current far-field fluorescence nanoscopes provide subdiffraction resolution by exploiting a mechanism of fluorescence inhibition. This mechanism is implemented such that features closer than the diffraction limit emit separately when simultaneously exposed to excitation light. A basic mechanism for such transient fluorescence inhibition is the depletion of the fluorophore ground state by transferring it (via a triplet) in a dark state, a mechanism which is workable in most standard dyes. Here we show that microscopy based on ground state depletion followed by individual molecule return (GSDIM) can effectively provide multicolor diffraction-unlimited resolution imaging of immunolabeled fixed and SNAP-tag labeled living cells. Implemented with standard labeling techniques, GSDIM is demonstrated to separate up to four different conventional fluorophores using just two detection channels and a single laser line. The method can be expanded to even more colors by choosing optimized dichroic mirrors and selecting marker molecules with negligible inhomogeneous emission broadening.

RNA polymerase II transcribes most eukaryotic genes. Photobleaching studies have revealed that living Chinese hamster ovary cells expressing the catalytic subunit of the polymerase tagged with the green fluorescent protein contain a large rapidly exchanging pool of enzyme, plus a smaller engaged fraction; genetic complementation shows this tagged polymerase to be fully functional. We investigated how transcriptional inhibitors--some of which are used therapeutically--affect the engaged fraction in living cells using fluorescence loss in photobleaching; all were used at concentrations that have reversible effects. Various kinase inhibitors (roscovitine, DRB, KM05283, alsterpaullone, isoquinolinesulfonamide derivatives H-7, H-8, H-89, H-9), proteasomal inhibitors (lactacystin, MG132), and an anti-tumour agent (cisplatin) all reduced the engaged fraction; an intercalator (actinomycin D), two histone deacetylase inhibitors (trichostatin A, sodium butyrate), and irradiation with ultra-violet light all increased it. The polymerase proves to be both a sensitive sensor and effector of the response to these inhibitors.

The photostability of fluorescent dyes is of crucial importance for the statistical accuracy of single-molecule detection (SMD) and for the image quality of scanning confocal microscopy. Concurrent results for the photostability were obtained by two different experimental techniques. First, the photostabilities of several coumarin and rhodamine derivatives in aqueous solution were obtained by monitoring the steady-state fluorescence decay in a quartz cell. Furthermore, an epi-illuminated microscope, continuous wave (CW) excitation at 514.5 nm, and fluorescence correlation spectroscopy (FCS) with a newly developed theory were used to study the photobleaching characteristics of rhodamines under conditions used for SMD. Depending on the rhodamine structure, the probability of photobleaching, p(b), is in the order of 10(-)(6)-10(-)(7) for irradiances below 10(3) W/cm(2). However, a considerable increase of p(b) for irradiances above this level was observed which can only be described by photobleaching reactions from higher excited states (two-step photolysis). In view of these observations, the probability of photobleaching, p(b), as well as a closed expression of its dependence on the CW excitation irradiance considering a five-level molecular electronic state model with the possibility of photobleaching from higher excited electronic states, is derived. From this model, optimal conditions for SMD with respect to the number of emitted fluorescence photons and to the signal-to-background ratio are discussed, taking into account both saturation and photobleaching. The additional photobleaching due to two-step photolysis limits the applicable irradiance.

This chapter discusses the theory and practical application of laser-induced fluorescence (LIF). Fluorescence, generally, is just another name for spontaneous emission. LIF is a two-step process: (1) absorption of the laser photon, followed by (2) emission.

The tegument protein UL94 is a human cytomegalovirus (HCMV) late protein and its function has yet to be determined. Using live cell fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP) imaging, we found that UL94 is able to shuttle between the nucleus and cytoplasm. Analysis of UL94 mutants fused to EGFP showed that two newly characterized nuclear localization sequences (NLSs) and amino acid 343 play key roles in UL94 nuclear localization. Mutation of these sequences can alter the intracellular distribution of UL94 and disrupt its nucleocytoplasmic shuttling. Amino acid 343 of UL94 was also found to be crucial for its interaction with another HCMV tegument protein pp28. Furthermore, one nuclear export sequence (NES) was identified within UL94. Mutation of the key amino acids in the NES can also alter the intracellular distribution of UL94 and disrupt its shuttling function. Like other proteins containing a leucine-rich export signal, nuclear export of the UL94 was affected by leptomycin B, indicating that it is exported via the Crm1-dependent pathway. Our data provide a basis for further understanding the character and function of HCMV UL94.