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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.

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...

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.

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...

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.

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

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.

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.

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.

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.

A novel nanophotonic method for enhancing the two-photon fluorescence signal of a fluorophore is presented. It utilizes the second harmonic (SH) of the exciting light generated by noble metal nanospheres in whose near-field the dye molecules are placed, to further enhance the dye's fluorescence signal in addition to the usual metal-enhanced fluorescence phenomenon. This method enables demonstration, for the first time, of two-photon fluorescence enhancement inside a biological system, namely live cells. A multishell hydrogel nanoparticle containing a silver core, a protective citrate capping, which serves also as an excitation quenching inhibitor spacer, a pH indicator dye shell, and a polyacrylamide cladding are employed. Utilizing this technique, an enhancement of up to 20 times in the two-photon fluorescence of the indicator dye is observed. Although a significant portion of the enhanced fluorescence signal is due to one-photon processes accompanying the SH generation of the exciting light, this method preserves all the advantages of infrared-excited, two-photon microscopy: enhanced penetration depth, localized excitation, low photobleaching, low autofluorescence, and low cellular damage.

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

The accumulation of misfolded proteins in the cytosol and nucleus of neuronal cells leads to neurodegenerative disorders. Polyglutamine diseases are caused by polyglutamine-expanded proteins, whereas mutations in superoxide dismutase 1 lead to amyotrophic lateral sclerosis. These structurally unstable mutant species perturb essential interactions between normal proteins and tend to aggregate because of the presence of exposed hydrophobic surfaces. Accumulating evidence suggests that soluble species, including misfolded monomers and oligomers, are more toxic than large insoluble aggregates or inclusions. Spectroscopic analysis, including fluorescence recovery after photobleaching and fluorescence loss in photobleaching, in living cells revealed that protein aggregates of misfolded proteins are dynamic structures that interact with other proteins, such as molecular chaperones. Fluorescence correlation spectroscopy analysis detected soluble oligomers/aggregates of misfolded proteins in cell extracts. Fluorescence resonance energy transfer analysis supported the notion that soluble oligomers/aggregates are formed before the formation of inclusions in vivo. Here, we reviewed the characteristics of oligomers and aggregates of misfolded proteins, with a particular focus on those revealed by spectroscopic analysis, and discussed how these oligomers may be toxic to cells.

Calculations have been done that allow developing a new type of illuminators optimized for dark-field microscopy and fluorescent nanoscopy, a new type of ultrahigh-resolution microscopy for which we have patent priority, and its later analogs. The concept proposed here substantiates the feasibility of uniformly illuminating different parts of an object to ensure equal probability of excitation and, in due time, simultaneous photobleaching of fluorescent molecules despite the random orientation of their light-absorbing oscillators. The latter is important because non-bleached fluorophores that accumulate in the specimen produce background noise and make it too difficult to locate the centers of spots produced by new fluorescent molecules.

The current advances of fluorescence microscopy and new fluorescent probes make fluorescence resonance energy transfer (FRET) a powerful technique for studying protein-protein interactions inside living cells. It is very hard to quantitatively analyze FRET efficiency using intensity-based FRET imaging microscopy due to the presence of autofluorescence and spectral crosstalks. In this study, we for the first time developed a novel photobleaching-based method to quantitatively detect FRET efficiency (Pb-FRET) by selectively photobleaching acceptor. The Pb-FRET method requires two fluorescence detection channels: a donor channel (CH 1 ) to selectively detect the fluorescence from donor, and a FRET channel (CH 2 ) which normally includes the fluorescence from both acceptor and donor due to emission spectral crosstalk. We used the Pb-FRET method to quantitatively measure the FRET efficiency of SCAT3, a caspase-3 indicator based on FRET, inside single living cells stably expressing SCAT3 during STS-induced apoptosis. At 0, 6 and 12 h after STS treatment, the FRET efficiency of SCAT3 obtained by Pb-FRET inside living cells was verified by two-photon excitation (TPE) fluorescence lifetime imaging microscopy (FLIM). The temporal resolution of Pb-FRET method is in second time-scale for ROI photobleaching, even in microsecond time-scale for spot photobleaching. Our results demonstrate that the Pb-FRET method is independent of photobleaching degree, and is very useful for quantitatively monitoring protein-protein interactions inside single living cell.

The fluorescence photobleaching recovery method with pulse-position modulation (PPM) of bleaching/probing irradiation is presented. This approach is modification of previously announced photobleaching recovery under decaying photobleaching (FRDP) approach, which employs the amplitude control of irradiation intensity. Underlying idea was to solve the problem of setup nonlinearity by methodical modification that was successfully done. The irradiation intensity is series of equal bleach-probe pulses with increasing distance. The more sophisticated series was proposed as a convolution of subseries, which one characterizing its own time scale. It allows to detect the fluorescence kinetics in the wide range of time and of different nature simultaneously. The method was applied on model systems as FITC-HSA in the water/glycerol mixture and FITC-DMPE in the POPC multibilayers. The method allowed to detect and investigate diffusion processes, presence immobile fraction, effect of limited area of liposomes and reversible fluorescence kinetics.

Fluorescence recovery after photobleaching and fluorescence correlation spectroscopy are the primary means for studying translational diffusion in biological systems. Both techniques, however, present numerous obstacles for measuring translational mobility in structures only slightly larger than optical resolution. We report a new method using through-prism total internal reflection fluorescence microscopy with continuous photobleaching (TIR-CP) to overcome these obstacles. Small structures, such as prokaryotic cells or isolated eukaryotic organelles, containing fluorescent molecules are adhered to a surface. This surface is continuously illuminated by an evanescent wave created by total internal reflection. The characteristic length describing the decay of the evanescent intensity with distance from the surface is smaller than the structures. The fluorescence decay rate resulting from continuous evanescent illumination is monitored as a function of the excitation intensity. The data at higher excitation intensities provide apparent translational diffusion coefficients for the fluorescent molecules within the structures because the decay results from two competing processes (the intrinsic photobleaching propensity and diffusion in the small structures). We present the theoretical basis for the technique and demonstrate its applicability by measuring the diffusion coefficient, 6.3 ± 1.1 µm2/sec, of green fluorescent protein (GFP) in Escherichia coli cells.

The woody secondary walls of plants represent the major sites of cellulose deposition. The polymerization of cellulose occurs at the plasma membrane by the secondary wall cellulose synthase complex (CSC). In the long, cylindrical cells that make up the xylem, secondary wall deposition is confined to discrete regions of the cell, and yellow fluorescent protein (YFP)-labeled CSCs are also localized to these regions. Using fluorescence loss in photobleaching (FLIP) of complete hoops containing YFP-CSCs, we demonstrate movement of the complexes beneath the nascent secondary wall in developing xylem vessels. We have devised a method for determining particle velocities for particles moving around a cylindrical object using data from FLIP. By applying this method to the hoops of YFP-CSCs of the developing vessels, we have obtained the first estimates of speed of these complexes. These speeds are calculated to be in excess of 7 microm s(-1) and are far higher than those speeds previously reported for the primary wall complex. These high speeds are unlikely to be consistent with CSC movement being attributed to cellulose synthesis alone, and suggest the existence of a highly motile compartment beneath the nascent secondary wall.

Silver island films (SIFs) were deposited on the glass substrates to serve as the supports. T-lymphocytic (PM1) cell lines were labeled by Alexa Fluor 680 dextran conjugates on the membranes or by YOYO in the nucleus, respectively. The fluorescence images of the cell lines were recorded in the emission intensity and lifetime using scanning confocal microscopy. The fluorescence signals by the fluorophores bound on the cell membranes were enhanced significantly by SIF supports as compared with on the glass. In addition to the increase in the intensity, there was a dramatic shortening of the emission lifetime. In contrast to the Alexa Fluor 680 fluorophores on the membranes, the YOYO fluorophores intercalated in the cell nucleus were not influenced significantly by the silver islands. This result can be interpreted by an effect of the distance on coupling between the fluorophores and metal particles: the fluorophores on the cell membranes are localized within but the fluorophores in the cell nucleus are beyond the region of metal-enhanced fluorescence. Thus, the metal supports can be used to improve the detection sensitivity to the target molecules on the cell surfaces when they are fluorescently labeled.

Genome activity and nuclear metabolism clearly depend on accessibility, but it is not known whether and to what extent nuclear structures limit the mobility and access of individual molecules. We used fluorescently labeled streptavidin with a nuclear localization signal as an average-sized, inert protein to probe the nuclear environment. The protein was injected into the cytoplasm of mouse cells, and single molecules were tracked in the nucleus with high-speed fluorescence microscopy. We analyzed and compared the mobility of single streptavidin molecules in structurally and functionally distinct nuclear compartments of living cells. Our results indicated that all nuclear subcompartments were easily and similarly accessible for such an average-sized protein, and even condensed heterochromatin neither excluded single molecules nor impeded their passage. The only significant difference was a higher frequency of transient trappings in heterochromatin, which lasted only tens of milliseconds. The streptavidin molecules, however, did not accumulate in heterochromatin, suggesting comparatively less free volume. Interestingly, the nucleolus seemed to exclude streptavidin, as it did many other nuclear proteins, when visualized by conventional fluorescence microscopy. The tracking of single molecules, nonetheless, showed no evidence for repulsion at the border but relatively unimpeded passage through the nucleolus. These results clearly show that single-molecule tracking can provide novel insights into mobility of proteins in the nucleus that cannot be obtained by conventional fluorescence microscopy. Our results suggest that nuclear processes may not be regulated at the level of physical accessibility but rather by local concentration of reactants and availability of binding sites.

We have observed single DNA strands labeled with a small fluorescent molecule, BODIPY-FL, using objective based total internal fluorescence microscopy. In spite of its photobleaching, this small fluorophore is potentially useful for monitoring biochemical processes like protein synthesis because it can be efficiently incorporated into proteins by the ribosome through a charged epsilon-labeled fluorescent lysine tRNA. Using evanescent wave laser excitation at 488 nm, we have been able to observe single Bodipy molecules using integration times as low as 20 ms with a good signal to noise ratio, and for several images before photobleaching. We have measured the fluorescence decay due to photobleaching and have been able to lengthen it by a factor of 5 using oxygen scavenger systems.

Summary Nuclear positioning and dynamic interactions of viral proteins with nuclear substructures play essen- tial roles during infection with DNA viruses. Visual- ization of the intranuclear interactions and motility of the parvovirus replication protein (NS1) in living cells gives insight into specific parvovirus protein- cellular structure interactions. Confocal analysis of highly synchronized infected Norden Laboratory Feline Kidney cells showed accumulation of nuclear NS1 in discrete interchromosomal foci. NS1 fused with enhanced yellow fluorescence protein (NS1- EYFP) provided a marker in live cells for dynamics of NS1 traced by photobleaching techniques. Fluo- rescence Recovery after Photobleaching suggested that the NS1 protein is not freely diffusing but undergoes transient interactions with nuclear com- partments. Fluorescence Loss in Photobleaching demonstrated for the first time the shuttling of a par- voviral protein between the nucleus and the cyto- plasm as assayed with NS1-EYFP. Finally, time-lapse imaging of infected cells revealed that the intra- nuclear distribution of NS1-EYFP evolves dramati- cally starting from the formation of NS1 foci and proceeding to a homogenous distribution extending throughout the nucleus.

Advanced multidimensional time-correlated single photon counting (mdTCSPC) and picosecond time-resolved fluorescence in combination with site-directed fluorescence labeling are valuable tools to study the properties of membrane protein surface segments on the pico- to nanoseconds time scale. Time-resolved fluorescence anisotropy changes of protein bound fluorescent probes reveal changes in protein dynamics and steric restriction. In addition, the change in fluorescence lifetime and intensity of the covalently bound fluorescent dye is indicative of environmental changes at the protein surface. In this study, we have measured the changes in fluorescence lifetime traces of the fluorescent dye fluorescein covalently bound to the first cytoplasmic loop of bacteriorhodopsin (bR) after light activation of protein function. The fluorescence is excited by a picosecond laser pulse. The retinylidene chromophore of bR is light-activated by a 10 ns laser pulse, which in turn triggers recording of a sequence of fluorescence lifetime traces in the mdTCSPC-module. The fluorescence decay changes upon protein function occur predominantly in the 100 ps time range. The kinetics of these changes shows two transitions between three intermediate states in the second part of the bR photocycle. Correlation with photocycle kinetics allows for the determination of reaction intermediates at the proteins surface which are coupled to changes in the retinal binding pocket.

We present a truly quantitative fluorescence recovery after photobleaching (FRAP) model for use with the confocal laser scanning microscope based on the photobleaching of a long line segment. The line FRAP method is developed to complement the disk FRAP method reported before. Although being more subject to the influence of noise, the line FRAP model has the advantage of a smaller bleach region, thus allowing for faster and more localized measurements of the diffusion coefficient and mobile fraction. The line FRAP model is also very well suited to examine directly the influence of the bleaching power on the effective bleaching resolution. We present the outline of the mathematical derivation, leading to a final analytical expression to calculate the fluorescence recovery. We examine the influence of the confocal aperture and the bleaching power on the measured diffusion coefficient to find the optimal experimental conditions for the line FRAP method. This will be done for R-phycoerythrin and FITC-dextrans of various molecular weights. The ability of the line FRAP method to measure correctly absolute diffusion coefficients in three-dimensional samples will be evaluated as well. Finally we show the application of the method to the simultaneous measurement of free green fluorescent protein diffusion in the cytoplasm and nucleus of living A549 cells.

Picosecond time-resolution fluorescence signal detection over many hours is possible using the time-correlated single photon counting (TCSPC) technique. Advanced TCSPC with clock oscillator set by the pulsed laser and data analysis provides a tool to investigate processes in single molecules on time scale from picoseconds to seconds. Optical imaging techniques combined with TCSPC allow one to study the spatial distribution of fluorescence properties in solution and on a surface. Mechanical manipulation of a single macromolecule by means of an atomic-force microscope makes it possible to detect fluorescence signal changes as a function of mechanical conformations of a fluorescent dye attached to a single DNA molecule. Microsc. Res. Tech., 2007. © 2007 Wiley-Liss, Inc.

The cell-wide mobility of PBSs was confirmed by synchronously monitoring the fluorescence recovery after photobleaching (FRAP) and the fluorescence loss in photobleaching (FLIP). On the other hand, a fluorescence recovery was still observed even if PBSs were immobile (PBSs fixed on the membranes by betaine and isolated PBSs fixed on the agar plate) or PBS mobility was unobservable (cell wholly bleached). Furthermore, it was proved that some artificial factors were involved not only in FRAP but also in FLIP, including renaturation of the reversibly denatured proteins, laser scanning-induced fluorescence loss and photo-damage to the cell. With consideration of the fast renaturation component in fluorescence recovery, the diffusion coefficient was estimated to be tenfold smaller than that without the component. Moreover, it was observed that the fluorescence intensity on the bleached area was always lower than that on the non-bleached area, even after 20 min, while it should be equal if PBSs were mobile freely. Based on the increasing proportion of the PBSs anti-washed to Triton X-100 (1%) with prolonged laser irradiation to the cells locked in light state 1 by PBQ, it was concluded that some PBSs became immobile due to photo-linking to PSII.

The steady-state dynamics of karyopherin-dependent nuclear transport in a living cell is examined. The kinetic model established by a number of experimentally obtained parameters reveals how each step of the transport system contributes to maintaining steady-state cargo gradient and fluxes across the nuclear envelope., Karyopherin-dependent molecular transport through the nuclear pore complex is maintained by constant recycling pathways of karyopherins coupled with the Ran-dependent cargo catch-and-release mechanism. Although many studies have revealed the bidirectional dynamics of karyopherins, the entire kinetics of the steady-state dynamics of karyopherin and cargo is still not fully understood. In this study, we used fluorescence recovery after photobleaching and fluorescence loss in photobleaching on live cells to provide convincing in vivo proof that karyopherin-mediated nucleocytoplasmic transport of cargoes is bidirectional. Continuous photobleaching of the cytoplasm of live cells expressing NLS cargoes led to progressive decrease of nuclear fluorescence signals. In addition, experimentally obtained kinetic parameters of karyopherin complexes were used to establish a kinetic model to explain the entire cargo import and export transport cycles facilitated by importin β. The results strongly indicate that constant shuttling of karyopherins, either free or bound to cargo, ensures proper balancing of nucleocytoplasmic distribution of cargoes and establishes effective regulation of cargo dynamics by RanGTP.