Photobleaching correction in fluorescence microscopy images

PostFocus: automated selective post-acquisition high-throughput focus restoration using diffusion model for label-free time-lapse microscopy

MOTIVATION

High-throughput time-lapse imaging is a fundamental tool for efficient living cell profiling at single-cell resolution. Label-free phase-contrast video microscopy enables noninvasive, nontoxic, and long-term imaging. The tradeoff between speed and throughput, however, implies that despite the state-of-the-art autofocusing algorithms, out-of-focus cells are unavoidable due to the migratory nature of immune cells (velocities >10 μm/min). Here, we propose PostFocus to (i) identify out-of-focus images within time-lapse sequences with a classifier, and (ii) deploy a de-noising diffusion probabilistic model to yield reliable in-focus images.

RESULTS

De-noising diffusion probabilistic model outperformed deep discriminative models with a superior performance on the whole image and around cell boundaries. In addition, PostFocus improves the accuracy of image analysis (cell and contact detection) and the yield of usable videos.

AVAILABILITY AND IMPLEMENTATION

Open-source code and sample data are available at: https://github.com/kwu14victor/PostFocus.

Interfacial Effects of Nanostructured Doubly Reentrant Surfaces on the Evolution of Local Concentration and Fluid Flow in an Evaporating Droplet

Surface modification, such as bioinspired nanostructured doubly reentrant surfaces that have presented superhydrophobic wettability even under low-surface-tension liquid, is a very promising technology for controlling droplet dynamics, heat transfer, and evaporation. In this article, we investigate the interfacial effects of nanostructured doubly reentrant surfaces on the flow behaviors and local concentration evolution during the evaporation of an ethanol/water multicomponent droplet. Using particle image velocimetry (PIV) and novel aggregate-induced emission-based (AIE) techniques, the flow patterns and local concentration distributions on both hydrophobic and nanostructured doubly reentrant surfaces were probed and compared. It is found that in addition to the established Marangoni flow-dominated stage, transition stage, and buoyancy-induced flow-dominated stage, a new transition stage and a rolling stage for the nanostructured doubly reentrant surface are detected in the late evaporation period. Differences in the local concentration distribution evolution occur depending on the hydrophobicity of the surface on which the droplet is placed. For the hydrophobic surface, a nonuniform local concentration distribution exists consistently, with a high water fraction in a shell-shaped region near the liquid-air interface and a secondary concentration gradient within this shell-shaped region. The concentration distribution on the nanostructured doubly reentrant surface evolves in a more complex manner, with a strip-shaped region of high water fraction forming in the intermediate stage and then reorganized by rolling flow in the late stage. Finally, theoretical analysis combining PIV and AIE visualization results reveals that the variations in droplet concentration distributions on surfaces with different hydrophobicities exert a significant impact on evaporative behaviors. These behaviors, in turn, affect the evolution of the local concentration distribution.

Fluorescence-based absolute quantification of near-infrared probes in tissue extracts for biodistribution analyses

In recent years, significant progress has been made in the development of fluorescent contrast agents for clinical applications. For the development of a fluorescent probe, it is crucial to evaluate its safety profile, including biodistribution. Specific methods need to be developed for the absolute quantification of fluorescent probes in tissue specimens from animals administered with test compounds in the framework of biodistribution/efficacy/toxicity studies. Here, we describe a new method for the absolute quantification of fluorescent probes in tissue specimens from animals administered with compounds that have absorption and emission wavelength in the Near-Infrared region (600-800 nm). The protocol is based on the standard addition approach in order to minimize the interference of the matrix on the analyte signal causing inaccuracy in the absolute determination of the concentration. The measurement of the fluorescence intensity is done via a microplate reader. The method has been fully validated and applied for the quantification of a fluorescence-guided surgery targeted contrast agent in a Good Laboratory Practice (GLP) biodistribution study. Results clearly demonstrate that this procedure is fully applicable in a preclinical setting and that it overcomes common issues associated with fluorescence signal quantification in tissue extracts.

Performance assessment of probe-based Raman spectroscopy systems for biomedical analysis

We present a methodology for evaluating the performance of probe-based Raman spectroscopy systems for biomedical analysis. This procedure uses a biological standard sample and data analysis approach to circumvent many of the issues related to accurately measuring and comparing the signal quality of Raman spectra between systems. Dairy milk is selected as the biological standard due to its similarity to tissue spectral properties and because its homogeneity eliminates the dependence of probe orientation on the measured spectrum. A spectral dataset is first collected from milk for each system configuration, followed by a model-based correction step to remove photobleaching artifacts and accurately calculate SNR. Results demonstrate that the proposed strategy, unlike current methods, produces an experimental SNR that agrees with the theoretical value. Four preconfigured imaging spectrographs that share similar manufacturer specifications were compared, showing that their capabilities to detect biological Raman spectra widely differ in terms of throughput and stray light rejection. While the methodology is used to compare spectrographs in this case, it can be adapted for other purposes, such as optimizing the design of a custom-built Raman spectrometer, evaluating inter-probe variability, or examining how altering system subcomponents affects signal quality.

Quantitative Single-Molecule Localization Microscopy

Super-resolution fluorescence microscopy allows the investigation of cellular structures at nanoscale resolution using light. Current developments in super-resolution microscopy have focused on reliable quantification of the underlying biological data. In this review, we first describe the basic principles of super-resolution microscopy techniques such as stimulated emission depletion (STED) microscopy and single-molecule localization microscopy (SMLM), and then give a broad overview of methodological developments to quantify super-resolution data, particularly those geared toward SMLM data. We cover commonly used techniques such as spatial point pattern analysis, colocalization, and protein copy number quantification but also describe more advanced techniques such as structural modeling, single-particle tracking, and biosensing. Finally, we provide an outlook on exciting new research directions to which quantitative super-resolution microscopy might be applied.

Actin assembly requirements of the formin Fus1 to build the fusion focus

In formin-family proteins, actin filament nucleation and elongation activities reside in the formin homology 1 (FH1) and FH2 domains, with reaction rates that vary by at least 20-fold between formins. Each cell expresses distinct formins that assemble one or several actin structures, raising the question of what confers each formin its specificity. Here, using the formin Fus1 in Schizosaccharomyces pombe, we systematically probed the importance of formin nucleation and elongation rates in vivo. Fus1 assembles the actin fusion focus, necessary for gamete fusion to form the zygote during sexual reproduction. By constructing chimeric formins with combinations of FH1 and FH2 domains previously characterized in vitro, we establish that changes in formin nucleation and elongation rates have direct consequences on fusion focus architecture, and that Fus1 native high nucleation and low elongation rates are optimal for fusion focus assembly. We further describe a point mutant in Fus1 FH2 that preserves native nucleation and elongation rates in vitro but alters function in vivo, indicating an additional FH2 domain property. Thus, rates of actin assembly are tailored for assembly of specific actin structures.

Spatiotemporal stop-and-go dynamics of the mitochondrial TOM core complex correlates with channel activity

Single-molecule studies can reveal phenomena that remain hidden in ensemble measurements. Here we show the correlation between lateral protein diffusion and channel activity of the general protein import pore of mitochondria (TOM-CC) in membranes resting on ultrathin hydrogel films. Using electrode-free optical recordings of ion flux, we find that TOM-CC switches reversibly between three states of ion permeability associated with protein diffusion. While freely diffusing TOM-CC molecules are predominantly in a high permeability state, non-mobile molecules are mostly in an intermediate or low permeability state. We explain this behavior by the mechanical binding of the two protruding Tom22 subunits to the hydrogel and a concomitant combinatorial opening and closing of the two β-barrel pores of TOM-CC. TOM-CC could thus represent a β-barrel membrane protein complex to exhibit membrane state-dependent mechanosensitive properties, mediated by its two Tom22 subunits.

Transcription-coupled DNA repair underlies variation in persister awakening and the emergence of resistance

Persisters constitute a population of temporarily antibiotic-tolerant variants in an isogenic bacterial population and are considered an important cause of relapsing infections. It is currently unclear how cellular damage inflicted by antibiotic action is reversed upon persister state exit and how this relates to antibiotic resistance development at the molecular level. We demonstrate that persisters, upon fluoroquinolone treatment, accumulate oxidative DNA damage, which is repaired through nucleotide excision repair. Detection of the damage occurs via transcription-coupled repair using UvrD-mediated backtracking or Mfd-controlled displacement of the RNA polymerase. This competition results in heterogeneity in persister awakening lags. Most persisters repair the oxidative DNA damage, displaying a mutation rate equal to the untreated population. However, the promutagenic factor Mfd increases the mutation rate in a persister subpopulation. Our data provide in-depth insight into the molecular mechanisms underlying persister survival and pinpoint Mfd as an important molecular factor linking persistence to resistance development.

Best practices and tools for reporting reproducible fluorescence microscopy methods

Although fluorescence microscopy is ubiquitous in biomedical research, microscopy methods reporting is inconsistent and perhaps undervalued. We emphasize the importance of appropriate microscopy methods reporting and seek to educate researchers about how microscopy metadata impact data interpretation. We provide comprehensive guidelines and resources to enable accurate reporting for the most common fluorescence light microscopy modalities. We aim to improve microscopy reporting, thus improving the quality, rigor and reproducibility of image-based science.

Increasing the Image Contrast via Fast Fluorescence Photobleaching

This paper focuses on the analysis of image sequences acquired during fast photobleaching using a standard wide-field microscope. We show that the photobleaching rate estimated for each pixel is not constant for the whole field of view, but it provides a new spatially variant parametric image related to the cell structure and diffusion of fluorophores. We also provide an alternative way to estimate a pixel-wise photobleaching rate with significantly less computation time than exponential model fitting.Clinical Relevance- This method provides an additional way how fluorescence photobleaching might be used for increasing the image contrast.

Combined Effects of Zeta-potential and Temperature of Nanopores on Diffusioosmotic Ion Transport

Diffusioosmosis (DO) results from ion transport near charged surfaces in the presence of electrolyte gradients and is critical in nanofluidic systems. However, DO has not yet been comprehensively studied because nanofabrication materials have limitations of low throughput and difficult quantification. Herein, we describe a self-assembled particle membrane (SAPM)-integrated microfluidic platform that can modulate the material properties (e.g., zeta-potential) and transport flux of nanopores. We quantify the effect of the zeta-potential on DO by measuring the electrical signals across three different nanopores/nanochannels of the SAPM. We then empirically quantify the effects of the temperature and ionic strength of the electrolytes on DO and reveal a nonlinear relationship with DO-driven ion transport; the ionic strengths govern the DO- or diffusion-effective ion transport phenomena. Finally, we demonstrate DO-driven electric power generation with enhanced performance as a potential application under optimized experimental conditions.

A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling

Stochastic signaling dynamics expand living cells' information processing capabilities. An increasing number of studies report that regulators encode information in their pulsatile dynamics. The evolutionary mechanisms that lead to complex signaling dynamics remain uncharacterized, perhaps because key interactions of signaling proteins are encoded in intrinsically disordered regions (IDRs), whose evolution is difficult to analyze. Here we focused on the IDR that controls the stochastic pulsing dynamics of Crz1, a transcription factor in fungi downstream of the widely conserved calcium signaling pathway. We find that Crz1 IDRs from anciently diverged fungi can all respond transiently to calcium stress; however, only Crz1 IDRs from the Saccharomyces clade support pulsatility, encode extra information, and rescue fitness in competition assays, while the Crz1 IDRs from distantly related fungi do none of the three. On the other hand, we find that Crz1 pulsing is conserved in the distantly related fungi, consistent with the evolutionary model of stabilizing selection on the signaling phenotype. Further, we show that a calcineurin docking site in a specific part of the IDRs appears to be sufficient for pulsing and show evidence for a beneficial increase in the relative calcineurin affinity of this docking site. We propose that evolutionary flexibility of functionally divergent IDRs underlies the conservation of stochastic signaling by stabilizing selection.

Bleach correction ImageJ plugin for compensating the photobleaching of time-lapse sequences

During the capturing of the time-lapse sequence of fluorescently labeled samples, fluorescence intensity exhibits decays. This phenomenon is known as 'photobleaching' and is a widely known problem in imaging in life sciences. The photobleaching can be attenuated by tuning the imaging set-up, but when such adjustments only partially work, the image sequence can be corrected for the loss of intensity in order to precisely segment the target structure or to quantify true intensity dynamics. We implemented an ImageJ plugin that allows the user to compensate for the photobleaching to estimate the non-bleaching condition with choice of three different algorithms: simple ratio, exponential fitting, and histogram matching methods. The histogram matching method is a novel algorithm for photobleaching correction. This article presents details and characteristics of each algorithm based on application to actual image sequences.

Quadruply Stranded Metallo-Supramolecular Helicate [Pd2(hextrz)4]4+ Acts as a Molecular Mimic of Cytolytic Peptides

[Pd₂(hextrz)₄]⁴⁺ is a quadruply stranded helicate, a novel bioinorganic complex designed to mimic the structure and function of proteins due to its high stability and supramolecular size. We have previously reported that [Pd₂(hextrz)₄]⁴⁺ exhibited cytotoxicity toward a range of cell lines, with IC₅₀ values ranging from 3 to 10 μM. Here we demonstrate that [Pd₂(hextrz)₄]⁴⁺ kills cells by forming pores within the cell membrane, a mechanism of cell death analogous to the naturally occurring cytolytic peptides. [Pd₂(hextrz)₄]⁴⁺ induced cell death is characterized by an initial influx of Ca²⁺, followed by nuclear condensation and mitochondrial swelling. This is accompanied by progressive cell membrane damage that results in the formation of large blebs at the cell surface. This allows the efflux of molecules from the cell leading to loss of cell viability. These data suggest that it may be possible to design metallo-supramolecular complexes to mimic the cytotoxic action of pore forming proteins and peptides and so provide a new class of drug to treat cancer, autoimmune disorders, and microbial infection.

Alkyne-Tagged PLGA Allows Direct Visualization of Nanoparticles In Vitro and Ex Vivo by Stimulated Raman Scattering Microscopy

Polymeric nanoparticles (NPs) are attractive candidates for the controlled and targeted delivery of therapeutics in vitro and in vivo. However, detailed understanding of the uptake, location, and ultimate cellular fate of the NPs is necessary to satisfy safety concerns, which is difficult because of the nanoscale size of these carriers. In this work, we show how small chemical labels can be appended to poly(lactic acid-co-glycolic acid) (PLGA) to synthesize NPs that can then be imaged by stimulated Raman scattering microscopy, a vibrational imaging technique that can elucidate bond-specific information in biological environments, such as the identification of alkyne signatures in modified PLGA terpolymers. We show that both deuterium and alkyne labeled NPs can be imaged within primary rat microglia, and the alkyne NPs can also be imaged in ex vivo cortical mouse brain tissue. Immunohistochemical analysis confirms that the NPs localize in microglia in the mouse brain tissue, demonstrating that these NPs have the potential to deliver therapeutics selectively to microglia.

Tailoring drug release rates in hydrogel-based therapeutic delivery applications using graphene oxide

Graphene oxide (GO) is increasingly used for controlling mass diffusion in hydrogel-based drug delivery applications. On the macro-scale, the density of GO in the hydrogel is a critical parameter for modulating drug release. Here, we investigate the diffusion of a peptide drug through a network of GO membranes and GO-embedded hydrogels, modelled as porous matrices resembling both laminated and ‘house of cards’ structures. Our experiments use a therapeutic peptide and show a tunable nonlinear dependence of the peptide concentration upon time. We establish models using numerical simulations with a diffusion equation accounting for the photo-thermal degradation of fluorophores and an effective percolation model to simulate the experimental data. The modelling yields an interpretation of the control of drug diffusion through GO membranes, which is extended to the diffusion of the peptide in GO-embedded agarose hydrogels. Varying the density of micron-sized GO flakes allows for fine control of the drug diffusion. We further show that both GO density and size influence the drug release rate. The ability to tune the density of hydrogel-like GO membranes to control drug release rates has exciting implications to offer guidelines for tailoring drug release rates in hydrogel-based therapeutic delivery applications.

Designing a rigorous microscopy experiment: Validating methods and avoiding bias

Images generated by a microscope are never a perfect representation of the biological specimen. Microscopes and specimen preparation methods are prone to error and can impart images with unintended attributes that might be misconstrued as belonging to the biological specimen. In addition, our brains are wired to quickly interpret what we see, and with an unconscious bias toward that which makes the most sense to us based on our current understanding. Unaddressed errors in microscopy images combined with the bias we bring to visual interpretation of images can lead to false conclusions and irreproducible imaging data. Here we review important aspects of designing a rigorous light microscopy experiment: validation of methods used to prepare samples and of imaging system performance, identification and correction of errors, and strategies for avoiding bias in the acquisition and analysis of images.

A Noisy Analog-to-Digital Converter Connects Cytosolic Calcium Bursts to Transcription Factor Nuclear Localization Pulses in Yeast

Several examples of transcription factors that show stochastic, unsynchronized pulses of nuclear localization have been described. Here we show that under constant calcium stress, nuclear localization pulses of the transcription factor Crz1 follow stochastic variations in cytosolic calcium concentration. We find that the size of the stochastic calcium bursts is positively correlated with the number of subsequent Crz1 pulses. Based on our observations, we propose a simple stochastic model of how the signaling pathway converts a constant external calcium concentration into a digital number of Crz1 pulses in the nucleus, due to the time delay from nuclear transport and the stochastic decoherence of individual Crz1 molecule dynamics. We find support for several additional predictions of the model and suggest that stochastic input to nuclear transport may produce noisy digital responses to analog signals in other signaling systems.

Compositional adaptability in NPM1-SURF6 scaffolding networks enabled by dynamic switching of phase separation mechanisms

The nucleolus, the site for ribosome biogenesis contains hundreds of proteins and several types of RNA. The functions of many non-ribosomal nucleolar proteins are poorly understood, including Surfeit locus protein 6 (SURF6), an essential disordered protein with roles in ribosome biogenesis and cell proliferation. SURF6 co-localizes with Nucleophosmin (NPM1), a highly abundant protein that mediates the liquid-like features of the granular component region of the nucleolus through phase separation. Here, we show that electrostatically-driven interactions between disordered regions of NPM1 and SURF6 drive liquid-liquid phase separation. We demonstrate that co-existing heterotypic (NPM1-SURF6) and homotypic (NPM1-NPM1) scaffolding interactions within NPM1-SURF6 liquid-phase droplets dynamically and seamlessly interconvert in response to variations in molecular crowding and protein concentrations. We propose a mechanism wherein NPM1-dependent nucleolar scaffolds are modulated by non-ribosomal proteins through active rearrangements of interaction networks that can possibly contribute to the directionality of ribosomal biogenesis within the liquid-like nucleolus.

The nucleolus is a membrane-less organelle and both Nucleophosmin (NPM1) and Surfeit locus protein 6 (SURF6) are abundant proteins within the nucleolus. Here the authors employ biophysical methods to study the properties of NPM1-S6N droplets and provide insights into the role of SURF6 in maintaining and modulating the liquid-like structure of the nucleolus.

Correcting for photodestruction in super-resolution optical fluctuation imaging

Super-resolution optical fluctuation imaging overcomes the diffraction limit by analyzing fluctuations in the fluorophore emission. A key assumption of the imaging is that the fluorophores are independent, though this is invalidated in the presence of photodestruction. In this work, we evaluate the effect of photodestruction on SOFI imaging using theoretical considerations and computer simulations. We find that photodestruction gives rise to an additional signal that does not present an easily interpretable view of the sample structure. This additional signal is strong and the resulting images typically exhibit less noise. Accordingly, these images may be mis-interpreted as being more visually pleasing or more informative. To address this uncertainty, we develop a procedure that can robustly estimate to what extent any particular experiment is affected by photodestruction. We also develop a detailed assessment methodology and use it to evaluate the performance of several correction algorithms. We identify two approaches that can correct for the presence of even strong photodestruction, one of which can be implemented directly in the SOFI calculation software.

Reliable measurement of E. coli single cell fluorescence distribution using a standard microscope set-up

Background

Quantifying gene expression at single cell level is fundamental for the complete characterization of synthetic gene circuits, due to the significant impact of noise and inter-cellular variability on the system’s functionality. Commercial set-ups that allow the acquisition of fluorescent signal at single cell level (flow cytometers or quantitative microscopes) are expensive apparatuses that are hardly affordable by small laboratories.

Methods

A protocol that makes a standard optical microscope able to acquire quantitative, single cell, fluorescent data from a bacterial population transformed with synthetic gene circuitry is presented. Single cell fluorescence values, acquired with a microscope set-up and processed with custom-made software, are compared with results that were obtained with a flow cytometer in a bacterial population transformed with the same gene circuitry.

Results

The high correlation between data from the two experimental set-ups, with a correlation coefficient computed over the tested dynamic range > 0.99, proves that a standard optical microscope– when coupled with appropriate software for image processing– might be used for quantitative single-cell fluorescence measurements. The calibration of the set-up, together with its validation, is described.

Conclusions

The experimental protocol described in this paper makes quantitative measurement of single cell fluorescence accessible to laboratories equipped with standard optical microscope set-ups. Our method allows for an affordable measurement/quantification of intercellular variability, whose better understanding of this phenomenon will improve our comprehension of cellular behaviors and the design of synthetic gene circuits. All the required software is freely available to the synthetic biology community (MUSIQ Microscope flUorescence SIngle cell Quantification).

Electronic supplementary material

The online version of this article (doi:10.1186/s13036-017-0050-y) contains supplementary material, which is available to authorized users.

Comparative evaluation of performance measures for shading correction in time-lapse fluorescence microscopy

Time-lapse fluorescence microscopy is a valuable technology in cell biology, but it suffers from the inherent problem of intensity inhomogeneity due to uneven illumination or camera nonlinearity, known as shading artefacts. This will lead to inaccurate estimates of single-cell features such as average and total intensity. Numerous shading correction methods have been proposed to remove this effect. In order to compare the performance of different methods, many quantitative performance measures have been developed. However, there is little discussion about which performance measure should be generally applied for evaluation on real data, where the ground truth is absent. In this paper, the state-of-the-art shading correction methods and performance evaluation methods are reviewed. We implement 10 popular shading correction methods on two artificial datasets and four real ones. In order to make an objective comparison between those methods, we employ a number of quantitative performance measures. Extensive validation demonstrates that the coefficient of joint variation (CJV) is the most applicable measure in time-lapse fluorescence images. Based on this measure, we have proposed a novel shading correction method that performs better compared to well-established methods for a range of real data tested.

bicoid mRNA localises to the Drosophila oocyte anterior by random Dynein-mediated transport and anchoring

bicoid mRNA localises to the Drosophila oocyte anterior from stage 9 of oogenesis onwards to provide a local source for Bicoid protein for embryonic patterning. Live imaging at stage 9 reveals that bicoid mRNA particles undergo rapid Dynein-dependent movements near the oocyte anterior, but with no directional bias. Furthermore, bicoid mRNA localises normally in shot^2A2, which abolishes the polarised microtubule organisation. FRAP and photo-conversion experiments demonstrate that the RNA is stably anchored at the anterior, independently of microtubules. Thus, bicoid mRNA is localised by random active transport and anterior anchoring. Super-resolution imaging reveals that bicoid mRNA forms 110-120 nm particles with variable RNA content, but constant size. These particles appear to be well-defined structures that package the RNA for transport and anchoring.

Correction for photobleaching in dynamic fluorescence microscopy: application in the assessment of pharmacokinetic parameters in ultrasound-mediated drug delivery

We have previously demonstrated the feasibility of monitoring ultrasound-mediated uptake of a hydrophilic model drug in real time with dynamic confocal fluorescence microscopy. In this study, we evaluate and correct the impact of photobleaching to improve the accuracy of pharmacokinetic parameter estimates. To model photobleaching of the fluorescent model drug SYTOX Green, a photobleaching process was added to the current two-compartment model describing cell uptake. After collection of the uptake profile, a second acquisition was performed when SYTOX Green was equilibrated, to evaluate the photobleaching rate experimentally. Photobleaching rates up to 5.0 10(-3) s(-1) were measured when applying power densities up to 0.2 W.cm(-2). By applying the three-compartment model, the model drug uptake rate of 6.0 10(-3) s(-1) was measured independent of the applied laser power. The impact of photobleaching on uptake rate estimates measured by dynamic fluorescence microscopy was evaluated. Subsequent compensation improved the accuracy of pharmacokinetic parameter estimates in the cell population subjected to sonopermeabilization.

Frontrunners of T cell activation: Initial, localized Ca2+ signals mediated by NAADP and the type 1 ryanodine receptor

The activation of T cells is the fundamental on switch for the adaptive immune system. Ca(2+) signaling is essential for T cell activation and starts as initial, short-lived, localized Ca(2+) signals. The second messenger nicotinic acid adenine dinucleotide phosphate (NAADP) forms rapidly upon T cell activation and stimulates early Ca(2+) signaling. We developed a high-resolution imaging technique using multiple fluorescent Ca(2+) indicator dyes to characterize these early signaling events and investigate the channels involved in NAADP-dependent Ca(2+) signals. In the first seconds of activation of either primary murine T cells or human Jurkat cells with beads coated with an antibody against CD3, we detected Ca(2+) signals with diameters close to the limit of detection and that were close to the activation site at the plasma membrane. In Jurkat cells in which the ryanodine receptor (RyR) was knocked down or in primary T cells from RyR1(-/-) mice, either these early Ca(2+) signals were not detected or the number of signals was markedly reduced. Local Ca(2+) signals observed within 20 ms upon microinjection of Jurkat cells with NAADP were also sensitive to RyR knockdown. In contrast, TRPM2 (transient receptor potential channel, subtype melastatin 2), a potential NAADP target channel, was not required for the formation of initial Ca(2+) signals in primary T cells. Thus, through our high-resolution imaging method, we characterized early Ca(2+) release events in T cells and obtained evidence for the involvement of RyR and NAADP in such signals.

High-resolution non-contact measurement of the electrical activity of plants in situ using optical recording

The limitations of conventional extracellular recording and intracellular recording make high-resolution multisite recording of plant bioelectrical activity in situ challenging. By combining a cooled charge-coupled device camera with a voltage-sensitive dye, we recorded the action potentials in the stem of Helianthus annuus and variation potentials at multiple sites simultaneously with high spatial resolution. The method of signal processing using coherence analysis was used to determine the synchronization of the selected signals. Our results provide direct visualization of the phloem, which is the distribution region of the electrical activities in the stem and leaf of H. annuus, and verify that the phloem is the main action potential transmission route in the stems of higher plants. Finally, the method of optical recording offers a unique opportunity to map the dynamic bioelectrical activity and provides an insight into the mechanisms of long-distance electrical signal transmission in higher plants.

Neutron, fluorescence, and optical imaging: An in situ combination of complementary techniques

An apparatus which enables the simultaneous combination of three complementary imaging techniques, optical imaging, fluorescence imaging, and neutron radiography, is presented. While each individual technique can provide information on certain aspects of the sample and their time evolution, a combination of the three techniques in one setup provides a more complete and consistent data set. The setup can be used in transmission and reflection modes and thus with optically transparent as well as opaque samples. Its capabilities are illustrated with two examples. A polymer hydrogel represents a transparent sample and the diffusion of fluorescent particles into and through this polymer matrix is followed. In reflection mode, the absorption of solvent by a nile red-functionalized mesoporous silica powder and the corresponding change in fluorescent signal are studied.

Differential laser-induced perturbation Raman spectroscopy: a comparison with Raman spectroscopy for analysis and classification of amino acids and dipeptides

Differential-laser induced perturbation spectroscopy (DLIPS) is a new spectral analysis technique for classification and identification, with key potential applications for analysis of complex biomolecular systems. DLIPS takes advantage of the complex ultraviolet (UV) laser–material interactions based on difference spectroscopy by coupling low intensity UV laser perturbation with a traditional spectroscopy probe. Here, we quantify the DLIPS performance using a Raman scattering probe in classification of basic constituents of collagenous tissues, namely, the amino acids glycine, L-proline, and L-alanine, and the dipeptides glycine–glycine, glycine–alanine and glycine–proline and compare the performance to a traditional Raman spectroscopy probe via several multivariate analyses. We find that the DLIPS approach yields an ~40% improvement in discrimination among these tissue building blocks. The effects of the 193-nm perturbation laser are further examined by assessing the photodestruction of targeted material molecular bonds. The DLIPS method with a Raman probe holds promise for future tissue diagnosis, either as a stand-alone technique or as part of an orthogonal biosensing scheme.

Photobleaching as a tool to measure the local strain field in fibrous membranes of connective tissues

Connective tissues are complex structures which contain collagen and elastin fibers. These fiber-based structures have a great influence on material mechanical properties and need to be studied at the microscopic scale. Several microscopy techniques have been developed in order to image such microstructures; among them are two-photon excited fluorescence microscopy and second harmonic generation. These observations have been coupled with mechanical characterization to link microstructural kinematics to macroscopic material parameter evolution. In this study, we present a new approach to measure local strain in soft biological tissues using a side-effect of fluorescence microscopy: photobleaching. Controlling the loss of fluorescence induced by photobleaching, we create a pattern on our sample that we can monitor during mechanical loading. The image analysis allows three-dimensional displacements of the patterns at various loading levels to be computed. Then, local strain distribution is derived using the finite element discretization on a four-node element mesh created from our photobleached pattern. Photobleaching tests on a human liver capsule have revealed that this technique is non-destructive and does not have any impact on mechanical properties. This method is likely to have other applications in biological material studies, considering that all collagen-elastin fiber-based biological tissues possess autofluorescence properties and thus can be photobleached.

Requirement of LIM domains for the transient accumulation of paxillin at damaged stress fibres

Cells recognize and respond to changes in intra- and extracellular mechanical conditions to maintain their mechanical homeostasis. Linear contractile bundles of actin filaments and myosin II known as stress fibres (SFs) mediate mechanical signals. Mechanical cues such as excessive stress driven by myosin II and/or external force may damage SFs and induce the local transient accumulation of SF-repair complexes (zyxin and VASP) at the damaged sites. Using an atomic force microscope mounted on a fluorescence microscope, we applied mechanical damage to cells expressing fluorescently tagged cytoskeletal proteins and recorded the subsequent mobilization of SF-repair complexes. We found that a LIM protein, paxillin, transiently accumulated at the damaged sites earlier than zyxin, while paxillin knockdown did not affect the kinetics of zyxin translocation. The C-terminal half of paxillin, comprising four-tandem LIM domains, can still translocate to damaged sites on SFs, suggesting that the LIM domain is essential for the mechanosensory function of paxillin. Our findings demonstrate a crucial role of the LIM domain in mechanosensing LIM proteins.

Deconvolution of calcium fluorescent indicator signal from AFM cantilever reflection

Atomic force microscopy (AFM) can be combined with fluorescence microscopy to measure the changes in intracellular calcium levels (indicated by fluorescence of Ca²⁺ sensitive dye fluo-4) in response to mechanical stimulation performed by AFM. Mechanical stimulation using AFM is associated with cantilever movement, which may interfere with the fluorescence signal. The motion of the AFM cantilever with respect to the sample resulted in changes of the reflection of light back to the sample and a subsequent variation in the fluorescence intensity, which was not related to changes in intracellular Ca²⁺ levels. When global Ca²⁺ responses to a single stimulation were assessed, the interference of reflected light with the fluorescent signal was minimal. However, in experiments where local repetitive stimulations were performed, reflection artifacts, correlated with cantilever motion, represented a significant component of the fluorescent signal. We developed a protocol to correct the fluorescence traces for reflection artifacts, as well as photobleaching. An added benefit of our method is that the cantilever reflection in the fluorescence recordings can be used for precise temporal correlation of the AFM and fluorescence measurements.

Denoising of LSFCM images with compensation for the photoblinking/photobleaching effects

Fluorescence confocal microscopy images present a low signal to noise ratio and a time intensity decay due to the so called photoblinking and photobleaching effects. These effects, together with the Poisson multiplicative noise that corrupts the images, make long time biological observation processes very difficult.