Observing secretory granules with a multiangle evanescent wave microscope

Three-dimensional total-internal reflection fluorescence nanoscopy with nanometric axial resolution by photometric localization of single molecules

Single-molecule localization microscopy enables far-field imaging with lateral resolution in the range of 10 to 20 nanometres, exploiting the fact that the centre position of a single-molecule’s image can be determined with much higher accuracy than the size of that image itself. However, attaining the same level of resolution in the axial (third) dimension remains challenging. Here, we present Supercritical Illumination Microscopy Photometric z-Localization with Enhanced Resolution (SIMPLER), a photometric method to decode the axial position of single molecules in a total internal reflection fluorescence microscope. SIMPLER requires no hardware modification whatsoever to a conventional total internal reflection fluorescence microscope and complements any 2D single-molecule localization microscopy method to deliver 3D images with nearly isotropic nanometric resolution. Performance examples include SIMPLER-direct stochastic optical reconstruction microscopy images of the nuclear pore complex with sub-20 nm axial localization precision and visualization of microtubule cross-sections through SIMPLER-DNA points accumulation for imaging in nanoscale topography with sub-10 nm axial localization precision.

Achieving high axial resolution is challenging in single-molecule localization microscopy. Here, the authors present a photometric method to decode the axial position of single molecules in a total internal reflection fluorescence microscope without hardware modification, and show nearly isotropic nanometric resolution.

State-of-the-Art Technologies for Understanding Brassinosteroid Signaling Networks

Brassinosteroids, the steroid hormones of plants, control physiological and developmental processes through its signaling pathway. The major brassinosteroid signaling network components, from the receptor to transcription factors, have been identified in the past two decades. The development of biotechnologies has driven the identification of novel brassinosteroid signaling components, even revealing several crosstalks between brassinosteroid and other plant signaling pathways. Herein, we would like to summarize the identification and improvement of several representative brassinosteroid signaling components through the development of new technologies, including brassinosteroid-insensitive 1 (BRI1), BRI1-associated kinase 1 (BAK1), BR-insensitive 2 (BIN2), BRI1 kinase inhibitor 1 (BKI1), BRI1-suppressor 1 (BSU1), BR signaling kinases (BSKs), BRI1 ethyl methanesulfonate suppressor 1 (BES1), and brassinazole resistant 1 (BZR1). Furthermore, improvement of BR signaling knowledge, such as the function of BKI1, BES1 and its homologous through clustered regularly interspaced short palindromic repeats (CRISPR), the regulation of BIN2 through single-molecule methods, and the new in vivo interactors of BIN2 identified by proximity labeling are described. Among these technologies, recent advanced methods proximity labeling and single-molecule methods will be reviewed in detail to provide insights to brassinosteroid and other phytohormone signaling pathway studies.

Calibrating Evanescent-Wave Penetration Depths for Biological TIRF Microscopy

Roughly half of a cell's proteins are located at or near the plasma membrane. In this restricted space, the cell senses its environment, signals to its neighbors, and exchanges cargo through exo- and endocytotic mechanisms. Ligands bind to receptors, ions flow across channel pores, and transmitters and metabolites are transported against concentration gradients. Receptors, ion channels, pumps, and transporters are the molecular substrates of these biological processes, and they constitute important targets for drug discovery. Total internal reflection fluorescence (TIRF) microscopy suppresses the background from the cell's deeper layers and provides contrast for selectively imaging dynamic processes near the basal membrane of live cells. The optical sectioning of TIRF is based on the excitation confinement of the evanescent wave generated at the glass/cell interface. How deep the excitation light actually penetrates the sample is difficult to know, making the quantitative interpretation of TIRF data problematic. Nevertheless, many applications like superresolution microscopy, colocalization, Förster resonance energy transfer, near-membrane fluorescence recovery after photobleaching, uncaging or photoactivation/switching as well as single-particle tracking require the quantitative interpretation of evanescent-wave-excited images. Here, we review existing techniques for characterizing evanescent fields, and we provide a roadmap for comparing TIRF data across images, experiments, and laboratories.

A primer on resolving the nanoscale structure of the plasma membrane with light and electron microscopy

Taraska reviews the imaging methods that are being used to understand the structure of the plasma membrane at the molecular level.

The plasma membrane separates a cell from its external environment. All materials and signals that enter or leave the cell must cross this hydrophobic barrier. Understanding the architecture and dynamics of the plasma membrane has been a central focus of general cellular physiology. Both light and electron microscopy have been fundamental in this endeavor and have been used to reveal the dense, complex, and dynamic nanoscale landscape of the plasma membrane. Here, I review classic and recent developments in the methods used to image and study the structure of the plasma membrane, particularly light, electron, and correlative microscopies. I will discuss their history and use for mapping the plasma membrane and focus on how these tools have provided a structural framework for understanding the membrane at the scale of molecules. Finally, I will describe how these studies provide a roadmap for determining the nanoscale architecture of other organelles and entire cells in order to bridge the gap between cellular form and function.

Nanometric axial resolution of fibronectin assembly units achieved with an efficient reconstruction approach for multi-angle-TIRF microscopy

High resolution imaging of molecules at the cell-substrate interface is required for understanding key biological processes. Here we propose a complete pipeline for multi-angle total internal reflection fluorescence microscopy (MA-TIRF) going from instrument design and calibration procedures to numerical reconstruction. Our custom setup is endowed with a homogeneous field illumination and precise excitation beam angle. Given a set of MA-TIRF acquisitions, we deploy an efficient joint deconvolution/reconstruction algorithm based on a variational formulation of the inverse problem. This algorithm offers the possibility of using various regularizations and can run on graphics processing unit (GPU) for rapid reconstruction. Moreover, it can be easily used with other MA-TIRF devices and we provide it as an open-source software. This ensemble has enabled us to visualize and measure with unprecedented nanometric resolution, the depth of molecular components of the fibronectin assembly machinery at the basal surface of endothelial cells.

Near-Membrane Refractometry Using Supercritical Angle Fluorescence

Total internal reflection fluorescence (TIRF) microscopy and its variants are key technologies for visualizing the dynamics of single molecules or organelles in live cells. Yet truly quantitative TIRF remains problematic. One unknown hampering the interpretation of evanescent-wave excited fluorescence intensities is the undetermined cell refractive index (RI). Here, we use a combination of TIRF excitation and supercritical angle fluorescence emission detection to directly measure the average RI in the "footprint" region of the cell during image acquisition. Our RI measurement is based on the determination on a back-focal plane image of the critical angle separating evanescent and far-field fluorescence emission components. We validate our method by imaging mouse embryonic fibroblasts and BON cells. By targeting various dyes and fluorescent-protein chimeras to vesicles, the plasma membrane, as well as mitochondria and the endoplasmic reticulum, we demonstrate local RI measurements with subcellular resolution on a standard TIRF microscope, with a removable Bertrand lens as the only modification. Our technique has important applications for imaging axial vesicle dynamics and the mitochondrial energy state or detecting metabolically more active cancer cells.

Axial superresolution via multiangle TIRF microscopy with sequential imaging and photobleaching

We report superresolution optical sectioning using a multiangle total internal reflection fluorescence (TIRF) microscope. TIRF images were constructed from several layers within a normal TIRF excitation zone by sequentially imaging and photobleaching the fluorescent molecules. The depth of the evanescent wave at different layers was altered by tuning the excitation light incident angle. The angle was tuned from the highest (the smallest TIRF depth) toward the critical angle (the largest TIRF depth) to preferentially photobleach fluorescence from the lower layers and allow straightforward observation of deeper structures without masking by the brighter signals closer to the coverglass. Reconstruction of the TIRF images enabled 3D imaging of biological samples with 20-nm axial resolution. Two-color imaging of epidermal growth factor (EGF) ligand and clathrin revealed the dynamics of EGF-activated clathrin-mediated endocytosis during internalization. Furthermore, Bayesian analysis of images collected during the photobleaching step of each plane enabled lateral superresolution (<100 nm) within each of the sections.

Dye distance mapping using waveguide evanescent field fluorescence microscopy and its application to cell biology

Previous studies have measured the distance between cells and the substratum at sites of adhesion via the emission of a fluorescent dye and waveguide methods. Here, we demonstrate a novel approach to measure the position of fluorescent dyes above a waveguide surface in the 10-200 nm distance range throughout an entire area, yielding a 2D dye distance map or a 3D contour plot. The dye is located in a multilayered Langmuir Blodgett (LB) film or in the plasma membrane of a cell. Waveguide evanescent field fluorescence (WEFF) images obtained using two different waveguide modes are employed allowing, with a simple mathematical approach, the calculation of dye distance maps. Ultra-thin steps made using LB technology, adhesion distances and the bending of the plasma membrane between focal adhesions of osteoblastic cells are shown as examples. The errors are discussed. False color representation of a dye distance map with four osteoblasts. The inset represents an overexposed WEFF image of the same field of view.

The physical basis of total internal reflection fluorescence (TIRF) microscopy and its cellular applications

Total internal reflection fluorescence (TIRF) microscopy has gained popularity in recent years among cell biologists due to its ability to clearly visualize events that occur at the adherent plasma membrane of cells. TIRF microscopy systems are now commercially available from nearly all microscope suppliers. This review aims to give the reader an introduction to the physical basis of TIRF and considerations that need to be made when purchasing a commercial system. We explain how TIRF can be combined with other microscopy modalities and describe how to use TIRF to study processes such as endocytosis, exocytosis, and focal adhesion dynamics. Finally, we provide a step-by-step guide to imaging and analyzing focal adhesion dynamics in a migrating cell using TIRF microscopy.

Fast high-resolution 3D total internal reflection fluorescence microscopy by incidence angle scanning and azimuthal averaging

Total internal reflection fluorescence microscopy (TIRFM) is the method of choice to visualize a variety of cellular processes in particular events localized near the plasma membrane of live adherent cells. This imaging technique not relying on particular fluorescent probes provides a high sectioning capability. It is, however, restricted to a single plane. We present here a method based on a versatile design enabling fast multiwavelength azimuthal averaging and incidence angles scanning to computationally reconstruct 3D images sequences. We achieve unprecedented 50-nm axial resolution over a range of 800 nm above the coverslip. We apply this imaging modality to obtain structural and dynamical information about 3D actin architectures. We also temporally decipher distinct Rab11a-dependent exocytosis events in 3D at a rate of seven stacks per second.

Eliminating unwanted far-field excitation in objective-type TIRF. Part I. identifying sources of nonevanescent excitation light

Total internal reflection fluorescence microscopy (TIRFM) achieves subdiffraction axial sectioning by confining fluorophore excitation to a thin layer close to the cell/substrate boundary. However, it is often unknown how thin this light sheet actually is. Particularly in objective-type TIRFM, large deviations from the exponential intensity decay expected for pure evanescence have been reported. Nonevanescent excitation light diminishes the optical sectioning effect, reduces contrast, and renders TIRFM-image quantification uncertain. To identify the sources of this unwanted fluorescence excitation in deeper sample layers, we here combine azimuthal and polar beam scanning (spinning TIRF), atomic force microscopy, and wavefront analysis of beams passing through the objective periphery. Using a variety of intracellular fluorescent labels as well as negative staining experiments to measure cell-induced scattering, we find that azimuthal beam spinning produces TIRFM images that more accurately portray the real fluorophore distribution, but these images are still hampered by far-field excitation. Furthermore, although clearly measureable, cell-induced scattering is not the dominant source of far-field excitation light in objective-type TIRF, at least for most types of weakly scattering cells. It is the microscope illumination optical path that produces a large cell- and beam-angle invariant stray excitation that is insensitive to beam scanning. This instrument-induced glare is produced far from the sample plane, inside the microscope illumination optical path. We identify stray reflections and high-numerical aperture aberrations of the TIRF objective as one important source. This work is accompanied by a companion paper (Pt.2/2).

Shadowless-illuminated variable-angle TIRF (siva-TIRF) microscopy for the observation of spatial-temporal dynamics in live cells

Total-internal-reflection fluorescence (TIRF) microscopy provides high optical-sectioning capability and a good signal-contrast ratio for structures near the surfaces of cells. In recent years, several improvements have been developed, such as variable-angle TIRF (VA-TIRF) and spinning TIRF (sp-TIRF), which permit quantitative image analysis and address non-uniform scattering fringes, respectively. Here, we present a dual-color DMD-based shadowless-illuminated variable-angle TIRF (siva-TIRF) system that provides a uniform illumination field. By adjusting the incidence angle of the illuminating laser on the back focal plane (BFP) of the objective, we can rapidly illuminate biological samples in layers of various thicknesses in TIRF or hollow-cone epi-fluorescence mode. Compared with other methods of accomplishing VA-TIRF/sp-TIRF illumination, our system is simple to build and cost-effective, and it provides optimal multi-plane dual-color images. By showing spatiotemporal correlated movement of clathrin-coated structures with microtubule filaments from various layers of live cells, we demonstrate that cortical microtubules are important spatial regulators of clathrin-coated structures. Moreover, our system can be used to prove superb axial information of three-dimensional movement of structures near the plasma membrane within live cells.

A novel multiple hypothesis based particle tracking method for clathrin mediated endocytosis analysis using fluorescence microscopy

In order to quantitatively analyze biological images and study underlying mechanisms of the cellular and subcellular processes, it is often required to track a large number of particles involved in these processes. Manual tracking can be performed by the biologists, but the workload is very heavy. In this paper, we present an automatic particle tracking method for analyzing an essential subcellular process, namely clathrin mediated endocytosis. The framework of the tracking method is an extension of the classical multiple hypothesis tracking (MHT), and it is designed to manage trajectories, solve data association problems, and handle pseudo-splitting/merging events. In the extended MHT framework, particle tracking becomes evaluating two types of hypotheses. The first one is the trajectory-related hypothesis, to test whether a recovered trajectory is correct, and the second one is the observation-related hypothesis, to test whether an observation from an image belongs to a real particle. Here, an observation refers to a detected particle and its feature vector. To detect the particles in 2D fluorescence images taken using total internal reflection microscopy, the images are segmented into regions, and the features of the particles are obtained by fitting Gaussian mixture models into each of the image regions. Specific models are developed according to the properties of the particles. The proposed tracking method is demonstrated on synthetic data under different scenarios and applied to real data.

Eliminating unwanted far-field excitation in objective-type TIRF. Part II. combined evanescent-wave excitation and supercritical-angle fluorescence detection improves optical sectioning

Azimuthal beam scanning makes evanescent-wave (EW) excitation isotropic, thereby producing total internal reflection fluorescence (TIRF) images that are evenly lit. However, beam spinning does not fundamentally address the problem of propagating excitation light that is contaminating objective-type TIRF. Far-field excitation depends more on the specific objective than on cell scattering. As a consequence, the excitation impurities in objective-type TIRF are only weakly affected by changes of azimuthal or polar beam angle. These are the main results of the first part of this study (Eliminating unwanted far-field excitation in objective-type TIRF. Pt.1. Identifying sources of nonevanescent excitation light). This second part focuses on exactly where up beam in the illumination system stray light is generated that gives rise to nonevanescent components in TIRF. Using dark-field imaging of scattered excitation light we pinpoint the objective, intermediate lenses and, particularly, the beam scanner as the major sources of stray excitation. We study how adhesion-molecule coating and astrocytes or BON cells grown on the coverslip surface modify the dark-field signal. On flat and weakly scattering cells, most background comes from stray reflections produced far from the sample plane, in the beam scanner and the objective lens. On thick, optically dense cells roughly half of the scatter is generated by the sample itself. We finally show that combining objective-type EW excitation with supercritical-angle fluorescence (SAF) detection efficiently rejects the fluorescence originating from deeper sample regions. We demonstrate that SAF improves the surface selectivity of TIRF, even at shallow penetration depths. The coplanar microscopy scheme presented here merges the benefits of beam spinning EW excitation and SAF detection and provides the conditions for quantitative wide-field imaging of fluorophore dynamics at or near the plasma membrane.

A hydrophilic gel matrix for single-molecule super-resolution microscopy

Background

Novel microscopic techniques which bypass the resolution limit in light microscopy are becoming routinely established today. The higher spatial resolution of super-resolution microscopy techniques demands for precise correction of drift, spectral and spatial offset of images recorded at different axial planes.

Methods

We employ a hydrophilic gel matrix for super-resolution microscopy of cellular structures. The matrix allows distributing fiducial markers in 3D, and using these for drift correction and multi-channel registration. We demonstrate single-molecule super-resolution microscopy with photoswitchable fluorophores at different axial planes. We calculate a correction matrix for each spectral channel, correct for drift, spectral and spatial offset in 3D.

Results and discussion

We demonstrate single-molecule super-resolution microscopy with photoswitchable fluorophores in a hydrophilic gel matrix. We distribute multi-color fiducial markers in the gel matrix and correct for drift and register multiple imaging channels. We perform two-color super-resolution imaging of click-labeled DNA and histone H2B in different axial planes, and demonstrate the quality of drift correction and channel registration quantitatively. This approach delivers robust microscopic data which is a prerequisite for data interpretation.

Quantitative dynamic footprinting microscopy

Quantitative dynamic footprinting (qDF) allows visualization of the footprints of live leukocytes rolling on a selectin-coated cover glass. qDF works on the principle of total internal reflection fluorescence, which involves fluorescence excitation in a thin slice (~200 nm) of the cell proximal to the cover glass while the rest of the cell remains dark. Dual color qDF (DqDF) is an advancement of qDF, which enables simultaneous visualization of two fluorochromes in the footprints of rolling leukocytes. When the fluorochrome is localized either in the cell cytoplasm or plasma membrane, the two-dimensional qDF image is used to create a three-dimensional rendition of the footprint topography. DqDF is a useful tool to study leukocyte adhesion under flow, and has recently been used to reveal mechanisms that enable neutrophils to roll at high shear stresses that prevail in venules during inflammation.

Cellular imaging using total internal reflection fluorescence microscopy: theory and instrumentation

Live cell fluorescent microscopy is important in elucidating dynamic cellular processes such as cell signaling, membrane trafficking, and cytoskeleton remodeling. Often, transient intermediate states are revealed only when imaged and quantitated at the single-molecule, vesicle, or organelle level. Such insight depends on the spatiotemporal resolution and sensitivity of a given microscopy method. Confocal microscopes optically section the cell and improve image contrast and axial resolution (>600 nm) compared with conventional epifluorescence microscopes. Another approach, which can selectively excite fluorophores in an even thinner optical plane (<100 nm) is total internal reflection fluorescence microscopy (TIRFM). The key principle of TIRFM is that a thin, exponentially decaying, evanescent field of excitation can be generated at the interface of two mediums of different refractive index (RI) (e.g., the glass coverslip and the biological specimen); as such, TIRFM is ill-suited to deep imaging of cells or tissue. However, for processes near the lower cell cortex, the sensitivity of TIRFM is exquisite. The recent availability of a very high numerical-aperture (NA) objective lens (>1.45) and turnkey TIRFM systems by all the major microscopy manufacturers has made TIRFM increasingly accessible and attractive to biologists, especially when performed in a quantitative manner and complemented with orthogonal genetic and molecular manipulations. This article discusses the optical principles of TIRFM (including a sample calculation of penetration depth), the components of a TIRFM setup, and the use of TIRFM in combination with other imaging modalities.

3-D reconstruction of microtubules from multi-angle total internal reflection fluorescence microscopy using Bayesian framework

Total internal reflection fluorescence (TIRF) microscopy excites a thin evanescent field which theoretically decays exponentially. Each TIRF image is actually the projection of a 3-D volume and hence cannot alone produce an accurate localization of structures in the z-dimension, however, it provides greatly improved axial resolution for biological samples. Multiple angle-TIRF microscopy allows controlled variation of the incident angle of the illuminating laser beam, thus generating a set of images of different penetration depths with the potential to reconstruct the 3-D volume of the sample. With the ultimate goal to quantify important biological parameters of microtubules, we present a method to reconstruct 3-D position and orientation of microtubules based on multi-angle TIRF data, as well as experimental calibration of the actual decay function of the evanescent field at each angle. We validate our method using computer simulations, by creating a phantom simulating the curvilinear characteristics of microtubules and project the artificially constructed volume into a set of TIRF image for different penetration depth. The reconstructed depth information for the phantom data is shown to be accurate and robust to noise. We apply our method to microtubule TIRF images of PtK(2) cells in vivo. By comparing microtubule curvatures of the reconstruction results and several electron microscopy (EM) images of vertically sliced sample of microtubules, we find that the curvature statistics of our reconstruction agree well with the ground truth (EM data). Quantifying the distribution of microtubule curvature reveals an interesting discovery that microtubules can buckle and form local bendings of considerably small radius of curvature which is also visually spotted on the EM images, while microtubule bendings on a larger scale generally have a much larger radius and cannot bear the stress of a large curvature. The presented method has the potential to provide a reliable tool for 3-D reconstruction and tracking of microtubules.

Estimation of 3D geometry of microtubules using multi-angle total internal reflection fluorescence microscopy

With the ultimate goal to quantify important biological parameters of microtubules, we present a method to estimate the 3D positions of microtubules from multi-angle TIRF data based on the calibrated decay profiles for each angle. Total Internal Reflection Fluorescence (TIRF) Microscopy images are actually projections of 3D volumes and hence cannot alone produce an accurate localization of structures in the z-dimension, however, they provide greatly improved axial resolution for biological samples. Multiple angle-TIRF microscopy allows controlled variation of the incident angle of the illuminating laser beam, thus generating a set of images of different penetration depths with the potential to estimate the 3D volume of the sample. Our approach incorporates prior information about intensity and geometric smoothness. We validate our method using computer simulated phantom data and test its robustness to noise. We apply our method to TIRF images of microtubules in PTK2 cells and compare the distribution of the microtubule curvatures with electron microscopy (EM) images.

Surface plasmon-enhanced and quenched two-photon excited fluorescence

This study investigated theoretically and experimentally that two-photon excited fluorescence is enhanced and quenched via surface plasmons (SPs) excited by total internal reflection with a silver film. The fluorescence intensity is fundamentally affected by the local electromagnetic field enhancement and the quantum yield change according to the surrounding structure and materials. By utilizing the Fresnel equation and classical dipole radiation modeling, local electric field enhancement, fluorescence quantum yield, and fluorescence emission coupling yield via SPs were theoretically analyzed at different dielectric spacer thicknesses between the fluorescence dye and the metal film. The fluorescence lifetime was also decreased substantially via the quenching effect. A two-photon excited total internal reflection fluorescence (TIRF) microscopy with a time-correlated single photon counting device has been developed to measure the fluorescence lifetimes, photostabilities, and enhancements. The experimental results demonstrate that the fluorescence lifetimes and the trend of the enhancements are consistent with the theoretical analysis. The maximum fluorescence enhancement factor in the surface plasmon-total internal reflection fluorescence (SP-TIRF) configuration can be increased up to 30 fold with a suitable thickness SiO(2) spacer. Also, to compromise for the fluorescence enhancement and the fluorophore photostability, we find that the SP-TIRF configuration with a 10 nm SiO(2) spacer can provide an enhanced and less photobleached fluorescent signal via the assistance of enhanced local electromagnetic field and quenched fluorescence lifetime, respectively.

Artifacts resulting from imaging in scattering media: a theoretical prediction

Scattering of illumination light from a laser is a severe problem especially when imaging in thick media. Although this effect occurs in nearly every imaging process, it can be well perceived and analyzed in configurations where the optical axes for illumination and detection are perpendicular to each other. In this paper I present a theoretical perspective of how to extend the point-spread function arithmetic from ideal imaging to realistic imaging including ghost images. These ghost images are generated by scattered light and are low-correlated with the ideal image. Numerical simulations of the propagation of four different types of illumination beams through a cluster of spheres illustrate the effects of inhomogeneous object illumination. Clear differences between a conventional plane-wave illumination, a static light-sheet, and a laterally scanned Gaussian beam, but also relative to a scanned Bessel beam, can be observed.

Surface plasmon-enhanced two-photon fluorescence microscopy for live cell membrane imaging

A surface plasmon-enhanced two-photon total-internal-reflection fluorescence (TIRF) microscope has been developed to provide fluorescent images of living cell membranes. The proposed microscope with the help of surface plasmons (SPs) not only provides brighter fluorescent images based on the mechanism of local electromagnetic field enhancement, but also reduces photobleaching due to having a shorter fluorophore lifetime. In comparison with a one-photon TIRF, the two-photon TIRF can achieve higher signal-to-noise ratio cell membrane imaging due its smaller excitation volume and lower scattering. By combining the SP enhancement and two-photon excitation TIRF, the microscope has demonstrated it's capability for brighter and more contrasted fluorescence membrane images of living monkey kidney COS-7 fibroblasts transfected with an EYFP-MEM or EGFP-WOX1 construct.

A programmable light engine for quantitative single molecule TIRF and HILO imaging

We report on a simple yet powerful implementation of objective-type total internal reflection fluorescence (TIRF) and highly inclined and laminated optical sheet (HILO, a type of dark-field) illumination. Instead of focusing the illuminating laser beam to a single spot close to the edge of the microscope objective, we are scanning during the acquisition of a fluorescence image the focused spot in a circular orbit, thereby illuminating the sample from various directions. We measure parameters relevant for quantitative image analysis during fluorescence image acquisition by capturing an image of the excitation light distribution in an equivalent objective backfocal plane (BFP). Operating at scan rates above 1 MHz, our programmable light engine allows directional averaging by circular spinning the spot even for sub-millisecond exposure times. We show that restoring the symmetry of TIRF/HILO illumination reduces scattering and produces an evenly lit field-of-view that affords on-line analysis of evanescnt-field excited fluorescence without pre-processing. Utilizing crossed acousto-optical deflectors, our device generates arbitrary intensity profiles in BFP, permitting variable-angle, multi-color illumination, or objective lenses to be rapidly exchanged.

Even illumination in total internal reflection fluorescence microscopy using laser light

In modern fluorescence microscopy, lasers are a widely used source of light, both for imaging in total internal reflection and epi-illumination modes. In wide-field imaging, scattering of highly coherent laser light due to imperfections in the light path typically leads to nonuniform illumination of the specimen, compromising image analysis. We report the design and construction of an objective-launch total internal reflection fluorescence microscopy system with excellent evenness of specimen illumination achieved by azimuthal rotation of the incoming illuminating laser beam. The system allows quick and precise changes of the incidence angle of the laser beam and thus can also be used in an epifluorescence mode.

Chapter 7: Total internal reflection fluorescence microscopy

Total internal reflection fluorescence microscopy (TIRFM), also known as evanescent wave microscopy, is used in a wide range of applications, particularly to view single molecules attached to planar surfaces and to study the position and dynamics of molecules and organelles in living culture cells near the contact regions with the glass coverslip. TIRFM selectively illuminates fluorophores only in a very thin (less than 100 nm deep) layer near the substrate, thereby avoiding excitation of fluorophores outside this subresolution optical section. This chapter reviews the history, current applications in cell biology and biochemistry, basic optical theory, combinations with numerous other optical and spectroscopic approaches, and a range of setup methods, both commercial and custom.

Noninvasive time-dependent cytometry monitoring by digital holography

Using a digital holographic microscope setup, it is possible to measure dynamic volume changes in living cells. The cells were investigated time-dependently in transmission mode for different kinds of stimuli affecting their morphology. The measured phase shift was correlated to the cellular optical thickness, and then of the cell volume as well as the refractive index were calculated and interpreted. For the characterization of the digital holographic microscope setup, we have developed a transparent three-dimensional (3-D) reference chart that can be used as a lateral resolution chart and step-height resolution chart included in one substrate. For the monitoring of living cells, a biocompatible and autoclavable flow chamber was designed, which allows us to add, exchange, or dilute the fluid within the flow chamber. An integrated changeable coverslip enables inverse microscopic applications. Trypsinization, cell swelling and shrinking induced by osmolarity changes, and apoptosis served as model processes to elucidate the potential of the digital holographic microscopy (DHM).

Laser‐Based Measurements in Cell Biology

In this chapter, we review the imaging techniques and methods of molecular interrogation made possible by integrating laser light sources with microscopy. We discuss the advantages of exciting fluorescence by laser illumination and review commonly used laser-based imaging techniques such as confocal, multiphoton, and total internal reflection microcopy. We also discuss emerging imaging modalities based on intrinsic properties of biological macromolecules such as second harmonic generation imaging and coherent anti-Raman resonance spectroscopy. Super resolution techniques are presented that exceed the theoretical diffraction-limited resolution of a microscope objective. This chapter also focuses on laser-based techniques that can report biophysical parameters of fluorescently labeled molecules within living cells. Photobleaching techniques, fluorescence lifetime imaging, and fluorescence correlation methods can measure kinetic rates, molecular diffusion, protein-protein interactions, and concentration of a fluorophore-bound molecule. This chapter provides an introduction to the field of laser-based microscopy enabling readers to determine how best to match their research questions to the current suite of techniques.

Insulin exocytotic mechanism by imaging technique

Insulin is stored in pancreatic beta cell granules, and released biphasically by the exocytotic mechanism induced by nutrient glucose. Insulin exocytosis must be critically regulated to finely control body glucose homeostasis because insulin is the only hormone that can promptly reduce the blood glucose level. Recent advanced techniques in molecular biology and electrophysiology revealed the molecular mechanism of insulin release in the process from glucose entry to increased [Ca(2+)](i). However, the insulin exocytotic process such as translocation, docking and fusion of insulin granules was largely unknown. In order to reveal the molecular mechanism of this process, we utilized a newly innovated imaging technique, TIRF imaging system. Here we review recent results of our studies into docking and fusion of insulin granules analyzed by TIRF system.

Analysis of transient behavior in complex trajectories: application to secretory vesicle dynamics

Analysis of trajectories of dynamical biological objects, such as breeding ants or cell organelles, is essential to reveal the interactions they develop with their environments. Many previous works used a global characterization based on parameters calculated for entire trajectories. In cases where transient behavior was detected, this usually concerned only a particular type, such as confinement or directed motion. However, these approaches are not appropriate in situations in which the tracked objects may display many different types of transient motion. We have developed a method to exhaustively analyze different kinds of transient behavior that the tracked objects may exhibit. The method discriminates stalled periods, constrained and directed motions from random dynamics by evaluating the diffusion coefficient, the mean-square displacement curvature, and the trajectory asymmetry along individual trajectories. To detect transient motions of various durations, these parameters are calculated along trajectories using a rolling analysis window whose width is variable. The method was applied to the study of secretory vesicle dynamics in the subplasmalemmal region of human carcinoid BON cells. Analysis of transitions between transient motion periods, combined with plausible assumptions about the origin of each motion type, leads to a model of dynamical subplasmalemmal organization.

Kir6.2DeltaC26 channel traffics to plasma membrane by constitutive exocytosis

Adenosine triphosphate (ATP)-sensitive K+ (KATP) channels regulate many cellular functions by coupling the metabolic state of the cell to the changes in membrane potential. Truncation of C-terminal 26 amino acid residues of Kir6.2 protein (Kir6.2DeltaC26) deletes its endoplasmic reticulum retention signal, allowing functional expression of Kir6.2 in the absence of sulfonylurea receptor subunit. pEGFP-Kir6.2DeltaC26 and pKir6.2DeltaC26-IRES2-EGFP expression plasmids were constructed and transfected into HEK293 cells. We identified that Kir6.2DeltaC26 was localized on the plasma membrane and trafficked to the plasmalemma by means of constitutive exocytosis of Kir6.2DeltaC26 transport vesicles, using epi-fluorescence and total internal reflection fluorescence microscopy. Our electrophysiological data showed that Kir6.2DeltaC26 alone expressed KATP currents, whereas EGFP-Kir6.2DeltaC26 fusion protein displayed no KATP channel activity.

Use of TIRF Microscopy to Visualize Actin and Microtubules in Migrating Cells

Total internal reflection fluorescence (TIRF) is the technique of choice to visualize and quantify cellular events localized at the basal plasma membrane of adherent cells. By selectively illuminating the first 200 nm above the basal membrane, it allows maximal resolution in the vertical z-axis. In this chapter, I describe a prism-based TIRF setup and the procedures to visualize the actin and microtubule cytoskeleton in migrating astrocytes. TIRF microscopy provides quantitative information on the organization of the cytoskeleton in both fixed and live migrating cells.

Noninvasive measurement of cell volume changes by negative staining

To maintain the intracellular concentration of ions and small molecules on osmotic challenges, nature has developed highly sophisticated transport systems for regulating water and ion content. An ideal measurement technique for volume changes of cells during osmotic challenges has to fulfil two requirements: it has to be osmotically inert, and it should allow online monitoring of cell volume changes. Here, a simple fluorescence microscopy-based approach is presented. Using fluorescein as a negative stain, it is possible to monitor cell volume changes without affecting the functionality of cell membranes and cell osmolarity. Measurement of Madine-Darby canine kidney (MDCK) cells after hypo- and hyperosmotic challenges reveals the main advantages of this approach: besides providing precise and reproducible quantitative data on reversible cell volume changes, the viability of the cells can be assessed directly by the appearance of stain in the cytoplasm. This becomes evident especially after hypo-osmotic challenge of glutaraldehyde-treated cells, which become leaky after fixation, followed by a massive volume change. This new approach represents a very sensitive measurement technique for cell volume changes resulting from water or ion flux, and thus seems to be an ideal tool for studying cell volume regulatory processes.

Experimental verification of near-wall hindered diffusion for the Brownian motion of nanoparticles using evanescent wave microscopy

A total internal reflection fluorescence microscopy technique coupled with three-dimensional tracking of nanoparticles is used to experimentally verify the theory on near-wall hindered Brownian motion [Goldman et al., Chem. Eng. Sci. 22, 637 (1967); Brenner, Chem. Eng. Sci. 16, 242 (1967)] very close to the solid surface (within approximately 1 microm). The measured mean square displacements (MSDs) in the lateral x-y directions show good agreement with the theory for all tested nanoparticles of radii 50, 100, 250, and 500 nm. However, the measured MSDs in the z direction deviate substantially from the theory particularly for the case of smaller particles of 50 and 100 nm radius. Since the theory considers only the hydrodynamic interaction of moving particles with a stationary solid wall, additionally possible interaction forces like gravitational forces, van der Waals forces, and electro-osmotic forces have been examined to delineate the physical reasons for the discrepancy.

Variable incidence angle fluorescence interference contrast microscopy for z-imaging single objects

Surface-generated structured illumination microscopies interrogate the position of fluorescently labeled objects near surfaces with nanometer resolution along the z axis. However, these techniques are either experimentally cumbersome or applicable to a limited set of experimental systems. We present a new type of surface-generated structured illumination fluorescence microscopy, variable incidence angle fluorescence interference contrast microscopy (VIA-FLIC), in which the fluorescent sample is assembled above a reflective Si surface and the incidence angle of excitation light is varied by placing annular photomasks with different radii in the aperture diaphragm plane of the microscope. The variation in incidence angle alters the interference pattern of excitation light, and hence the intensity of detected fluorescence. Quantitative VIA-FLIC is tested by using a set of fluorophore-containing supported membranes separated from the Si surface by SiO2 layers of variable thicknesses. The resulting fluorescence intensity versus incidence angle curves depends on the separation from the Si surface and when fit with an appropriate model yield precise SiO2 thicknesses that are accurate with respect to the known SiO2 thicknesses. Since only a simple modification to a standard epifluorescence microscope is required, VIA-FLIC offers a versatile method to produce z-reconstructions with high resolution for a wide range of biological systems.

Motion of Single DNA Molecules at a Liquid−Solid Interface As Revealed by Variable-Angle Evanescent-Field Microscopy

A variable-angle total-internal-reflection fluorescence microscope (VATIRFM) capable of providing a large range of incident angles was constructed for imaging single DNA molecule dynamics at a solid/liquid interface. An algorithm using a public-domain image-processing program, ImageJ, was developed for single-molecule counting. The experimental counts at various incident angles with different evanescent-field layer (EFL) thicknesses are affected by molecular diffusion. The dynamics of molecules near the surface and the observed counts in the VATIRFM are elucidated using a limited one-dimensional random-walk diffusion model. The simulation fits well with the experimental counting results. Further analysis using the simulation reveals the details of single-molecule motion. One implication is that the measured intensities cannot be used directly to determine the distances of molecules from the surface, though the majority of fluorescence does come from the EFL. Another implication is that rather than providing molecular concentrations within EFL the experimental counting results depict the distance-dependent dynamics of molecules near the surface. Thus, the VATIRFM could be a powerful technique to study the surface repulsion/attraction of molecules within a few hundred nanometers of the surface. Further studies show that molecules at low ionic strengths experience electrostatic repulsion at distances much further away from the surface than the calculated thickness of the electrical double layer.

Effect of taper geometries and launch angle on evanescent wave penetration depth in optical fibers

A large penetration depth of an evanescent wave is the key to success for developing an ultra high-resolution fiber-based evanescent wave biosensor. Tapering the fiber and launching light at an angle has the potential of increasing the penetration depth of evanescent wave manifolds. The effects of tapering, launch angle and taper length of the fiber have been explored in detail using a ray-tracing model to calculate the highest possible penetration depth of the evanescent field. Evanescent wave penetration depths of the order of the size of living cells have been achieved by optimizing the parameters relating geometry of tapered fibers.

An Integrated Metal Clad Leaky Waveguide Sensor for Detection of Bacteria

An integrated optical metal clad leaky waveguide (MCLW) sensor device has been developed for the detection of bacteria. This is more sensitive than waveguide sensors currently in use. The MCLW device has been fabricated to extend the evanescent field to provide significant light intensity over the entire volume of the bacteria bound on the chip surface within this field. This in turn increases the interaction of the light with the entire volume of the bacteria. MCLW devices have been used for detecting refractive index changes, scattering, and fluorescence from bacterial spores captured on an immobilized antibody. The detection limit of Bacillus subtilis var. niger bacterial spores using refractive index detection was 8 x10(4) spores/mL. The scattering intensity of the BG spores was found to be three times greater than the scattering intensity generated using surface plasmon resonance. The extended light propagation along the direction of flow for a few millimeters provides an effective interrogation approach to increase the area of detection to detect low concentrations down to 1 x 10(4) spores/mL. The sensor was then optimized by studying the key factors affecting sensor performance including changing the pH of the medium, type of antibody immobilization matrix, sensor surface regeneration approaches, and longevity of the sensor.

Correlation of syntaxin-1 and SNAP-25 clusters with docking and fusion of insulin granules analysed by total internal reflection fluorescence microscopy

AIMS/HYPOTHESIS

The interaction of syntaxin-1 and SNAP-25 with insulin exocytosis was examined using the diabetic Goto-Kakizaki (GK) rat and a total internal reflection fluorescence (TIRF) imaging system.

METHODS

Primary rat pancreatic beta cells were immunostained with anti-syntaxin-1A, anti-SNAP-25 and anti-insulin antibodies, and then observed by TIRF microscopy. The real-time image of GFP-labelled insulin granules motion was monitored by TIRF.

RESULTS

The number of syntaxin-1A and SNAP-25 clusters, and the number of docked insulin granules on the plasma membrane were reduced in GK beta cells. When GK rats were treated with daily insulin injection for 2 weeks, the number of syntaxin-1 and SNAP-25 clusters was restored, along with the number of docked insulin granules. The infection of GK beta cells with Adex1CA SNAP-25 increased the number of docked insulin granules. TIRF imaging analysis demonstrated that the decreased number of fusion events from previously docked insulin granules in GK beta cells was restored when the number of docked insulin granules increased by insulin treatment or Adex1CA SNAP-25 infection.

CONCLUSIONS/INTERPRETATION

There was a close correlation between the number of syntaxin-1 and SNAP-25 clusters and the number of docked insulin granules, which is associated with the fusion of insulin granules.

TIRF imaging of docking and fusion of single insulin granule motion in primary rat pancreatic beta-cells: different behaviour of granule motion between normal and Goto-Kakizaki diabetic rat beta-cells

We imaged and analysed the motion of single insulin secretory granules near the plasma membrane in live pancreatic beta-cells, from normal and diabetic Goto-Kakizaki (GK) rats, using total internal reflection fluorescence microscopy (TIRFM). In normal rat primary beta-cells, the granules that were fusing during the first phase originate from previously docked granules, and those during the second phase originate from 'newcomers'. In diabetic GK rat beta-cells, the number of fusion events from previously docked granules were markedly reduced, and, in contrast, the fusion from newcomers was still preserved. The dynamic change in the number of docked insulin granules showed that, in GK rat beta-cells, the total number of docked insulin granules was markedly decreased to 35% of the initial number after glucose stimulation. Immunohistochemistry with anti-insulin antibody observed by TIRFM showed that GK rat beta-cells had a marked decline of endogenous insulin granules docked to the plasma membrane. Thus our results indicate that the decreased number of docked insulin granules accounts for the impaired insulin release during the first phase of insulin release in diabetic GK rat beta-cells.

Fluorescence imaging with two-photon evanescent wave excitation

We demonstrate broad-field, non-scanning, two-photon excitation fluorescence (2PEF) close to a glass/cell interface by total internal reflection of a femtosecond-pulsed infrared laser beam. We exploit the quadratic intensity dependence of 2PEF to provide non-linear evanescent wave (EW) excitation in a well-defined sample volume and to eliminate scattered background excitation. A simple model is shown to describe the resulting 2PEF intensity and to predict the effective excitation volume in terms of easily measurable beam, objective and interface properties. We demonstrate non-linear evanescent wave excitation at 860 nm of acridine orange-labelled secretory granules in live chromaffin cells, and excitation at 900 nm of TRITC-phalloidin-actin/GPI-GFP double-labelled fibroblasts. The confined excitation volume and the possibility of simultaneous multi-colour excitation of several fluorophores make EW 2PEF particularly advantageous for quantitative microscopy, imaging biochemistry inside live cells, or biosensing and screening applications in miniature high-density multi-well plates.

Quantifying axial secretory-granule motion with variable-angle evanescent-field excitation

The trajectory of secretory vesicles to their fusion sites at the plasma membrane is expected to give insight into the mechanisms that underlie vesicle transport, maturation and the initiation of membrane fusion. Evanescent-wave (EW) microscopy allows the tracking of fluorescently labeled granules and vesicles prior to fusion with nanometer precision in xy-direction. At the same time, the exponential sensitivity of granular fluorescence to experimental parameters can preclude quantitative estimates of the granule's approach to the plasma membrane. Thus, it has remained controversial to which extent axial distance can be obtained from simple intensity measurements. We used the information contained in a stack of images acquired at 80-125 nm penetration depth of the EW field to estimate individual granule diameter and axial distance. A population analysis on 90 granules revealed an average diameter of 305 +/- 47 nm, below the diffraction-limited 352 +/- 31 nm obtained from xy measurements at fixed depth penetration. Stimulation of exocytosis by potassium depolarization resulted in the selective loss of the 18 +/- 5% of granules located closest to the plasma membrane, while a second population of granules located 60 nm deeper within the cytoplasm increased by recruitment of granules previously located at > or = 120 nm depth. These measurements extend and corroborate previous observations at fixed penetration depth of functionally distinct granule populations. Parameters influencing the accuracy of the parameter estimation are evaluated in the appendix.

Ion channels in secretory granules of the pancreas and their role in exocytosis and release of secretory proteins

Regulated secretion in exocrine and neuroendocrine cells occurs through exocytosis of secretory granules and the subsequent release of stored small molecules and proteins. The introduction of biophysical techniques with high temporal and spatial resolution, and the identification of Ca(2+)-dependent and -independent "docking" and "fusion" proteins, has greatly enhanced our understanding of exocytosis. The cloning of families of ion channel proteins, including intracellular ion channels, has also revived interest in the role of secretory granule ion channels in exocytotic secretion. Thus secretory granules of pancreatic acinar cell express a ClC-2 Cl(-) channel, a HCO-permeable member of the CLCA Ca(2+)-dependent anion channel family, and a KCNQ1 K(+) channel. Evidence suggests that these channels may facilitate the release of digestive enzymes and/or prevent exocytosed granules from collapsing during "kiss and run" recycling. In pancreatic beta-cells, a granular ClC-3 Cl(-) channel provides a shunt pathway for a vacuolar-type H(+)-ATPase. Acidification "primes" the granules for Ca(2+)-dependent exocytosis and release of insulin. In summary, secretory granules are equipped with specific sets of ion channels, which modulate regulated exocytosis and the release of macromolecules. These channels could represent excellent targets for therapeutic interventions to control exocytotic secretion in relevant diseases, such as pancreatitis, cystic fibrosis, or diabetes mellitus.

High refractive index substrates for fluorescence microscopy of biological interfaces with high z contrast

Total internal reflection fluorescence microscopy is widely used to confine the excitation of a complex fluorescent sample very close to the material on which it is supported. By working with high refractive index solid supports, it is possible to confine even further the evanescent field, and by varying the angle of incidence, to obtain quantitative information on the distance of the fluorescent object from the surface. We report the fabrication of hybrid surfaces consisting of nm layers of SiO(2) on lithium niobate (LiNbO(3), n = 2.3). Supported lipid bilayer membranes can be assembled and patterned on these hybrid surfaces as on conventional glass. By varying the angle of incidence of the excitation light, we are able to obtain fluorescent contrast between 40-nm fluorescent beads tethered to a supported bilayer and fluorescently labeled protein printed on the surface, which differ in vertical position by only tens of nm. Preliminary experiments that test theoretical models for the fluorescence-collection factor near a high refractive index surface are presented, and this factor is incorporated into a semiquantitative model used to predict the contrast of the 40-nm bead/protein system. These results demonstrate that it should be possible to profile the vertical location of fluorophores on the nm distance scale in real time, opening the possibility of many experiments at the interface between supported membranes and living cells. Improvements in materials and optical techniques are outlined.