Lighting up the cell surface with evanescent wave microscopy

C-reactive protein (CRP) aptamer binds to monomeric but not pentameric form of CRP

Native C-reactive protein (CRP) is composed of five identical subunits arranged in a pentameric structure (pCRP). Binding of pCRP to damaged cell membranes produces a second isoform, modified CRP, which has similar antigenicity to isolated monomeric subunits of CRP (mCRP). Emerging evidence indicates that modified CRP plays a role in inflammation and atherosclerosis, however, there are very few techniques that can distinguish the different isoforms of CRP. Here we show that an RNA aptamer binds specifically to mCRP and not to pCRP. Using this aptamer, we describe a simple, fast, and sensitive assay to detect nanomolar concentrations of mCRP using fluorescence anisotropy. In addition, we show that this aptamer can be used to detect mCRP in polyacrylamide gels and bound to a surface using total internal reflection fluorescence microscopy. The biological activity of the mCRP we prepared by heating pCRP with 0.1% sodium dodecyl sulfate was confirmed by observing binding to the complement protein, C1q. This probe provides an important tool for CRP research and has the potential to improve clinical diagnostics that predict risk for cardiovascular disease.

Imaging techniques for assaying lymphocyte activation in action

Imaging techniques have greatly improved our understanding of lymphocyte activation. Technical advances in spatial and temporal resolution and new labelling tools have enabled researchers to directly observe the activation process. Consequently, research using imaging approaches to study lymphocyte activation has expanded, providing an unprecedented level of cellular and molecular detail in the field. As a result, certain models of lymphocyte activation have been verified, others have been revised and yet others have been replaced with new concepts. In this article, we review the current imaging techniques that are used to assess lymphocyte activation in different contexts, from whole animals to single molecules, and discuss the advantages and potential limitations of these methods.

Dlg1 binds GKAP to control dynein association with microtubules, centrosome positioning, and cell polarity

The small GTPase Cdc42 regulates interactions of dynein with microtubules through the polarity protein Dlg1 and the scaffolding protein GKAP.

Centrosome positioning is crucial during cell division, cell differentiation, and for a wide range of cell-polarized functions including migration. In multicellular organisms, centrosome movement across the cytoplasm is thought to result from a balance of forces exerted by the microtubule-associated motor dynein. However, the mechanisms regulating dynein-mediated forces are still unknown. We show here that during wound-induced cell migration, the small G protein Cdc42 acts through the polarity protein Dlg1 to regulate the interaction of dynein with microtubules of the cell front. Dlg1 interacts with dynein via the scaffolding protein GKAP and together, Dlg1, GKAP, and dynein control microtubule dynamics and organization near the cell cortex and promote centrosome positioning. Our results suggest that, by modulating dynein interaction with leading edge microtubules, the evolutionary conserved proteins Dlg1 and GKAP control the forces operating on microtubules and play a fundamental role in centrosome positioning and cell polarity.

Linear optics based nanoscopy

Classically, optical systems are considered to have a fundamental resolution limit due to wave nature of light. This article presents a novel method for observing sub-wavelength features in a conventional optical microscope using linear optics. The operation principle is based on a random and time varying flow of nanoparticles moving in proximity to the inspected sample. Those particles excite the evanescent waves and couple them into harmonic waves. The sub-wavelength features are encoded and later on digitally decoded by proper image processing of a sequence of images. The achievable final resolution limit corresponds to the size of the nanoparticles. Experimental proof of principle validation of the technique is reported.

Detection of C-reactive protein in evanescent wave field using microparticle-tracking velocimetry

A new technique is developed to measure the nanoparticles' brownian motions by employing microparticle-tracking velocimetry (micro-PTV) in evanescent wave field, which can provide high signal-to-noise ratio images for analyzing nanoparticles' movements. This method enables real-time detection of C-reactive proteins (CRPs) during the rapid interaction between CRPs and anti-CRP-coated nanobeads as CRP concentrations are related to the nanobeads' brownian velocity in the equilibrium state. The smallest observable nanobeads with 185 nm were utilized in this experiment to detect CRP concentrations as low as 0.1 microg/mL even in a high-viscosity solution. Further, the dissociation constant, K(D), can be evaluated based on the experimental results.

Imaging lipids in living cells

The investigation of lipids in living cells is one of the underdeveloped areas in cell biology. Although it is possible to analyze the global lipid composition of a cell type, fractionation of the various types of membranes from cells is extraordinarily difficult, mainly because most membranes appear to be in contact with each other. Therefore, we know the lipid components, but we have a difficult time finding out their exact position, how dynamically they change location, and how rapidly they are metabolized. Imaging lipids in cells seems to be the obvious solution to the problem. The most common way to image molecules is by the artificial addition of a fluorescent tag. The use of fluorescent proteins has become the mainstay of protein imaging, but this method is, of course, not suitable for small molecules such as lipids. Unfortunately, the fluorescent tag is usually as large as the lipid and is therefore likely to have a severe influence on lipid location and metabolism. To circumvent this problem, two solutions have been developed--namely, the use of fluorescently labeled proteins that specifically recognize lipids and a chemical method to introduce the fluorescent tag inside the cell. This article describes procedures necessary to image lipids by fluorescently tagged lipid-binding domains and by labeling lipid derivatives in fixed and living cells.

Regulation of multidrug resistance-associated protein 2 by calcium signaling in mouse liver

Multidrug resistance associated protein 2 (Mrp2) is a canalicular transporter responsible for organic anion secretion into bile. Mrp2 activity is regulated by insertion into the plasma membrane; however, the factors that control this are not understood. Calcium (Ca(2+)) signaling regulates exocytosis of vesicles in most cell types, and the type II inositol 1,4,5-triphosphate receptor (InsP(3)R2) regulates Ca(2+) release in the canalicular region of hepatocytes. However, the role of InsP(3)R2 and of Ca(2+) signals in canalicular insertion and function of Mrp2 is not known. The aim of this study was to determine the role of InsP(3)R2-mediated Ca(2+) signals in targeting Mrp2 to the canalicular membrane. Livers, isolated hepatocytes, and hepatocytes in collagen sandwich culture from wild-type (WT) and InsP(3)R2 knockout (KO) mice were used for western blots, confocal immunofluorescence, and time-lapse imaging of Ca(2+) signals and of secretion of a fluorescent organic anion. Plasma membrane insertion of green fluorescent protein (GFP)-Mrp2 expressed in HepG2 cells was monitored by total internal reflection microscopy. InsP(3)R2 was concentrated in the canalicular region of WT mice but absent in InsP(3)R2 KO livers, whereas expression and localization of InsP(3)R1 was preserved, and InsP(3)R3 was absent from both WT and KO livers. Ca(2+) signals induced by either adenosine triphosphate (ATP) or vasopressin were impaired in hepatocytes lacking InsP(3)R2. Canalicular secretion of the organic anion 5-chloromethylfluorescein diacetate (CMFDA) was reduced in KO hepatocytes, as well as in WT hepatocytes treated with 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA). Moreover, the choleretic effect of tauroursodeoxycholic acid (TUDCA) was impaired in InsP(3)R2 KO mice. Finally, ATP increased GFP-Mrp2 fluorescence in the plasma membrane of HepG2 cells, and this also was reduced by BAPTA.

CONCLUSION

InsP(3)R2-mediated Ca(2+) signals enhance organic anion secretion into bile by targeting Mrp2 to the canalicular membrane.

Blue-emitting small silica particles incorporating ZnSe-based nanocrystals prepared by reverse micelle method

ZnSe-based nanocrystals (ca. 4-5 nm in diameter) emitting in blue region (ca. 445 nm) were incorporated in spherical small silica particles (20–40 nm in diameter) by a reverse micelle method. During the preparation, alkaline solution was used to deposit the hydrolyzed alkoxide on the surface of nanocrystals. It was crucially important for this solution to include Zn²⁺ ions and surfactant molecules (thioglycolic acid) to preserve the spectral properties of the final silica particles. This is because these substances in the solution prevent the surface of nanocrystals from deterioration by dissolution during processing. The resultant silica particles have an emission efficiency of 16% with maintaining the photoluminescent spectral width and peak wavelength of the initial colloidal solution.

Interference reflection microscopy

Interference reflection microscopy (IRM) is an optical technique used to study cell adhesion or cell mobility on a glass coverslip. The interference of reflected light waves generates images with high contrast and definition. IRM can be used to examine almost any cell that will rest upon a glass surface, although it is most useful in examining sites of close contact between a cell and substratum. This unit presents methods for obtaining IRM images of cells with particular emphasis on IRM imaging with a laser scanning confocal microscope (LSCM), as most LSCM are already capable of recording these images without any modification of the instrument. Techniques are presented for imaging fixed and live cells, as well as simultaneous multi-channel capture of fluorescence and reflection images.

Venus fly trap domain of mGluR1 functions as a dominant negative against group I mGluR signaling

Metabotropic glutamate receptors (mGluRs) form covalently linked homodimers and contain large, N-terminal extracellular ligand binding, "venus fly trap" (VFT) domains. These domains, when expressed separately, are secreted as disulfide linked dimers and can dimerize with full-length receptors. mGluR splice variants have been described that contain only this domain, but the consequences of their interaction on receptor signaling have not been explored. Here it is shown that an mGluR1 mutant containing only the VFT is retained on the cell surface when a full-length receptor is co-expressed. Further, when expressed in rat superior cervical ganglion (SCG) neurons and modulation of native calcium currents is used as an assay for receptor activity, the VFT acts as a dominant negative with respect to mGluR1 signaling. Although full-length mGluR1 and mGluR5 are not known to heterodimerize, the mGluR5 VFT partially occludes mGluR1 signaling and the mGluR1 VFT potently occludes mGluR5 signaling in SCG neurons. In addition, an mGluR1 point mutant, mGluR1 C140G, which cannot covalently dimerize, functions like the wild-type receptor when expressed alone. The C140G mutant is inhibited by the mGluR1 VFT construct but does not retain the mGluR1 VFT on the cell surface, suggesting that the loss of C140 renders the interaction reversible. Finally, a peptide designed to disrupt mGluR1 dimerization reduced signaling through the C140G mutant receptor, but only when applied intracellularly for several hours, indicating that loss of signaling requires disruption of dimerization prior to plasma membrane insertion.

Role of the polybasic sequence in the Doc2alpha C2B domain in dense-core vesicle exocytosis in PC12 cells

The double C2 (Doc2) family is characterized by an N-terminal Munc13-1-interacting domain and C-terminal tandem C2 domains, and it comprises three isoforms, Doc2alpha, Doc2beta, and Doc2gamma, in humans and mice. Doc2alpha, the best-characterized, brain-specific isoform, exhibits Ca(2+)-dependent phospholipid-binding activity through its C2A domain, and the Ca(2+)-binding activity is thought to be important for the regulation of Ca(2+)-dependent exocytosis. In contrast to the C2A domain, however, nothing is known about the physiological functions of the C2B domain in regulated exocytosis. In this study, we demonstrated by a mutation analysis that the polybasic sequence in the C2B domain of Doc2alpha (306 KKSKHKTCVKKK 317) is required for binding of syntaxin-1a/synaptosome-associated protein of 25 kDa (SNAP-25) heterodimer. We also investigated the effect of Lys-to-Gln (named KQ) mutations in the polybasic sequence of the C2B domain on vesicle dynamics by total internal reflection fluorescence microscopy in PC12 cells. A Doc2alpha(KQ) mutant, which lacks binding activity toward syntaxin-1a/SNAP-25 heterodimer, significantly decreased the number of plasma membrane-docked vesicles before stimulation and strongly inhibited high-KCl-induced exocytosis from the plasma membrane-docked vesicles. These results indicate that the polybasic sequence in the C2B domain functions as a binding site for syntaxin-1a/SNAP-25 heterodimer and controls the number of 'readily releasable' vesicles in neuroendocrine cells.

Fluorescence microscopy: a concise guide to current imaging methods

The field of fluorescence microscopy is rapidly growing, providing ever increasing imaging capabilities for cell and neurobiologists. Over the last decade, many new technologies and techniques have been developed which allow for deeper, faster, or higher resolution imaging. For the non-expert microscopist, it can be difficult to match the best imaging technique to the biological question to be examined. Picking the right technique requires a basic understanding of the underlying imaging physics for each technique, as well as an informed comparison and balancing of competing imaging properties in the context of the sample to be imaged. This unit provides concise descriptions of a range of commercially available imaging techniques and provides a tabular guide to choosing among them. Techniques covered include structured light, confocal, total internal reflection fluorescence (TIRF), two-photon, and stimulated emission depletion (STED) microscopy.

Single-photon atomic force microscopy

In the last few years, an array of novel technologies, especially the big family of scanning probe microscopy, now often integrated with other powerful imaging tools such as laser confocal microscopy and total internal reflection fluorescence microscopy, have been widely applied in the investigation of biomolecular interactions and dynamics. But it is still a great challenge to directly monitor the dynamics of biomolecular interactions with high spatial and temporal resolution in living cells. An innovative method termed "single-photon atomic force microscopy" (SP-AFM), superior to existing techniques in tracing biomolecular interactions and dynamics in vivo, was proposed on the basis of the combination of atomic force microscopy with the technologies of carbon nanotubes and single-photon detection. As a unique tool, SP-AFM, capable of simultaneous topography imaging and molecular identification at the subnanometer level by synchronous acquisitions and analyses of the surface topography and fluorescent optical signals while scanning the sample, could play a very important role in exploring biomolecular interactions and dynamics in living cells or in a complicated biomolecular background.

Microtubule dynamics at the cell cortex probed by TIRF microscopy

Total internal reflection fluorescence (TIRF) microscopy is a technique that allows selective excitation of fluorescence at a liquid/solid interface within a short distance from the boundary. The penetration depth of TIRF microscopy depends on the angle of illumination resulting in a range of depths, which typically vary from approximately similar 70-200 nm up to reverse approximately 500 nm. The advantages of TIRF microscopy include excellent signal-to-noise ratio, high sensitivity, low photobleaching, and low photodamage. TIRF microscopy is widely used for studying cell adhesion, exo- and endocytosis, and the dynamics of plasma membrane-associated molecules. TIRF microscopy can also be applied for selective visualization of any other cellular processes that occur near the basal membrane even if their localization is not restricted to this part of the cell. For example, microtubules are distributed throughout the cytoplasm, but the use of TIRF microscopy makes it possible to visualize specifically the microtubule subpopulation in the vicinity of the basal cortex and thus study cortical microtubule attachment and stabilization, interactions between microtubules and matrix adhesion structures, and the behavior of specific molecules involved in these processes. In this chapter we describe the application of a commercially available setup to analyze microtubule behavior in live mammalian cells using TIRF microscopy.

High-resolution total-internal-reflection fluorescence microscopy using periodically nanostructured glass slides

We compare the performance of a total-internal-reflection fluorescence microscope under varying illumination and substrate conditions. The samples are deposited on a standard homogeneous glass slide or on a grating and illuminated by one or two interfering beams at various incident angles. A conjugate gradient with positivity a priori information is used to reconstruct the fluorophore density from the images. Numerical studies demonstrate that when the sample lies on an optimized grating, the lateral resolution of the microscope is greatly improved, up to fourfold, the best result being obtained when the grating is illuminated by two interfering beams.

Endocytic events in TCR signaling: focus on adapters in microclusters

Although the critical role of T-cell receptor (TCR) microclusters in T-cell activation is now widely accepted, the mechanisms of regulation of these TCR-rich structures, which also contain enzymes, adapters, and effectors, remain poorly defined. Soon after microcluster formation, several signaling proteins rapidly dissociate from the TCR. Recent studies from our laboratory demonstrated that the movement of the adapters linker for activation of T cells (LAT) and Src homology 2 domain-containing leukocyte protein of 76 kDa (SLP-76) away from initial microcluster formation sites represents endocytic events. Ubiquitylation, Cbl proteins, and multiple endocytic pathways are involved in the internalization events that disassemble signaling microclusters. Several recent studies have indicated that microcluster movement and centralization plays an important role in signal termination. We suggest that microcluster movement is directly linked to endocytic events, thus implicating endocytosis of microclusters as a means to regulate signaling output of the T cell.

Compartmentalization of the outer hair cell demonstrated by slow diffusion in the extracisternal space

In the outer hair cell (OHC), the extracisternal space (ECiS) is a conduit and reservoir of the molecular and ionic substrates of the lateral wall, including those necessary for electromotility. To determine the mechanisms through which molecules are transported in the ECiS of the OHC, we selectively imaged the time-dependent spatial distribution of fluorescent molecules in a <100 nm layer near the cell/glass interface of the recording chamber after their photolytic activation in a diffraction-limited volume. The effective diffusion coefficient was calculated using the analytical solution of the diffusion equation. It was found that diffusion in the ECiS is isotropic and not affected by depolarizing the OHC. Compared with free solution, the diffusion of 10 kDa dextran was slowed down in both the ECiS and the axial core by a factor of 4.6 and 1.6, respectively.

Low-temperature single-molecule spectroscopy on photosynthetic pigment-protein complexes from purple bacteria

The primary reactions of purple bacterial photosynthesis take place within two well characterized pigment-protein complexes, the core Reaction Center-Light Harvesting 1 (RC-LH1) complex and the more peripheral Light Harvesting 2 (LH2) complex. These antenna complexes serve to absorb incident solar radiation and to transfer it to the reaction-centers, where it is used to 'power' the photosynthetic redox reaction. This review provides an overview of how the character of the electronically excited states of these pigment-protein complexes are determined by quantum mechanics and how the respective spectral signatures can be observed by single-molecule spectroscopy.

Illuminating the life of GPCRs

The investigation of biological systems highly depends on the possibilities that allow scientists to visualize and quantify biomolecules and their related activities in real-time and non-invasively. G-protein coupled receptors represent a family of very dynamic and highly regulated transmembrane proteins that are involved in various important physiological processes. Since their localization is not confined to the cell surface they have been a very attractive "moving target" and the understanding of their intracellular pathways as well as the identified protein-protein-interactions has had implications for therapeutic interventions. Recent and ongoing advances in both the establishment of a variety of labeling methods and the improvement of measuring and analyzing instrumentation, have made fluorescence techniques to an indispensable tool for GPCR imaging. The illumination of their complex life cycle, which includes receptor biosynthesis, membrane targeting, ligand binding, signaling, internalization, recycling and degradation, will provide new insights into the relationship between spatial receptor distribution and function. This review covers the existing technologies to track GPCRs in living cells. Fluorescent ligands, antibodies, auto-fluorescent proteins as well as the evolving technologies for chemical labeling with peptide- and protein-tags are described and their major applications concerning the GPCR life cycle are presented.

Exocyst is involved in polarized cell migration and cerebral cortical development

Neuronal migration is essential for proper development of the cerebral cortex. As a first step, a postmitotic cell extends its leading process, presumably by adding new membrane at the growing tip, which would enable directed locomotion. The goal of the present study was to determine if biosynthetic exocytic pathway is polarized in migrating cells and whether polarized exocytosis promotes directed cell migration. A promising candidate for controlling the spatial sites of vesicle tethering and fusion at the plasma membrane is a protein complex called the exocyst. We found that cell migration in a wound assay, as well as cortical neuronal migration during embryonic development was impaired when the exocyst was disturbed. By combining TIRF microscopy and a stochastic model of exocytosis, we found that vesicle exocytosis is preferentially distributed close to the leading edge of polarized cells, that the exocytic process is organized into hotspots, and that the polarized delivery of vesicles and their clustering in hotspots depend on the intact exocyst complex. The exocyst complex seems to achieve this spatial regulation by determining the sites at the membrane where secretory vesicles tether. Thus, our study supports the notion that polarized membrane traffic regulated by the exocyst is an essential component of cell migration and that its deficit may lead to cortical abnormalities involving cortical neuronal malpositioning.

Dynamic adhesions and MARCKS in melanoma cells

Cell motility necessitates the rapid formation and disassembly of cell adhesions. We have studied adhesions in a highly motile melanoma cell line using various biochemical approaches and microscopic techniques to image close adhesions. We report that WM-1617 melanoma cells contain at least two types of close adhesion: classic focal adhesions and more extensive, irregularly shaped adhesions that tend to occur along lamellipodial edges. In contrast to focal adhesions, these latter adhesions are highly dynamic and can be disassembled rapidly via protein kinase C (PKC) activation (e.g. by eicosanoid) and MARCKS phosphorylation. MARCKS overexpression, however, greatly increases the area of close adhesions and renders them largely refractory to PKC stimulation. This indicates that nonphosphorylated MARCKS is an adhesion stabilizer. Unlike focal adhesions, the dynamic adhesions contain alpha3 integrin and MARCKS, but they do not contain the focal adhesion marker vinculin. Overall, these results begin to define the molecular and functional properties of dynamic close adhesions involved in cell motility.

Imaging glucose-regulated insulin secretion and gene expression in single islet beta-cells: control by AMP-activated protein kinase

The mechanisms by which changes in glucose concentration regulate gene expression and insulin secretion in pancreatic islet beta-cells are only partly understood. Here we describe the development of new technologies for examining these processes at the level of single living beta-cells. We also present recent findings, made using these and other techniques, which implicate a role for adenosine 5'-monophosphate-activated protein kinase in glucose signaling in these cells.

Recruitment of vimentin to the cell surface by beta3 integrin and plectin mediates adhesion strength

Much effort has been expended on analyzing how microfilament and microtubule cytoskeletons dictate the interaction of cells with matrix at adhesive sites called focal adhesions (FAs). However, vimentin intermediate filaments (IFs) also associate with the cell surface at FAs in endothelial cells. Here, we show that IF recruitment to FAs in endothelial cells requires beta3 integrin, plectin and the microtubule cytoskeleton, and is dependent on microtubule motors. In CHO cells, which lack beta3 integrin but contain vimentin, IFs appear to be collapsed around the nucleus, whereas in CHO cells expressing beta3 integrin (CHOwtbeta3), vimentin IFs extend to FAs at the cell periphery. This recruitment is regulated by tyrosine residues in the beta3 integrin cytoplasmic tail. Moreover, CHOwtbeta3 cells exhibit significantly greater adhesive strength than CHO or CHO cells expressing mutated beta3 integrin proteins. These differences require an intact vimentin network. Therefore, vimentin IF recruitment to the cell surface is tightly regulated and modulates the strength of adhesion of cells to their substrate.

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.

Analyzing protein-protein spatial-temporal dependencies from image sequences using fuzzy temporal random sets

Total Internal Reflection Fluorescence Microscopy (TIRFM) allows us to image fluorescenttagged proteins near the plasma membrane of living cells with high spatial-temporal resolution. Using TIRFM imaging of GFP-tagged clathrin endocytic proteins, areas of fluorescence are observed as overlapping spots of different sizes and durations. Standard procedures to measure protein-protein colocalization of dual labeled samples threshold the original graylevel images to segment areas covered by different proteins. This binary logic is not appropriate as it leaves a free tuning parameter which can influence the conclusions. Moreover, these procedures rely on simple statistical analysis based on correlation coefficients or visual inspection. We propose a probabilistic model to examine spatial-temporal dependencies. Image sequences of two proteins are modeled as a realization of a bivariate fuzzy temporal random set. Spatial-temporal dependencies are described by means of the pair-correlation function and the K-function and are tested using a Monte Carlo test. Five simulated image sequences were used to validate the performance of the procedure. Spatial and spatial-temporal dependencies were generated using a linked pairs model and a Poisson cluster model for the germs. To demonstrate the applicability in addressing current biological questions, we applied the procedure to fluorescent-tagged proteins involved in endocytosis (Clathrin, Hip1R, Epsin, and Caveolin). Results show that this procedure allows biologists to automatically quantify dependencies between molecules in a more formal and robust way. Image sequences and a Matlab toolbox for simulation and testing are available at http://www.uv.es/tracs/.

Live cell imaging of the HIV-1 life cycle

Technology developed in the past 10 years has dramatically increased the ability of researchers to directly visualize and measure various stages of the HIV type 1 (HIV-1) life cycle. In many cases, imaging-based approaches have filled critical gaps in our understanding of how certain aspects of viral replication occur in cells. Specifically, live cell imaging has allowed a better understanding of dynamic, transient events that occur during HIV-1 replication, including the steps involved in viral fusion, trafficking of the viral nucleoprotein complex in the cytoplasm and even the nucleus during infection and the formation of new virions from an infected cell. In this review, we discuss how researchers have exploited fluorescent microscopy methodologies to observe and quantify these events occurring during the replication of HIV-1 in living cells.

Fluorescence resonance energy transfer imaging of PKC signalling in living cells using genetically encoded fluorescent probes

Perception of ligands in the extracellular space by transmembrane receptors initiates signal transduction. The conformation change of the receptor induces changes of intracellular signalling components, including altered cellular concentration, altered subcellular location, altered conformation and altered interacting partners. Biochemical approaches have yielded a lot of information about these processes. However, methods that are compatible with analysis of single living cells are often preferred, since cells are highly organized and their response is usually spatially heterogeneous. In addition, the study of signalling cascades requires high temporal resolution. Fluorescence imaging approaches meet these requirements. Moreover, imaging approaches can be combined with genetically encoded green fluorescent protein-based probes that have a high selectivity and sensitivity for the process/molecule of interest. Nowadays, many genetically encoded probes are available for visualizing signalling in living cells. This review is centred on a key regulator of cellular signalling, protein kinase C (PKC). We will discuss imaging approaches that are used for analysing the molecules involved in activation of PKC, visualizing the dynamics of the location of PKC, measuring the conformation of PKC and quantifying the activity of PKC. These approaches are of general interest since they can be applied to study the dynamics, conformation and activity of any protein in living cells.

Imaging a target of Ca2+ signalling: dense core granule exocytosis viewed by total internal reflection fluorescence microscopy

Ca²⁺ ions are the most ubiquitous second messenger found in all cells, and play a significant role in controlling regulated secretion from neurons, endocrine, neuroendocrine and exocrine cells. Here, we describe microscopic techniques to image regulated secretion, a target of Ca²⁺ signalling. The first of these, total internal reflection fluorescence (TIRF), is well suited for optical sectioning at cell–substrate regions with an unusually thin region of fluorescence excitation (<150 nm). It is thus particularly useful for studies of regulated hormone secretion. A brief summary of this approach is provided, as well as a description of the physical basis for the technique and the tools to implement TIRF using a standard fluorescence microscope. We also detail the different fluorescent probes which can be used to detect secretion and how to analyze the data obtained. A comparison between TIRF and other imaging modalities including confocal and multiphoton microscopy is also included.

Measuring spatiotemporal dependencies in bivariate temporal random sets with applications to cell biology

Analyzing spatio-temporal dependencies between different types of events is highly relevant to numerous biological phenomena (e.g. signalling and trafficking) especially as advances in probes and microscopy have facilitated imaging of dynamic processes in living cells. For many types of events, the segmented areas can overlap spatially and temporally forming random clumps. In this paper, we model binary image sequences of two different event types as a realization of a bivariate temporal random set and propose a non-parametric approach to quantify spatial and spatio-temporal interrelations using the pair-correlation, cross-covariance and the Ripley IK functions. Based on these summary statistics we propose a randomization procedure to test independence between event types by applying random toroidal shifts and Monte Carlo tests. A simulation study assessed the performance of the proposed estimators and showed that these statistics capture the spatio-temporal dependencies accurately. The estimation of the spatio-temporal interval of interactions was also obtained. The method was successfully applied to analyze the interdependencies of several endocytic proteins using image sequences of living cells and validated the procedure as a new way to automatically quantify dependencies between proteins in a formal and robust manner.

Combined scanning probe and total internal reflection fluorescence microscopy

Combining scanning probe and optical microscopy represents a powerful approach for investigating structure-function relationships and dynamics of biomolecules and biomolecular assemblies, often in situ and in real-time. This platform technology allows us to obtain three-dimensional images of individual molecules with nanometer resolution, while simultaneously characterizing their structure and interactions though complementary techniques such as optical microscopy and spectroscopy. We describe herein the practical strategies for the coupling of scanning probe and total internal reflection fluorescence microscopy along with challenges and the potential applications of such platforms, with a particular focus on their application to the study of biomolecular interactions at membrane surfaces.

A novel subcellular collagen organization process visualized by total internal reflection fluorescence microscopy

The alpha1beta1 and alpha2beta1 integrins belong to a family of cell-surface molecules involved in structural contacts and signal-transduction events across the cell membrane. Employing two-dimensional substrates coated with fluorescently labeled type I collagen, we have discovered a novel subcellular matrix remodeling event that is particular to cells that express the fibrillar collagen receptor alpha2beta1. Cells expressing alpha1beta1 also perform this collagen organization process, but less proficiently. This work will provide a basis for subsequent studies of cell-mediated collagen fibril assembly.

Total internal reflection fluorescence microscopy for high-resolution imaging of cell-surface events

The wavelength of light imposes a physical limit of approximately 400 nm on the maximum resolution that can be achieved using light microscopy. This unit will describe the use of total internal reflection fluorescence microscopy (TIR-FM), or evanescent wave microscopy, an approach that partially overcomes this physical limit and permits one to selectively image just those fluorophores in the optical plane (along the z axis) within 50 nm of the cell surface. TIR-FM works by means of limiting the depth of penetration of the excitation light within this narrow region. This narrow excitatory plane not only provides a high signal-to-noise ratio but also minimizes the photodamage to the cell.

Regulated motion of glycoproteins revealed by direct visualization of a single cargo in the endoplasmic reticulum

The quality of cargo proteins in the endoplasmic reticulum (ER) is affected by their motion during folding. To understand how the diffusion of secretory cargo proteins is regulated in the ER, we directly analyze the motion of a single cargo molecule using fluorescence imaging/fluctuation analyses. We find that the addition of two N-glycans onto the cargo dramatically alters their diffusion by transient binding to membrane components that are confined by hyperosmolarity. Via simultaneous observation of a single cargo and ER exit sites (ERESs), we could exclude ERESs as the binding sites. Remarkably, actin cytoskeleton was required for the transient binding. These results provide a molecular basis for hypertonicity-induced immobilization of cargo, which is dependent on glycosylation at multiple sites but not the completion of proper folding. We propose that diffusion of secretory glycoproteins in the ER lumen is controlled from the cytoplasm to reduce the chances of aggregation.

Nano-scale characterization of the dynamics of the chloroplast Toc translocon

Translocons are macromolecular nano-scale machines that facilitate the selective translocation of proteins across membranes. Although common in function, different translocons have evolved diverse molecular mechanisms for protein translocation. Subcellular organelles of endosymbiotic origin such as the chloroplast and mitochondria had to evolve/acquire translocons capable of importing proteins whose genes were transferred to the host genome. These gene products are expressed on cytosolic ribosomes as precursor proteins and targeted back to the organelle by an N-terminal extension called the transit peptide or presequence. In chloroplasts the transit peptide is specifically recognized by the Translocon of the Outer Chloroplast membrane (Toc) which is composed of receptor GTPases that potentially function as gate-like switches, where GTP binding and hydrolysis somehow facilitate preprotein binding and translocation. Compared to other translocons, the dynamics of the Toc translocon are probably more complex and certainly less understood. We have developed biochemical/biophysical, imaging, and computational techniques to probe the dynamics of the Toc translocon at the nanoscale. In this chapter we provide detailed protocols for kinetic and binding analysis of precursor interactions in organeller, measurement of the activity and nucleotide binding of the Toc GTPases, native electrophoretic analysis of the assembly/organization of the Toc complex, visualization of the distribution and mobility of Toc apparatus on the surface of chloroplasts, and conclude with the identification and molecular modeling Toc75 POTRA domains. With these new methodologies we discuss future directions of the field.

Fast 4D Microscopy

Many cellular processes involve fast movements of weakly labeled cellular structures in all directions, which should be recorded in 3D time-lapse microscopy (4D microscopy). This chapter introduces fast 4D imaging, which is used for sampling the cell's volume by collecting focal planes in time-lapse mode as rapidly as possible, without perturbing the sample by strong illumination. The final images should contain sufficient contrast allowing for the isolation of structures of interest by segmentation and the analysis of their intracellular movements by tracking. Because they are the most sensitive, systems using wide-field microscopy and deconvolution techniques are discussed in greater depth. We discuss important points to consider, including system components and multifunctionality, spatial resolution and sampling conditions, and mechanical and optical stability and how to test for it. We consider image formation using high numerical aperture optics and discuss the influence of optical blur and noise on image formation of living cells. Spherical aberrations, their consequences for axial image quality, and their impact on the success of deconvolution of low intensity image stacks are explained in detail. Simple protocols for acquiring and treating point spread functions (PSFs) and live cells are provided. A compromise for counteracting spherical aberration involving the use of a kit of immersion oils for PSF and cell acquisition is illustrated. Recommendations for evaluating acquisition conditions and deconvolution parameters are given. Finally, we discuss future developments based on the use of adaptive optics which will push back many of today's limits.

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.

Analysis of spatial dependencies of endocytic proteins based on temporal random sets

Statistical image analysis has emerged as a basic methodology in the study of many real phenomena, which can be represented by sequences of binary images. Recent techniques, such as total internal reflection fluorescent microscopy, allow us to image simultaneously two fluorescent-tagged proteins which are relevant in important cellular processes, such as endocytosis. Here, we model these biological pairs of image sequences as realizations of a 3D non-isotropic bivariate random set, in which one dimension corresponds to time. We analyze their second-order properties by means of the cross-covariance and the pair correlation function in order to study colocalization between proteins. Results show the proposed methodology allows us to study spatial dependencies in a formal and robust way.

Quantification of protein based on single-molecule counting by total internal reflection fluorescence microscopy with adsorption equilibrium

We developed a sensitive single-molecule imaging method for quantification of protein by total internal reflection fluorescence microscopy with adsorption equilibrium. In this method, the adsorption equilibrium of protein was achieved between solution and glass substrate. Then, fluorescence images of protein molecules in a evanescent wave field were taken by a highly sensitive electron multiplying charge coupled device. Finally, the number of fluorescent spots corresponding to the protein molecules in the images was counted. Alexa Fluor 488-labeled goat anti-rat IgG(H+L) was chosen as the model protein. The spot number showed an excellent linear relationship with protein concentration. The concentration linear range was 5.4 x 10(-11) to 8.1 x 10(-10) mol L(-1).

Parallel two-channel near- and far-field fluorescence microscopy

We report a new two-channel fluorescence microscopy technique for surface-generated fluorescence. The realized fluorescence microscope allows high resolution imaging of aqueous samples. The core element of the instrument is a parabolic mirror objective that is used to collect the fluorescence at large surface angles above the critical angle of the waterglass interface. An aspheric lens, incorporated into the solid parabolic element, is used for diffraction-limited laser focusing and for collecting fluorescence at low angles with respect to the optical axis. By separated collection of the fluorescence emitted into supercritical and subcritical angles, two detection volumes strongly differing in their axial resolution are generated at the surface of a glass cover slip. The collection of supercritical angle fluorescence (SAF) results in a strict surface confinement of the detection volume, whereas collecting below the critical angle allows gathering the fluorescence emitted several microns deep inside the sample. Consequently, the signals from surface-bound and unbound diffusing fluorescent molecules can be obtained simultaneously.

Calcium-dependent trapping of mitochondria near plasma membrane in stimulated astrocytes

Growing evidence suggests that astrocytes are the active partners of neurons in many brain functions. Astrocytic mitochondria are highly motile organelles which regulate the temporal and spatial patterns of Ca( 2+ ) dynamics, in addition to being a major source of ATP and reactive oxygen species. Previous studies have shown that mitochondria translocate to endoplasmic reticulum during Ca( 2+ ) release from internal stores, but whether a similar spatial interaction between mitochondria and plasma membrane occurs is not known. Using total internal reflection fluorescence (TIRF) microscopy we show that a fraction of mitochondria became trapped near the plasma membrane of cultured hippocampal astrocytes during exposure to the transmitters glutamate or ATP, resulting in net translocation of the mitochondria to the plasma membrane. This translocation was dependent on the intracellular Ca( 2+ ) rise because it was blocked by pre-incubation with BAPTA AM and mimicked by application of the Ca( 2+ ) ionophore ionomycin. Transmembrane Ca( 2+ ) influx induced by raising external Ca( 2+ ) also caused mitochondrial trapping, which occurred more rapidly than that produced by glutamate or ATP. In astrocytes treated with the microtubule-disrupting agent nocodazole, intracellular Ca( 2+ ) rises failed to induce trapping of mitochondria near plasma membrane, suggesting a role for microtubules in this phenomenon. Our data reveal the Ca( 2+ )-dependent trapping of mitochondria near the plasma membrane as a novel form of mitochondrial regulation, which is likely to control the perimembrane Ca( 2+ ) dynamics and regulate signaling by mitochondria-derived reactive oxygen species.