High-resolution near-field optical imaging of single nuclear pore complexes under physiological conditions

Ultra-structural analysis of human spermatozoa by aperture scanning near-field optical microscopy

Scanning near-field optical microscopy (SNOM) represents a potential candidate for investigation of ultrastructure in human spermatozoa. It is a noninvasive optical technique that offers two main advantages: minimal sample preparation and simultaneous topographical and optical images acquisition with a spatial resolution beyond the diffraction limit. This enables the combination of surface characterization and information from the inner cellular organization in a single acquisition providing an immediate and comprehensive analysis of the cellular portions. In this work spermatozoa are immobilized on poly-L-lysine coated coverslips, fixed according to a standard protocol and imaged by aperture-SNOM in air. In the SNOM images, all peculiar sperm portions show well-resolved optical features, which exhibit good similarities with the structures revealed in transmission electron microscopy images, as compared with literature data. The optical features of anomalous spermatozoa are clearly different as respect with those observed for healthy ones. This analysis reveals the potentialities of SNOM and opens to its application to high-resolution analysis of sperm morphological alterations, which might be relevant in reproductive medicine.

Live endothelial cells imaged by Scanning Near-field Optical Microscopy (SNOM): capabilities and challenges

The scanning near-field optical microscopy (SNOM) shows a potential to study details of biological samples, since it provides the optical images of objects with nanometric spatial resolution (50-200 nm) and the topographic information at the same time. The goal of this work is to demonstrate the capabilities of SNOM in transmission configuration to study human endothelial cells and their morphological changes, sometimes very subtle, upon inflammation. Various sample preparations were tested for SNOM measurements and promising results are collected to show: 1) the influence of α tumor necrosis factor (TNF-α) on EA.hy 926 cells (measurements of the fixed cells); 2) high resolution images of various endothelial cell lines, i.e. EA.hy 926 and HLMVEC (investigations of the fixed cells in buffer environment); 3) imaging of live endothelial cells in physiological buffers. The study demonstrate complementarity of the SNOM measurements performed in air and in liquid environments, on fixed as well as on living cells. Furthermore, it is proved that the SNOM is a very useful method for analysis of cellular morphology and topography. Changes in the cell shape and nucleus size, which are the symptoms of inflammatory reaction, were noticed in TNF-α activated EA.hy 926 cells. The cellular structures of submicron size were observed in high resolution optical images of cells from EA.hy 926 and HLMVEC lines.

Decoupling absorption and emission processes in super-resolution localization of emitters in a plasmonic hotspot

The absorption process of an emitter close to a plasmonic antenna is enhanced due to strong local electromagnetic (EM) fields. The emission, if resonant with the plasmonic system, re-radiates to the far-field by coupling with the antenna via plasmonic states, whose presence increases the local density of states. Far-field collection of the emission of single molecules close to plasmonic antennas, therefore, provides mixed information of both the local EM field strength and the local density of states. Moreover, super-resolution localizations from these emission-coupled events do not report the real position of the molecules. Here we propose using a fluorescent molecule with a large Stokes shift in order to spectrally decouple the emission from the plasmonic system, leaving the absorption strongly resonant with the antenna's enhanced EM fields. We demonstrate that this technique provides an effective way of mapping the EM field or the local density of states with nanometre spatial resolution.

Reporting the position of molecules and the electromagnetic enhancement in a plasmonic hotspot is difficult. Here Mack et al. use a large Stokes-shifted molecule to spectrally decouple the emission process of the dye from the plasmonic system, keeping the absorption on resonance with the plasmon resonance of the antenna.

Total internal reflection fluorescence quantification of receptor pharmacology

Total internal reflection fluorescence (TIRF) microscopy has been widely used as a single molecule imaging technique to study various fundamental aspects of cell biology, owing to its ability to selectively excite a very thin fluorescent volume immediately above the substrate on which the cells are grown. However, TIRF microscopy has found little use in high content screening due to its complexity in instrumental setup and experimental procedures. Inspired by the recent demonstration of label-free evanescent wave biosensors for cell phenotypic profiling and drug screening with high throughput, we had hypothesized and demonstrated that TIRF imaging is also amenable to receptor pharmacology profiling. This paper reviews key considerations and recent applications of TIRF imaging for pharmacology profiling.

Structural analysis and mapping of individual protein complexes by infrared nanospectroscopy

Mid-infrared spectroscopy is a widely used tool for material identification and secondary structure analysis in chemistry, biology and biochemistry. However, the diffraction limit prevents nanoscale protein studies. Here we introduce mapping of protein structure with 30 nm lateral resolution and sensitivity to individual protein complexes by Fourier transform infrared nanospectroscopy (nano-FTIR). We present local broadband spectra of one virus, ferritin complexes, purple membranes and insulin aggregates, which can be interpreted in terms of their α-helical and/or β-sheet structure. Applying nano-FTIR for studying insulin fibrils—a model system widely used in neurodegenerative disease research—we find clear evidence that 3-nm-thin amyloid-like fibrils contain a large amount of α-helical structure. This reveals the surprisingly high level of protein organization in the fibril’s periphery, which might explain why fibrils associate. We envision a wide application potential of nano-FTIR, including cellular receptor in vitro mapping and analysis of proteins within quaternary structures.

Mid-infrared spectroscopy offers important chemical and structural information about biological samples but diffraction prevents nanoscale studies. Amenabar et al. demonstrate Fourier transform infrared nanospectroscopy for analysing the secondary structure of protein complexes with 30 nm spatial resolution.

Operation of a wet near-field scanning optical microscope in stable zones by minimizing the resonance change of tuning forks

A resonant shift and a decrease of resonance quality of a tuning fork attached to a conventional fiber optic probe in the vicinity of liquid is monitored systematically while varying the protrusion length and immersion depth of the probe. Stable zones where the resonance modification as a function of immersion depth is minimized are observed. A wet near-field scanning optical microscope (wet-NSOM) is operated for a sample within water by using such a stable zone.

The crocidolite fibres interaction with human mesothelial cells as investigated by combining electron microscopy, atomic force and scanning near-field optical microscopy

In this study, we have performed a morphological analysis of crocidolite fibres interaction with mesothelial cells (MET5A) by combining conventional electron microscopy with atomic force (AFM) and scanning near-field optical microscopy (SNOM). After 6-h exposure at a crocidolite dose of 5 μg cm(-2), 90% of MET5A cells interact with fibres that under these conditions have a low cytotoxic effect. SEM images point out that fibres can be either engulfed by the cells that lose their typical morphology or they can accumulate over or partially inside the cells, which preserve their typical spread morphology. By using AFM we are able to directly visualize the entry-site of nanometric-sized fibres at the plasma membrane of the spread mesothelial cells. More importantly, the crocidolite fibres that are observed to penetrate the plasma membrane in SNOM topography can be simultaneously followed beneath the cell surface in the SNOM optical images. The analysis of SNOM data demonstrates the entrance of crocidolite fibres in proximity of nuclear compartment, as observed also in the TEM images. Our findings indicate that the combination of conventional electron microscopy with novel nanoscopic techniques can be considered a promising approach to achieve a comprehensive morphological description of the interaction between asbestos fibres and mesothelial cells that represents the early event in fibre pathogenesis.

Exploiting the light–metal interaction for biomolecular sensing and imaging

The ability of metal surfaces and nanostructures to localize and enhance optical fields is the primary reason for their application in biosensing and imaging. Local field enhancement boosts the signal-to-noise ratio in measurements and provides the possibility of imaging with resolutions significantly better than the diffraction limit. In fluorescence imaging, local field enhancement leads to improved brightness of molecular emission and to higher detection sensitivity and better discrimination. We review the principles of plasmonic fluorescence enhancement and discuss applications ranging from biosensing to bioimaging.

The role of nanophotonics in regenerative medicine

Cells respond to biochemical and mechanical stimuli through a series of steps that begin at the molecular, nanometre level, and translate finally in global cell response. Defects in biochemical- and/or mechanical-sensing, transduction or cellular response are the cause of multiple diseases, including cancer and immune disorders among others. Within the booming field of regenerative medicine, there is an increasing need for developing and applying nanotechnology tools to bring understanding on the cellular machinery and molecular interactions at the nanoscale. Nanotechnology, nanophotonics and in particular, high-resolution-based fluorescence approaches are already delivering crucial information on the way that cells respond to their environment and how they organize their receptors to perform specialized functions. This chapter focuses on emerging super-resolution optical techniques, summarizing their principles, technical implementation, and reviewing some of the achievements reached so far.

A guide to super-resolution fluorescence microscopy

For centuries, cell biology has been based on light microscopy and at the same time been limited by its optical resolution. However, several new technologies have been developed recently that bypass this limit. These new super-resolution technologies are either based on tailored illumination, nonlinear fluorophore responses, or the precise localization of single molecules. Overall, these new approaches have created unprecedented new possibilities to investigate the structure and function of cells.

Molecular recognition imaging using tuning fork-based transverse dynamic force microscopy

We demonstrate simultaneous transverse dynamic force microscopy and molecular recognition imaging using tuning forks as piezoelectric sensors. Tapered aluminum-coated glass fibers were chemically functionalized with biotin and anti-lysozyme molecules and attached to one of the prongs of a 32kHz tuning fork. The lateral oscillation amplitude of the tuning fork was used as feedback signal for topographical imaging of avidin aggregates and lysozyme molecules on mica substrate. The phase difference between the excitation and detection signals of the tuning fork provided molecular recognition between avidin/biotin or lysozyme/anti-lysozyme. Aggregates of avidin and lysozyme molecules appeared as features with heights of 1-4nm in the topographic images, consistent with single molecule atomic force microscopy imaging. Recognition events between avidin/biotin or lysozyme/anti-lysozyme were detected in the phase image at high signal-to-noise ratio with phase shifts of 1-2 degrees. Because tapered glass fibers and shear-force microscopy based on tuning forks are commonly used for near-field scanning optical microscopy (NSOM), these results open the door to the exciting possibility of combining optical, topographic and biochemical recognition at the nanometer scale in a single measurement and in liquid conditions.

Imaging individual proteins and nanodomains on intact cell membranes with a probe-based optical antenna

Optical antennas that confine and enhance electromagnetic fields in a nanometric region hold great potential for nanobioimaging and biosensing. Probe-based monopole optical antennas are fabricated to enhance fields localized to <30 nm near the antenna apex in aqueous conditions. These probes are used under appropriate excitation antenna conditions to image individual antibodies with an unprecedented resolution of 26 +/- 4 nm and virtually no surrounding background. On intact cell membranes in physiological conditions, the obtained resolution is 30 +/- 6 nm. Importantly, the method allows individual proteins to be distinguished from nanodomains and the degree of clustering to be quantified by directly measuring physical size and intensity of individual fluorescent spots. Improved antenna geometries should lead to true live cell imaging below 10-nm resolution with position accuracy in the subnanometric range.

Nanoscale imaging of epidermal growth factor receptor clustering: effects of inhibitors

The development of some solid tumors is associated with overexpression of the epidermal growth factor receptor (EGFR) and often correlates with poor prognosis. Near field scanning optical microscopy, a technique with subdiffraction-limited optical resolution, was used to examine the influence of two inhibitors (the chimeric 225 antibody and tyrosine phosphorylation inhibitor AG1478) on the nanoscale clustering of EGFR in HeLa cells. The EGFR is organized in small clusters, average diameter of 150 nm, on the plasma membrane for both control and EGF-treated cells. The numbers of receptors in individual clusters vary from as few as one or two proteins to greater than 100. Both inhibitors yield an increased cluster density and an increase in the fraction of clusters with smaller diameters and fewer receptors. Exposure to AG1478 also decreases the fraction of EGFR that colocalizes with both rafts and caveolae. EGF stimulation results in a significant loss of the full-length EGFR from the plasma membrane with the concomitant appearance of low molecular mass proteolytic products. By contrast, AG1478 reduces the level of EGFR degradation. Changes in receptor clustering provide one mechanism for regulating EGFR signaling and are relevant to the design of strategies for therapeutic interventions based on modulating EGFR signaling.

Near-field optical study of protein transport kinetics at a single nuclear pore

The kinetics of proteins passing through individual nuclear pore complexes (NPCs) of the nuclear envelope (NE) was studied using near-field scanning optical microscopy (NSOM) in combination with fluorescence correlation spectroscopy (FCS). The NSOM probe was placed over a single pore in an unsupported native NE to observe fluorescence-labeled NTF2 moving in the transport channel. A correlation analysis of the arising fluorescence fluctuations enabled us to characterize the translocation as driven by Brownian motion and to determine the related kinetic constants. Though trapped in the pore, NTF2 turned out to be highly mobile within a large axial extension. Our findings support the idea that molecules in transit interact with NPC proteins containing phenylalanine-glycine-repeat domains at the periphery of the channel. NSOM-FCS may help to understand the facilitated translocation in more detail and offers a new way to study single molecule mobility on a nanoscale.

Near-field scanning optical microscopy detects nanoscale glycolipid domains in the plasma membrane

The localization of asialo-GM1 in ordered membrane raft domains in HeLa cells has been examined using a combination of membrane fractionation and fluorescence imaging. The glycolipid is enriched in Triton X-100 insoluble membrane fractions that contain high concentrations of cholesterol and caveolin-1 but is also found in detergent soluble membrane fractions. Near-field fluorescence microscopy shows that a fraction of the asialo-GM1 is localized in small nanoscale clusters that have an upper limit for the average diameter of approximately 90 nm and are partially colocalized with caveolae membrane domains. In addition to clusters, a diffuse, non-clustered population of asialo-GM1 is observed and is hypothesized to correspond to glycolipid isolated in detergent soluble membrane fractions.

Imaging of membrane proteins using antenna-based optical microscopy

The localization and identification of individual proteins is of key importance for the understanding of biological processes on the molecular scale. Here, we demonstrate near-field fluorescence imaging of single proteins in their native cell membrane. Incident laser radiation is localized and enhanced with an optical antenna in the form of a spherical gold particle attached to a pointed dielectric tip. Individual proteins can be identified with a diffraction-unlimited spatial resolution of ∼50 nm. Besides determining the concentration and distribution of specific membrane proteins, this approach makes it possible to study the colocalization of different membrane proteins. Moreover, it enables a simultaneous recording of the membrane topology. Protein distributions can be correlated with the local membrane topology, thereby providing important information on the chemical and structural organization of cellular membranes.

Nuclear pore disassembly from endoplasmic reticulum membranes promotes Ca2+ signalling competency

The functionality of the endoplasmic reticulum (ER) as a Ca(2+) storage organelle is supported by families of Ca(2+) pumps, buffers and channels that regulate Ca(2+) fluxes between the ER lumen and cytosol. Although many studies have identified heterogeneities in Ca(2+) fluxes throughout the ER, the question of how differential functionality of Ca(2+) channels is regulated within proximal regions of the same organelle is unresolved. Here, we studied the in vivo dynamics of an ER subdomain known as annulate lamellae (AL), a cytoplasmic nucleoporin-containing organelle widely used in vitro to study the mechanics of nuclear envelope breakdown. We show that nuclear pore complexes (NPCs) within AL suppress local Ca(2+) signalling activity, an inhibitory influence relieved by heterogeneous dissociation of nucleoporins to yield NPC-denuded ER domains competent at Ca(2+) signalling. Consequently, we propose a novel generalized role for AL - reversible attenuation of resident protein activity - such that regulated AL (dis)assembly via a kinase/phosphatase cycle allows cells to support rapid gain/loss-of-function transitions in cellular physiology.

Vertebrate membrane proteins: structure, function, and insights from biophysical approaches

Membrane proteins are key targets for pharmacological intervention because they are vital for cellular function. Here, we analyze recent progress made in the understanding of the structure and function of membrane proteins with a focus on rhodopsin and development of atomic force microscopy techniques to study biological membranes. Membrane proteins are compartmentalized to carry out extra- and intracellular processes. Biological membranes are densely populated with membrane proteins that occupy approximately 50% of their volume. In most cases membranes contain lipid rafts, protein patches, or paracrystalline formations that lack the higher-order symmetry that would allow them to be characterized by diffraction methods. Despite many technical difficulties, several crystal structures of membrane proteins that illustrate their internal structural organization have been determined. Moreover, high-resolution atomic force microscopy, near-field scanning optical microscopy, and other lower resolution techniques have been used to investigate these structures. Single-molecule force spectroscopy tracks interactions that stabilize membrane proteins and those that switch their functional state; this spectroscopy can be applied to locate a ligand-binding site. Recent development of this technique also reveals the energy landscape of a membrane protein, defining its folding, reaction pathways, and kinetics. Future development and application of novel approaches during the coming years should provide even greater insights to the understanding of biological membrane organization and function.

Antenna-based optical imaging of single Ca2+ transmembrane proteins in liquids

Understanding the diversity of biological processes requires methods that can address single proteins in their natural environment and provide insights into structural and functional properties, as well as the local distribution of each individual protein. We use an optical antenna in the form of a single gold nanoparticle to localize incident laser radiation to 50 nm, significantly smaller than the diffraction limit of light. Our approach enables us to optically resolve individual plasma-membrane-bound Ca2+ pumps (PMCA4) immersed in aqueous environments and to determine the distribution of interprotein distances. We are able to correlate the protein maps with local topology. Improved antenna geometries will make it possible to resolve, identify, and probe single membrane proteins in live cells with true protein resolution of 5-10 nm.

NSOM/QD-based nanoscale immunofluorescence imaging of antigen-specific T-cell receptor responses during an in vivo clonal Vγ2Vδ2 T-cell expansion

Nanoscale imaging of an in vivo antigen-specific T-cell immune response has not been reported. Here, the combined near-field scanning optical microscopy- and fluorescent quantum dot-based nanotechnology was used to perform immunofluorescence imaging of antigen-specific T-cell receptor (TCR) response in an in vivo model of clonal T-cell expansion. The near-field scanning optical microscopy/quantum dot system provided a best-optical-resolution (<50 nm) nano-scale imaging of Vgamma2Vdelta2 TCR on the membrane of nonstimulated Vgamma2Vdelta2 T cells. Before Ag-induced clonal expansion, these nonstimulating Vgamma2Vdelta2 TCRs appeared to be distributed differently from their alphabeta TCR counterparts on the cell surface. Surprisingly, Vgamma2Vdelta2 TCR nanoclusters not only were formed but also sustained on the membrane during an in vivo clonal expansion of Vgamma2Vdelta2 T cells after phosphoantigen treatment or phosphoantigen plus mycobacterial infection. The TCR nanoclusters could array to form nanodomains or microdomains on the membrane of clonally expanded Vgamma2Vdelta2 T cells. Interestingly, expanded Vgamma2Vdelta2 T cells bearing TCR nanoclusters or nanodomains were able to rerecognize phosphoantigen and to exert better effector function. These studies provided nanoscale insight into the in vivo T-cell immune response.

Trends in fluorescence imaging and related techniques to unravel biological information

Optical microscopy is among the most powerful tools that the physical sciences have ever provided biology. It is indispensable for basic lab work, as well as for cutting edge research, as the visual monitoring of life processes still belongs to the most compelling evidences for a multitude of biomedical applications. Along with the rapid development of new probes and methods for the analysis of laser induced fluorescence, optical microscopy over past years experienced a vast increase of both new techniques and novel combinations of established methods to study biological processes with unprecedented spatial and temporal precision. On the one hand, major technical advances have significantly improved spatial resolution. On the other hand, life scientists are moving toward three- and even four-dimensional cell biology and biophysics involving time as a crucial coordinate to quantitatively understand living specimen. Monitoring the whole cell or tissue in real time, rather than producing snap-shot-like two-dimensional projections, will enable more physiological and, thus, more clinically relevant experiments, whereas an increase in temporal resolution facilitates monitoring fast nonperiodic processes as well as the quantitative analysis of characteristic dynamics.

Single-molecule fluorescence analysis of cellular nanomachinery components

Recent progress in proteomics suggests that the cell can be conceived as a large network of highly refined, nanomachine-like protein complexes. This working hypothesis calls for new methods capable of analyzing individual protein complexes in living cells and tissues at high speed. Here, we examine whether single-molecule fluorescence (SMF) analysis can satisfy that demand. First, recent technical progress in the visualization, localization, tracking, conformational analysis, and true resolution of individual protein complexes is highlighted. Second, results obtained by the SMF analysis of protein complexes are reviewed, focusing on the nuclear pore complex as an instructive example. We conclude that SMF methods provide powerful, indispensable tools for the structural and functional characterization of protein complexes. However, the transition from in vitro systems to living cells is in the initial stages. We discuss how current limitations in the nanoscopic analysis of living cells and tissues can be overcome to create a new paradigm, nanoscopic biomedicine.

The nuclear pore complex up close

Transport between the nucleus and cytoplasm is mediated by nuclear pore complexes (NPCs), perforations in the double-membrane of the nuclear envelope. NPCs are huge protein assemblies made up of distinct subcomplexes. The complex modular nature of the NPC and limitations in the current experimental approaches render the analysis of NPCs and nucleocytoplasmic transport at the molecular level difficult. Recent efforts in the NPC/nucleocytoplasmic transport field have focused on elucidating the core components that make up NPC structure (or the lack thereof) and function. These include results obtained by more conventional methods, such as electron microscopy or biochemical strategies, as well as more advanced applications, such as X-ray crystallography and atomic force microscopy.

From the trap to the basket: getting to the bottom of the nuclear pore complex

Nuclear pore complexes (NPCs) are large supramolecular assemblies that perforate the double-membraned nuclear envelope and serve as the sole gateways of molecular exchange between the cytoplasm and the nucleus in interphase cells. Combining novel specimen preparation regimes with innovative use of high-resolution scanning electron microscopy, Hans Ris produced in the late eighties stereo images of the NPC with unparalleled clarity and structural detail, thereby setting new standards in the field. Since that time, efforts undertaken to resolve the molecular structure and architecture, and the numerous interactions that occur between NPC proteins (nucleoporins), soluble transport receptors, and the small GTPase Ran, have led to a deeper understanding of the functional role of NPCs in nucleocytoplasmic transport. In spite of these breakthroughs, getting to the bottom of the actual cargo translocation mechanism through the NPC remains elusive and controversial. Here, we review recent insights into NPC function by correlating structural findings with biochemical data. By introducing new experimental and computational results, we reexamine how NPCs can discriminate between receptor-mediated and passive cargo to promote vectorial translocation in a highly regulated manner. Moreover, we comment on the importance and potential benefits of identifying and experimenting with individual key components implicated in the translocation mechanism. We conclude by dwelling on questions that we feel are pertinent to a more rational understanding of the physical aspects governing NPC mechanics. Last but not least, we substantiate these uncertainties by boldly suggesting a new direction in NPC research as a means to verify such novel concepts, for example, a de novo designed 'minimalist' NPC.