Macromolecular-scale resolution in biological fluorescence microscopy

mMaple: a photoconvertible fluorescent protein for use in multiple imaging modalities

Recent advances in fluorescence microscopy have extended the spatial resolution to the nanometer scale. Here, we report an engineered photoconvertible fluorescent protein (pcFP) variant, designated as mMaple, that is suited for use in multiple conventional and super-resolution imaging modalities, specifically, widefield and confocal microscopy, structured illumination microscopy (SIM), and single-molecule localization microscopy. We demonstrate the versatility of mMaple by obtaining super-resolution images of protein organization in Escherichia coli and conventional fluorescence images of mammalian cells. Beneficial features of mMaple include high photostability of the green state when expressed in mammalian cells and high steady state intracellular protein concentration of functional protein when expressed in E. coli. mMaple thus enables both fast live-cell ensemble imaging and high precision single molecule localization for a single pcFP-containing construct.

Superresolution microscopy in heart - cardiac nanoscopy

Detailed understanding of the adaptive nature of cardiac cells in health and disease requires investigation of proteins and membranes in their native physiological environment, ideally by noninvasive optical methods. However, conventional light microscopy does not resolve the spatial characteristics of small fluorescently labeled protein or membrane structures in cells. Due to diffraction limiting resolution to half the wavelength of light, adjacent fluorescent molecules spaced at less than ~250 nm are not separately visualized. This fundamental problem has lead to a rapidly growing area of research, superresolution fluorescence microscopy, also called nanoscopy. We discuss pioneering applications of superresolution microscopy relevant to the heart, emphasizing different nanoscopy strategies toward new insight in cardiac cell biology. Here, we focus on molecular and structural readouts from subcellular nanodomains and organelles related to Ca(2+) signaling during excitation-contraction (EC) coupling, including live cell imaging strategies. Based on existing data and superresolution techniques, we suggest that an important future aim will be subcellular in situ structure-function analysis with nanometric resolving power in organotypic cells.

Transcription factories

There is considerable evidence that transcription does not occur homogeneously or diffusely throughout the nucleus, but rather at a number of specialized, discrete sites termed transcription factories. The factories are composed of ~4–30 RNA polymerase molecules, and are associated with many other molecules involved in transcriptional activation and mRNA processing. Some data suggest that the polymerase molecules within a factory remain stationary relative to the transcribed DNA, which is thought to be reeled through the factory site. There is also some evidence that transcription factories could help organize chromatin and nuclear structure, contributing to both the formation of chromatin loops and the clustering of active and co-regulated genes.

Effect of Nanohole Spacing on the Self-Imaging Phenomenon Created by the Three-Dimensional Propagation of Light through Periodic Nanohole Arrays

We present a detailed study of the inter-nanohole distance that governs the self-imaging phenomenon created by the three-dimensional propagation of light through periodic nanohole arrays on plasmonic substrates. We used scanning near-field optical microscopy (SNOM) to map the light intensity distributions at various heights above 10×10 nanohole arrays of varying pitch sizes on silver films. Our results suggest the inter-hole spacing has to be greater than the wavelength of the incident light to create the self-imaging phenomenon. We also present Finite-Difference Time-Domain (FDTD) calculations which show qualitative corroboration of our experimental results. Both our experimental and FDTD results show that the self-imaging phenomenon is more pronounced for structures with larger pitch sizes. We believe this self-imaging phenomenon is related to the Talbot imaging effect that has also been modified by a plasmonic component and can potentially be used to provide the basis for a new class of optical microscopes.

Adaptive optics enables 3D STED microscopy in aberrating specimens

Stimulated emission depletion (STED) microscopy allows fluorescence far-field imaging with diffraction-unlimited resolution. Unfortunately, extending this technique to three-dimensional (3D) imaging of thick specimens has been inhibited by sample-induced aberrations. Here we present the first implementation of adaptive optics in STED microscopy to allow 3D super-resolution imaging in strongly aberrated imaging conditions, such as those introduced by thick biological tissue.

Sharper fluorescent super-resolution spot generated by azimuthally polarized beam in STED microscopy

A novel method is proposed for generating sharper fluorescent super-resolution spot by azimuthally polarized beam in stimulated emission depletion (STED) microscopy. The incoherent superposition of azimuthally polarized beam with five-zone binary phase plate and the same beam with quadrant 0/πphase plate can yield a tightly focused doughnut spot surrounded completely and uniformly. And azimuthally polarized beam modulated by a vortex 0-2π phase plate works as pump beam. Compared with known effective excitation spot yielded by circular polarized STED beam, the azimuthally polarized beam result is shaper, as well as energy-saving, costing only ~50% of the energy cost by circular polarized beam. A STED beam of less intensity has the potential to reduce fluorescence photobleaching and photodamage in living cell imaging. In addition, the influence of Ez absence as well as FWHM of pump beam in the focal field is discussed.

Nanoparticle-assisted stimulated-emission-depletion nanoscopy

We show that metal nanoparticles can be used to improve the performance of super-resolution fluorescence nanoscopes based on stimulated-emission-depletion (STED). Compared with a standard STED nanoscope, we show theoretically a resolution improvement by more than an order of magnitude, or equivalently, depletion intensity reductions by more than 2 orders of magnitude and an even stronger photostabilization. Our scheme may allow improvement of existing STED nanoscopes and assist in the development of low-power, low-cost nanoscopes. This has the potential to increase the availability of STED nanoscopes and lead to a significant expansion of our understanding of biological and biochemical phenomena occurring on the nanoscale.

Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy

We demonstrate three-dimensional (3D) super-resolution in live multicellular organisms using structured illumination microscopy (SIM). Sparse multifocal illumination patterns generated by a digital micromirror device (DMD) allowed us to physically reject out-of-focus light, enabling 3D subdiffractive imaging in samples eightfold thicker than had been previously imaged with SIM. We imaged samples at one 2D image per second, at resolutions as low as 145 nm laterally and 400 nm axially. In addition to dual-labeled, whole fixed cells, we imaged GFP-labeled microtubules in live transgenic zebrafish embryos at depths >45 μm. We captured dynamic changes in the zebrafish lateral line primordium and observed interactions between myosin IIA and F-actin in cells encapsulated in collagen gels, obtaining two-color 4D super-resolution data sets spanning tens of time points and minutes without apparent phototoxicity. Our method uses commercially available parts and open-source software and is simpler than existing SIM implementations, allowing easy integration with wide-field microscopes.

Strategies to maximize the performance of a STED microscope

In stimulated emission depletion (STED) microscopy, the spatial resolution scales as the inverse square root of the STED beam's intensity. However, to fully exploit the maximum effective resolution achievable for a given STED beam's intensity, several experimental precautions have to be considered. We focus our attention on the temporal alignment between the excitation and STED pulses and the polarization state of the STED beam. We present a simple theoretical framework that help to explain their influence on the performance of a STED microscope and we validate the results by imaging calibration and biological samples with a custom made STED architecture based on a supercontinuum laser source. We also highlight the advantages of using time gating detection in terms of temporal alignment.

Chemotaxis in Campylobacter jejuni

Chemotaxis is the common way of flagellated bacteria to direct their locomotion to sites of most favourable living conditions, that are sites with the highest concentrations of energy sources and the lowest amounts of bacteriotoxic substances. The general prerequisites for chemotaxis are chemoreceptors, a chemosensory signal-transduction system and the flagellar apparatus. Epsilonproteobacteria like Campylobacter sp. show specific variations of the common chemotaxis components. CheV, a CheW-like linking-protein with an additional response regulator (RR) domain, was identified as commonly used coupling scaffold protein of Campylobacter jejuni. It attaches the histidine autokinase (CheAY), which also has an additional RR-domain, to the chemoreceptors signalling domains. These additional RR-domains seem to play an important role in the regulation of the CheAY-phosphorylation state and thereby in sensory adaptation. The Campylobacter-chemoreceptors are arranged into the three groups A, B, and C. Group A contains membrane-anchored receptors sensing periplasmic signals, group B consists only of one receptor with two cytoplasmic ligand-proteins representing a bipartite energy taxis system that senses pyruvate and fumarate, and group C receptors are cytoplasmic signalling domains with mostly unknown cytoplasmic ligand-binding proteins as sensory constituents. Recent findings demonstrating different alleles of the TLP7 chemoreceptor, specific for formic acid, led to an amendment of this grouping.

Super-resolution imaging prompts re-thinking of cell biology mechanisms: selected cases using stimulated emission depletion microscopy

The use of super-resolution imaging techniques in cell biology has yielded a wealth of information regarding cellular elements and processes that were invisible to conventional imaging. Focusing on images obtained by stimulated emission depletion (STED) microscopy, we discuss how the new high-resolution data influence the ways in which we use and interpret images in cell biology. Super-resolution images have lent support to some of our current hypotheses. But, more significantly, they have revealed unexpectedly complex processes that cannot be accounted for by the simpler models based on diffraction-limited imaging. The super-resolution imaging data challenge cell biologists to change their theoretical framework, by including, for instance, interpretations that describe multiple functions, functional errors or lack of function for cellular elements. In this context, we argue that descriptive research using super-resolution microscopy is now as necessary as hypothesis-driven research.

STED microscopy and its applications: new insights into cellular processes on the nanoscale

For about a decade, superresolution fluorescence microscopy has been advancing steadily, maturing from the proof-of-principle stage to routine application. Of the various techniques, STED (stimulated emission depletion) microscopy was the first to break the diffraction barrier. Today, it is a prominent and versatile form of superresolution light microscopy. STED microscopy has shed a sharper light on numerous topics in cell biology, but also in material sciences. Both disciplines extend into the nanometer range, making detailed studies of structural and functional relationships difficult or even impossible to achieve using diffraction-limited microscopy. With recent advancements like spectral multiplexing or live-cell imaging, STED microscopy makes nanoscale materials and components of the cell accessible for fluorescence-based investigations. With multicolor superresolution imaging, even the interactions between biological and engineered nanostructures can be studied in detail. This review gives an introduction into the working principle of STED microscopy, provides a detailed overview of recent advancements and new techniques implemented for use with STED microscopy and shows how these have been applied in the life sciences and nanotechnologies.

Colocalization of fluorescent probes: accurate and precise registration with nanometer resolution

Colocalization of fluorescent probes is commonly used in cell biology to discern the proximity of two proteins in the cell. Considering that the resolution limit of optical microscopy is on the order of 250 nm, there has not been a need for high-resolution colocalization techniques. However, with the advent of higher resolution techniques for cell biology and single-molecule biophysics, colocalization must also improve. For diffraction-limited applications, a geometric transformation (i.e., translation, scaling, and rotation) is typically applied to one color channel to align it with the other; however, to achieve high-resolution colocalization, this is not sufficient. Single-molecule high-resolution colocalization (SHREC) of single probes uses the local weighted mean transformation to achieve a colocalization resolution of at least 10 nm. This article describes the process of collecting a calibration data set of fiducials and the appropriate analysis to determine the transformation for colocalization.

Superlocalization spectral imaging microscopy of a multicolor quantum dot complex

The key factor of realizing super-resolution optical microscopy at the single-molecule level is to separately position two adjacent molecules. An opportunity to independently localize target molecules is provided by the intermittency (blinking) in fluorescence of a quantum dot (QD) under the condition that the blinking of each emitter can be recorded and identified. Herein we develop a spectral imaging based color nanoscopy which is capable of determining which QD is blinking in the multicolor QD complex through tracking the first-order spectrum, and thus, the distance at tens of nanometers between two QDs is measured. Three complementary oligonucleotides with lengths of 15, 30, and 45 bp are constructed as calibration rulers. QD585 and QD655 are each linked at one end. The measured average distances are in good agreement with the calculated lengths with a precision of 6 nm, and the intracellular dual-color QDs within a diffraction-limited spot are distinguished.

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.

Advances in light-based imaging of three-dimensional cellular ultrastructure

Visualization methods are key to gaining insights into cellular structure and function. Since diffraction has long confined optical microscopes to a resolution no better than hundreds of nanometers, the observation of ultrastructural features has traditionally been the domain of electron microscopes (EM). In the past decade, however, advances in super-resolution fluorescence microscopy have considerably expanded the capability of light-based imaging techniques. Advantages of fluorescent labeling such as high sensitivity, specificity, and multichannel capability, can now be exploited to dissect ultrastructural features of cells. With recent methods capable of imaging specific proteins with a resolution on the order of a few tens of nanometers in 3-dimensions, this has made it possible to elucidate the molecular organization of many complex cellular structures.

Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus

Recently, single-molecule imaging and photocontrol have enabled superresolution optical microscopy of cellular structures beyond Abbe's diffraction limit, extending the frontier of noninvasive imaging of structures within living cells. However, live-cell superresolution imaging has been challenged by the need to image three-dimensional (3D) structures relative to their biological context, such as the cellular membrane. We have developed a technique, termed superresolution by power-dependent active intermittency and points accumulation for imaging in nanoscale topography (SPRAIPAINT) that combines imaging of intracellular enhanced YFP (eYFP) fusions (SPRAI) with stochastic localization of the cell surface (PAINT) to image two different fluorophores sequentially with only one laser. Simple light-induced blinking of eYFP and collisional flux onto the cell surface by Nile red are used to achieve single-molecule localizations, without any antibody labeling, cell membrane permeabilization, or thiol-oxygen scavenger systems required. Here we demonstrate live-cell 3D superresolution imaging of Crescentin-eYFP, a cytoskeletal fluorescent protein fusion, colocalized with the surface of the bacterium Caulobacter crescentus using a double-helix point spread function microscope. Three-dimensional colocalization of intracellular protein structures and the cell surface with superresolution optical microscopy opens the door for the analysis of protein interactions in living cells with excellent precision (20-40 nm in 3D) over a large field of view (12 12 μm).

The fate of synaptic vesicle components upon fusion

Neurotransmitter release relies on the fusion of synaptic vesicles with the plasma membrane of synaptic boutons, which is followed by the recycling of vesicle components and formation of new vesicles. It is not yet clear whether upon fusion the vesicles persist as multimolecular patches in the plasma membrane, or whether they segregate into individual components. Evidence supporting each of these two models has been suggested in recent years. Using diffraction-unlimited imaging (stimulated emission depletion, or STED) of native synaptic vesicle proteins, we have proposed that vesicle proteins remain in clusters on the neuronal surface. These clusters do not appear to intermix. We discuss here these findings in the context of previous studies on synaptic vesicle fusion, and we propose a recycling model which accounts for most of the recent findings on the post-fusion fate of synaptic vesicle components.

Total internal reflection STED microscopy

Stimulated emission depletion (STED) microscopy achieves diffraction-unlimited resolution in far-field fluorescence microscopy well below 100 nm. As common for (single-lens) far-field microscopy techniques, the lateral resolution is better than the axial sectioning capabilities. Here we present the first implementation of total internal reflection (TIR) illumination into STED microscopy which limits fluorophore excitation to ~70 nm in the vicinity of the cover slip while simultaneously providing ~50 nm lateral resolution. We demonstrate the performance of this new microscope technique with fluorescent bead test samples as well as immuno-stained microtubules. Total internal reflection STED microscopy provides superior axial sectioning capabilities with the potential to reduce photo-bleaching and photo-damage in live cell imaging.

Sharper low-power STED nanoscopy by time gating

Applying pulsed excitation together with time-gated detection improves the fluorescence on-off contrast in continuous-wave stimulated emission depletion (CW-STED) microscopy, thus revealing finer details in fixed and living cells using moderate light intensities. This method also enables super-resolution fluorescence correlation spectroscopy with CW-STED beams, as demonstrated by quantifying the dynamics of labeled lipid molecules in the plasma membrane of living cells.

STED nanoscopy with mass-produced laser diodes

We show that far-field fluorescence nanoscopy by stimulated emission depletion (STED) can be realized with compact off-the-shelf laser diodes, such as those used in laser pointers and DVDs. A spatial resolution of 40-50 nm is attained by pulsing a 660 nm DVD-diode. The efficacy of these low-cost STED microscopes in biological imaging is demonstrated by differentiating between clusters of the synaptic protein bassoon and transport vesicles in hippocampal neurons, based on the feature diameter. Our results facilitate the implementation of this all-molecular-transition based superresolution method in many applications ranging from nanoscale fluorescence imaging to nanoscale fluorescence sensing.

Far-field optical nanoscopy with reduced number of state transition cycles

We report on a method to reduce the number of state transition cycles that a molecule undergoes in far-field optical nanoscopy of the RESOLFT type, i.e. concepts relying on saturable (fluorescence) state transitions induced by a spatially modulated light pattern. The method is exemplified for stimulated emission depletion (STED) microscopy which uses stimulated emission to transiently switch off the capability of fluorophores to fluoresce. By switching fluorophores off only if there is an adjacent fluorescent feature to be recorded, the method reduces the number of state transitions as well as the average time a dye is forced to reside in an off-state. Thus, the photobleaching of the sample is reduced, while resolution and recording speed are preserved. The power of the method is exemplified by imaging immunolabeled glial cells with up to 8-fold reduced photobleaching.

Electrons, photons, and force: quantitative single-molecule measurements from physics to biology

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution.

Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes

We demonstrate 3D superresolution microscopy in whole fixed cells using photoactivated localization microscopy (PALM). The use of the bright, genetically expressed fluorescent marker photoactivatable mCherry (PA-mCherry1) in combination with near diffraction-limited confinement of photoactivation using two-photon illumination and 3D localization methods allowed us to investigate a variety of cellular structures at <50 nm lateral and <100 nm axial resolution. Compared to existing methods, we substantially reduce excitation and bleaching of unlocalized markers, enabling 3D PALM imaging with high localization density in thick structures. Our 3D localization algorithms based on cross-correlation do not rely on idealized noise models or specific optical configurations, allowing flexible instrument design. Generation of appropriate fusion constructs and expression in Cos7 cells allowed us to image invaginations of the nuclear membrane, vimentin fibrils, the mitochondrial network, and the endoplasmic reticulum at depths greater than 8 μm.

STED Super-resolution Microscopy in Drosophila Tissue and in Mammalian Cells

Far-field super-resolution microscopy is a rapidly emerging method that is opening up opportunities for biological imaging beyond the optical diffraction limit. We have implemented a Stimulated Emission Depletion (STED) microscope to image single dye, cell, and tissue samples with 50-80 nm resolution. First, we compare the STED performance imaging single molecules of several common dyes and report a novel STED dye. Then we apply STED to image planar cell polarity protein complexes in intact fixed Drosophila tissue for the first time. Finally, we present a preliminary study of the centrosomal protein Cep164 in mammalian cells. Our images suggest that Cep164 is arranged in a nine-fold symmetric pattern around the centriole, consistent with findings suggested by cryoelectron tomography. Our work demonstrates that STED microscopy can be used for superresolution imaging in intact tissue and provides ultrastructural information in biological samples as an alternative to immuno-electron microscopy.

Formation of arenicin-1 microdomains in bilayers and their specific lipid interaction revealed by Z-scan FCS

Z-scan fluorescence correlation spectroscopy (FCS) is employed to characterize the interaction between arenicin-1 and supported lipid bilayers (SLBs) of different compositions. Lipid analogue C8-BODIPY 500/510C5-HPC and ATTO 465 labelled arenicin-1 are used to detect changes in lipid and peptide diffusion upon addition of unlabelled arenicin-1 to SLBs. Arenicin-1 decreases lipid mobility in negatively charged SLBs. According to diffusion law analysis, microdomains of significantly lower lipid mobility are formed. The analysis of peptide FCS data confirms the presence of microdomains for anionic SLBs. No indications of microdomain formation are detected in SLBs composed purely of zwitterionic lipids. Additionally, our FCS results imply that arenicin-1 exists in the form of oligomers and/or aggregates when interacting with membranes of both compositions.

Two-photon fluorescence lysosomal bioimaging with a micelle-encapsulated fluorescent probe

We report two-photon fluorescence microscopy (2PFM) imaging and in vitro cell viability of a new, efficient, lysosome-selective system based on a two-photon absorbing (2PA) fluorescent probe (I) encapsulated in Pluronic® F-127 micelles. Preparation of dye I was accomplished via microwave-assisted synthesis, resulting in improved yields and reduced reaction times. Photophysical characterization revealed notable 2PA efficiency of this probe.

Molecular strategies to read and write at the nanoscale with far-field optics

Diffraction prevents the focusing of ultraviolet and visible radiations within nanoscaled volumes and, as a result, the imaging and patterning of nanostructures with conventional far-field illumination. Specifically, the irradiation of a fluorescent or photosensitive material with focused light results in the simultaneous excitation of multiple chromophores distributed over a large area, relative to the dimensions of single molecules. It follows that the spatial control of fluorescence and photochemical reactions with molecular precision is impossible with conventional illumination configurations. However, the photochemical and photophysical properties of organic chromophores can be engineered to overcome diffraction in combination with patterned or reiterative illumination. These ingenious strategies offer the opportunity to confine excited chromophores within nanoscaled volumes and, therefore, restrict fluorescence or photochemical reactions within subdiffraction areas. Indeed, information can be "read" in the form of fluorescence and "written" in the form of photochemical products with resolution down to the nanometre level on the basis of these innovative approaches. In fact, these promising far-field optical methods permit the convenient imaging of biological samples and fabrication of miniaturized objects with unprecedented resolution and can have long-term and profound implications in biomedical research and information technology.

Nanoscopy of cell architecture: The actin-membrane interface

It was light microscopy that first revealed the hidden world of bacteria and the unit of life the "cell." From these first observations, made in the late 1600s, it has been clear that seeing is an important tool in biology. The merging of the fields of fluorescence and microscopy created the possibility to see subcellular structures and proteins. In the 1990s the use of the confocal microscopes, where cells/tissue could be optically sectioned, further improved the resolution of object visualization. From this microworld view we now move forward to the exciting prospects of the nanoworld view of biology. In this review I propose a nanoimaging approach, nanoscopy, which could be used to reveal cell architecture at the level of proteins and protein complexes. Nanoscopy includes, the F-techniques, superresolution microscopy, correlative light and electron microscopy and atomic force microscopy. To illustrate the biology that could be investigated by nanoscopy we focus on structures formed at the actin-membrane interface. In particular, focal adhesions and stress fibres have been analyzed using nanoscopy. Many of the proteins present in focal adhesions and stress fibres are shared with structures such as filopodia, lamellipodia, endocytic vesicles, actin pedestals and invadopodia. It is likely that nanoscopy of cells will reveal mechanistic details of biology at the level of individual proteins and protein complexes and importantly in a physiological context.

Spatial Organization and Dynamics of Transcription Elongation and Pre-mRNA Processing in Live Cells

During the last 30 years, systematic biochemical and functional studies have significantly expanded our knowledge of the transcriptional molecular components and the pre-mRNA processing machinery of the cell. However, our current understanding of how these functions take place spatiotemporally within the highly compartmentalized eukaryotic nucleus remains limited. Moreover, it is increasingly clear that “the whole is more than the sum of its parts” and that an understanding of the dynamic coregulation of genes is essential for fully characterizing complex biological phenomena and underlying diseases. Recent technological advances in light microscopy in addition to novel cell and molecular biology approaches have led to the development of new tools, which are being used to address these questions and may contribute to achieving an integrated and global understanding of how the genome works at a cellular level. Here, we review major hallmarks and novel insights in RNA polymerase II activity and pre-mRNA processing in the context of nuclear organization, as well as new concepts and challenges arising from our ability to gather extensive dynamic information at the single-cell resolution.

Imaging on the Nanoscale: Super-Resolution Fluorescence Microscopy

Although the resolution of a light microscope is fundamentally limited by diffraction to about half of the wavelength of light, in recent years several techniques have been developed that can overcome this limitation in fluorescence microscopy, allowing imaging with nanometre scale resolution. Many of these techniques are based on photoswitchable molecules that can switch between a bright, fluorescent and a dark, nonfluorescent state. Some of these techniques, as well as their limitations, are discussed.

Recent Advances in Mapping the Sub-cellular Distribution of Metal-Based Anticancer Drugs

There are increasing reports of novel metal-based chemotherapeutics that have either improved cancer cell selectivity, or alternative mechanisms of action, to existing anticancer drugs, and techniques are required for determining their sub-cellular molecular targets. Imaging methods offer many distinct advantages over destructive fractionation techniques, including the preservation of useful morphological information; however, mapping the intracellular distribution of metal ions inside tumour cells still remains challenging. Recent advances in three modes of imaging are discussed in this review, with a particular focus on the application to metal-based cancer chemotherapy – fluorescence microscopy, electron microscopy (including energy-filtered transmission electron microscopy (EFTEM)), and a new technique, Nano-scale secondary ion mass spectrometry (NanoSIMS).

Revisiting Bragg's X-ray microscope: scatter based optical transient grating detection of pulsed ionising radiation

Transient optical gratings for detecting ultrafast signals are routine for temporally resolved photochemical investigations. Many processes can contribute to the formation of such gratings; we indicate use of optically scattering centres that can be formed with highly variable latencies in different materials and devices using ionising radiation. Coherent light scattered by these centres can form the short-wavelength-to-optical-wavelength, incoherent-to-coherent basis of a Bragg X-ray microscope, with inherent scope for optical phasing. Depending on the dynamics of the medium chosen, the way is open to both ultrafast pulsed and integrating measurements. For experiments employing brief pulses, we discuss high-dynamic-range short-wavelength diffraction measurements with real-time optical reconstructions. Applications to optical real-time X-ray phase-retrieval are considered.

Single-molecule fluorescence characterization in native environment

Single-molecule detection (SMD) with fluorescence is a widely used microscopic technique for biomolecule structure and function characterization. The modern light microscope with high numerical aperture objective and sensitive CCD camera can image the brightly emitting organic and fluorescent protein tags with reasonable time resolution. Single-molecule imaging gives an unambiguous bottom-up biomolecule characterization that avoids the "missing information" problem characteristic of ensemble measurements. It has circumvented the diffraction limit by facilitating single-particle localization to ~1 nm. Probes developed specifically for SMD applications extend the advantages of single-molecule imaging to high probe density regions of cells and tissues. These applications perform under conditions resembling the native biomolecule environment and have been used to detect both probe position and orientation. Native, high density SMD may have added significance if molecular crowding impacts native biomolecule behavior as expected inside the cell.

Quantum lithography beyond the diffraction limit via Rabi oscillations

We propose a quantum optical method to do the subwavelength lithography. Our method is similar to the traditional lithography but adding a critical step before dissociating the chemical bound of the photoresist. The subwavelength pattern is achieved by inducing the multi-Rabi oscillation between the two atomic levels. The proposed method does not require multiphoton absorption and the entanglement of photons. It is expected to be realizable using current technology.

Advances in cellular, subcellular, and nanoscale imaging in vitro and in vivo

This review focuses on technical advances in fluorescence microscopy techniques including laser scanning techniques, fluorescence-resonance energy transfer (FRET) microscopy, fluorescence lifetime imaging (FLIM), stimulated emission depletion (STED)-based super-resolution microscopy, scanning confocal endomicroscopes, thin-sheet laser imaging microscopy (TSLIM), and tomographic techniques such as early photon tomography (EPT) as well as on clinical laser-based endoscopic and microscopic techniques. We will also discuss the new developments in the field of fluorescent dyes and fluorescent genetic reporters that enable new possibilities in high-resolution and molecular imaging both in in vitro and in vivo. Small animal and tissue imaging benefit from the development of new fluorescent proteins, dyes, and sensing constructs that operate in the far red and near-infrared spectrum.

The interaction of cells and bacteria with surfaces structured at the nanometre scale

The current development of nanobiotechnologies requires a better understanding of cell-surface interactions on the nanometre scale. Recently, advances in nanoscale patterning and detection have allowed the fabrication of appropriate substrates and the study of cell-substrate interactions. In this review we discuss the methods currently available for nanoscale patterning and their merits, as well as techniques for controlling the surface chemistry of materials at the nanoscale without changing the nanotopography and the possibility of truly characterizing the surface chemistry at the nanoscale. We then discuss the current knowledge of how a cell can interact with a substrate at the nanoscale and the effect of size, morphology, organization and separation of nanofeatures on cell response. Moreover, cell-substrate interactions are mediated by the presence of proteins adsorbed from biological fluids on the substrate. Many questions remain on the effect of nanotopography on protein adsorption. We review papers related to this point. As all these parameters have an influence on cell response, it is important to develop specific studies to point out their relative influence, as well as the biological mechanisms underlying cell responses to nanotopography. This will be the basis for future research in this field. An important topic in tissue engineering is the effect of nanoscale topography on bacteria, since cells have to compete with bacteria in many environments. The limited current knowledge of this topic is also discussed in the light of using topography to encourage cell adhesion while limiting bacterial adhesion. We also discuss current and prospective applications of cell-surface interactions on the nanoscale. Finally, based on questions raised previously that remain to be solved in the field, we propose future directions of research in materials science to help elucidate the relative influence of the physical and chemical aspects of nanotopography on bacteria and cell response with the aim of contributing to the development of nanobiotechnologies.

Three-dimensional nano-localization of single fluorescent emitters

We present a combination of self-interference microscopy with lateral super-resolution microscopy and introduce a novel approach for localizing a single nano-emitter to within a few nanometers in all three dimensions over a large axial range. We demonstrate nanometer displacements of quantum dots placed on top of polymer bilayers that undergo swelling when changing from an air to a water environment, achieving standard deviations below 10 nm for axial and lateral localization.