Ultrahigh-resolution multicolor colocalization of single fluorescent probes

The evolution of immune profiling: will there be a role for nanoparticles?

Immune profiling provides insights into the functioning of the immune system, including the distribution, abundance, and activity of immune cells. This understanding is essential for deciphering how the immune system responds to pathogens, vaccines, tumors, and other stimuli. Analyzing diverse immune cell types facilitates the development of personalized medicine approaches by characterizing individual variations in immune responses. With detailed immune profiles, clinicians can tailor treatment strategies to the specific immune status and needs of each patient, maximizing therapeutic efficacy while minimizing adverse effects. In this review, we discuss the evolution of immune profiling, from interrogating bulk cell samples in solution to evaluating the spatially-rich molecular profiles across intact preserved tissue sections. We also review various multiplexed imaging platforms recently developed, based on immunofluorescence and imaging mass spectrometry, and their impact on the field of immune profiling. Identifying and localizing various immune cell types across a patient's sample has already provided important insights into understanding disease progression, the development of novel targeted therapies, and predicting treatment response. We also offer a new perspective by highlighting the unprecedented potential of nanoparticles (NPs) that can open new horizons in immune profiling. NPs are known to provide enhanced detection sensitivity, targeting specificity, biocompatibility, stability, multimodal imaging features, and multiplexing capabilities. Therefore, we summarize the recent developments and advantages of NPs, which can contribute to advancing our understanding of immune function to facilitate precision medicine. Overall, NPs have the potential to offer a versatile and robust approach to profile the immune system with improved efficiency and multiplexed imaging power.

ColocZStats: a z-stack signal colocalization extension tool for 3D slicer

Confocal microscopy has evolved to be a widely adopted imaging technique in molecular biology and is frequently utilized to achieve accurate subcellular localization of proteins. Applying colocalization analysis on image z-stacks obtained from confocal fluorescence microscopes is a dependable method of revealing the relationship between different molecules. In addition, despite the established advantages and growing adoption of 3D visualization software in various microscopy research domains, there have been few systems that can support colocalization analysis within a user-specified region of interest (ROI). In this context, several broadly employed biological image visualization platforms are meticulously explored in this study to understand the current landscape. It has been observed that while these applications can generate three-dimensional (3D) reconstructions for z-stacks, and in some cases transfer them into an immersive virtual reality (VR) scene, there is still little support for performing quantitative colocalization analysis on such images based on a user-defined ROI and thresholding levels. To address these issues, an extension called ColocZStats (pronounced Coloc-Zee-Stats) has been developed for 3D Slicer, a widely used free and open-source software package for image analysis and scientific visualization. With a custom-designed user-friendly interface, ColocZStats allows investigators to conduct intensity thresholding and ROI selection on imported 3D image stacks. It can deliver several essential colocalization metrics for structures of interest and produce reports in the form of diagrams and spreadsheets.

A Brief Introduction to Single-Molecule Fluorescence Methods

One of the most popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which will be the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches will be addressed, we will first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we will review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We will end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, single-molecule localization super-resolution microscopy, to distance measurements with Förster resonance energy transfer and orientation measurements with fluorescence polarization.

Achieving nanoscale precision using neuromorphic localization microscopy

Neuromorphic cameras are a new class of dynamic-vision-inspired sensors that encode the rate of change of intensity as events. They can asynchronously record intensity changes as spikes, independent of the other pixels in the receptive field, resulting in sparse measurements. This recording of such sparse events makes them ideal for imaging dynamic processes, such as the stochastic emission of isolated single molecules. Here we show the application of neuromorphic detection to localize nanoscale fluorescent objects below the diffraction limit, with a precision below 20 nm. We demonstrate a combination of neuromorphic detection with segmentation and deep learning approaches to localize and track fluorescent particles below 50 nm with millisecond temporal resolution. Furthermore, we show that combining information from events resulting from the rate of change of intensities improves the classical limit of centroid estimation of single fluorescent objects by nearly a factor of two. Additionally, we validate that using post-processed data from the neuromorphic detector at defined windows of temporal integration allows a better evaluation of the fractalized diffusion of single particle trajectories. Our observations and analysis is useful for event sensing by nonlinear neuromorphic devices to ameliorate real-time particle localization approaches at the nanoscale.

Spatially modulated illumination microscopy: application perspectives in nuclear nanostructure analysis

Thousands of genes and the complex biochemical networks for their transcription are packed in the micrometer sized cell nucleus. To control biochemical processes, spatial organization plays a key role. Hence the structure of the cell nucleus of higher organisms has emerged as a main topic of advanced light microscopy. So far, a variety of methods have been applied for this, including confocal laser scanning fluorescence microscopy, 4Pi-, STED- and localization microscopy approaches, as well as (laterally) structured illumination microscopy (SIM). Here, we summarize the state of the art and discuss application perspectives for nuclear nanostructure analysis of spatially modulated illumination (SMI). SMI is a widefield-based approach to using axially structured illumination patterns to determine the axial extension (size) of small, optically isolated fluorescent objects between less than or equal to 200 nm and greater than or equal to 40 nm diameter with a precision down to the few nm range; in addition, it allows the axial positioning of such structures down to the 1 nm scale. Combined with SIM, a three-dimensional localization precision of less than or equal to 1 nm is expected to become feasible using fluorescence yields typical for single molecule localization microscopy applications. Together with its nanosizing capability, this may eventually be used to analyse macromolecular complexes and other nanostructures with a topological resolution, further narrowing the gap to Cryoelectron microscopy.

This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 2)’.

Intelligent Probabilistic System for Digital Tracing Cellular Origin of Individual Clinical Extracellular Vesicles

Extracellular vesicles (EVs) are small vesicles secreted by various cell types to mediate cell-to-cell communication through the transfer of macromolecules. EVs carry multiple cargo molecules that reflect the origins of their donor cells; thus, they can be considered reliable biomarkers for early cancer diagnosis. However, the diverse cellular origin of EV masks the detection signals generated by both tumor- and nontumor-derived cells. Thereby, the capability to recognize the cellular origin of EVs is the prerequisite for their diagnostic applications. In the present study, we develop an intelligent probabilistic system for tracing the cellular origin of individual EVs using single-molecule multicolor imaging. Through the analysis of the expression profile of two typical membrane protein markers, CD9 and CD63, on single EVs, accurate and rapid probabilistic recognition of EVs derived from individual tumor and nontumor cells in clinical samples is achieved. The correlation between cellular origin and surface protein phenotyping on single EVs is also exemplified. The proposed system holds great potential for advancing EVs as reliable clinical indicators and exploring their biological functions.

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.

Photonic technologies for liquid biopsies: recent advances and open research challenges

The recent development of sophisticated techniques capable of detecting extremely low concentrations of circulating tumor biomarkers in accessible body fluids, such as blood or urine, could contribute to a paradigm shift in cancer diagnosis and treatment. By applying such techniques, clinicians can carry out liquid biopsies, providing information on tumor presence, evolution, and response to therapy. The implementation of biosensing platforms for liquid biopsies is particularly complex because this application domain demands high selectivity/specificity and challenging limit-of-detection (LoD) values. The interest in photonics as an enabling technology for liquid biopsies is growing owing to the well-known advantages of photonic biosensors over competing technologies in terms of compactness, immunity to external disturbance, and ultra-high spatial resolution. Some encouraging experimental results in the field of photonic devices and systems for liquid biopsy have already been achieved by using fluorescent labels and label-free techniques and by exploiting super-resolution microscopy, surface plasmon resonance, surface-enhanced Raman scattering, and whispering gallery mode resonators. This paper critically reviews the current state-of-the-art, starting from the requirements imposed by the detection of the most common circulating biomarkers. Open research challenges are considered together with competing technologies, and the most promising paths of improvement are discussed for future applications.

Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning

Traces from single-molecule fluorescence microscopy (SMFM) experiments exhibit photophysical artifacts that typically necessitate human expert screening, which is time-consuming and introduces potential for user-dependent expectation bias. Here, we use deep learning to develop a rapid, automatic SMFM trace selector, termed AutoSiM, that improves the sensitivity and specificity of an assay for a DNA point mutation based on single-molecule recognition through equilibrium Poisson sampling (SiMREPS). The improved performance of AutoSiM is based on accepting both more true positives and fewer false positives than the conventional approach of hidden Markov modeling (HMM) followed by hard thresholding. As a second application, the selector is used for automated screening of single-molecule Förster resonance energy transfer (smFRET) data to identify high-quality traces for further analysis, and achieves ~90% concordance with manual selection while requiring less processing time. Finally, we show that AutoSiM can be adapted readily to novel datasets, requiring only modest Transfer Learning.

Hyperspectral infrared microscopy with visible light

Hyperspectral microscopy is an imaging technique that provides spectroscopic information with high spatial resolution. When applied in the relevant wavelength region, such as in the infrared (IR), it can reveal a rich spectral fingerprint across different regions of a sample. Challenges associated with low efficiency and high cost of IR light sources and detector arrays have limited its broad adoption. Here, we introduce a new approach to IR hyperspectral microscopy, where the IR spectral map is obtained with off-the-shelf components built for visible light. The method is based on the nonlinear interference of correlated photons generated via parametric down-conversion. In this proof-of-concept we demonstrate the chemical mapping of a patterned sample, where different areas have distinctive IR spectroscopic fingerprints. The method provides a wide field of view, fast readout, and negligible heat delivered to the sample, which opens prospects for its further development for applications in material and biological studies.

Colocalized Particle Counting Platform for Zeptomole Level Multiplexed Quantification

For multiplexed detection, it is important yet challenging to simultaneously meet the requirement of sensitivity, throughput, and implementation convenience for practical applications. Using the detection of DNAs and miRNAs for illustration, we present a colocalized particle counting platform that can realize the separation-free multiplexed detection of 6 nucleic acid targets with a zeptomole sensitivity and a dynamic range of up to 5 orders of magnitude. The presence of target induces the formation of a sandwich nanostructure via hybridization; thus, there is an occurrence of colocalization of two microbeads with two different colors. The sequence specific coding is realized by an arbitrary combination of two fluorescence channels with different emitting colors. The platform presents robustness in detecting multiple nucleic acid targets with a minimal cross talk and matrix effect as well as the ability to distinguish the specific miRNA from members of the same family. The results of simultaneous detection of 3 miRNAs in 3 different cell lines present straight consistency with that of the standard qRT-PCR. This platform can be adapted to other multiplexing designs such as the "turn-off" mode, in which the proportion of colocalized microbeads is decreased due to the strand-displacement reaction initiated by the specific target. This separation-free platform offers the possibility to achieve the on-site multiplexed detection with compatibility to different experimental designs and extensibility to other signal sources for enumeration.

Super-resolution Scanning Electrochemical Microscopy

To achieve super-resolution scanning electrochemical microscopy (SECM), we must overcome the theoretical limitation associated with noncontact electrochemical imaging of surface-generated species. This is the requirement for mass transfer to the electrode, which gives rise to the diffusional broadening of surface features. In this work, a procedure is developed for overcoming this limitation and thus generating "super-resolved" images using point spread function (PSF)-based deconvolution, where the point conductor plays the same role as the point emitter in optical imaging. In contrast to previous efforts in SECM towards this goal, our method uses a finite element model to generate a pair of corresponding blurred and sharp images for PSF estimation, avoiding the need to perform parameter optimization for effective deconvolution. It can therefore be used for retroactive data treatment and an enhanced understanding of the structure-property relationships that SECM provides.

Single Quantum Dot Tracking Illuminates Neuroscience at the Nanoscale

The use of nanometer-sized semiconductor crystals, known as quantum dots, allows us to directly observe individual biomolecular transactions through a fluorescence microscope. Here, we review the evolution of single quantum dot tracking over the past two decades, highlight key biophysical discoveries facilitated by quantum dots, briefly discuss biochemical and optical implementation strategies for a single quantum dot tracking experiment, and report recent accomplishments of our group at the interface of molecular neuroscience and nanoscience.

A Brief Introduction to Single-Molecule Fluorescence Methods

One of the more popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which will be the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches will be addressed, we will first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we will review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We will end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, single-molecule localization super-resolution microscopy, to distance measurements with Förster Resonance Energy Transfer and orientation measurements with fluorescence polarization.

Single-Molecule Localization Microscopy in Eukaryotes

Super-resolution fluorescence imaging by photoactivation or photoswitching of single fluorophores and position determination (single-molecule localization microscopy, SMLM) provides microscopic images with subdiffraction spatial resolution. This technology has enabled new insights into how proteins are organized in a cellular context, with a spatial resolution approaching virtually the molecular level. A unique strength of SMLM is that it delivers molecule-resolved information, along with super-resolved images of cellular structures. This allows quantitative access to cellular structures, for example, how proteins are distributed and organized and how they interact with other biomolecules. Ultimately, it is even possible to determine protein numbers in cells and the number of subunits in a protein complex. SMLM thus has the potential to pave the way toward a better understanding of how cells function at the molecular level. In this review, we describe how SMLM has contributed new knowledge in eukaryotic biology, and we specifically focus on quantitative biological data extracted from SMLM images.

Navigating challenges in the application of superresolution microscopy

In 2014, the Nobel Prize in Chemistry was awarded to three scientists who have made groundbreaking contributions to the field of superresolution (SR) microscopy (SRM). The first commercial SR microscope came to market a decade earlier, and many other commercial options have followed. As commercialization has lowered the barrier to using SRM and the awarding of the Nobel Prize has drawn attention to these methods, biologists have begun adopting SRM to address a wide range of questions in many types of specimens. There is no shortage of reviews on the fundamental principles of SRM and the remarkable achievements made with these methods. We approach SRM from another direction: we focus on the current practical limitations and compromises that must be made when designing an SRM experiment. We provide information and resources to help biologists navigate through common pitfalls in SRM specimen preparation and optimization of image acquisition as well as errors and artifacts that may compromise the reproducibility of SRM data.

Advances in single quantum dot-based nanosensors

We review the advances in single quantum dot-based nanosensors and their biomedical applications. We highlight their challenges and future direction.

Super-Resolution Imaging of a Dielectric Microsphere Is Governed by the Waist of Its Photonic Nanojet

Dielectric microspheres with appropriate refractive index can image objects with super-resolution, that is, with a precision well beyond the classical diffraction limit. A microsphere is also known to generate upon illumination a photonic nanojet, which is a scattered beam of light with a high-intensity main lobe and very narrow waist. Here, we report a systematic study of the imaging of water-immersed nanostructures by barium titanate glass microspheres of different size. A numerical study of the light propagation through a microsphere points out the light focusing capability of microspheres of different size and the waist of their photonic nanojet. The former correlates to the magnification factor of the virtual images obtained from linear test nanostructures, the biggest magnification being obtained with microspheres of ∼6-7 μm in size. Analyzing the light intensity distribution of microscopy images allows determining analytically the point spread function of the optical system and thereby quantifies its resolution. We find that the super-resolution imaging of a microsphere is dependent on the waist of its photonic nanojet, the best resolution being obtained with a 6 μm Ø microsphere, which generates the nanojet with the minimum waist. This comparison allows elucidating the super-resolution imaging mechanism.

Simultaneous nano-tracking of multiple motor proteins via spectral discrimination of quantum dots

Simultaneous nanometric tracking of multiple motor proteins was achieved by combining multicolor fluorescent labeling of target proteins and imaging spectroscopy, revealing dynamic behaviors of multiple motor proteins at the sub-diffraction-limit scale. Using quantum dot probes of distinct colors, we experimentally verified the localization precision to be a few nanometers at temporal resolution of 30 ms or faster. One-dimensional processive movement of two heads of a single myosin molecule and multiple myosin molecules was successfully traced. Furthermore, the system was modified for two-dimensional measurement and applied to tracking of multiple myosin molecules. Our approach is useful for investigating cooperative movement of proteins in supramolecular nanomachinery.

From single-molecule spectroscopy to super-resolution imaging of the neuron: a review

For more than 20 years, single-molecule spectroscopy has been providing invaluable insights into nature at the molecular level. The field has received a powerful boost with the development of the technique into super-resolution imaging methods, ca. 10 years ago, which overcome the limitations imposed by optical diffraction. Today, single molecule super-resolution imaging is routinely used in the study of macromolecular function and structure in the cell. Concomitantly, computational methods have been developed that provide information on numbers and positions of molecules at the nanometer-scale. In this overview, we outline the technical developments that have led to the emergence of localization microscopy techniques from single-molecule spectroscopy. We then provide a comprehensive review on the application of the technique in the field of neuroscience research.

IR-Live: fabrication of a low-cost plastic microfluidic device for infrared spectromicroscopy of living cells

Water is a strong mid-infrared absorber, which has hindered the full exploitation of label-free and non-invasive infrared (IR) spectromicroscopy techniques for the study of living biological samples. To overcome this barrier, many researchers have built sophisticated fluidic chambers or microfluidic chips wherein the depth of the liquid medium in the sample compartment is limited to 10 μm or less. Here we report an innovative and simple way to fabricate plastic devices with infrared transparent view-ports enabling infrared spectromicroscopy of living biological samples; therefore the device is named "IR-Live". Advantages of this approach include lower production costs, a minimal need to access a micro-fabrication facility, and unlimited mass or waste exchange for the living samples surrounding the view-port area. We demonstrate that the low-cost IR-Live in combination with microfluidic perfusion techniques enables long term (>60 h) cell culture, which broadens the capability of IR spectromicroscopy for studying living biological samples. To illustrate this, we first applied the device to study protein and lipid polarity in migrating REF52 fibroblasts by collecting 2-dimensional spectral chemical maps at a micrometer spatial resolution. Then, we demonstrated the suitability of our approach to study dynamic cellular events by collecting a time series of spectral maps of U937 monocytes during the early stage of cell attachment to a bio-compatible surface.

Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture)

The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 90s, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later super-resolution microscopy with single molecules. In the room temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized.

Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture)

The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 90s, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later super-resolution microscopy with single molecules. In the room temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized.

Stochastic approach to the molecular counting problem in superresolution microscopy

Superresolution imaging methods--now widely used to characterize biological structures below the diffraction limit--are poised to reveal in quantitative detail the stoichiometry of protein complexes in living cells. In practice, the photophysical properties of the fluorophores used as tags in superresolution methods have posed a severe theoretical challenge toward achieving this goal. Here we develop a stochastic approach to enumerate fluorophores in a diffraction-limited area measured by superresolution microscopy. The method is a generalization of aggregated Markov methods developed in the ion channel literature for studying gating dynamics. We show that the method accurately and precisely enumerates fluorophores in simulated data while simultaneously determining the kinetic rates that govern the stochastic photophysics of the fluorophores to improve the prediction's accuracy. This stochastic method overcomes several critical limitations of temporal thresholding methods.

Cryogenic colocalization microscopy for nanometer-distance measurements

The main limiting factor in spatial resolution of localization microscopy is the number of detected photons. Recently we showed that cryogenic measurements improve the photostability of fluorophores, giving access to Angstrom precision in localization of single molecules. Here, we extend this method to colocalize two fluorophores attached to well-defined positions of a double-stranded DNA. By measuring the separations of the fluorophore pairs prepared at different design positions, we verify the feasibility of cryogenic distance measurement with sub-nanometer accuracy. We discuss the important challenges of our method as well as its potential for further improvement and various applications.

Fluorescence tracking of motor proteins in vitro

Motor proteins convert the chemical energy of adenosine triphosphate (ATP) hydrolysis into directed movement along filamentous tracks, such as DNA, microtubule, and actin. The motile properties of motors are essential to their wide variety of cellular functions, including cargo transport, mitosis, cell motility, nuclear positioning, and ciliogenesis. Detailed understanding of the biophysical mechanisms of motor motility is therefore essential to understanding the physical basis of these processes. In which direction is the motor going? How fast and how far can a single motor walk down its track? How is ATP hydrolysis coupled to directed motion? How do multiple subunits of a motor coordinate with each other during motility? These questions can be addressed directly by tracking motors at a single-molecule level. This chapter will focus on high-resolution fluorescence tracking techniques of the processive cytoskeletal motors: myosins, kinesins, and cytoplasmic dynein. We outline the theoretical and practical considerations for studying these motors in vitro using fluorescence tracking at nanometer precision.

Quantum dots in diagnostics and detection: principles and paradigms

Quantum dots are semiconductor nanocrystals that exhibit exceptional optical and electrical behaviors not found in their bulk counterparts. Following seminal work in the development of water-soluble quantum dots in the late 1990's, researchers have sought to develop interesting and novel ways of exploiting the extraordinary properties of quantum dots for biomedical applications. Since that time, over 10,000 articles have been published related to the use of quantum dots in biomedicine, many of which regard their use in detection and diagnostic bioassays. This review presents a didactic overview of fundamental physical phenomena associated with quantum dots and paradigm examples of how these phenomena can and have been readily exploited for manifold uses in nanobiotechnology with a specific focus on their implementation in in vitro diagnostic assays and biodetection.

Localization microscopy coming of age: from concepts to biological impact

Super-resolution fluorescence imaging by single-molecule photoactivation or photoswitching and position determination (localization microscopy) has the potential to fundamentally revolutionize our understanding of how cellular function is encoded at the molecular level. Among all powerful, high-resolution imaging techniques introduced in recent years, localization microscopy excels because it delivers single-molecule information about molecular distributions, even giving absolute numbers of proteins present in subcellular compartments. This provides insight into biological systems at a molecular level that can yield direct experimental feedback for modeling the complexity of biological interactions. In addition, efficient new labeling methods and strategies to improve localization are emerging that promise to achieve true molecular resolution. This raises localization microscopy as a powerful complementary method for correlative light and electron microscopy experiments.

Towards a spectrum-based bar code for identification of weakly fluorescent microparticles

Spectrally resolved detection of fluorescent probes can be used to identify multiple labeled target molecules in an unknown mixture. We study how the spectral shape, the experimental noise, and the number of spectral detection channels affect the success of identification of weakly fluorescent beads on basis of their emission spectra. The proposed formalism allows to estimate the performance of the spectral identification procedure with a given set of spectral codes on the basis of the reference spectra only. We constructed a simple prism-based setup for spectral detection and demonstrate that seven distinct but overlapping spectral codes realized by combining up to three fluorescent dyes bound to a single bead in a barcode-based manner can be reliably identified. The procedure allows correct identification even in the presence of known autofluorescence background stronger than the actual signal.

Solid-phase single molecule biosensing using dual-color colocalization of fluorescent quantum dot nanoprobes

The development of solid-phase surface-based single molecule imaging technology has attracted significant interest during the past decades. Here we demonstrate a sandwich hybridization method for highly sensitive detection of a single thrombin protein at a solid-phase surface based on the use of dual-color colocalization of fluorescent quantum dot (QD) nanoprobes. Green QD560-modified thrombin binding aptamer I (QD560-TBA I) were deposited on a positive poly(l-lysine) assembled layer, followed by bovine serum albumin blocking. It allowed the thrombin protein to mediate the binding of the easily detectable red QD650-modified thrombin binding aptamer II (QD650-TBA II) to the QD560-TBA I substrate. Thus, the presence of the target thrombin can be determined based on fluorescent colocalization measurements of the nanoassemblies, without target amplification or probe separation. The detection limit of this assay reached 0.8 pM. This fluorescent colocalization assay has enabled single molecule recognition in a separation-free detection format, and can serve as a sensitive biosensing platform that greatly suppresses the nonspecific adsorption false-positive signal. This method can be extended to other areas such as multiplexed immunoassay, single cell analysis, and real time biomolecule interaction studies.

Correlation of dual colour single particle trajectories for improved detection and analysis of interactions in living cells

Interactions between objects inside living cells are often investigated by looking for colocalization between fluorescence microscopy images that are recorded in separate colours corresponding to the fluorescent label of each object. The fundamental limitation of this approach in the case of dynamic objects is that coincidental colocalization cannot be distinguished from true interaction. Instead, correlation between motion trajectories obtained by dual colour single particle tracking provides a much stronger indication of interaction. However, frequently occurring phenomena in living cells, such as immobile phases or transient interactions, can limit the correlation to small parts of the trajectories. The method presented here, developed for the detection of interaction, is based on the correlation inside a window that is scanned along the trajectories, covering different subsets of the positions. This scanning window method was validated by simulations and, as an experimental proof of concept, it was applied to the investigation of the intracellular trafficking of polymeric gene complexes by endosomes in living retinal pigment epithelium cells, which is of interest to ocular gene therapy.

Investigating cellular structures at the nanoscale with organic fluorophores

Super-resolution fluorescence imaging can provide insights into cellular structure and organization with a spatial resolution approaching virtually electron microscopy. Among all the different super-resolution methods single-molecule-based localization microscopy could play an exceptional role in the future because it can provide quantitative information, for example, the absolute number of biomolecules interacting in space and time. Here, small organic fluorophores are a decisive factor because they exhibit high fluorescence quantum yields and photostabilities, thus enabling their localization with nanometer precision. Besides past progress, problems with high-density and specific labeling, especially in living cells, and the lack of suited standards and long-term continuous imaging methods with minimal photodamage render the exploitation of the full potential of the method currently challenging.

Polymeric nanoparticles with sequential and multiple FRET cascade mechanisms for multicolor and multiplexed imaging

The ability to map multiple biomarkers at the same time has far-reaching biomedical and diagnostic applications. Here, a series of biocompatible poly(D,L-lactic-co-glycolic acid) and polyethylene glycol particles for multicolor and multiplexed imaging are reported. More than 30 particle formulations that exhibit distinct emission signatures (ranging from the visible to NIR wavelength region) are designed and synthesized. These particles are encapsulated with combinations of carbocyanine-based fluorophores DiO, Dil, DiD, and DiR, and are characterized as <100 nm in size and brighter than commercial quantum dots. A particle formulation is identified that simultaneously emits fluorescence at three different wavelengths upon a single excitation at 485 nm via sequential and multiple FRET cascade events for multicolor imaging. Three other particles that display maximum fluorescence intensities at 570, 672, or 777 nm for multiplexed imaging are also identified. These particles are individually conjugated with specific (Herceptin or IgG2A11 antibody) or nonspecific (heptaarginine) ligands for targeting and, thus, could be applied to differentiate different cancer cells from a cell mixture according to the expressions of cell-surface human epidermal growth factor receptor 2 and the receptor for advanced glycation endproducts. Using an animal model subcutaneously implanted with the particles, it is further demonstrated that the developed platform could be useful for in vivo multiplexed imaging.

Stochastic optical reconstruction microscopy (STORM): a method for superresolution fluorescence imaging

The relatively low spatial resolution of the optical microscope presents significant limitations for the observation of biological ultrastructure. Subcellular structures and molecular complexes essential for biological function exist on length scales from nanometers to micrometers. When observed with light, however, structural features smaller than ∼0.2 µm are blurred and are difficult or impossible to resolve. In this article, we describe stochastic optical reconstruction microscopy (STORM), a method for superresolution imaging based on the high accuracy localization of individual fluorophores. It uses optically switchable fluorophores: molecules that can be switched between a nonfluorescent and a fluorescent state by exposure to light. The article discusses photoswitchable fluorescent molecules, STORM microscope design and the imaging procedure, data analysis, imaging of cultured cells, multicolor STORM, and three-dimensional (3D) STORM. This approach is generally applicable to biological imaging and requires relatively simple experimental apparatus; its spatial resolution is theoretically unlimited, and a resolution improvement of an order of magnitude over conventional optical microscopy has been experimentally demonstrated.

Rapid spectral-domain localization

We present a method to dynamically image structures at nanometer spatial resolution with far-field instruments. We propose the use of engineered nanoprobes with distinguishable spectral responses and the measurement of coherent scattering, rather than fluorescence. Approaches such as PALM/STORM have relied on the rarity of emission events in time to distinguish signals from distinct probes. By distinguishing signals in the spectral domain, we enable the acquisition of data in a multiplex fashion and thus circumvent the fundamental problem of slow data acquisition of current techniques. The described method has the potential to image dynamic systems with a spatial resolution only limited to the size of the scattering probes.

Dynamic full-field infrared imaging with multiple synchrotron beams

Microspectroscopic imaging in the infrared (IR) spectral region allows for the examination of spatially resolved chemical composition on the microscale. More than a decade ago, it was demonstrated that diffraction-limited spatial resolution can be achieved when an apertured, single-pixel IR microscope is coupled to the high brightness of a synchrotron light source. Nowadays, many IR microscopes are equipped with multipixel Focal Plane Array (FPA) detectors, which dramatically improve data acquisition times for imaging large areas. Recently, progress been made toward efficiently coupling synchrotron IR beamlines to multipixel detectors, but they utilize expensive and highly customized optical schemes. Here we demonstrate the development and application of a simple optical configuration that can be implemented on most existing synchrotron IR beamlines to achieve full-field IR imaging with diffraction-limited spatial resolution. Specifically, the synchrotron radiation fan is extracted from the bending magnet and split into four beams that are combined on the sample, allowing it to fill a large section of the FPA. With this optical configuration, we are able to oversample an image by more than a factor of 2, even at the shortest wavelengths, making image restoration through deconvolution algorithms possible. High chemical sensitivity, rapid acquisition times, and superior signal-to-noise characteristics of the instrument are demonstrated. The unique characteristics of this setup enabled the real-time study of heterogeneous chemical dynamics with diffraction-limited spatial resolution for the first time.

Photoinitiated release of an aziridinium ion precursor for the temporally controlled alkylation of nucleophiles

A photo-activatable aziridinium precursor has been developed to investigate the possibility of a photo-initiated traditional nucleophilic reaction. The photolysis of a quaternary amine yields a tertiary amine and has allowed us to temporally control aziridinium formation and subsequent alkylation of a colorimetric nucleophilic reporter molecule. We have also used this photo-initiated reaction to alkylate a sulfhydryl group. This new photo-initiated alkylation strategy is water-soluble and expands the toolkit of photo-activated crosslinkers for protein labeling research.

A novel method for quantified, superresolved, three-dimensional colocalisation of isotropic, fluorescent particles

Colocalisation, the overlap of subcellular structures labelled with different colours, is a key step to characterise cellular phenotypes. We have developed a novel bioimage informatics approach for quantifying colocalisation of round, blob-like structures in two-colour, highly resolved, three-dimensional fluorescence microscopy datasets. First, the algorithm identifies isotropic fluorescent particles, of relative brightness compared to their immediate neighbourhood, in three dimensions and for each colour. The centroids of these spots are then determined, and each object in one location of a colour image is checked for a corresponding object in the other colour image. Three-dimensional distance maps between the centroids of differently coloured spots then display where and how closely they colocalise, while histograms allow to analyse all colocalisation distances. We use the method to reveal sparse colocalisation of different human leukocyte antigen receptors in choriocarcinoma cells. It can also be applied to other isotropic subcellular structures such as vesicles, aggresomes and chloroplasts. The simple, robust and fast approach yields superresolved, object-based colocalisation maps and provides a first indication of protein-protein interactions of fluorescent, isotropic particles.

Breaking the resolution limit in light microscopy

The advancement in fluorescence microscopy has dramatically enhanced the obtainable optical resolution enabling the users to inspect the structures of interest at finer and finer level of detail. This chapter describes some of these methods and how they break the classical resolution limit. The labeling of targets, such as individual genetic loci, specific proteins, or organelles, is possible inside living cells, which led to the extensive use of fluorescence microscopy in life sciences. Other microscopic modes usually lack this high specificity but sometimes provide other useful information such as the orientation of molecular species in polarization microscopy. Modes, such as differential interference contrast, phase contrast, or dark field, are useful to discriminate and follow cells or structures within them without the need for specific labeling. However, classically the resolution of all of these light microscopic modes was far below that of the electron microscope, and only some recent approaches have made significant progress in resolution increase. Recently, many microscopy methods have dramatically enhanced the resolution. Gradually, these methods are now applied to solve biological problems. The most promising approaches are all based on fluorescence and use either nonlinear interaction of light with the sample (STED, nonlinear structured illumination, dynamic saturation optical microscopy, or saturation in the time domain) or precise localization of individual particles or molecules with subsequent image generation.

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.

Single-molecule localization super-resolution microscopy: deeper and faster

For over a decade fluorescence microscopy has demonstrated the capacity to achieve single-molecule localization accuracies of a few nanometers, well below the ≈ 200 nm lateral and ≈ 500 nm axial resolution limit of conventional microscopy. Yet, only the recent development of new fluorescence labeling modalities, the increase in sensitivity of imaging hardware, and the creation of novel image analysis tools allow for the emergence of single-molecule-based super-resolution imaging techniques. Novel methods such as photoactivated localization microscopy and stochastic optical reconstruction microscopy can typically reach a tenfold increase in resolution compared to standard microscopy methods. Their implementation is relatively easy only requiring minimal changes to a conventional wide-field or total internal reflection fluorescence microscope. The recent translation of these two methods into commercial imaging systems has made them further accessible to researchers in biology. However, these methods are still evolving rapidly toward imaging live samples with high temporal resolution and depth. In this review, we recall the roots of single-molecule localization microscopy, summarize major recent developments, and offer perspective on potential applications.