Organic fluorescent probes for stochastic optical reconstruction microscopy (STORM): Recent highlights and future possibilities

Fluorescent probes in autoimmune disease research: current status and future prospects

Autoimmune diseases (AD) present substantial challenges for early diagnosis and precise treatment due to their intricate pathogenesis and varied clinical manifestations. While existing diagnostic methods and treatment strategies have advanced, their sensitivity, specificity, and real-time applicability in clinical settings continue to exhibit significant limitations. In recent years, fluorescent probes have emerged as highly sensitive and specific biological imaging tools, demonstrating substantial potential in AD research.This review examines the response mechanisms and historical evolution of various types of fluorescent probes, systematically summarizing the latest research advancements in their application to autoimmune diseases. It highlights key applications in biomarker detection, dynamic monitoring of immune cell functions, and assessment of drug treatment efficacy. Furthermore, this article analyzes the technical challenges currently encountered in probe development and proposes potential directions for future research. With ongoing advancements in materials science, nanotechnology, and bioengineering, fluorescent probes are anticipated to achieve higher sensitivity and enhanced functional integration, thereby facilitating early detection, dynamic monitoring, and innovative treatment strategies for autoimmune diseases. Overall, fluorescent probes possess substantial scientific significance and application value in both research and clinical settings related to autoimmune diseases, signaling a new era of personalized and precision medicine.

Advancing Platelet Research Through Live-Cell Imaging: Challenges, Techniques, and Insights

Platelet cells are essential to maintain haemostasis and play a critical role in thrombosis. They swiftly respond to vascular injury by adhering to damaged vessel surfaces, activating signalling pathways, and aggregating with each other to control bleeding. This dynamic process of platelet activation is intricately coordinated, spanning from membrane receptor maturation to intracellular interactions to whole-cell responses. Live-cell imaging has become an invaluable tool for dissecting these complexes. Despite its benefits, live imaging of platelets presents significant technical challenges. This review addresses these challenges, identifying key areas in need of further development and proposing possible solutions. We also focus on the dynamic processes of platelet adhesion, activation, and aggregation in haemostasis and thrombosis, applying imaging capacities from the microscale to the nanoscale. By exploring various live imaging techniques, we demonstrate how these approaches offer crucial insights into platelet biology and deepen our understanding of these three core events. In conclusion, this review provides an overview of the imaging methods currently available for studying platelet dynamics, guiding researchers in selecting suitable techniques for specific studies. By advancing our knowledge of platelet behaviour, these imaging methods contribute to research on haemostasis, thrombosis, and platelet-related diseases, ultimately aiming to improve clinical outcomes.

Single-Particle Fluorescence Spectroscopy for Elucidating Charge Transfer and Catalytic Mechanisms on Nanophotocatalysts

Photocatalysis is a cost-effective approach to producing renewable energy. A thorough comprehension of carrier separation at the micronano level is crucial for enhancing the photochemical conversion capabilities of photocatalysts. However, the heterogeneity of photocatalyst nanoparticles and complex charge migration processes limit the profound understanding of photocatalytic reaction mechanisms. By establishing the precise interrelationship between microscopic properties and photophysical behaviors of photocatalysts, single-particle fluorescence spectroscopy can elucidate the carrier separation and catalytic mechanism of the photocatalysts in situ, which provides perspectives for improving the photocatalytic efficiency. This Review primarily focuses on the basic principles and advantages of single-particle fluorescence spectroscopy and its progress in the study of plasmonic and semiconductor photocatalysis, especially emphasizing its importance in understanding the charge separation and photocatalytic reaction mechanism, which offers scientific guidance for designing efficient photocatalytic systems. Finally, we summarize and forecast the future development prospects of single-particle fluorescence spectroscopy technology, especially the insights into its technological upgrading.

Nanoparticles and plants: A focus on analytical characterization techniques

Nanotechnology has brought about significant progress through the use of goods based on nanomaterials. However, concerns remain about the accumulation of these materials in the environment and their potential toxicity to living organisms. Plants have the ability to take in nanomaterials (NMs), which can cause changes in their physiology and morphology. On the other hand, nanoparticles (NPs) have been used to increase plant development and control pests in agriculture by including them into agrochemicals. The challenges of the interaction, internalization, and accumulation of NMs within plant tissues are enormous, mainly because of the various characteristics of NMs and the absence of reliable analytical tools. As our knowledge of the interactions between NMs and plant cells expands, we are able to create novel NMs that are tailored, targeted, and designed to be safe, thus minimizing the environmental consequences of nanomaterials. This review provides a thorough examination and comparison of the main microscopy techniques, spectroscopic methods, and far-field super-resolution methodologies used to examine nanomaterials within the cell walls of plants.

Enhancing resolution and contrast in fibre bundle-based fluorescence microscopy using generative adversarial network

Fibre bundle (FB)-based endoscopes are indispensable in biology and medical science due to their minimally invasive nature. However, resolution and contrast for fluorescence imaging are limited due to characteristic features of the FBs, such as low numerical aperture (NA) and individual fibre core sizes. In this study, we improved the resolution and contrast of sample fluorescence images acquired using in-house fabricated high-NA FBs by utilising generative adversarial networks (GANs). In order to train our deep learning model, we built an FB-based multifocal structured illumination microscope (MSIM) based on a digital micromirror device (DMD) which improves the resolution and the contrast substantially compared to basic FB-based fluorescence microscopes. After network training, the GAN model, employing image-to-image translation techniques, effectively transformed wide-field images into high-resolution MSIM images without the need for any additional optical hardware. The results demonstrated that GAN-generated outputs significantly enhanced both contrast and resolution compared to the original wide-field images. These findings highlight the potential of GAN-based models trained using MSIM data to enhance resolution and contrast in wide-field imaging for fibre bundle-based fluorescence microscopy. Lay Description: Fibre bundle (FB) endoscopes are essential in biology and medicine but suffer from limited resolution and contrast for fluorescence imaging. Here we improved these limitations using high-NA FBs and generative adversarial networks (GANs). We trained a GAN model with data from an FB-based multifocal structured illumination microscope (MSIM) to enhance resolution and contrast without additional optical hardware. Results showed significant enhancement in contrast and resolution, showcasing the potential of GAN-based models for fibre bundle-based fluorescence microscopy.

Tuning the excitation laser power in a stochastic optical reconstruction microscope for Alexa Fluor 647 dye in Vectashield mounting media

Super-resolution imaging techniques have fundamentally changed our understanding of cellular architecture and dynamics by surpassing the diffraction limit and enabling the visualization of subcellular details. The popular super-resolution method known as stochastic optical reconstruction microscopy (STORM) relies on the exact localization of single fluorescent molecules. The significance of employing Vectashield as a mounting medium for the super-resolution imaging scheme called direct STORM has recently been explored. Alexa Fluor 647 (AF647), one of the most popular dyes, shows significant blinking in Vectashield. However, to observe prominent blinking of the fluorophore for the reconstruction of super-resolved images, the power of the excitation laser needs to be tuned. This work demonstrates the tuning of excitation power density in the sample plane for superior imaging performance using AF647 in Vectashield. Samples comprising MDA-MB-231 breast cancer cell line are used for the experiments. The actin filaments of the cell are stained with phalloidin-conjugated AF647 dye. For the experiment, we employ a low-cost openFrame-based STORM system equipped with a programmable Arduino-regulated laser source emitting at 638 nm. An excitation power density of 0.60 kW/cm2 at 638 nm in the sample plane is observed to maximize the signal-to-noise ratio, the number of switching events, and the number of photons detected per event during image acquisition, thereby leading to the best imaging performance in terms of resolution. The outcome of this work will promote further STORM-based super-resolved imaging applications in cell biology using Alexa Fluor 647 in Vectashield.

Near-Infrared Spontaneously Blinking Fluorophores for Live Cell Super-Resolution Imaging with Minimized Phototoxicity

Single-molecule localization microscopy (SMLM) requires high-intensity laser irradiation, typically exceeding kW/cm2, to yield a sufficient photon count. However, this intense visible light exposure incurs substantial cellular toxicity, hindering its use in living cells. Here, we developed a class of near-infrared (NIR) spontaneously blinking fluorophores for SMLM. These NIR fluorophores are a combination of rhodamine spirolactams and merocyanine derivatives, where the rhodamine spirolactam component converts between a bright and dark state based on pH-dependent spirocyclization and merocyanine derivatives shift the excitation wavelength into the infrared. Single-molecule characterizations demonstrated their potential for SMLM. At a moderate power density of 3.93 kW/cm2, these probes exhibit duty cycle as low as 0.18% and an emission rate as high as 26,700 photons/s. Phototoxicity assessment under single-molecule imaging conditions reveals that NIR illumination (721 nm) minimizes harm to living cells. Employing these NIR fluorophores, we successfully captured time-lapse super-resolution tracking of mitochondria at a Fourier ring correlation (FRC) resolution of 69.4 nm and reconstructed the ultrastructures of endoplasmic reticulum (ER) in living cells.

Molecular probes for super-resolution imaging of drug dynamics

Super-resolution molecular probes (SRMPs) are essential tools for visualizing drug dynamics within cells, transcending the resolution limits of conventional microscopy. In this review, we provide an overview of the principles and design strategies of SRMPs, emphasizing their role in accurately tracking drug molecules. By illuminating the intricate processes of drug distribution, diffusion, uptake, and metabolism at a subcellular and molecular level, SRMPs offer crucial insights into therapeutic interventions. Additionally, we explore the practical applications of super-resolution imaging in disease treatment, highlighting the significance of SRMPs in advancing our understanding of drug action. Finally, we discuss future perspectives, envisioning potential advancements and innovations in this field. Overall, this review serves to inform and practitioners about the utility of SRMPs in driving innovation and progress in pharmacology, providing valuable insights for drug development and optimization.

Targeted Photoconvertible BODIPYs Based on Directed Photooxidation-Induced Conversion for Applications in Photoconversion and Live Super-Resolution Imaging

Photomodulable fluorescent probes are drawing increasing attention due to their applications in advanced bioimaging. Whereas photoconvertible probes can be advantageously used in tracking, photoswitchable probes constitute key tools for single-molecule localization microscopy to perform super-resolution imaging. Herein, we shed light on a red and far-red BODIPY, namely, BDP-576 and BDP-650, which possess both properties of conversion and switching. Our study demonstrates that these pyrrolyl-BODIPYs convert into typical green- and red-emitting BODIPYs that are perfectly adapted to microscopy. We also showed that this pyrrolyl-BODIPYs undergo Directed Photooxidation Induced Conversion, a photoconversion mechanism that we recently introduced, where the pyrrole moiety plays a central role. These unique features were used to develop targeted photoconvertible probes toward different organelles or subcellular units (plasma membrane, mitochondria, nucleus, actin, Golgi apparatus, etc.) using chemical targeting moieties and a Halo tag. We notably showed that BDP-650 could be used to track intracellular vesicles over more than 20 min in two-color imagings with laser scanning confocal microscopy, demonstrating its robustness. The switching properties of these photoconverters were studied at the single-molecule level and were then successfully used in live single-molecule localization microscopy in epithelial cells and neurons. Both membrane- and mitochondria- targeted probes could be used to decipher membrane 3D architecture and mitochondrial dynamics at the nanoscale. This study builds a bridge between the photoconversion and photoswitching properties of probes undergoing directed photooxidation and shows the versatility and efficacy of this mechanism in advanced live imaging.

Folic acid-mediated enhancement of the diagnostic potential of luminescent europium-doped hydroxyapatite nanocrystals for cancer biomaging

Early and accurate cancer diagnosis is crucial for improving patient survival rates. Luminescent nanoparticles have emerged as a promising tool in fluorescence bioimaging for cancer diagnosis. To enhance diagnostic accuracy, ligands promoting endocytosis into cancer cells are commonly incorporated onto nanoparticle surfaces. Folic acid (FA) is one such ligand, known to specifically bind to folate receptors (FR) overexpressed in various cancer cells such as cervical and ovarian carcinoma. Therefore, surface modification of luminescent nanoparticles with FA can enhance both luminescence efficiency and diagnostic accuracy. In this study, luminescent europium-doped hydroxyapatite (EuHAp) nanocrystals were prepared via hydrothermal method and subsequently modified with (3-Aminopropyl)triethoxysilane (APTES) followed by FA to target FR-positive human cervical adenocarcinoma cell line (HeLa) cells. The sequential grafting of APTES and then FA formed a robust covalent linkage between the nanocrystals and FA. Rod-shaped FA-modified EuHAp nanocrystals, approximately 100 nm in size, exhibited emission peaks at 589, 615, and 650 nm upon excitation at 397 nm. Despite a reduction in photoluminescence intensity following FA modification, fluorescence microscopy revealed a remarkable 120-fold increase in intensity compared to unmodified EuHAp, attributed to the enhanced uptake of FA-modified EuHAp. Additionally, confocal microscope observations confirmed the specificity and the internalization of FA-modified EuHAp nanocrystals in HeLa cells. In conclusion, the modification of EuHAp nanocrystals with FA presents a promising strategy to enhance the diagnostic potential of cancer bioimaging probes.

Squaraine Dyes Exhibit Spontaneous Fluorescence Blinking That Enables Live-Cell Nanoscopy

Hampered by their susceptibility to nucleophilic attack and chemical bleaching, electron-deficient squaraine dyes have long been considered unsuitable for biological imaging. This study unveils a surprising twist: in aqueous environments, bleaching is not irreversible but rather a reversible spontaneous quenching process. Leveraging this new discovery, we introduce a novel deep-red squaraine probe tailored for live-cell super-resolution imaging. This probe enables single-molecule localization microscopy (SMLM) under physiological conditions without harmful additives or intense lasers and exhibits spontaneous blinking orchestrated by biological nucleophiles, such as glutathione or hydroxide anion. With a low duty cycle (∼0.1%) and high-emission rate (∼6 × 104 photons/s under 400 W/cm2), the squaraine probe surpasses the benchmark Cy5 dye by 4-fold and Si-rhodamine by a factor of 1.7 times. Live-cell SMLM with the probe reveals intricate structural details of cell membranes, which demonstrates the high potential of squaraine dyes for next-generation super-resolution imaging.

Recent advances in super-resolution optical imaging based on aggregation-induced emission

Super-resolution imaging has rapidly emerged as an optical microscopy technique, offering advantages of high optical resolution over the past two decades; achieving improved imaging resolution requires significant efforts in developing super-resolution imaging agents characterized by high brightness, high contrast and high sensitivity to fluorescence switching. Apart from technical requirements in optical systems and algorithms, super-resolution imaging relies on fluorescent dyes with special photophysical or photochemical properties. The concept of aggregation-induced emission (AIE) was proposed in 2001, coinciding with unprecedented advancements and innovations in super-resolution imaging technology. AIE probes offer many advantages, including high brightness in the aggregated state, low background signal, a larger Stokes shift, ultra-high photostability, and excellent biocompatibility, making them highly promising for applications in super-resolution imaging. In this review, we summarize the progress in implementation methods and provide insights into the mechanism of AIE-based super-resolution imaging, including fluorescence switching resulting from photochemically-converted aggregation-induced emission, electrostatically controlled aggregation-induced emission and specific binding-regulated aggregation-induced emission. Particularly, the aggregation-induced emission principle has been proposed to achieve spontaneous fluorescence switching, expanding the selection and application scenarios of super-resolution imaging probes. By combining the aggregation-induced emission principle and specific molecular design, we offer some comprehensive insights to facilitate the applications of AIEgens (AIE-active molecules) in super-resolution imaging.

Visualizing the intracellular aggregation behavior of gold nanoclusters via structured illumination microscopy and scanning transmission electron microscopy

Given the growing concerns about nanotoxicity, numerous studies have focused on providing mechanistic insights into nanotoxicity by imaging the intracellular fate of nanoparticles. A suitable imaging strategy is necessary to uncover the intracellular behavior of nanoparticles. Although each conventional technique has its own limitations, scanning transmission electron microscopy (STEM) and three-dimensional structured illumination microscopy (3D-SIM) combine the advantages of chemical element mapping, ultrastructural analysis, and cell dynamic tracking. Gold nanoclusters (AuNCs), synthesized using 6-aza-2 thiothymine (ATT) and L-arginine (Arg) as reducing and protecting ligands, referred to as Arg@ATT-AuNCs, have been widely used in biological sensing and imaging, medicine, and catalyst yield. Based on their intrinsic fluorescence and high electron density, Arg@ATT-AuNCs were selected as a model. STEM imaging showed that both the single-particle and aggregated states of Arg@ATT-AuNCs were compartmentally distributed within a single cell. Real-time 3D-SIM imaging showed that the fluorescent Arg@ATT-AuNCs gradually aggregated after being located in the lysosomes of living cells, causing lysosomal damage. The aggregate formation of Arg@ATT-AuNCs was triggered by the low-pH medium, particularly in the lysosomal acidic environment. The proposed dual imaging strategy was verified using other types of AuNCs, which is valuable for studying nano-cell interactions and any associated cytotoxicity, and has the potential to be a useful approach for exploring the interaction of cells with various nanoparticles.

Quantitative Super-Resolution Microscopy Reveals the Relationship between CENP-A Stoichiometry and Centromere Physical Size

Centromeric chromatin is thought to play a critical role in ensuring the faithful segregation of chromosomes during mitosis. However, our understanding of this role is presently limited by our poor understanding of the structure and composition of this unique chromatin. The nucleosomal variant, CENP-A, localizes to narrow regions within the centromere, where it plays a major role in centromeric function, effectively serving as a platform on which the kinetochore is assembled. Previous work found that, within a given cell, the number of microtubules within kinetochores is essentially unchanged between CENP-A-localized regions of different physical sizes. However, it is unknown if the amount of CENP-A is also unchanged between these regions of different sizes, which would reflect a strict structural correspondence between these two key characteristics of the centromere/kinetochore assembly. Here, we used super-resolution optical microscopy to image and quantify the amount of CENP-A and DNA within human centromere chromatin. We found that the amount of CENP-A within CENP-A domains of different physical sizes is indeed the same. Further, our measurements suggest that the ratio of CENP-A- to H3-containing nucleosomes within these domains is between 8:1 and 11:1. Thus, our results not only identify an unexpectedly strict relationship between CENP-A and microtubules stoichiometries but also that the CENP-A centromeric domain is almost exclusively composed of CENP-A nucleosomes.

Xanthene, cyanine, oxazine and BODIPY: the four pillars of the fluorophore empire for super-resolution bioimaging

In the realm of biological research, the invention of super-resolution microscopy (SRM) has enabled the visualization of ultrafine sub-cellular structures and their functions in live cells at the nano-scale level, beyond the diffraction limit, which has opened up a new window for advanced biomedical studies to unravel the complex unknown details of physiological disorders at the sub-cellular level with unprecedented resolution and clarity. However, most of the SRM techniques are highly reliant on the personalized special photophysical features of the fluorophores. In recent times, there has been an unprecedented surge in the development of robust new fluorophore systems with personalized features for various super-resolution imaging techniques. To date, xanthene, cyanine, oxazine and BODIPY cores have been authoritatively utilized as the basic fluorophore units in most of the small-molecule-based organic fluorescent probe designing strategies for SRM owing to their excellent photophysical characteristics and easy synthetic acquiescence. Since the future of next-generation SRM studies will be decided by the availability of advanced fluorescent probes and these four fluorescent building blocks will play an important role in progressive new fluorophore design, there is an urgent need to review the recent advancements in designing fluorophores for different SRM methods based on these fluorescent dye cores. This review article not only includes a comprehensive discussion about the recent developments in designing fluorescent probes for various SRM techniques based on these four important fluorophore building blocks with special emphasis on their effective integration into live cell super-resolution bio-imaging applications but also critically evaluates the background of each of the fluorescent dye cores to highlight their merits and demerits towards developing newer fluorescent probes for SRM.

DNA Nanoribbon-Assisted Intracellular Biosynthesis of Fluorescent Gold Nanoclusters for Cancer Cell Imaging

Metal nanoclusters (NCs) have emerged as a promising class of fluorescent probes for cellular imaging due to their high resistance to photobleaching and low toxicity. Nevertheless, their widespread use in clinical diagnosis is limited by their unstable intracellular fluorescence. In this study, we develop an intracellularly biosynthesized fluorescent probe, DNA nanoribbon-gold NCs (DNR/AuNCs), for long-term cellular tracking. Our results show that DNR/AuNCs exhibit a 4-fold enhancement of intracellular fluorescence intensity compared to free AuNCs. We also investigated the mechanism underlying the fluorescence enhancement of AuNCs by DNRs. Our findings suggest that the higher synthesis efficiency and stability of AuNCs in the lysosome may contribute to their fluorescence enhancement, which enables long-term (up to 15 days) fluorescence imaging of cancer cells (enhancement of ∼60 times compared to free AuNCs). Furthermore, we observe similar results with other metal NCs, confirming the generality of the DNR-assisted biosynthesis approach for preparing highly bright and stable fluorescent metal NCs for cancer cell imaging.

Beyond DNA: new probes for PAINT super-resolution microscopy

In the last decade, point accumulation for imaging in nanoscale topography (PAINT) has emerged as a versatile tool for single-molecule localization microscopy (SMLM). Currently, DNA-PAINT is the most widely used, in which a transient stochastically binding DNA docking-imaging pair is used to reconstruct specific characteristics of biological or synthetic materials on a single-molecule level. Slowly, the need for PAINT probes that are not dependent on DNA has emerged. These probes can be based on (i) endogenous interactions, (ii) engineered binders, (iii) fusion proteins, or (iv) synthetic molecules and provide complementary applications for SMLM. Therefore, researchers have been expanding the PAINT toolbox with new probes. In this review, we provide an overview of the currently existing probes that go beyond DNA and their applications and challenges.

Fluorescent Organic Small Molecule Probes for Bioimaging and Detection Applications

The activity levels of key substances (metal ions, reactive oxygen species, reactive nitrogen, biological small molecules, etc.) in organisms are closely related to intracellular redox reactions, disease occurrence and treatment, as well as drug absorption and distribution. Fluorescence imaging technology provides a visual tool for medicine, showing great potential in the fields of molecular biology, cellular immunology and oncology. In recent years, organic fluorescent probes have attracted much attention in the bioanalytical field. Among various organic fluorescent probes, fluorescent organic small molecule probes (FOSMPs) have become a research hotspot due to their excellent physicochemical properties, such as good photostability, high spatial and temporal resolution, as well as excellent biocompatibility. FOSMPs have proved to be suitable for in vivo bioimaging and detection. On the basis of the introduction of several primary fluorescence mechanisms, the latest progress of FOSMPs in the applications of bioimaging and detection is comprehensively reviewed. Following this, the preparation and application of fluorescent organic nanoparticles (FONPs) that are designed with FOSMPs as fluorophores are overviewed. Additionally, the prospects of FOSMPs in bioimaging and detection are discussed.

Choosing the Probe for Single-Molecule Fluorescence Microscopy

Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.

Ultra-bright and narrow-band emission from Ag atomic sized nanoclusters in a self-assembled plasmonic resonator

We have proposed, implemented and investigated a novel, efficient quantum emitter based on an atomic-sized Ag nanocluster in a plasmonic resonator. The quantum emitter enables the realization of: (1) ultra-bright fluorescence, (2) narrow-band emission down to 4 nm, (3) ultra-short fluorescence lifetime. The fluorescence cross-section of a quantum emitter is on the order of σ ∼ 10^-14 cm², which is comparable to the largest fluorescence cross-sections of dye molecules and quantum dots, and enables a light source with a record high intensity known only for plasmon nanolasers. The results presented suggest a unique method for fabricating nanoprobes with high brightness and wavelength-tunable spectrally narrow fluorescence, which is needed for multiplex diagnostics and detection of substances at extremely low concentrations.

Blood Cell Analysis: From Traditional Methods to Super-Resolution Microscopy

Blood cell analysis is essential for the diagnosis and identification of hematological malignancies. The use of digital microscopy systems has been extended in clinical laboratories. Super-resolution microscopy (SRM) has attracted wide attention in the medical field due to its nanoscale spatial resolution and high sensitivity. It is considered to be a potential method of blood cell analysis that may have more advantages than traditional approaches such as conventional optical microscopy and hematology analyzers in certain examination projects. In this review, we firstly summarize several common blood cell analysis technologies in the clinic, and analyze the advantages and disadvantages of these technologies. Then, we focus on the basic principles and characteristics of three representative SRM techniques, as well as the latest advances in these techniques for blood cell analysis. Finally, we discuss the developmental trend and possible research directions of SRM, and provide some discussions on further development of technologies for blood cell analysis.

A coordinate-based co-localization index to quantify and visualize spatial associations in single-molecule localization microscopy

Visualizing the subcellular distribution of proteins and determining whether specific proteins co-localize is one of the main strategies in determining the organization and potential interactions of protein complexes in biological samples. The development of super-resolution microscopy techniques such as single-molecule localization microscopy (SMLM) has tremendously increased the ability to resolve protein distribution at nanometer resolution. As super-resolution imaging techniques are becoming instrumental in revealing novel biological insights, new quantitative approaches that exploit the unique nature of SMLM datasets are required. Here, we present a new, local density-based algorithm to quantify co-localization in dual-color SMLM datasets. We show that this method is broadly applicable and only requires molecular coordinates and their localization precision as inputs. Using simulated point patterns, we show that this method robustly measures the co-localization in dual-color SMLM datasets, independent of localization density, but with high sensitivity towards local enrichments. We further validated our method using SMLM imaging of the microtubule network in epithelial cells and used it to study the spatial association between proteins at neuronal synapses. Together, we present a simple and easy-to-use, but powerful method to analyze the spatial association of molecules in dual-color SMLM datasets.

Investigating the Performances of Wide-Field Raman Microscopy with Stochastic Optical Reconstruction Post-Processing

Super-resolution fluorescence microscopy based on localization algorithms has tremendously impacted the field of imaging by improving the spatial resolution of optical measurements with specific blinking fluorophores and concomitant reduction of acquisition time. In vibrational spectroscopy and imaging, various methods have been developed to surpass the diffraction limit including near-field scattering methods, such as in tip-enhanced Raman and infrared spectroscopies. Although these scanning-probe techniques can provide exquisite spatial resolution, they often require long acquisition times and tedious fabrication of nano-scale scanning probes. Herein, stochastic optical reconstruction microscopy (STORM) protocol is applied on Raman measurements acquired using a wide-field home-built microscopy setup. We explore how the fluctuations of the Raman signal acquired over a series of time-lapse images at specific spectral ranges can be exploited with STORM processing, possibly revealing details with improved spatial resolution, under lower irradiance and with faster acquisition speed that cannot be achieved in point scanning mode over the same field of view. Samples studied here include patterned silicon, polystyrene microspheres on a silicon wafer, and graphene on a silicon/silicon dioxide substrate. The outcome presents an effective way to collect Raman images at selected spectral ranges with spatial resolutions of ∼200 nm over a large field of view under 532 nm excitation together with an acquisition speed improved by two orders of magnitude and under a significantly reduced irradiance compared to confocal laser scanning acquisition.

Single-Molecule Localization Microscopy of Subcellular Protein Distribution in Neurons

Over the past years several forms of superresolution fluorescence microscopy have been developed that offer the possibility to study cellular structures and protein distribution at a resolution well below the diffraction limit of conventional fluorescence microscopy (<200 nm). A particularly powerful superresolution technique is single-molecule localization microscopy (SMLM). SMLM enables the quantitative investigation of subcellular protein distribution at a spatial resolution up to tenfold higher than conventional imaging, even in live cells. Not surprisingly, SMLM has therefore been used in many applications in biology, including neuroscience. This chapter provides a step-by-step SMLM protocol to visualize the nanoscale organization of endogenous proteins in dissociated neurons but can be extended to image other adherent cultured cells. We outline a number of methods to visualize endogenous proteins in neurons for live-cell and fixed application, including immunolabeling, the use of intrabodies for live-cell SMLM, and endogenous tagging using CRISPR/Cas9.

Conjugated Polymers: Optical Toolbox for Bioimaging and Cancer Therapy

Conjugated polymers (CPs) are capable of coordinating the electron coupling phenomenon to bestow powerful optoelectronic features. The light-harvesting and light-amplifying properties of CPs are extensively used in figuring out the biomedical issues with special emphasis on accurate diagnosis, effective treatment, and precise theranostics. This review summarizes the recent progress of CP materials in bioimaging, cancer therapeutics, and introduces the design strategies by rationally tuning the optical properties. The recent advances of CPs in bioimaging applications are first summarized and the challenges to clear the future directions of CPs in the respective area are discussed. In the following sections, the focus is on the burgeoning applications of CPs in phototherapy of the tumor, and illustrates the underlying photo-transforming mechanism for further molecular designing. Besides, the recent progress in the CPs-assistant drug therapy, mainly including drug delivery, gene therapeutic, the optical-activated reversion of tumor resistance, and synergistic therapy has also been discussed elaborately. In the end, the potential challenges and future developments of CPs on cancer diagnosis and therapy are also illuminated for the improvement of optical functionalization and the promotion of clinical translation.

Quantitative dSTORM super-resolution microscopy localizes Aurora kinase A/AURKA in the mitochondrial matrix

BACKGROUND INFORMATION

Mitochondria are dynamic organelles playing essential metabolic and signaling functions in cells. Their ultrastructure has largely been investigated with electron microscopy (EM) techniques. However, quantifying protein-protein proximities using EM is extremely challenging. Super-resolution microscopy techniques as direct stochastic optical reconstruction microscopy (dSTORM) now provide a fluorescent-based, quantitative alternative to EM. Recently, super-resolution microscopy approaches including dSTORM led to valuable advances in our knowledge of mitochondrial ultrastructure, and in linking it with new insights in organelle functions. Nevertheless, dSTORM is mostly used to image integral mitochondrial proteins, and there is little or no information on proteins transiently present at this compartment. The cancer-related Aurora kinase A/AURKA is a protein localized at various subcellular locations, including mitochondria.

RESULTS

We first demonstrate that dSTORM coupled to GcoPS can resolve protein proximities within individual submitochondrial compartments. Then, we show that dSTORM provides sufficient spatial resolution to visualize and quantify the most abundant pool of endogenous AURKA in the mitochondrial matrix, as previously shown for overexpressed AURKA. In addition, we uncover a smaller pool of AURKA localized at the OMM, which could have a potential functional readout. We conclude by demonstrating that aldehyde-based fixatives are more specific for the OMM pool of the kinase instead.

CONCLUSIONS

Our results indicate that dSTORM coupled to GcoPS colocalization analysis is a suitable approach to explore the compartmentalization of non-integral mitochondrial proteins as AURKA, in a qualitative and quantitative manner. This method also opens up the possibility of analyzing the proximity between AURKA and its multiple mitochondrial partners with exquisite spatial resolution, thereby allowing novel insights into the mitochondrial functions controlled by AURKA.

SIGNIFICANCE

Probing and quantifying the presence of endogenous AURKA - a cell cycle-related protein localized at mitochondria - in the different organelle subcompartments, using quantitative dSTORM super-resolution microscopy.

Super-Resolution Imaging with Graphene

Super-resolution optical imaging is a consistent research hotspot for promoting studies in nanotechnology and biotechnology due to its capability of overcoming the diffraction limit, which is an intrinsic obstacle in pursuing higher resolution for conventional microscopy techniques. In the past few decades, a great number of techniques in this research domain have been theoretically proposed and experimentally demonstrated. Graphene, a special two-dimensional material, has become the most meritorious candidate and attracted incredible attention in high-resolution imaging domain due to its distinctive properties. In this article, the working principle of graphene-assisted imaging devices is summarized, and recent advances of super-resolution optical imaging based on graphene are reviewed for both near-field and far-field applications.

Systematic overview on the most widespread techniques for inducing and visualizing the DNA double-strand breaks

DNA double-strand breaks (DSBs) are one of the most frequent causes of initiating cancerous malformations, therefore, to reduce the risk, cells have developed sophisticated DNA repair mechanisms. These pathways ensure proper cellular function and genome integrity. However, any alteration or malfunction during DNA repair can influence cellular homeostasis, as improper recognition of the DNA damage or dysregulation of the repair process can lead to genome instability. Several powerful methods have been established to extend our current knowledge in the field of DNA repair. For this reason, in this review, we focus on the methods used to study DSB repair, and we summarize the advantages and disadvantages of the most commonly used techniques currently available for the site-specific induction of DSBs and the subsequent tracking of the repair processes in human cells. We highlight methods that are suitable for site-specific DSB induction (by restriction endonucleases, CRISPR-mediated DSB induction and laser microirradiation) as well as approaches [e.g., fluorescence-, confocal- and super-resolution microscopy, chromatin immunoprecipitation (ChIP), DSB-labeling and sequencing techniques] to visualize and follow the kinetics of DSB repair.

Modular Synthetic Approach to Silicon-Rhodamine Homologues and Analogues via Bis-aryllanthanum Reagents

A modular synthetic approach toward diverse analogues of the far-red fluorophore silicon-rhodamine (SiR), based on a regioselective double nucleophilic addition of aryllanthanum reagents to esters, anhydrides, and lactones, is proposed. The reaction has improved functional group tolerance and represents a unified strategy toward cell-permeant, spontaneously blinking, and photoactivatable SiR fluorescent labels. In tandem with Pd-catalyzed hydroxy- or aminocarbonylation, it serves a streamlined synthetic pathway to a series of validated live-cell-compatible fluorescent dyes.

Super-resolution Microscopy for Biological Imaging

Studying the ultra-fine structures and functions of the subcellular organelles and exploring the dynamic biological events in depth are the key issues in contemporary biological research. Fluorescence bio-imaging has been used to study cell biology for decades. However, the structures and functions of the subcellular organelles which fall under the diffraction limit are still not explored fully at a nanoscale level. Several super-resolution microscopy (SRM) techniques have been devised over the years which can be utilized to overcome diffraction limit. These techniques have opened a new window in biological research. However, SRM methods are highly vulnerable to the lack of appropriate fluorophores and other sophisticated technical considerations. Therefore, this chapter briefly summarizes the basic principles of various SRM methods which have been frequently utilized in biological imaging. The chapter not only gives an overview of the technical advantages and drawbacks about using different SRM techniques for bio-imaging applications but also briefly articulates the nitty-gritties of selecting a proper fluorescent probe for a specific SRM experiment with biological samples.

Nanoscale Infrared Spectroscopy and Chemometrics Enable Detection of Intracellular Protein Distribution

Determination of the intracellular location of proteins is one of the fundamental tasks of microbiology. Conventionally, label-based microscopy and super-resolution techniques are employed. In this work, we demonstrate a new technique that can determine intracellular protein distribution at nanometer spatial resolution. This method combines nanoscale spatial resolution chemical imaging using the photothermal-induced resonance (PTIR) technique with multivariate modeling to reveal the intracellular distribution of cell components. Here, we demonstrate its viability by imaging the distribution of major cellulases and xylanases in Trichoderma reesei using the colocation of a fluorescent label (enhanced yellow fluorescence protein, EYFP) with the target enzymes to calibrate the chemometric model. The obtained partial least squares model successfully shows the distribution of these proteins inside the cell and opens the door for further studies on protein secretion mechanisms using PTIR.

ICT and AIE Characteristics Two Cyano-Functionalized Probes and Their Photophysical Properties, DFT Calculations, Cytotoxicity, and Cell Imaging Applications

Two probes, AIE-1 and AIE-2, were synthesized to investigate the effect of substitutional functional group on aggregation (aggregation-caused quenching (ACQ) or aggregation-induced emission (AIE)) and intramolecular charge transfer (ICT) behavior as well as on the cell imaging aspect. The yellow-color non-substituted probe AIE-1 showed weak charge-transfer absorption and an emission band at 377 nm and 432 nm, whereas the yellowish-orange color substituted probe AIE-2 showed a strong charge-transfer absorption and an emission band at 424 nm and 477 nm in THF solvent. The UV-Vis studies of AIE-1 and AIE-2 in THF and THF with different water fractions showed huge absorption changes in AIE-2 with high water fractions due to its strong aggregation behavior, but no such noticeable absorption changes were observed for AIE-1. Interestingly, the fluorescence intensity of AIE-1 at 432 nm gradually decreased with increasing water fractions and became almost non-emissive at 90% water. However, the monomer-type emission of AIE-2 at 477 nm was shifted to 584 nm with a 6-fold increase in fluorescence intensity in THF-H2O (1:9, v/v) solvent mixtures due to the restriction of intramolecular rotation on aggregation in high water fractions. This result indicates that the probe AIE-1 shows ACQ and probe AIE-2 shows AIE behaviors in THF-H2O solvent mixtures. Furthermore, the emission spectra of AIE-1 and AIE-2 were carried out in different solvent and with different concentrations to see the solvent- or concentration-dependent aggregation behavior. Scanning electron microscope (SEM) and dynamic light scattering (DLS) experiments were also conducted to assess the morphology and particle size of two probes before and after aggregation. Both of the probes, AIE-1 and AIE-2, showed less toxicity on HeLa cells and were suitable for cell imaging studies. Density functional theory (DFT) calculation was also carried out to confirm the ICT process from an electron-rich indole moiety to an electron-deficient cyano-phenyl ring of AIE-1 or AIE-2.

Nanoliposomes Co-Encapsulating Photoswitchable Probe and Photosensitizer for Super-Resolution Optical Imaging and Photodynamic Therapy

Photosensitizers (PSs) are ideal cancer theranostic drugs that can be administered as both fluorescence imaging reagents and photodynamic therapy (PDT) drugs. To improve the tumoritropic behavior of PSs, nanoliposomes are presently being considered as optimal PSs carriers. Although nanoliposomal PSs have been utilized in clinical therapy, PSs localization and photosensitive processing in nanoliposomal PSs are rarely observed on nanoscale. Investigating changes in the fine structure of nanoliposomes under photosensitive processing will further our understanding of the photosensitive effect on nanoliposomal PSs. In this study, nanoliposomes co-encapsulating the PSs benzoporphyrin derivative monoacid A (BPD) and the photoswitchable probe Cy5-927 were prepared to realize PDT and nanoscale super-resolution optical imaging. The fine structures of nanoliposomal BPD and Cy5-927 (LBC) were visualized by a home-built stochastic optical reconstruction microscopy (STORM). Our PDT results showed that the photorelease and PDT efficiency of BPD were not decreased by co-encapsulating with Cy5-927 in LBC. Taken together, LBC can be used as a new optical probe and PDT reagent for investigating changes in nanoliposomes fine structure and micro-interaction in the cellular process of PDT. Therefore, our results deepened our understanding of liposome-based PDT for optimizing cancer treatment. © 2019 International Society for Advancement of Cytometry.

Redefining the photo-stability of common fluorophores with triplet state quenchers: mechanistic insights and recent updates

Light microscopy can offer certain advantages over electron microscopy in terms of acquiring detailed insights into the biological/intra-cellular milieu. In recent years, with the development of new fluorescence imaging technologies, it has become extremely important to assess the role of designing appropriate fluorophores in acquiring desired biological information without encountering any untoward hitches. Over the years, external fluorophores have been prevalently used in fluorescence microscopy and single-molecule fluorescence microscopy-based studies. Photostable fluorogenic probes with high extinction coefficients and quantum yields, exhibiting minimum autofluorescence and photobleaching properties, are preferred in single-molecule microscopy as they can tolerate long-term laser exposure. Therefore, the development of triplet state quenchers and/or any other suitable new strategy to ensure the photo-stability of the fluorophores during long-term live cell imaging exercises is highly anticipated. In this feature article, various strategies for stabilizing fluorophores, including the mechanisms of TSQ-induced stabilization, have been thoroughly reviewed considering contemporary literature reports and applications.