Photobleaching kinetics of fluorescein in quantitative fluorescence microscopy

Scanning Switch-off Microscopy for Super-Resolution Fluorescence Imaging

Super-resolution (SR) microscopy provides a revolutionary optical imaging approach by breaking the diffraction limit of light, while the commonly required special instrumentation with complex optical setup hampers its popularity. Here, we present a scanning switch-off microscopy (SSM) concept that exploits the omnipresent switch-off response of fluorophores to enable super-resolution imaging using a commercial confocal microscope. We validated the SSM model with theoretical calculations and experiments. An imaging resolution of ∼100 nm was obtained for DNA origami nanostructures and cellular cytoskeletons using fluorescent labels of Alexa 405, Alexa 488, Cy3, and Atto 488. Notably, super-resolution imaging of live cells was realized with SSM, by employing a dronpa fluorescent protein as the fluorescent label. In principle, this SSM method can be applied to any excitation laser scanning-based microscope.

Singlet Oxygen Photophysics: From Liquid Solvents to Mammalian Cells

Molecular oxygen, O2, has long provided a cornerstone for studies in chemistry, physics, and biology. Although the triplet ground state, O2(X3Σg-), has garnered much attention, the lowest excited electronic state, O2(a1Δg), commonly called singlet oxygen, has attracted appreciable interest, principally because of its unique chemical reactivity in systems ranging from the Earth's atmosphere to biological cells. Because O2(a1Δg) can be produced and deactivated in processes that involve light, the photophysics of O2(a1Δg) are equally important. Moreover, pathways for O2(a1Δg) deactivation that regenerate O2(X3Σg-), which address fundamental principles unto themselves, kinetically compete with the chemical reactions of O2(a1Δg) and, thus, have practical significance. Due to technological advances (e.g., lasers, optical detectors, microscopes), data acquired in the past ∼20 years have increased our understanding of O2(a1Δg) photophysics appreciably and facilitated both spatial and temporal control over the behavior of O2(a1Δg). One goal of this Review is to summarize recent developments that have broad ramifications, focusing on systems in which oxygen forms a contact complex with an organic molecule M (e.g., a liquid solvent). An important concept is the role played by the M+•O2-• charge-transfer state in both the formation and deactivation of O2(a1Δg).

Light-Sheet Microscopic Imaging of Whole-Mouse Vascular Network with Fluorescent Microsphere Perfusion

Visualizing the whole vascular network system is crucial for understanding the pathogenesis of specific diseases and devising targeted therapeutic interventions. Although the combination of light sheet microscopy and tissue-clearing methods has emerged as a promising approach for investigating the blood vascular network, leveraging the spatial resolution down to the capillary level and the ability to image centimeter-scale samples remains difficult. Especially, as the resolution improves, the issue of photobleaching outside the field of view poses a challenge to image the whole vascular network of adult mice at capillary resolution. Here, we devise a fluorescent microsphere vascular perfusion method to enable labeling of the whole vascular network in adult mice, which overcomes the photobleaching limit during the imaging of large samples. Moreover, by combining the utilization of a large-scale light-sheet microscope and tissue clearing protocols for whole-mouse samples, we achieve the capillary-level imaging resolution (3.2 × 3.2 × 6.5 μm) of the whole vascular network with dimensions of 45 × 15 × 82 mm in adult mice. This method thus holds great potential to deliver mesoscopic resolution images of various tissue organs for whole-animal imaging.

Fast, Accurate, and Versatile Data Analysis Platform for the Quantification of Molecular Spatiotemporal Signals

Optical recording of intricate molecular dynamics is becoming an indispensable technique for biological studies, accelerated by the development of new or improved biosensors and microscopy technology. This creates major computational challenges to extract and quantify biologically meaningful spatiotemporal patterns embedded within complex and rich data sources, many of which cannot be captured with existing methods. Here, we introduce Activity Quantification and Analysis (AQuA2), a fast, accurate, and versatile data analysis platform built upon advanced machine learning techniques. It decomposes complex live imaging-based datasets into elementary signaling events, allowing accurate and unbiased quantification of molecular activities and identification of consensus functional units. We demonstrate applications across a wide range of biosensors, cell types, organs, animal models, and imaging modalities. As exemplar findings, we show how AQuA2 identified drug-dependent interactions between neurons and astroglia, and distinct sensorimotor signal propagation patterns in the mouse spinal cord.

Studying the viability and growth kinetics of vancomycin-resistant Enterococcus faecalis V583 following femtosecond laser irradiation (420-465 nm)

Enterococcus faecalis is among the most resistant bacteria found in infected root canals. The demand for cutting-edge disinfection methods has rekindled research on photoinactivation with visible light. This study investigated the bactericidal activity of femtosecond laser irradiation against vancomycin-resistant Enterococcus faecalis V583 (VRE). The effect of parameters such as wavelength and energy density on the viability and growth kinetics of VRE was studied to design an optimized laser-based antimicrobial photoinactivation approach without any prior addition of exogenous photosensitizers. The most effective wavelengths were 430 nm and 435 nm at a fluence of 1000 J/cm2, causing a nearly 2-log reduction (98.6% and 98.3% inhibition, respectively) in viable bacterial counts. The colony-forming units and growth rate of the laser-treated cultures were progressively decreased as energy density or light dose increased at 445 nm but reached a limit at 1250 J/cm2. At a higher fluence of 2000 J/cm2, the efficacy was reduced due to a photobleaching phenomenon. Our results highlight the importance of optimizing laser exposure parameters, such as wavelength and fluence, in bacterial photoinactivation experiments. To our knowledge, this is the first study to report an optimized wavelength for the inactivation of VRE using visible femtosecond laser light.

A statistical resolution measure of fluorescence microscopy with finite photons

First discovered by Ernest Abbe in 1873, the resolution limit of a far-field microscope is considered determined by the numerical aperture and wavelength of light, approximatelyλ 2 N A . With the advent of modern fluorescence microscopy and nanoscopy methods over the last century, this definition is insufficient to fully describe a microscope's resolving power. To determine the practical resolution limit of a fluorescence microscope, photon noise remains one essential factor yet to be incorporated in a statistics-based theoretical framework. We proposed an information density measure quantifying the theoretical resolving power of a fluorescence microscope in the condition of finite photons. The developed approach not only allows us to quantify the practical resolution limit of various fluorescence and super-resolution microscopy modalities but also offers the potential to predict the achievable resolution of a microscopy design under different photon levels.

Awareness for artifacts in fluorescence microscopy of β-TCP

Fluorescence analysis of β-TCP ceramics is often used to describe cells found on said ceramics. However, we found, to our knowledge, so far undescribed artifacts which might sometimes be hard to differentiate from cells due to shape and fluorescence behavior. We tried prolonged ultrasound washing as well as Technovit 9100 fixation to reduce these artifacts. While untreated dowels showed no reduction in artifacts no matter the further treatment, Technovit fixation reduced the artifacts with even further reduction achieved by mechanical cleaning. As a consequence, scientists working with these dowels and likely even other types should try to avoid creating false positive results by considering the existence of these artifacts, checking additional filters for unusual fluorescence and by reducing them by using Technovit fixation when possible.

Unleashing Precision and Freedom in Optical Manipulation: Software-Assisted Real-Time Precision Opto-Control of Intracellular Molecular Activities and Cell Functions

The traditional method in biological science to regulate cell functions often employs chemical interventions, which commonly lack precision in space and time. While optical manipulation offers superior spatial precision, existing technologies are constrained by limitations in flexibility, accuracy, and response time. Here, we present an adaptable and interactive optical manipulation platform that integrates laser scanning, chemical sensing, synchronized multi-laser control, adaptable target selection, flexible decision-making, and real-time monitoring of sample responses. This software-assisted real-time precision opto-control (S-RPOC) platform facilitates automatic target selection driven by optical signals while permitting user-defined manual delineation. It allows the treatment of mobile or stationary targets with varying laser dosages and wavelengths simultaneously at diffraction-limited spatial precision and optimal accuracy. Significantly, S-RPOC showcases versatile capabilities including adaptive photobleaching, comprehensive quantification of protein dynamics, selective organelle perturbation, control of cell division, and manipulation of individual cell behaviors within a population. With its unprecedented spatiotemporal precision and adaptable decision-making, S-RPOC holds the potential for extensive applications in biological science.

Harmonization of ANA testing challenge: quantification strategy to accurately predict end-point titers avoiding serial dilution

Despite the advantages of automated systems for antinuclear antibody (ANA) analysis, the prediction of end-point titers avoiding serial dilutions is still in progress. The aims of this study were to set a conversion table providing discriminant ranges of fluorescence signal intensity values (FI) corresponding to the end-point titers and validate this tool in a real-life laboratory setting. Eight hundred ninety-four serum samples were analyzed for ANA using Image Navigator System. In order to classify FI into non-overlapping groups corresponding to conventional end-point titers, statistical discriminant analysis was used. Validation study was performed calculating agreement and error rates between visual readings and conversion table of 1119 routine ANA positive samples. Setting of FI ranges corresponding to the end-point titers for different staining patterns was computed. For samples showing single pattern, the overall agreement between visual readings and conversion table was 98.4% for all titers ranging from 1:160 to 1:2560, of which 68.0% had the same titer and 30.4% were within ± one titer difference. Concordance rates according to ANA patterns were as follows: (1) nuclear 98.4%, of which 67.0% had the same titer and 31.4% ± one titer; (2) cytoplasmic 100%, of which 72.7% had the same titer and 27.3% than ± one titer; (3) mitotic 66.6%, of which 33.3% had more ± one titer. Our study developed a quantification method for autoantibodies titers assessment based on just one single sample dilution instead of traditional serial dilution approach, providing significant advantages in routine laboratory in terms of reduction in hand-on time and harmonization of results.

In Operando Visualization of Elementary Turnovers in Photocatalytic Organic Synthesis

We report the in operando visualization of the photocatalytic turnovers on single eosin Y (EY) through a redox-induced photoblinking phenomenon. The photocatalytic cyclization of thiobenzamide (TB) catalyzed by EY was investigated. The analysis of the intensity-versus-time trajectories of single EYs revealed the kinetics and dynamics of the elementary photocatalytic turnovers and the heterogeneity of the activity of individual EYs. The quenching turnover time showed a fast population and a slow population, which could be attributed to the singlet and triplet states of photoexcited EY. The slow quenching turnovers were more dominant at higher TB concentrations. The activity heterogeneity of EYs was studied over a series of reactant concentrations. Excess quenching reagent was found to decrease the percentage of active EYs. The method can be broadly applied to studying the elementary processes of photocatalytic organic reactions in operando.

Kinetics of Structural Transitions Induced by Sodium Dodecyl Sulfate in α-Chymotrypsin

The temporal changes in circular dichroism at 222 and 260 nm were recorded by using stopped-flow spectroscopy after mixing α-chymotrypsin solutions with sodium dodecyl sulfate solutions. Simultaneously with the circular dichroism signal, the fluorescence emission was recorded. Changes in the secondary and tertiary structures of chymotrypsin induced by sodium dodecyl sulfate are characterized by either three or four one-way reactions with relaxation amplitudes and times precisely determined by an advanced numerical procedure of Kuzmič. Quantitatively, transitions within the secondary and tertiary structures of the protein are significantly different. Moreover, changes in the tertiary structure depend on the type of recorded signal (either circular dichroism or fluorescence) and the wavelength of the incident radiation. The latter observation is particularly interesting as it indicates that the contributions of protein's different tryptophans to the total recorded fluorescence depend on the excitation wavelength. We present several results justifying this hypothesis.

Micro- and nanofabrication of dynamic hydrogels with multichannel information

Creating micro/nanostructures containing multi-channel information within responsive hydrogels presents exciting opportunities for dynamically changing functionalities. However, fabricating these structures is immensely challenging due to the soft and dynamic nature of hydrogels, often resulting in unintended structural deformations or destruction. Here, we demonstrate that dehydrated hydrogels, treated by a programmable femtosecond laser, can allow for a robust fabrication of micro/nanostructures. The dehydration enhances the rigidity of the hydrogels and temporarily locks the dynamic behaviours, significantly promoting their structural integrity during the fabrication process. By utilizing versatile dosage domains of the femtosecond laser, we create micro-grooves on the hydrogel surface through the use of a high-dosage mode, while also altering the fluorescent intensity within the rest of the non-ablated areas via a low-dosage laser. In this way, we rationally design a pixel unit containing three-channel information: structural color, polarization state, and fluorescent intensity, and encode three complex image information sets into these channels. Distinct images at the same location were simultaneously printed onto the hydrogel, which can be observed individually under different imaging modes without cross-talk. Notably, the recovered dynamic responsiveness of the hydrogel enables a multi-information-encoded surface that can sequentially display different information as the temperature changes.

Dielectric Metasurface Enabled Compact, Single-Shot Digital Holography for Quantitative Phase Imaging

Quantitative phase imaging (QPI) enables nondestructive, real-time, label-free imaging of transparent specimens and can reveal information about their fundamental properties such as cell size and morphology, mass density, particle dynamics, and cellular fluctuations. Development of high-performance and low-cost quantitative phase imaging systems is thus required in many fields, including on-site biomedical imaging and industrial inspection. Here, we propose an ultracompact, highly stable interferometer based on a single-layer dielectric metasurface for common path off-axis digital holography and experimentally demonstrate quantitative phase imaging. The interferometric imaging system leveraging an ultrathin multifunctional metasurface captures image plane holograms in a single shot and provides quantitative phase information on the test samples for extraction of its physical properties. With the benefits of planar engineering and high integrability, the proposed metasurface-based method establishes a stable miniaturized QPI system for reliable and cost-effective point-of-care devices, live cell imaging, 3D topography, and edge detection for optical computing.

Illuminating the path: aggregation-induced emission for food contaminants detection

Food safety is a global concern that deeply affects human health. To ensure the profitability of the food industry and consumer safety, there is an urgent need to develop rapid, sensitive, accurate, and cost-effective detection methods for food contaminants. Recently, the Aggregation-Induced Emission (AIE) has been successfully used to detect food contaminants. AIEgens, fluorescent dyes that cause AIE, have several valuable properties including high quantum yields, photostability, and large Stokes shifts. This review provides a detailed introduction to the principles and advantages of AIE-triggered detection, followed by a focus on the past five years' applications of AIE in detecting various food contaminants including pesticides, veterinary drugs, mycotoxins, food additives, ions, pathogens, and biogenic amines. Each detection principle and component is comprehensively covered and explained. Moreover, the similarities and differences among different types of food contaminants are summarized, aiming to inspire future researchers. Finally, this review concludes with a discussion of the prospects for incorporating AIEgens more effectively into the detection of food contaminants.

2-λ5-Phosphaquinolin-2-ones as Non-cytotoxic, Targetable, and pH-Stable Fluorophores

Several phosphaquinolinone derivatives have been synthesized and characterized to explore their usefulness in the realm of cell imaging. Solution-state photophysical properties in both aqueous and organic solutions were collected for these derivatives. Additionally, CCK-8 cell viability assays and fluorescent imaging in HeLa cells incubated with the new heterocyclic derivatives show evidence of favorable cell permeability, cell viability, and moderate intracellular localization when appended with the well-known morpholine targeting motif.

Nanoscatterer-Assisted Fluorescence Amplification Technique

Weak fluorescence signals, which are important in research and applications, are often masked by the background. Different amplification techniques are actively investigated. Here, a broadband, geometry-independent and flexible feedback scheme based on the random scattering of dielectric nanoparticles allows the amplification of a fluorescence signal by partial trapping of the radiation within the sample volume. Amplification of up to a factor of 40 is experimentally demonstrated in ultrapure water with dispersed TiO2 nanoparticles (30 to 50 nm in diameter) and fluorescein dye at 200 μmol concentration (pumped with 5 ns long, 3 mJ laser pulses at 490 nm). The measurements show a measurable reduction in linewidth at the emission peak, indicating that feedback-induced stimulated emission contributes to the large gain observed.

Optically active organic and inorganic nanomaterials for biological imaging applications: A review

Recent advancements in the field of nanotechnology have enabled targeted delivery of drug agents in vivo with minimal side effects. The use of nanoparticles for bio-imaging has revolutionized the field of nanomedicine by enabling non-invasive targeting and selective delivery of active drug moieties in vivo. Various inorganic nanomaterials like mesoporous silica nanoparticles, gold nanoparticles, magnetite nanoparticles graphene-based nanomaterials etc., have been created for multimodal therapies with varied multi-imaging modalities. These nanomaterials enable us to overcome the disadvantages of conventional imaging contrast agents (organic dyes) such as lack of stability in vitro and in vivo, high reactivity, low-quantum yield and poor photo stability. Inorganic nanomaterials can be easily fabricated, functionalised and modified as per requirements. Recently, advancements in synthesis techniques, such as the ability to generate molecules and construct supramolecular structures for specific functionalities, have boosted the usage of engineered nanomaterials. Their intrinsic physicochemical properties are unique and they possess excellent biocompatibility. Inorganic nanomaterial research has developed as the most actively booming research fields in biotechnology and biomedicine. Inorganic nanomaterials like gold nanoparticles, magnetic nanoparticles, mesoporous silica nanoparticles, graphene-based nanomaterials and quantum dots have shown excellent use in bioimaging, targeted drug delivery and cancer therapies. Biocompatibility of nanomaterials is an important aspect for the evolution of nanomaterials in the bench to bedside transition. The conduction of thorough and meticulous study for safety and efficacy in well-designed clinical trials is absolutely necessary to determine the functional and structural relationship between the engineered nanomaterial and its toxicity. In this article an attempt is made to throw some light on the current scenario and developments made in the field of nanomaterials in bioimaging.

Fluorescent protein lifetimes report densities and phases of nuclear condensates during embryonic stem-cell differentiation

Fluorescent proteins (FP) are frequently used for studying proteins inside cells. In advanced fluorescence microscopy, FPs can report on additional intracellular variables. One variable is the local density near FPs, which can be useful in studying densities within cellular bio-condensates. Here, we show that a reduction in fluorescence lifetimes of common monomeric FPs reports increased levels of local densities. We demonstrate the use of this fluorescence-based variable to report the distribution of local densities within heterochromatin protein 1α (HP1α) in mouse embryonic stem cells (ESCs), before and after early differentiation. We find that local densities within HP1α condensates in pluripotent ESCs are heterogeneous and cannot be explained by a single liquid phase. Early differentiation, however, induces a change towards a more homogeneous distribution of local densities, which can be explained as a liquid-like phase. In conclusion, we provide a fluorescence-based method to report increased local densities and apply it to distinguish between homogeneous and heterogeneous local densities within bio-condensates.

Monomer and Oligomer Transition of Zinc Phthalocyanine Is Key for Photobleaching in Photodynamic Therapy

Photodynamic therapy (PDT) is recognized as a powerful method to inactivate cells. However, the photosensitizer (PS), a key component of PDT, has suffered from undesired photobleaching. Photobleaching reduces reactive oxygen species (ROS) yields, leading to the compromise of and even the loss of the photodynamic effect of the PS. Therefore, much effort has been devoted to minimizing photobleaching in order to ensure that there is no loss of photodynamic efficacy. Here, we report that a type of PS aggregate showed neither photobleaching nor photodynamic action. Upon direct contact with bacteria, the PS aggregate was found to fall apart into PS monomers and thus possessed photodynamic inactivation against bacteria. Interestingly, the disassembly of the bound PS aggregate in the presence of bacteria was intensified by illumination, generating more PS monomers and leading to an enhanced antibacterial photodynamic effect. This demonstrated that on a bacterial surface, the PS aggregate photo-inactivated bacteria via PS monomer during irradiation, where the photodynamic efficiency was retained without photobleaching. Further mechanistic studies showed that PS monomers disrupted bacterial membranes and affected the expression of genes related to cell wall synthesis, bacterial membrane integrity, and oxidative stress. The results obtained here are applicable to other types of PSs in PDT.

A nanoparticle-based molecular beacon for directly detecting attomolar small RNA from plasma without purification

Molecular beacons (MBs) are DNA-based probes that detect DNA or RNA fragments and hold promise for monitoring diseases and studying protein-nucleic acid interactions. MBs usually use fluorescent molecules as fluorophores for reporting the target detection event. However, the fluorescence of the traditional fluorescent molecules can bleach and even be interfered with the background autofluorescence, reducing the detection performance. Hence, we propose to develop a nanoparticle-based MB (NPMB) that uses upconversion nanoparticles (UCNPs) as a fluorophore, which can be excited by near-infrared light to avoid background autofluorescence and thus enables us to detect small RNA from complicated clinical samples such as plasma. Specifically, we employ a DNA hairpin structure, with one segment complementary to the target RNA, to position a quencher (gold nanoparticles, Au NPs) and the UCNP fluorophore in close proximity, leading to the quenching of the fluorescence of UCNPs in the absence of a target nucleic acid. Only when the hairpin structure is complementary with the detection target, will the hairpin structure be destroyed to separate Au NPs and UCNPs, resulting in the instant recovery of the fluorescence signal of UCNPs and the consequent ultrasensitive detection of the target concentrations. The NPMB has an ultra-low background signal because UCNPs can be excited with NIR light with a wavelength longer than the emitted visible light. We demonstrate that the NPMB can successfully detect a small (22-nt) RNA (using a microRNA cancer biomarker, miR-21, as an example) and a small single-stranded DNA (complementing the cDNA of miR-21) in aqueous solutions from 1 aM to 1 pM, with the linear detection range being 10 aM to 1 pM for the former and 1 aM to 100 fM for the latter. We further show that the NPMB can be used to detect unpurified small RNA (miR-21) in clinical samples such as plasma with the same detection region. Our work suggests that the NPMB is a promising label-free and purification-free method for detecting small nucleic acid biomarkers in clinical samples with a detection limit as low as the aM level.

Fluorescence excitation enhancement by waveguiding nanowires

The optical properties of vertical semiconductor nanowires can allow an enhancement of fluorescence from surface-bound fluorophores, a feature proven useful in biosensing. One of the contributing factors to the fluorescence enhancement is thought to be the local increase of the incident excitation light intensity in the vicinity of the nanowire surface, where fluorophores are located. However, this effect has not been experimentally studied in detail to date. Here, we quantify the excitation enhancement of fluorophores bound to a semiconductor nanowire surface by combining modelling with measurements of fluorescence photobleaching rate, indicative of the excitation light intensity, using epitaxially grown GaP nanowires. We study the excitation enhancement for nanowires with a diameter of 50-250 nm and show that excitation enhancement reaches a maximum for certain diameters, depending on the excitation wavelength. Furthermore, we find that the excitation enhancement decreases rapidly within tens of nanometers from the nanowire sidewall. The results can be used to design nanowire-based optical systems with exceptional sensitivities for bioanalytical applications.

Continuous Glucose Monitoring Enabled by Fluorescent Nanodiamond Boronic Hydrogel

Continuous monitoring of glucose allows diabetic patients to better maintain blood glucose level by altering insulin dosage or diet according to prevailing glucose values and thus to prevent potential hyperglycemia and hypoglycemia. However, current continuous glucose monitoring (CGM) relies mostly on enzyme electrodes or micro-dialysis probes, which suffer from insufficient stability, susceptibility to corrosion of electrodes, weak or inconsistent correlation, and inevitable interference. A fluorescence-based glucose sensor in the skin will likely be more stable, have improved sensitivity, and can resolve the issues of electrochemical interference from the tissue. This study develops a fluorescent nanodiamond boronic hydrogel system in porous microneedles for CGM. Fluorescent nanodiamond is one of the most photostable fluorophores with superior biocompatibility. When surface functionalized, the fluorescent nanodiamond can integrate with boronic polymer and form a hydrogel, which can produce fluorescent signals in response to environmental glucose concentration. In this proof-of-concept study, the strategy for building a miniatured device with fluorescent nanodiamond hydrogel is developed. The device demonstrates remarkable long-term photo and signal stability in vivo with both small and large animal models. This study presents a new strategy of fluorescence based CGM toward treatment and control of diabetes.

Practical Guidance for Developing Small-Molecule Optical Probes for In Vivo Imaging

The WMIS Education Committee (2019-2022) reached a consensus that white papers on molecular imaging could be beneficial for practitioners of molecular imaging at their early career stages and other scientists who are interested in molecular imaging. With this consensus, the committee plans to publish a series of white papers on topics related to the daily practice of molecular imaging. In this white paper, we aim to provide practical guidance that could be helpful for optical molecular imaging, particularly for small molecule probe development and validation in vitro and in vivo. The focus of this paper is preclinical animal studies with small-molecule optical probes. Near-infrared fluorescence imaging, bioluminescence imaging, chemiluminescence imaging, image-guided surgery, and Cerenkov luminescence imaging are discussed in this white paper.

PLATERO: A calibration protocol for plate reader green fluorescence measurements

One of the most common sources of information in Synthetic Biology is the data coming from plate reader fluorescence measurements. These experiments provide a measure of the light emitted by a certain fluorescent molecule, such as the Green Fluorescent Protein (GFP). However, these measurements are generally expressed in arbitrary units and are affected by the measurement device gain. This limits the range of measurements in a single experiment and hampers the comparison of results among experiments. In this work, we describe PLATERO, a calibration protocol to express fluorescence measures in concentration units of a reference fluorophore. The protocol removes the gain effect of the measurement device on the acquired data. In addition, the fluorescence intensity values are transformed into units of concentration using a Fluorescein calibration model. Both steps are expressed in a single mathematical expression that returns normalized, gain-independent, and comparable data, even if the acquisition was done at different device gain levels. Most important, the PLATERO embeds a Linearity and Bias Analysis that provides an assessment of the uncertainty of the model estimations, and a Reproducibility and Repeatability analysis that evaluates the sources of variability originating from the measurements and the equipment. All the functions used to build the model, exploit it with new data, and perform the uncertainty and variability assessment are available in an open access repository.

A temperature-tuned electrochemiluminescence layer for reversibly imaging cell topography

Investigating electrochemiluminescence (ECL) scenarios under different temperatures is important to expand its imaging scope near an electrode surface. Here, we develop a temperature-tuned ECL layer by recording the evolution of shadow regions of adherent cells. Finite element simulation and experimental results demonstrate that the thickness of the ECL layer (TEL) is reversibly regulated by electrode temperature (T _e), so that single cell topography at different heights is imaged. The TEL in two ECL routes shows different regulation ranges with elevated T _e, thus providing a flexible approach to adjust the imaging scope within specific heights. In addition, a heated electrode significantly improves the image quality of cell adhesion in heterogeneous electrochemical rate-determined situations. Thus, the contrast in cell regions shows a reversible response to T _e. This work provides a new approach to regulate the TEL and is promising for monitoring transient heat generation from biological entities.

Technologies Enabling Single-Molecule Super-Resolution Imaging of mRNA

The transient nature of RNA has rendered it one of the more difficult biological targets for imaging. This difficulty stems both from the physical properties of RNA as well as the temporal constraints associated therewith. These concerns are further complicated by the difficulty in imaging endogenous RNA within a cell that has been transfected with a target sequence. These concerns, combined with traditional concerns associated with super-resolution light microscopy has made the imaging of this critical target difficult. Recent advances have provided researchers the tools to image endogenous RNA in live cells at both the cellular and single-molecule level. Here, we review techniques used for labeling and imaging RNA with special emphases on various labeling methods and a virtual 3D super-resolution imaging technique.

Comparison of the effect of reporting cytoplasmic patterns as anti-nuclear antibody positive and anti-nuclear antibody negative on reflex test ordering

Objective Anti-nuclear antibody (ANA) patterns are classified as nuclear, cytoplasmic or mitotic. The International Consensus on ANA patterns (ICAP) suggests three parameters for ANA reporting – assay type, results and advice for reflex testing – but has not yet reached a consensus on the reporting of cytoplasmic/mitotic patterns as ANA-negative or positive. We investigated the effect of ICAP’s two proposals for reporting cytoplasmic patterns as ANA-positive and negative with a view to the recommendation for reflex testing in a country that has no national reimbursement policies for automatic reflex testing.

Methods This non-interventional descriptive study included 1241 patients with positive cytoplasmic ANA patterns. 442 patients were reported as ANA-negative and 799 as ANA-positive. Patients were followed up for a two-year period to determine testing recommendations based upon nuclear and cytoplasmic patterns. For statistical analysis, the t-test was used, with a significance threshold of p-value<0.05.

Results Appropriate reflex orders were seen more commonly with cytoplasmic patterns reported as ANA-positive (27.30%) than with those reported as ANA-negative (5.51%, p-value<0.05). However, ANA-positive reports led to higher ordering of nuclear pattern reflex tests (12.97%) compared with ANA-negative reports (1.10%, p-value<0.05). A large group of patients (59.73% ANA-positive, 93.39% ANA-negative) did not receive reflex testing.

Conclusion Reporting cytoplasmic patterns as ANA-positive was considered more significant, but reading the result report without considering the pattern and recommendation notes could lead to inappropriate reflex testing. Besides reaching a consensus for reporting cytoplasmic patterns as ANA-negative or positive, it is important to consider solutions to reimbursement policies for automatic reflex testing to decrease the impediments in reporting cytoplasmic ANA patterns.

Image segmentation and separation of spectrally similar dyes in fluorescence microscopy by dynamic mode decomposition of photobleaching kinetics

BACKGROUND

Image segmentation in fluorescence microscopy is often based on spectral separation of fluorescent probes (color-based segmentation) or on significant intensity differences in individual image regions (intensity-based segmentation). These approaches fail, if dye fluorescence shows large spectral overlap with other employed probes or with strong cellular autofluorescence.

RESULTS

Here, a novel model-free approach is presented which determines bleaching characteristics based on dynamic mode decomposition (DMD) and uses the inferred photobleaching kinetics to distinguish different probes or dye molecules from autofluorescence. DMD is a data-driven computational method for detecting and quantifying dynamic events in complex spatiotemporal data. Here, DMD is first used on synthetic image data and thereafter used to determine photobleaching characteristics of a fluorescent sterol probe, dehydroergosterol (DHE), compared to that of cellular autofluorescence in the nematode Caenorhabditis elegans. It is shown that decomposition of those dynamic modes allows for separating probe from autofluorescence without invoking a particular model for the bleaching process. In a second application, DMD of dye-specific photobleaching is used to separate two green-fluorescent dyes, an NBD-tagged sphingolipid and Alexa488-transferrin, thereby assigning them to different cellular compartments.

CONCLUSIONS

Data-based decomposition of dynamic modes can be employed to analyze spatially varying photobleaching of fluorescent probes in cells and tissues for spatial and temporal image segmentation, discrimination of probe from autofluorescence and image denoising. The new method should find wide application in analysis of dynamic fluorescence imaging data.

Two-Photon Fluorescence in Red and Violet Conjugated Polymer Microspheres

We investigate the two-photon fluorescence (TPF) of conjugated polymer (CP) microspheres with diameters up to tens of micrometers. Two polymers, emitting in either the violet or red, were first synthesized and characterized in terms of their one-photon fluorescence and three-dimensional internal microstructure. Under femtosecond infrared excitation, both types of microspheres showed a strong TPF, which was investigated by the excitation intensity dependence, emission spectroscopy, time-resolved luminescence, and photobleaching dynamics. While the violet-fluorescent microspheres performed similarly compared to dye-doped polystyrene counterparts emitting at a similar wavelength, the red-fluorescent microspheres showed a two-orders-of-magnitude stronger TPF. This excellent performance is attributed to enhanced hyperpolarizability associated with intermolecular interactions in the polymer solid, indicating a route toward designed CP microspheres that could outperform currently-available microparticles for sensing or imaging applications involving two-photon fluorescence.

Fabrication of heterogeneous chemical patterns on stretchable hydrogels using single-photon lithography

Curved hydrogel surfaces bearing chemical patterns are highly desirable in various applications, including artificial blood vessels, wearable electronics, and soft robotics. However, previous studies on the fabrication of chemical patterns on hydrogels employed two-photon lithography, which is still not widely accessible to most laboratories. This work demonstrates a new patterning technique for fabricating curved hydrogels with chemical patterns on their surfaces without two-photon microscopy. In this work, we show that exposing hydrogels in fluorophore solutions to single photons via confocal microscopy enables the patterning of fluorophores on hydrogels. By applying this technique to highly stretchable hydrogels, we demonstrate three applications: (1) improving pattern resolution by fabricating patterns on stretched hydrogels and then returning the hydrogels to their initial, unstretched length; (2) modifying the local stretchability of hydrogels at a microscale resolution; and (3) fabricating perfusable microchannels with chemical patterns by winding chemically patterned hydrogels around a template, embedding the hydrogels in a second hydrogel, and then removing the template. The patterning method demonstrated in this work may facilitate a better mimicking of the physicochemical properties of organs in tissue engineering and may be used to make hydrogel robots with specific chemical functionalities.

Self-Assembly of Amphiphilic BODIPY Derivatives on Micropatterned Ionic Liquid Surfaces for Fluorescent Films with Excellent Stability and Sensing Performance

Fluorescent films have been widely recognized as one of the most powerful tools for trace analyte detection. However, their use has been limited due to the poor photochemical stability of fluorophores at a gas-solid interface and inefficient film mass transfer. Herein, novel fluorescent films were developed through self-assembly of amphiphilic BODIPY derivatives on micropatterned ionic liquid surfaces. Unlike solid-state films, the obtained monolayer films exhibit excellent photochemical stability, similar to that of a solution. Moreover, the interfacial assembly of amphiphilic fluorophores can avoid gas diffusion inside the microdroplets, significantly improving the sensing performance. The 1/1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]BF₄) monolayer exhibits high sensitivity, high selectivity, and a fast response to detect diethylchlorophosphate (DCP) vapor. The detection limit was 226 ppt, with a response time to DCP of 2.0 s. Importantly, the 1/[BMIM]BF₄ monolayer can be reused for at least 50 cycles with no obvious signal fading. This study is expected to benefit the development of new strategies for designing fluorescence sensing films and lay a solid foundation for the fabrication of multifunctional sensing devices with excellent photochemical stability and sensing performance.

Cellulose Acetate-Based Plasmonic Crystals for Surface-Enhanced Raman and Fluorescence Spectroscopy

In order to meet environmental concerns, there is an increasing demand for biodegradable and sustainable materials in many areas, including photonics. Cellulose and its derivatives are potentially eco-friendly alternatives to conventional plastics, because of their abundance and lower environmental impact. Here, we report the fabrication of plasmonic structures by molding cellulose acetate into submicrometric periodic lattices, using soft lithography. The fabricated platforms can be used for the enhancement of Raman and fluorescence signals of a range of analytes including a model immunoassay utilizing a streptavidin-conjugated dye, which is characterized by a 23-fold enhancement in fluorescence signal intensity, which shows the potential of the platform to be further used for the assay-based development of diagnostic tools.

Reversible photonic hydrogel sensors via holographic interference lithography

Continuous monitoring of physiological conditions and biomarkers via optical holographic sensors is an area of growing interest to facilitate the expansion of personalised medicine. Here, a facile laser-induced dual polymerization method is developed to fabricate holographic hydrogel sensors for the continuous and reversible colorimetric determination of pH variations over a physiological range in serum (pH 7-9). Readout parameters simulated through a Finite-difference time-domain Yee's algorithm retrieve the spectral response through expansion. Laser lithography of holographic hydrogel sensor fabrication is achieved via a single 355 nm laser pulse to initiate polymerization of ultrafine hydrogel fringes. Eliminating the requirement for complex processing of toxic components and streamlining the synthetic procedure provides a simpler route to mass production. Optimised pH-responsive hydrogels contain amine bearing functional co-monomers demonstrating reversible Bragg wavelength shifts of 172 nm across the entire visible wavelength range with pH variation from 7.0 to 9.0 upon illumination with broadband light. Photolithographic recording of information shows the ability to convey detailed information to users for qualitative identification of pH. Holographic sensor reversibility over 20 cycles showed minimal variation in replay wavelength supporting reliable and consistent readout, with optimised sensors showing rapid response times of <5 min. The developed sensors demonstrate the application to continuous monitoring in biological fluids, withstanding interference from electrolytes, saccharides, and proteins colorimetrically identifying bovine serum pH over a physiological range. The holographic sensors benefit point-of-care pH analysis of biological analytes which could be applied to the identification of blood gas disorders and wound regeneration monitoring through colorimetric readouts.

Chaotropic Perturbation of Noncovalent Interactions of the Hemagglutinin Tag Monoclonal Antibody Fragment Enables Superresolution Molecular Census

Antibody-antigen interactions represent one of the most exploited biomolecular interactions in experimental biology. While numerous techniques harnessed immobilized antibodies for nanoscale fluorescence imaging, few utilized their reversible binding kinetics. Here, we investigated noncovalent interactions of the monoclonal hemagglutinin (HA) epitope tag antibody, 12CA5, in the fixed cellular environment. We observed that the use of a chaotropic agent, potassium thiocyanate (KSCN), promoted the dissociation of the 12CA5 antibody fragment (Fab), which already displayed faster dissociation compared to its immunoglobulin G (IgG) counterpart. Molecular dynamic simulations revealed notable root-mean-square deviations and destabilizations in the presence of KSCN, while the hydrogen-bonding network remained primarily unaffected at the antigen-binding site. The reversible interactions enabled us to achieve a superresolution molecular census of local populations of 3xHA tagged microtubule fibers with improved molecular quantification consistency compared to single-molecule localization microscopy (SMLM) techniques utilizing standard immunofluorescence staining for sample labeling. Our technique, termed superresolution census of molecular epitope tags (SR-COMET), highlights the utilization of reversible antibody-antigen interactions for SMLM-based quantitative superresolution imaging.

A biocompatible two-photon absorbing fluorescent mitochondrial probe for deep in vivo bioimaging

We reported a mitochondria-targeted two-photon fluorescent dye with an excellent two-photon absorption cross-section. With this dye, we reached an imaging depth of ca. 640 μm during mitochondrial imaging of cortical cells in live animals.

Optimised Electroporation for Loading of Extracellular Vesicles with Doxorubicin

The clinical use of chemotherapeutics is limited by several factors, including low cellular uptake, short circulation time, and severe adverse effects. Extracellular vesicles (EVs) have been suggested as a drug delivery platform with the potential to overcome these limitations. EVs are cell-derived, lipid bilayer nanoparticles, important for intercellular communication. They can transport bioactive cargo throughout the body, surmount biological barriers, and target a variety of tissues. Several small molecule drugs have been successfully incorporated into the lumen of EVs, permitting efficient transport to tumour tissue, increasing therapeutic potency, and reducing adverse effects. However, the cargo loading is often inadequate and refined methods are a prerequisite for successful utilisation of the platform. By systematically evaluating the effect of altered loading parameters for electroporation, such as total number of EVs, drug to EV ratio, buffers, pulse capacitance, and field strength, we were able to distinguish tendencies and correlations. This allowed us to design an optimised electroporation protocol for loading EVs with the chemotherapeutic drug doxorubicin. The loading technique demonstrated improved cargo loading and EV recovery, as well as drug potency, with a 190-fold increased response compared to naked doxorubicin.

Analysis insights for three FRET pairs of chemically unlinked two-molecule FRET cytometry

Förster resonance energy transfer (FRET) is the direct energy exchange between two-component fluorescent molecules. FRET methods utilize chemically linked molecules or unlinked fluorescence protein-protein interactions. FRET is therefore a powerful indicator of molecular proximity, but standardized determination of FRET efficiency is challenged when investigating natural (chemically unlinked) interactions. In this paper, we have examined the interactions of tumor necrosis factor receptor-1 (TNFR1) molecules expressed as recombinant fusion proteins of cyan, yellow, or red fluorescent protein (-CFP, -YFP, or -RFP) to evaluate two-molecule chemically unlinked FRET by flow cytometry. We demonstrate three independent FRET pairs CFP→YFP (FRET-1), YFP→RFP (FRET-2) and CFP→RFP (FRET-3), comparing TNFR1+TNFR1 with non-interacting TNFR1+CD27 proteins, on both LSR-II and Fortessa X-20 cytometers. We describe genuine FRET activities reflecting TNFR1 homotypic interactions. FRET events can be visualized during sample acquisition via the use of "spiked" FRET donor cells, together with TNFR1+TNFR1 co-transfected cells, as FRET channel MFI overlays. FRET events are subsequentially indicated by comparing concatenated files of cells expressing either FRET positive events (TNFR1+TNFR1) or FRET negative events (TNFR1+CD27) to generate single-cell scatter plots showing loss of FRET donor brightness. Robust determination of FRET efficiency is then confirmed at the single-cell level by applying matrix calculations based on the measurements of FRET donor, acceptor and FRET fluorescent intensities (I), detector channel emission coefficient (S), fluorescent protein extinction coefficients (ε) and α factor. In this TNFR based system, the mean CFP→YFP FRET-1 efficiency is 0.43 (LSR-II) and 0.41 (Fortessa), the mean YFP→RFP FRET-2 efficiency is 0.30 (LSR-II) and 0.29 (Fortessa), and the mean CFP→RFP FRET-3 efficiency is 0.56 (LSR-II) and 0.54 (Fortessa). This study also embraces multidimensional clustering using t-SNE, Fit-SNE, UMAP, Tri-Map and PaCMAP to further demonstrate FRET. These approaches establish a robust system for standardized detection of chemically unlinked TNFR1 homotypic interactions with three individual FRET pairs.

Rapid ensemble measurement of protein diffusion and probe blinking dynamics in cells

We present a fluorescence fluctuation image correlation analysis method that can rapidly and simultaneously measure the diffusion coefficient, photoblinking rates, and fraction of diffusing particles of fluorescent molecules in cells. Unlike other image correlation techniques, we demonstrated that our method could be applied irrespective of a nonuniformly distributed, immobile blinking fluorophore population. This allows us to measure blinking and transport dynamics in complex cell morphologies, a benefit for a range of super-resolution fluorescence imaging approaches that rely on probe emission blinking. Furthermore, we showed that our technique could be applied without directly accounting for photobleaching. We successfully employed our technique on several simulations with realistic EMCCD noise and photobleaching models, as well as on Dronpa-C12-labeled β-actin in living NIH/3T3 and HeLa cells. We found that the diffusion coefficients measured using our method were consistent with previous literature values. We further found that photoblinking rates measured in the live HeLa cells varied as expected with changing excitation power.

Development of a New Approach for Low-Laser-Power Super-Resolution Fluorescence Imaging

The development of super-resolution fluorescence microscopy over the past decade has drastically improved the resolution of light microscopy to ∼10 nm. Stochastic optical reconstruction microscopy (STORM) can be used to achieve subdiffraction-limit resolution by sequentially imaging and localizing individual fluorophores. In principle, the super-resolution of STORM can be obtained by high-accuracy localization of photoswitchable fluorophores, which require fast photoswitching and bright fluorescence intensity from a single emitter. It is known that the switching rate of photoswitchable fluorophores depends on the laser power─a high laser power being required for the enhancement of imaging resolution. However, high laser power is usually harmful to biological specimens and limits the imaging time because of its photobleaching effects and high phototoxicity. In this study, we attempted to overcome this problem by improving the STORM resolution at a lower laser power. Through the quantitative analysis of the photoswitching behavior of single fluorophores under different laser power conditions, we developed a new approach to achieve super-resolution fluorescence images at a laser power 10 times lower than had previously been reported. This approach is expected to play an increasingly significant role in super-resolution imaging of power-sensitive samples.

Three-dimensional dynamics optical coherence tomography for tumor spheroid evaluation

We present a completely label-free three-dimensional (3D) optical coherence tomography (OCT)-based tissue dynamics imaging method for visualization and quantification of the metabolic and necrotic activities of tumor spheroid. Our method is based on a custom 3D scanning protocol that is designed to capture volumetric tissue dynamics tomography images only in a few tens of seconds. The method was applied to the evaluation of a tumor spheroid. The time-course viability alteration and anti-cancer drug response of the spheroid were visualized qualitatively and analyzed quantitatively. The similarity between the OCT-based dynamics images and fluorescence microscope images was also demonstrated.

Photobleaching step analysis for robust determination of protein complex stoichiometries

The counting of discrete photobleaching steps in fluorescence microscopy is ideally suited to study protein complex stoichiometry in situ. The counting range of photobleaching step analysis has been significantly improved with more-sophisticated algorithms for step detection, albeit at an increasing computational cost and with the necessity for high-quality data. Here, we address concerns regarding robustness, automation, and experimental validation, optimizing both data acquisition and analysis. To make full use of the potential of photobleaching step analysis, we evaluate various labeling strategies with respect to their molecular brightness, photostability, and photoblinking. The developed analysis algorithm focuses on automation and computational efficiency. Moreover, we validate the developed methods with experimental data acquired on DNA origami labeled with defined fluorophore numbers, demonstrating counting of up to 35 fluorophores. Finally, we show the power of the combination of optimized trace acquisition and automated data analysis by counting labeled nucleoporin 107 in nuclear pore complexes of intact U2OS cells. The successful in situ application promotes this framework as a new resource enabling cell biologists to robustly determine the stoichiometries of molecular assemblies at the single-molecule level in an automated manner.

Photoactivation of Erythrosine in simulated body fluids

Photodynamic Therapy (PDT) is a powerful technique for the treatment of cancer and non-cancerous diseases. The precise PDT treatment protocol definition must consider the performance difference between in vitroand in vivoapplications. This also occurs in other biological studies, and to partially overcome this difficulty, the simulated body fluids are generally applied as a prior understanding of the particularities of the different systems. However, in PDT these studies are scarce. In this work, we investigated the photoactivation of Erythrosine, a photosensitizer widely used in PDT, in different simulated body fluids. Differences in the photodegradation kinetics, triplet lifetime, and singlet oxygen generation were observed. The results can help to explain and to define PDT application protocols.

Single-molecule photocatalytic dynamics at individual defects in two-dimensional layered materials

The insightful comprehension of in situ catalytic dynamics at individual structural defects of two-dimensional (2D) layered material, which is crucial for the design of high-performance catalysts via defect engineering, is still missing. Here, we resolved single-molecule trajectories resulted from photocatalytic activities at individual structural features (i.e., basal plane, edge, wrinkle, and vacancy) in 2D layered indium selenide (InSe) in situ to quantitatively reveal heterogeneous photocatalytic dynamics and surface diffusion behaviors. The highest catalytic activity was found at vacancy in a four-layer InSe, up to ~30× higher than that on the basal plane. Moreover, lower adsorption strength of reactant and slower dissociation/diffusion rates of product were found at more photocatalytic active defects. These distinct dynamic properties are determined by lattice structures/electronic energy levels of defects and layer thickness of supported InSe. Our findings shed light on the fundamental understanding of photocatalysis at defects and guide the rational defect engineering.

Vinyl-Fluorene Molecular Wires for Voltage Imaging with Enhanced Sensitivity and Reduced Phototoxicity

Fluorescent voltage indicators are an attractive alternative for studying the electrical activity of excitable cells; however, the development of indicators that are both highly sensitive and low in toxicity over long-term experiments remains a challenge. Previously, we reported a fluorene-based voltage-sensitive fluorophore that exhibits much lower phototoxicity than previous voltage indicators in cardiomyocyte monolayers, but suffers from low sensitivity to membrane potential changes. Here, we report that the addition of a single vinyl spacer in the fluorene molecular wire scaffold improves the voltage sensitivity 1.5- to 3.5-fold over fluorene-based voltage probes. Furthermore, we demonstrate the improved ability of the new vinyl-fluorene VoltageFluors to monitor action potential kinetics in both mammalian neurons and human-induced pluripotent stem cell-derived cardiomyocytes. Addition of the vinyl spacer between the aniline donor and fluorene monomer results in indicators that are significantly less phototoxic in cardiomyocyte monolayers. These results demonstrate how structural modification to the voltage sensing domain have a large effect on improving the overall properties of molecular wire-based voltage indicators.

The effect of femtosecond laser irradiation on the growth kinetics of Staphylococcus aureus: An in vitro study

We investigated the effect of femtosecond laser irradiation on the growth kinetics of Staphylococcus aureus. In order to improve laser-based antimicrobial therapy and develop a clinically viable modality, various laser parameters such as laser light wavelength, laser power, exposure time, and energy density were studied. The INSPIRE HF100 laser system (Spectra Physics) provided the femtosecond laser light, which was pumped by a mode-locked femtosecond Ti: sapphire laser MAI TAI HP (Spectra Physics). The survival of the bacterial cells was monitored after irradiation by determination of growth rate using optical density, which is a rapid, simple, and reliable method. The growth rate of laser-exposed cultures was compared to control cultures. Fifteen minutes of exposure to femtosecond laser radiation with a wavelength of 390 nm and 400 nm at an average power of 50 mW was enough to significantly reduce bacterial viability, with a lag in the growth phase of 5 h longer than the control culture (P < 0.0001 by ANOVA and Tukey test).

Peptide-MHC I complex stability measured by nanoscale differential scanning fluorimetry reveals molecular mechanism of thermal denaturation

Recombinant major histocompatibility complex class I molecules are used in diagnostic and therapeutic approaches in cancer immunotherapy, with many studies exploring their binding to antigenic peptides. Current techniques for kinetic peptide binding studies are hampered by high sample consumption, low throughput, interference with protein stability, and/or high background signal. Here, we validate nanoscale differential scanning fluorimetry (nanoDSF), a method using the tryptophan fluorescence of class I molecules, for class I/peptide binding, and we use it to determine the molecular mechanism of the thermal denaturation of HLA-A*02:01.