The fluorescent toolbox for assessing protein location and function

Ultrahigh-Throughput Detection of Enzymatic Alcohol Dehydrogenase Activity in Microfluidic Droplets with a Direct Fluorogenic Assay

The exploration of large DNA libraries of metagenomic or synthetic origin is greatly facilitated by ultrahigh‐throughput assays that use monodisperse water‐in‐oil emulsion droplets as sequestered reaction compartments. Millions of samples can be generated and analysed in microfluidic devices at kHz speeds, requiring only micrograms of reagents. The scope of this powerful platform for the discovery of new sequence space is, however, hampered by the limited availability of assay substrates, restricting the functions and reaction types that can be investigated. Here, we broaden the scope of detectable biochemical transformations in droplet microfluidics by introducing the first fluorogenic assay for alcohol dehydrogenases (ADHs) in this format. We have synthesized substrates that release a pyranine fluorophore (8‐hydroxy‐1,3,6‐pyrenetrisulfonic acid, HPTS) when enzymatic turnover occurs. Pyranine is well retained in droplets for >6 weeks (i. e. 14‐times longer than fluorescein), avoiding product leakage and ensuring excellent assay sensitivity. Product concentrations as low as 100 nM were successfully detected, corresponding to less than one turnover per enzyme molecule on average. The potential of our substrate design was demonstrated by efficient recovery of a bona fide ADH with an >800‐fold enrichment. The repertoire of droplet screening is enlarged by this sensitive and direct fluorogenic assay to identify dehydrogenases for biocatalytic applications.

Super-resolving Microscopy in Neuroscience

Fluorescence imaging techniques play a pivotal role in our understanding of the nervous system. The emergence of various super-resolution microscopy methods and specialized fluorescent probes enables direct insight into neuronal structure and protein arrangements in cellular subcompartments with so far unmatched resolution. Super-resolving visualization techniques in neurons unveil a novel understanding of cytoskeletal composition, distribution, motility, and signaling of membrane proteins, subsynaptic structure and function, and neuron-glia interaction. Well-defined molecular targets in autoimmune and neurodegenerative disease models provide excellent starting points for in-depth investigation of disease pathophysiology using novel and innovative imaging methodology. Application of super-resolution microscopy in human brain samples and for testing clinical biomarkers is still in its infancy but opens new opportunities for translational research in neurology and neuroscience. In this review, we describe how super-resolving microscopy has improved our understanding of neuronal and brain function and dysfunction in the last two decades.

Modular fluorescent nanoparticle DNA probes for detection of peptides and proteins

Fluorescently labeled antibody and aptamer probes are used in biological studies to characterize binding interactions, measure concentrations of analytes, and sort cells. Fluorescent nanoparticle labels offer an excellent alternative to standard fluorescent labeling strategies due to their enhanced brightness, stability and multivalency; however, challenges in functionalization and characterization have impeded their use. This work introduces a straightforward approach for preparation of fluorescent nanoparticle probes using commercially available reagents and common laboratory equipment. Fluorescent polystyrene nanoparticles, Thermo Fisher Scientific FluoSpheres, were used in these proof-of-principle studies. Particle passivation was achieved by covalent attachment of amine-PEG-azide to carboxylated particles, neutralizing the surface charge from - 43 to - 15 mV. A conjugation-annealing handle and DNA aptamer probe were attached to the azide-PEG nanoparticle surface either through reaction of pre-annealed handle and probe or through a stepwise reaction of the nanoparticles with the handle followed by aptamer annealing. Nanoparticles functionalized with DNA aptamers targeting histidine tags and VEGF protein had high affinity (EC50s ranging from 3 to 12 nM) and specificity, and were more stable than conventional labels. This protocol for preparation of nanoparticle probes relies solely on commercially available reagents and common equipment, breaking down the barriers to use nanoparticles in biological experiments.

Emerging imaging methods to study whole-brain function in rodent models

In the past decade, the idea that single populations of neurons support cognition and behavior has gradually given way to the realization that connectivity matters and that complex behavior results from interactions between remote yet anatomically connected areas that form specialized networks. In parallel, innovation in brain imaging techniques has led to the availability of a broad set of imaging tools to characterize the functional organization of complex networks. However, each of these tools poses significant technical challenges and faces limitations, which require careful consideration of their underlying anatomical, physiological, and physical specificity. In this review, we focus on emerging methods for measuring spontaneous or evoked activity in the brain. We discuss methods that can measure large-scale brain activity (directly or indirectly) with a relatively high temporal resolution, from milliseconds to seconds. We further focus on methods designed for studying the mammalian brain in preclinical models, specifically in mice and rats. This field has seen a great deal of innovation in recent years, facilitated by concomitant innovation in gene-editing techniques and the possibility of more invasive recordings. This review aims to give an overview of currently available preclinical imaging methods and an outlook on future developments. This information is suitable for educational purposes and for assisting scientists in choosing the appropriate method for their own research question.

Out-of-Phase Imaging after Optical Modulation (OPIOM) for Multiplexed Fluorescence Imaging Under Adverse Optical Conditions

Fluorescence imaging has become a powerful tool for observations in biology. Yet it has also encountered limitations to overcome optical interferences of ambient light, autofluorescence, and spectrally interfering fluorophores. In this account, we first examine the current approaches which address these limitations. Then we more specifically report on Out-of-Phase Imaging after Optical Modulation (OPIOM), which has proved attractive for highly selective multiplexed fluorescence imaging even under adverse optical conditions. After exposing the OPIOM principle, we detail the protocols for successful OPIOM implementation.

New contrast agents for photoacoustic imaging and theranostics: Recent 5-year overview on phthalocyanine/naphthalocyanine-based nanoparticles

The phthalocyanine (Pc) and naphthalocyanine (Nc) nanoagents have drawn much attention as contrast agents for photoacoustic (PA) imaging due to their large extinction coefficients and long absorption wavelengths in the near-infrared region. Many investigations have been conducted to enhance Pc/Ncs' photophysical properties and address their poor solubility in an aqueous solution. Many diverse strategies have been adopted, including centric metal chelation, structure modification, and peripheral substitution. This review highlights recent advances on Pc/Nc-based PA agents and their extended use for multiplexed biomedical imaging, multimodal diagnostic imaging, and image-guided phototherapy.

Advancing biological super-resolution microscopy through deep learning: a brief review

Biological super-resolution microscopy is a new generation of imaging techniques that overcome the ~200 nm diffraction limit of conventional light microscopy in spatial resolution. By providing novel spatial or spatiotemporal information on biological processes at nanometer resolution with molecular specificity, it plays an increasingly important role in biomedical sciences. However, its technical constraints also require trade-offs to balance its spatial resolution, temporal resolution, and light exposure of samples. Recently, deep learning has achieved breakthrough performance in many image processing and computer vision tasks. It has also shown great promise in pushing the performance envelope of biological super-resolution microscopy. In this brief review, we survey recent advances in using deep learning to enhance the performance of biological super-resolution microscopy, focusing primarily on computational reconstruction of super-resolution images. Related key technical challenges are discussed. Despite the challenges, deep learning is expected to play an important role in the development of biological super-resolution microscopy. We conclude with an outlook into the future of this new research area.

Molecular mechanism of hippocampal long-term potentiation - Towards multiscale understanding of learning and memory

Long-term potentiation (LTP) of synaptic transmission is considered to be a cellular counterpart of learning and memory. Activation of postsynaptic NMDA type glutamate receptor (NMDA-R) induces trafficking of AMPA type glutamate receptors (AMPA-R) and other proteins to the synapse in sequential fashion. At the same time, the dendritic spine expands for long-term and modulation of actin underlies this (structural LTP or sLTP). How these changes persist despite constant diffusion and turnover of the component proteins have been the central focus of the current LTP research. Signaling triggered by Ca²⁺-influx via NMDA-R triggers kinase including Ca²⁺/calmodulin-dependent protein kinase II (CaMKII). CaMKII can sustain longer-term biochemical signaling by forming a reciprocally-activating kinase-effector complex with its substrate proteins including Tiam1, thereby regulating persistence of the downstream signaling. Furthermore, activated CaMKII can condense at the synapse through the mechanism of liquid-liquid phase separation (LLPS). This increases the binding capacity at the synapse, thereby contributing to the maintenance of enlarged protein complexes. It may also serve as the synapse tag, which captures newly synthesized proteins.

A NIR fluorescent probe for fatty acid amide hydrolase bioimaging and its application in development of inhibitors

Fatty acid amide hydrolase (FAAH) is primarily responsible for the inactivation of fatty acid ethanolamide (FAE) and is involved in a variety of biological functions related to diseases of the nervous system. Herein, we developed a highly selective and sensitive FAAH-activated near-infrared fluorescent probe named DAND and achieved the real-time detection and imaging of FAAH activity in complex biosystems. Moreover, a visual high-throughput screening method was established using DAND, piperine was identified as a novel inhibitor of FAAH. Based on the interaction of piperine with FAAH, a more potent FAAH inhibitor (11f) was designed and synthesized which possessed an IC₅₀ value of 0.65 μM. Furthermore, 11f could attenuate the liposaccharide (LPS)-induced activation of BV2 cells, exhibiting an excellent anti-inflammatory activity. These results indicated that DAND could be used as a promising molecular tool for exploring FAAH activity and for rapidly screening potential FAAH inhibitors. In addition, piperine and its derivatives could serve as potential candidate drugs for the treatment of neurodegenerative diseases in the future.

Orthogonal coiled coils enable rapid covalent labelling of two distinct membrane proteins with peptide nucleic acid barcodes

Templated chemistry offers the prospect of addressing specificity challenges occurring in bioconjugation reactions. Here, we show two peptide-templated amide-bond forming reactions that enable the concurrent labelling of two different membrane proteins with two different peptide nucleic acid (PNA) barcodes. The reaction system is based on the mutually selective coiled coil interaction between two thioester-linked PNA–peptide conjugates and two cysteine peptides serving as genetically encoded peptide tags. Orthogonal coiled coil templated covalent labelling is highly specific, quantitative and proceeds within a minute. To demonstrate the usefulness, we evaluated receptor internalisation of two membranous receptors EGFR (epidermal growth factor) and ErbB2 (epidermal growth factor receptor 2) by first staining PNA-tagged proteins with fluorophore–DNA conjugates and then erasing signals from non-internalized receptors via toehold-mediated strand displacement.

A pair of orthogonal coiled coils templates highly specific live cell bioconjugation of two different proteins. PNA tagging and hybridisation with fluorophore–DNA reporters enables rapid dual receptor internalisation analysis of EGFR and ErbB2.

Imaging therapeutic peptide transport across intestinal barriers

Oral delivery is a highly preferred method for drug administration due to high patient compliance. However, oral administration is intrinsically challenging for pharmacologically interesting drug classes, in particular pharmaceutical peptides, due to the biological barriers associated with the gastrointestinal tract. In this review, we start by summarizing the pharmacological performance of several clinically relevant orally administrated therapeutic peptides, highlighting their low bioavailabilities. Thus, there is a strong need to increase the transport of peptide drugs across the intestinal barrier to realize future treatment needs and further development in the field. Currently, progress is hampered by a lack of understanding of transport mechanisms that govern intestinal absorption and transport of peptide drugs, including the effects of the permeability enhancers commonly used to mediate uptake. We describe how, for the past decades, mechanistic insights have predominantly been gained using functional assays with end-point read-out capabilities, which only allow indirect study of peptide transport mechanisms. We then focus on fluorescence imaging that, on the other hand, provides opportunities to directly visualize and thus follow peptide transport at high spatiotemporal resolution. Consequently, it may provide new and detailed mechanistic understanding of the interplay between the physicochemical properties of peptides and cellular processes; an interplay that determines the efficiency of transport. We review current methodology and state of the art in the field of fluorescence imaging to study intestinal barrier transport of peptides, and provide a comprehensive overview of the imaging-compatible in vitro, ex vivo, and in vivo platforms that currently are being developed to accelerate this emerging field of research.

A self-labeling protein based on the small ultra-red fluorescent protein, smURFP

Self-labeling proteins have revolutionized super-resolution and sensor imaging. Tags recognize a bioorthogonal substrate for covalent attachment. We show the small Ultra-Red Fluorescent Protein (smURFP) is a self-labeling protein. The substrate is fluorogenic, fluoresces when attached, and quenches fluorescent cargo. The smURFP-tag has novel properties for tool development.

New Extensibility and Scripting Tools in the ImageJ Ecosystem

ImageJ provides a framework for image processing across scientific domains while being fully open source. Over the years ImageJ has been substantially extended to support novel applications in scientific imaging as they emerge, particularly in the area of biological microscopy, with functionality made more accessible via the Fiji distribution of ImageJ. Within this software ecosystem, work has been done to extend the accessibility of ImageJ to utilize scripting, macros, and plugins in a variety of programming scenarios, e.g., from Groovy and Python and in Jupyter notebooks and cloud computing. We provide five protocols that demonstrate the extensibility of ImageJ for various workflows in image processing. We focus first on Fluorescence Lifetime Imaging Microscopy (FLIM) data, since this requires significant processing to provide quantitative insights into the microenvironments of cells. Second, we show how ImageJ can now be utilized for common image processing techniques, specifically image deconvolution and inversion, while highlighting the new, built-in features of ImageJ-particularly its capacity to run completely headless and the Ops matching feature that selects the optimal algorithm for a given function and data input, thereby enabling processing speedup. Collectively, these protocols can be used as a basis for automating biological image processing workflows. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Using PyImageJ for FLIM data processing Alternate Protocol: Groovy FLIMJ in Jupyter Notebooks Basic Protocol 2: Using ImageJ Ops for image deconvolution Support Protocol 1: Using ImageJ Ops matching feature for image inversion Support Protocol 2: Headless ImageJ deconvolution.

9-Cyanopyronin probe palette for super-multiplexed vibrational imaging

Multiplexed optical imaging provides holistic visualization on a vast number of molecular targets, which has become increasingly essential for understanding complex biological processes and interactions. Vibrational microscopy has great potential owing to the sharp linewidth of vibrational spectra. In 2017, we demonstrated the coupling between electronic pre-resonant stimulated Raman scattering (epr-SRS) microscopy with a proposed library of 9-cyanopyronin-based dyes, named Manhattan Raman Scattering (MARS). Herein, we develop robust synthetic methodology to build MARS probes with different core atoms, expansion ring numbers, and stable isotope substitutions. We discover a predictive model to correlate their vibrational frequencies with structures, which guides rational design of MARS dyes with desirable Raman shifts. An expanded library of MARS probes with diverse functionalities is constructed. When coupled with epr-SRS microscopy, these MARS probes allow us to demonstrate not only many versatile labeling modalities but also increased multiplexing capacity. Hence, this work opens up next-generation vibrational imaging with greater utilities.

Characterization of DNA-protein complexes by nanoparticle tracking analysis and their association with systemic lupus erythematosus

Nanotechnology enables investigations of single biomacromolecules, but technical challenges have limited the application in liquid biopsies, for example, blood plasma. Nonetheless, tools to characterize single molecular species in such samples represent a significant unmet need with the increasing appreciation of the physiological importance of protein structural changes at nanometer scale. Mannose-binding lectin (MBL) is an oligomeric plasma protein and part of the innate immune system through its ability to activate complement. MBL also serves a role as a scavenger for cellular debris, especially DNA. This may link functions of MBL with several inflammatory diseases in which cell-free DNA now appears to play a role, but mechanistic insight has been lacking. By making nanoparticle tracking analysis possible in human plasma, we now show that superoligomeric structures of MBL form nanoparticles with DNA. These oligomers correlate with disease activity in systemic lupus erythematosus patients. With the direct quantification of the hydrodynamic radius, calculations following the principles of Taylor dispersion in the blood stream connect the size of these complexes to endothelial inflammation, which is among the most important morbidities in lupus. Mechanistic insight from an animal model of lupus supported that DNA-stabilized superoligomers stimulate the formation of germinal center B cells and drive loss of immunological tolerance. The formation involves an inverse relationship between the concentration of MBL superoligomers and antibodies to double-stranded DNA. Our approach implicates the structure of DNA-protein nanoparticulates in the pathobiology of autoimmune diseases.

Photoluminescent Nanoparticles for Chemical and Biological Analysis and Imaging

Research related to the development and application of luminescent nanoparticles (LNPs) for chemical and biological analysis and imaging is flourishing. Novel materials and new applications continue to be reported after two decades of research. This review provides a comprehensive and heuristic overview of this field. It is targeted to both newcomers and experts who are interested in a critical assessment of LNP materials, their properties, strengths and weaknesses, and prospective applications. Numerous LNP materials are cataloged by fundamental descriptions of their chemical identities and physical morphology, quantitative photoluminescence (PL) properties, PL mechanisms, and surface chemistry. These materials include various semiconductor quantum dots, carbon nanotubes, graphene derivatives, carbon dots, nanodiamonds, luminescent metal nanoclusters, lanthanide-doped upconversion nanoparticles and downshifting nanoparticles, triplet-triplet annihilation nanoparticles, persistent-luminescence nanoparticles, conjugated polymer nanoparticles and semiconducting polymer dots, multi-nanoparticle assemblies, and doped and labeled nanoparticles, including but not limited to those based on polymers and silica. As an exercise in the critical assessment of LNP properties, these materials are ranked by several application-related functional criteria. Additional sections highlight recent examples of advances in chemical and biological analysis, point-of-care diagnostics, and cellular, tissue, and in vivo imaging and theranostics. These examples are drawn from the recent literature and organized by both LNP material and the particular properties that are leveraged to an advantage. Finally, a perspective on what comes next for the field is offered.

Phospholipid Analogues as Chemotherapeutic Agents Against Trypanosomatids

BACKGROUND

Neglected tropical diseases (NTDs) represent a serious problem in a number of countries around the world and especially in Africa and South America, affecting mostly the poor population which has limited access to the healthcare system. The drugs currently used for the treatment of NTDs are dated many decades ago and consequently, present in some cases very low efficacy, high toxicity and development of drug resistance. In the search for more efficient chemotherapeutic agents for NTDs, a large number of different compound classes have been synthesized and tested. Among them, ether phospholipids, with their prominent member miltefosine, are considered one of the most promising.

OBJECTIVE

This review summarizes the literature concerning the development of antiparasitic phospholipid derivatives, describing the efforts towards more efficient and less toxic analogues while providing an overview of the mechanism of action of this compound class against trypanosomatids.

CONCLUSION

Phospholipid analogues are already known for their antiprotozoal activity. Several studies have been conducted in order to synthesize novel derivatives with the aim to improve current treatments such as miltefosine, with promising results. Photolabeling and fluorescent alkyl phospholipid analogues have contributed to the clarification of the mode of action of this drug family.

Optobiochemistry: Genetically Encoded Control of Protein Activity by Light

Optobiochemical control of protein activities allows the investigation of protein functions in living cells with high spatiotemporal resolution. Over the last two decades, numerous natural photosensory domains have been characterized and synthetic domains engineered and assembled into photoregulatory systems to control protein function with light. Here, we review the field of optobiochemistry, categorizing photosensory domains by chromophore, describing photoregulatory systems by mechanism of action, and discussing protein classes frequently investigated using optical methods. We also present examples of how spatial or temporal control of proteins in living cells has provided new insights not possible with traditional biochemical or cell biological techniques.

Nanohoop Rotaxane Design to Enhance the Selectivity of Reaction-Based Probes: A Proof-of-Principle Study

Mechanical interlocking of a nanohoop fluorophore and a reactive thread couples the benefits of a reaction-based probe with a sterically congested active site for enhanced selectivity. Advantageously, the thread design uses dual function stoppers that act as both a quencher and a trigger for sensing. In progress toward expanding this approach to biologically relevant analytes, this system is used to demonstrate steric differentiation and provide a selective turn-on fluorescent response with size selectivity for HS^- rather than larger thiolates.

Parameter estimation in fluorescence recovery after photobleaching: quantitative analysis of protein binding reactions and diffusion

Fluorescence recovery after photobleaching (FRAP) is a common experimental method for investigating rates of molecular redistribution in biological systems. Many mathematical models of FRAP have been developed, the purpose of which is usually the estimation of certain biological parameters such as the diffusivity and chemical reaction rates of a protein, this being accomplished by fitting the model to experimental data. In this article, we consider a two species reaction–diffusion FRAP model. Using asymptotic analysis, we derive new FRAP recovery curve approximation formulae, and formally re-derive existing ones. On the basis of these formulae, invoking the concept of Fisher information, we predict, in terms of biological and experimental parameters, sufficient conditions to ensure that the values all model parameters can be estimated from data. We verify our predictions with extensive computational simulations. We also use computational methods to investigate cases in which some or all biological parameters are theoretically inestimable. In these cases, we propose methods which can be used to extract the maximum possible amount of information from the FRAP data.

In vivo Fluorescence Imaging of Extracellular ATP in the Mouse Cerebral Cortex with a Hybrid-type Optical Sensor

Adenosine 5'-triphosphate (ATP) works as an extracellular signaling molecule for cells in the brain, such as neurons and glia. Cellular communication via release of ATP is involved in a range of processes required for normal brain functions, and aberrant communication is associated with brain disorders. To investigate the mechanisms underlying these cellular processes, various techniques have been developed for the measurement of extracellular ATP. To monitor the dynamics of extracellular ATP signaling with high spatiotemporal resolution, we recently developed a hybrid-type ATP optical sensor (ATPOS) that enables in vivo fluorescence imaging of extracellular ATP dynamics in the brain. ATPOS is synthesized by labeling an ATP-binding protein, Bacillus FoF1-ATP synthase ε subunit, with a small-molecular fluorescent dye Cy3. Injection of ATPOS into the cerebral cortex of living mice enables visualization of the wave-like propagation of extracellular ATP release in response to electrical stimulation. The protocol described here should be useful for visualizing ATP signaling in diverse processes involved in intercellular communication in the brain.

Cationic Tricyclic AIEgens for Concomitant Bacterial Discrimination and Inhibition

New ionic compounds with aggregation-induced emission (AIE) feature has been widely studied. These AIE-based luminogens (AIEgens) not only effectively resolve aggregation-caused quenching (ACQ) problems that are encountered for most of conventional fluorescent dyes, but also exhibit promising applications in biological imaging, potentially for a wide variety of diseases. However, such an AIE system needs to be further developed. In this work, a series of novel cationic AIEgens that are comprised of tricyclic 2-aminopyridinium derivatives with seven-membered rings are designed and synthesized via a simple, multicomponent reaction. Notably, these AIEgens exhibit the ability to specifically stain gram-positive bacteria. Moreover, a specific AIEgen, BMTAP-7, possesses highly efficient bacteriostatic ability for Staphylococcus aureus (S. aureus) in both liquid medium and solid agar plates, which have a minimum inhibitory concentration (MIC) between 4 and 8 µg mL^-1 . Using live-cell imaging and a wash-free process, it is observed that hydrophilic AIEgens are localized to mitochondria, whereas lipophilic AIEgens display specific staining of lysosomes. These AIEgens with bacteriostatic activity hold great promise for distinguishing between bacterial types and inhibiting bacterial infections in situ.

A Bottom-Up Approach to Red-Emitting Molecular-Based Nanoparticles with Natural Stealth Properties and their Use for Single-Particle Tracking Deep in Brain Tissue

Fluorescent nanoparticles dedicated to bioimaging applications should possess specific properties that have to be maintained in the aqueous, reactive, and crowded biological environment. These include chemical and photostability, small size (on the scale of subcellular structures), biocompatibility, high brightness, and good solubility. The latter is a major challenge for inorganic nanoparticles, which require surface coating to be made water soluble. Molecular-based fluorescent organic nanoparticles (FONs) may prove a promising, spontaneously water-soluble alternative, whose bottom-up design allows for the fine-tuning of individual properties. Here, the critical challenge of controlling the interaction of nanoparticles with cellular membranes is addressed. This is a report on bright, size-tunable, red-emitting, naturally stealthy FONs that do not require the use of antifouling agents to impede interactions with cellular membranes. As a proof of concept, single FONs diffusing up to 150 µm deep in brain tissue are imaged and tracked.

Fluorescent proteins of the EosFP clade: intriguing marker tools with multiple photoactivation modes for advanced microscopy

Optical fluorescence microscopy has taken center stage in the exploration of biological structure and dynamics, especially on live specimens, and super-resolution imaging methods continue to deliver exciting new insights into the molecular foundations of life. Progress in the field, however, crucially hinges on advances in fluorescent marker technology. Among these, fluorescent proteins (FPs) of the GFP family are advantageous because they are genetically encodable, so that live cells, tissues or organisms can produce these markers all by themselves. A subclass of them, photoactivatable FPs, allow for control of their fluorescence emission by light irradiation, enabling pulse-chase imaging and super-resolution microscopy. In this review, we discuss FP variants of the EosFP clade that have been optimized by amino acid sequence modification to serve as markers for various imaging techniques. In general, two different modes of photoactivation are found, reversible photoswitching between a fluorescent and a nonfluorescent state and irreversible green-to red photoconversion. First, we describe their basic structural and optical properties. We then summarize recent research aimed at elucidating the photochemical processes underlying photoactivation. Finally, we briefly introduce various advanced imaging methods facilitated by specific EosFP variants, and show some exciting sample applications.

Azide-based bioorthogonal chemistry: Reactions and its advances in cellular and biomolecular imaging

Since the term "bioorthogonal" was first demonstrated in 2003, new tools for bioorthogonal chemistry have been rapidly developed. Bioorthogonal chemistry has now been widely utilized for applications in imaging various biomolecules, such as proteins, glycoconjugates, nucleic acids, and lipids. Contrasting the chemical reactions or synthesis that are typically executed in vitro with organic solvents, bioorthogonal reactions can occur inside cells under physiological conditions. Functional groups or chemical reporters for bioorthogonal chemistry are highly selective and will not perturb the native functions of biological systems. Advances in azide-based bioorthogonal chemical reporters make it possible to perform chemical reactions in living systems for wide-ranging applications. This review discusses the milestones of azide-based bioorthogonal reactions, from Staudinger ligation and copper(I)-catalyzed azide-alkyne cycloaddition to strain-promoted azide-alkyne cycloaddition. The development of bioorthogonal reporters and their capability of being built into biomolecules in vivo have been extensively applied in cellular imaging. We focus on strategies used for metabolic incorporation of chemically tagged molecular building blocks (e.g., amino acids, carbohydrates, nucleotides, and lipids) into cells via cellular machinery systems. With the aid of exogenous bioorthogonally compatible small fluorescent probes, we can selectively visualize intracellular architectures, such as protein, glycans, nucleic acids, and lipids, with high specificity to help in answering complex biological problems.

Optically Modulated and Optically Activated Delayed Fluorescent Proteins through Dark State Engineering

Modulating fluorescent protein emission holds great potential for increasing readout sensitivity for applications in biological imaging and detection. Here, we identify and engineer optically modulated yellow fluorescent proteins (EYFP, originally 10C, but renamed EYFP later, and mVenus) to yield new emitters with distinct modulation profiles and unique, optically gated, delayed fluorescence. The parent YFPs are individually modulatable through secondary illumination, depopulating a long-lived dark state to dynamically increase fluorescence. A single point mutation introduced near the chromophore in each of these YFPs provides access to a second, even longer-lived modulatable dark state, while a different double mutant renders EYFP unmodulatable. The naturally occurring dark state in the parent YFPs yields strong fluorescence modulation upon long-wavelength-induced dark state depopulation, allowing selective detection at the frequency at which the long wavelength secondary laser is intensity modulated. Distinct from photoswitches, however, this near IR secondary coexcitation repumps the emissive S₁ level from the long-lived triplet state, resulting in optically activated delayed fluorescence (OADF). This OADF results from secondary laser-induced, reverse intersystem crossing (RISC), producing additional nanosecond-lived, visible fluorescence that is delayed by many microseconds after the primary excitation has turned off. Mutation of the parent chromophore environment opens an additional modulation pathway that avoids the OADF-producing triplet state, resulting in a second, much longer-lived, modulatable dark state. These Optically Modulated and Optically Activated Delayed Fluorescent Proteins (OMFPs and OADFPs) are thus excellent for background- and reference-free, high sensitivity cellular imaging, but time-gated OADF offers a second modality for true background-free detection. Our combined structural and spectroscopic data not only gives additional mechanistic details for designing optically modulated fluorescent proteins but also provides the opportunity to distinguish similarly emitting OMFPs through OADF and through their unique modulation spectra.

Photoelectrochemical imaging system with high spatiotemporal resolution for visualizing dynamic cellular responses

Photoelectrochemical imaging has great potential in the label-free investigation of cellular processes. Herein, we report a new fast photoelectrochemical imaging system (PEIS) for DC photocurrent imaging of live cells, which combines high speed with excellent lateral resolution and high photocurrent stability, which are all crucial for studying dynamic cellular processes. An analog micromirror was adopted to raster the sensor substrate, enabling high-speed imaging. α-Fe₂O₃ (hematite) thin films synthesized via electrodeposition were used as a robust substrate with high photocurrent and good spatial resolution. The capabilities of this system were demonstrated by monitoring cell responses to permeabilization with Triton X-100. The ability to carry out dynamic functional imaging of multiple cells simultaneously provides improved confidence in the data than could be achieved with the slower electrochemical single-cell imaging techniques described previously. When monitoring pH changes, the PEIS can achieve frame rates of 8 frames per second.

Strategies for Site-Specific Labeling of Receptor Proteins on the Surfaces of Living Cells by Using Genetically Encoded Peptide Tags

Fluorescence microscopy imaging enables receptor proteins to be investigated within their biological context. A key challenge is to site-specifically incorporate reporter moieties into proteins without interfering with biological functions or cellular networks. Small peptide tags offer the opportunity to combine inducible labeling with small tag sizes that avoid receptor perturbation. Herein, we review the current state of live-cell labeling of peptide-tagged cell-surface proteins. Considering their importance as targets in medicinal chemistry, we focus on membrane receptors such as G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). We discuss peptide tags that i) are subject to enzyme-mediated modification reactions, ii) guide the complementation of reporter proteins, iii) form coiled-coil complexes, and iv) interact with metal complexes. Given our own contributions in the field, we place emphasis on peptide-templated labeling chemistry.

One-for-all phototheranostics: Single component AIE dots as multi-modality theranostic agent for fluorescence-photoacoustic imaging-guided synergistic cancer therapy

Construction of single component theranostic agent with one-for-all features to concurrently afford both multi-modality imaging and therapy is an appealing yet significantly challenging task. Herein, a type of luminogens with aggregation-induced emission (AIE) characteristics are tactfully designed and facilely synthesized. These AIE luminogens (AIEgens) exhibit long emission wavelengths, good photostability, remarkable biocompatibility, good reactive oxygen species (ROS) generation performance and excellent photothermal conversion efficiency, which allow them to be powerfully utilized for in vitro and in vivo cancer phototheranostics. The results show that one of the AIEgens is capable of precisely diagnosing solid tumors of mice by means of combined near-infrared-I/II (NIR-I/II) fluorescence-photoacoustic imaging, meanwhile this AIEgen can activate photodynamic and photothermal synergistic therapy (PDT-PTT) upon laser irradiation, resulting in excellent tumor elimination efficacy with only once injection and irradiation. This study thus provides a versatile platform for practical cancer theranostics.

State-of-the-art microscopy to understand islets of Langerhans: what to expect next?

The discovery of Langerhans and microscopic description of islets in the pancreas were crucial steps in the discovery of insulin. Over the past 150 years, many discoveries in islet biology and type 1 diabetes have been made using powerful microscopic techniques. In the past decade, combination of new probes, animal and tissue models, application of new biosensors and automation of light and electron microscopic methods and other (sub)cellular imaging modalities have proven their potential in understanding the beta cell under (patho)physiological conditions. The imaging evolution, from fluorescent jellyfish to real‐time intravital functional imaging, the revolution in automation and data handling and the increased resolving power of analytical imaging techniques are now converging. Here, we review innovative approaches that address islet biology from new angles by studying cells and molecules at high spatiotemporal resolution and in live models. Broad implementation of these cellular imaging techniques will shed new light on cause/consequence of (mal)function in islets of Langerhans in the years to come.

DNA-templated silver nanoclusters as an efficient catalyst for reduction of nitrobenzene derivatives: a systematic study

Nitrobenzene compounds are highly toxic pollutants with good stability, and they have a major negative impact on both human health and the ecological environment. Herein, it was found for the first time that fluorescent DNA-silver nanoclusters (DNA-AgNCs) can catalyze the reduction of toxic and harmful nitro compounds into less toxic amino compounds with excellent tolerance to high temperature and organic solvents. In this study, the reduction of p-nitrophenol (4-NP) as a model was systematically investigated, followed by expending the substrate to disclose the versatility of this reaction. This report not only expanded the conditions for utilizing catalytic reduction conditions of DNA-AgNCs as an efficient catalyst in the control of hazardous chemicals but also widened the substrate range of DNA-AgNCs reduction, providing a new angle for the application of noble metal nanoclusters.

Subcellular proteomics

The eukaryotic cell is compartmentalized into subcellular niches, including membrane-bound and membrane-less organelles. Proteins localize to these niches to fulfil their function, enabling discreet biological processes to occur in synchrony. Dynamic movement of proteins between niches is essential for cellular processes such as signalling, growth, proliferation, motility and programmed cell death, and mutations causing aberrant protein localization are associated with a wide range of diseases. Determining the location of proteins in different cell states and cell types and how proteins relocalize following perturbation is important for understanding their functions, related cellular processes and pathologies associated with their mislocalization. In this Primer, we cover the major spatial proteomics methods for determining the location, distribution and abundance of proteins within subcellular structures. These technologies include fluorescent imaging, protein proximity labelling, organelle purification and cell-wide biochemical fractionation. We describe their workflows, data outputs and applications in exploring different cell biological scenarios, and discuss their main limitations. Finally, we describe emerging technologies and identify areas that require technological innovation to allow better characterization of the spatial proteome.

Recent progress in natural product-based inhibitor screening with enzymatic fluorescent probes

Drug discovery is a complex process in which many challenges need to be overcome, from the discovery of a drug candidate to ensuring the efficacy and safety of the candidate in humans. Modern analytical methods allow tens of thousands of drug candidates to be screened for their inhibition of specific enzymes or receptors. In recent years, fluorescent probes have been used for the detection and diagnosis of human pathogens as well as high-throughput screening. This review focuses on recent progress in organic small-molecule based enzyme-activated fluorescent probes for screening of inhibitors from natural products. The contents include the construction of fluorescent probes, working mechanism and the process of inhibitor screening. The progress suggests that fluorescent probes are a vital and rapidly growing technology for inhibitor screening of enzymes, in particular, inhibitor screening in situ.

Properties and regulation of Gly-Sar uptake and transport in bovine intestinal epithelial cells

Intestinal absorption of peptides is vital for the overall health and productivity of dairy cows. This study investigated the regulation, uptake and transport of dipeptides in bovine intestinal epithelial cells (BIECs). We also evaluated the effects of time, pH, concentration of the dipeptides, temperature, presence of diethylpyrocarbonate (DEPC)-an inhibitor of PepT1, and other dipeptides (Met-Met, Lys-Lys or Met-Lys), on the uptake and transport of Gly-Sar-FITC, which was a common fluorophore-labelled dipeptide. Under controlled experiments, BIECs were treated with 25 μM LY294002 (a phosphatidylinositol 3-kinase (PI3K) inhibitor) and 25 μM Perifosine (a protein kinase B (AKT) inhibitor). The subsequent expression of PepT1 in the BIECs was assessed by reverse transcriptase polymerase chain reaction (RT-PCR) and Western blotting. It was found that the uptake and transport of Gly-Sar-FITC were significant high at 37℃ than that at 4℃. The optimal pH for transport and uptake of Gly-Sar-FITC was 6.0-6.5, whereas the two properties decreased significantly in the presence of DEPC, Met-Met, Lys-Lys and Met-Lys (p < 0.05). The apical-to-basolateral transport was also found to be significantly higher than the reverse transport (p < 0.05). PI3K and AKT inhibitors were found to significantly suppress the expression of PepT1, thus impairing uptake and transport of Gly-Sar-FITC. Findings of this study thus suggest that the uptake and transport of Gly-Sar-FITC in BIECs are mediated by PepT1, and the PI3K/AKT signalling pathway regulates the absorption of small peptides.

Fluorescent Silica Nanoparticles to Label Metastatic Tumor Cells in Mineralized Bone Microenvironments

During breast cancer bone metastasis, tumor cells interact with bone microenvironment components including inorganic minerals. Bone mineralization is a dynamic process and varies spatiotemporally as a function of cancer-promoting conditions such as age and diet. The functional relationship between skeletal dissemination of tumor cells and bone mineralization, however, is unclear. Standard histological analysis of bone metastasis frequently relies on prior demineralization of bone, while methods that maintain mineral are often harsh and damage fluorophores commonly used to label tumor cells. Here, fluorescent silica nanoparticles (SNPs) are introduced as a robust and versatile labeling strategy to analyze tumor cells within mineralized bone. SNP uptake and labeling efficiency of MDA-MB-231 breast cancer cells is characterized with cryo-scanning electron microscopy and different tissue processing methods. Using a 3D in vitro model of marrow-containing, mineralized bone as well as an in vivo model of bone metastasis, SNPs are demonstrated to allow visualization of labeled tumor cells in mineralized bone using various imaging modalities including widefield, confocal, and light sheet microscopy. This work suggests that SNPs are valuable tools to analyze tumor cells within mineralized bone using a broad range of bone processing and imaging techniques with the potential to increase the understanding of bone metastasis.

Re-expression of glucuronyl C5-epimerase in the mutant MEF cells increases heparan sulfate epimerization but has no influence on the Golgi localization and enzymatic activity of 2-O-sulfotransferase

Heparan sulfate (HS) is a linear and complex polysaccharide that modulates the biological activities through protein recognition and interaction. Evidence indicates that protein-binding properties of HS are largely dependent on distinctive sulfation and epimerization patterns that are modified by a series of Golgi-localized enzymes. In particular, the glucuronyl C5-epimerase (Hsepi) converts D-glucuronic acid residues to L-iduronic acid, and 2-O-sulfotransferase (2OST) catalyzes sulfation at C2 position of IdoA and rarely GlcA residues. Mice lacking both Hsepi and 2OST display multiple development defects, indicating the importance of IdoA in HS. Here, to gain greater insights of HS structure-function relationships, as well as a better understanding of the regulatory mechanisms of Hsepi and 2OST, the fine structure and cellular signaling functions of HS were investigated after restoration of Hsepi in the mutant mouse embryonic fibroblast cells. Introduction of Hsepi into the Hsepi mutant MEF cells led to robustly increased proportion of IdoA residues, which rescued the cell signaling in responding to FGF2. However, we found that Hsepi knockout had no influence on either cellular transportation or enzymatic activity of 2OST in the MEF cells, which is not in accord with the findings reported, suggesting that the enzymatic activity and cellular transportation of 2OST and Hsepi might be differently regulated.

Naphthalenediimides with High Fluorescence Quantum Yield: Bright-Red, Stable, and Responsive Fluorescent Dyes

The naphthalenediimide (NDI) scaffold in contrast to its higher congeners possess low-fluorescence. In spite of elegant synthetic developments, a highly emissive NDI is quite rare to find, as well as, a green-light-emitting NDI is yet to be explored. Herein, we report a novel class of symmetric and asymmetric NH₂ -substituted core-NDIs (1-5) with tunable fluorescence in the visible region and extending to the NIR frontier. Importantly, the bis-NH₂ -substituted NDI 2 revealed quantum yield, Φ f of ≈81 and ≈68 % in toluene and DMSO, respectively, suggesting versatility of the fluorophore in a wide range of solvent polarity. The dye 1 is shown to be the first NDI-based green-light emitter. The donor piperidine group in 5 diminish the Φ f by 40-fold providing a lever to modulate the excited-state intramolecular proton transfer (ESIPT) process. Our synthetic protocol applies a Pd catalyst and a benign hydride source simplifying the non-trivial -NH₂ group integration at the NDI-core. TD-DFT calculations predicted strong intramolecular hydrogen bonds in the excited state in the bulk nonpolar medium and responsiveness to solvent polarity. The maximization of the NDI emission outlined here would further boost the burgeoning repertoire of applications of the NDI scaffold.

Ultrasound lighting up AIEgens for potential surgical navigation

Multifunctional contrast-enhanced agents suitable for application in surgical navigation by taking advantage of the merits of their diverse imaging modalities at different surgical stages are highly sought-after. Herein, an amphipathic polymer composed of aggregation-induced emission fluorogens (AIEgens) and Gd³⁺ chelates was successfully synthesized and assembled into ultrasound responsive microbubbles (AIE-Gd MBs) to realize potential tri-modal contrast-enhanced ultrasound (US) imaging, magnetic resonance imaging (MRI), and AIEgen-based fluorescence imaging (FI) during the perioperative period. Through ultrasound targeted microbubble destruction (UTMD) and cavitation effect, the as-prepared AIE-Gd MBs went through a MBs-to-nanoparticles (NPs) conversion, which not only resulted in targeted accumulation in tumor tissues but also led to stronger fluorescence being exhibited due to the more aggregated AIE-Gd molecules in the NPs. As a proof-of-concept, our work proposes a strategy of US-lit-up AIEgens in tumors which could offer a simple and powerful tool for surgical navigation in the future.

Single cell imaging reveals cisplatin regulating interactions between transcription (co)factors and DNA

Cisplatin is an extremely successful anticancer drug, and is commonly thought to target DNA. However, the way in which cisplatin-induced DNA lesions regulate interactions between transcription factors/cofactors and genomic DNA remains unclear. Herein, we developed a dual-modal microscopy imaging strategy to investigate, in situ, the formation of ternary binding complexes of the transcription cofactor HMGB1 and transcription factor Smad3 with cisplatin crosslinked DNA in single cells. We utilized confocal microscopy imaging to map EYFP-fused HMGB1 and fluorescent dye-stained DNA in single cells, followed by the visualization of cisplatin using high spatial resolution (200-350 nm) time of flight secondary ion mass spectrometry (ToF-SIMS) imaging of the same cells. The superposition of the fluorescence and the mass spectrometry (MS) signals indicate the formation of HMGB1-Pt-DNA ternary complexes in the cells. More significantly, for the first time, similar integrated imaging revealed that the cisplatin lesions at Smad-binding elements, for example GGC(GC)/(CG) and AGAC, disrupted the interactions of Smad3 with DNA, which was evidenced by the remarkable reduction in the expression of Smad-specific luciferase reporters subjected to cisplatin treatment. This finding suggests that Smad3 and its related signalling pathway are most likely involved in the intracellular response to cisplatin induced DNA damage.

Secretion of Recombinant Human Annexin V in Fusion with the Super Folder GFP for Labelling Phosphatidylserine-Exposing Membranes

Annexin V (ANXV), mostly characterized by its ability to interact with biological membranes in a calcium-dependent manner. ANXV interacts mainly with phosphatidylserine (PS), for that fluorescent ANXV widely produced and used as a sensitive and specific probe to mark apoptotic cells or any PS-containing bilayers membranes. Many reports described the prokaryotic expression of recombinant human ANXV. To overcome some of E. coli expression limitations, we aimed in this work to investigate unconventional alternative expression system in mammalian cells for producing secreted human ANXV in fusion with the super folder green fluorescent protein (sfGFP). HEK239T cells were transfected using polyethylenimine (PEI) and pcDNA-sfGFP-ANXV plasmid. Forty-eight hours post transfection, direct fluorescence measurement, immunoblotting and ELISA confirmed the presence of secreted sfGFP-ANXV in cells supernatant. The yield of secreted 6 × His-tagged sfGFP-ANXV after affinity purification was estimated to be around 2 µg per 1 ml of cells supernatant. The secretion system was proper to produce a fully functional sfGFP-ANXV fusion protein in quantities enough to recognize and bind PS-containing surfaces or liposomes. Besides, biological assays such as flow cytometry and fluorescent microscopy confirmed the capacity of the secreted sfGFP-ANXV to detect PS exposure on apoptotic cells. Taken together, we present mammalian expression as a quick, affordable and endotoxin-free system to produce sfGFP-ANXV fusion protein. The secreted sfGFP-ANXV in eukaryotic system is a promising biotechnological tool, it opens up new horizons for additional applications in the detection of PS bearing surfaces and apoptosis in vitro and in vivo assays.

Visualization of integrin molecules by fluorescence imaging and techniques

Integrin molecules are transmembrane αβ heterodimers involved in cell adhesion, trafficking, and signaling. Upon activation, integrins undergo dynamic conformational changes that regulate their affinity to ligands. The physiological functions and activation mechanisms of integrins have been heavily discussed in previous studies and reviews, but the fluorescence imaging techniques -which are powerful tools for biological studies- have not. Here we review the fluorescence labeling methods, imaging techniques, as well as Förster resonance energy transfer assays used to study integrin expression, localization, activation, and functions.

An Integrated Electrochemical Nanodevice for Intracellular RNA Collection and Detection in Single Living Cell

New tools for single-cell interrogation enable deeper understanding of cellular heterogeneity and associated cellular behaviors and functions. Information of RNA expression in single cell could contribute to our knowledge of the genetic regulatory circuits and molecular mechanism of disease development. Although significant progresses have been made for intracellular RNA analysis, existing methods have a trade-off between operational complexity and practical feasibility. We address this challenge by combining the ionic current rectification property of nanopipette reactor with duplex-specific nuclease-assisted hybridization chain reaction for signal amplification to realize a simple and practical intracellular nanosensor with minimal invasiveness, which enables single-cell collection and electrochemical detection of intracellular RNA with cell-context preservation. Systematic studies on differentiation of oncogenic miR-10b expression levels in non-malignant breast cells, metastatic breast cancer cells as well as non-metastatic breast cancer cells were then realized by this nanotool accompanied by assessment of different drugs effects. This work has unveiled the ability of electrochemistry to probe intracellular RNA and opened new opportunities to study the gene expression and heterogeneous complexity under physiological conditions down to single-cell level.

Application of Advanced Light Microscopy to the Study of HIV and Its Interactions with the Host

This review highlights the significant observations of human immunodeficiency virus (HIV) assembly, release and maturation made possible with advanced light microscopy techniques. The advances in technology which now enables these light microscopy measurements are discussed with special emphasis on live imaging approaches including Total Internal Reflection Fluorescence (TIRF), high-resolution light microscopy techniques including PALM and STORM and single molecule measurements, including Fluorescence Resonance Energy Transfer (FRET). The review concludes with a discussion on what new insights and understanding can be expected from these measurements.