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Genetically encoded fluorescent indicators, combined with optical imaging, enable the detection of physiologically or behaviorally relevant neural activity with high spatiotemporal resolution. Recent developments in protein engineering and screening strategies have improved the dynamic range, kinetics, and spectral properties of genetically encoded fluorescence indicators of brain chemistry. Such indicators have detected neurotransmitter and calcium dynamics with high signal-to-noise ratio at multiple temporal and spatial scales in vitro and in vivo. This review summarizes the current trends in these genetically encoded fluorescent indicators of neurotransmitters and calcium, focusing on their key metrics and in vivo applications.

[This corrects the article DOI: 10.1371/journal.pone.0206568.].

Copper ion pollution will cause serious damage to the ecological environment and harm the human body through the enrichment of the food chain. To quickly and accurately detect copper ions, a fluorescence probe L1 with high sensitivity and easy preparation was prepared based on pyrene. In a DMSO buffer solvent (PBS, 0.02 M, pH 7.4, V/V = 9:1), probe L1 may specifically detect Cu 2+ . The anti-interference capability of fluorescent probe L1 in detecting Cu 2+ was examined, demonstrating its good selectivity and sensitivity for copper ions. Within the Cu 2+ concentration range of 0 to 24 μM, the fluorescence intensity of probe L1 at 477 nm exhibited a strong linear correlation (R 2 = 0.986) with Cu 2+ concentration. The limit of detection (LOD) for probe L1 about Cu 2+ was determined using the 3σ/k technique, yielding a value of 1.699 × 10 −2 μM. It is appropriate for the detection of copper ions in near-neutral and alkaline environments.

Many luminescent stimuli responsive materials are based on fluorescence emission, while stimuli-responsive room temperature phosphorescent materials are less explored. Here, we show a kind of stimulus-responsive room temperature phosphorescence materials by the covalent linkage of phosphorescent chromophore of arylboronic acid and polymer matrix of poly(vinylalcohol). Attributed to the rigid environment offered from hydrogen bond and B-O covalent bond between arylboronic acid and poly(vinylalcohol), the yielded polymer film exhibits ultralong room temperature phosphorescence with lifetime of 2.43 s and phosphorescence quantum yield of 7.51%. Interestingly, the RTP property of this film is sensitive to the water and heat stimuli, because water could destroy the hydrogen bonds between adjacent poly(vinylalcohol) polymers, then changing the rigidity of this system. Furthermore, by introducing another two fluorescent dyes to this system, the color of afterglow with stimulus response effect could be adjusted from blue to green to orange through triplet-to-singlet Förster-resonance energy-transfer. Finally, due to the water/heat-sensitive, multicolor and completely aqueous processable feature for these three afterglow hybrids, they are successfully applied in multifunctional ink for anti-counterfeit, screen printing and fingerprint record. Stimuli responsive luminescent materials are important in applied research but many of these materials are based on fluorescent stimuli responsive materials. Here, the authors report a stimulus-responsive room temperature phosphorescent materials composed of a phosphorescent chromophore of arylboronic acid and poly(vinylalcohol) with color tunable and water process able properties.

This paper mainly studies the preparation of nitrogen-doped carbon nanoparticles (N-CNPs), which are used as fluorescent probes for the detection of copper ions (Cu2+) in actual environmental water samples. The novel synthesis method is simple, fast, efficient, low-cost, and environmentally friendly, enabling effective detection of pollutants in environmental water samples. The fluorescence intensity of the N-CNPs can be selectively quenched by Cu2+. The experimental results show that the N-CNPs exhibit a good linear relationship with Cu2+ concentration and demonstrate high selectivity. The N-CNPs have been used to detect the Cu2+ concentration of the environmental water samples, and the recovery rate of standard addition is about 100%.

NIR-II fluorophores have shown great promise for biomedical applications with superior in vivo optical properties. To date, few small-molecule NIR-II fluorophores have been discovered with donor-acceptor-donor (D-A-D) or symmetrical structures, and upconversion-mitochondria-targeted NIR-II dyes have not been reported. Herein, we report development of D-A type thiopyrylium-based NIR-II fluorophores with frequency upconversion luminescence (FUCL) at ~580 nm upon excitation at ~850 nm. H4-PEG-PT can not only quickly and effectively image mitochondria in live or fixed osteosarcoma cells with subcellular resolution at 1 nM, but also efficiently convert optical energy into heat, achieving mitochondria-targeted photothermal cancer therapy without ROS effects. H4-PEG-PT has been further evaluated in vivo and exhibited strong tumor uptake, specific NIR-II signals with high spatial and temporal resolution, and remarkable NIR-II image-guided photothermal therapy. This report presents the first D-A type thiopyrylium NIR-II theranostics for synchronous upconversion-mitochondria-targeted cell imaging, in vivo NIR-II osteosarcoma imaging and excellent photothermal efficiency. Currently available mitochondria-targeted fluorescent dyes emit only one color in the visible or NIR-I and their applications are limited. Here, the authors develop upconversion mitochondria-targeted NIR-II fluorophores for synchronous upconversion-mitochondria-targeted cell imaging, in vivo NIR-II osteosarcoma imaging and photothermal efficiency

Owing to reduced light scattering and tissue autofluorescence, in vivo fluorescence imaging in the 1,000–3,000-nm near-infrared II (NIR-II) spectral range can afford non-invasive imaging at depths of millimetres within biological tissue. Infrared fluorescent probes labelled with antibodies or other targeting ligands also enable NIR-II molecular imaging at the single-cell level. Here we present recent developments in the design of fluorophores and probes emitting in the NIR-II window based on organic synthesis and nanoscience approaches. We also review advances in NIR-II wide-field and microscopy imaging modalities, with a focus on preclinical imaging and promising clinical translation case studies. Finally, we outline current issues and challenges for the wider adoption of NIR-II imaging in biomedical research and clinical imaging. A review of NIR-II fluorescence imaging is presented, with a focus on fluorophores, probes and imaging techniques.

Fluorescence imaging in near-infrared IIb (NIR-IIb, 1500–1700 nm) spectrum holds a great promise for tissue imaging. While few inorganic NIR-IIb fluorescent probes have been reported, their organic counterparts are still rarely developed, possibly due to the shortage of efficient materials with long emission wavelength. Herein, we propose a molecular design philosophy to explore pure organic NIR-IIb fluorophores by manipulation of the effects of twisted intramolecular charge transfer and aggregation-induced emission at the molecular and morphological levels. An organic fluorescent dye emitting up to 1600 nm with a quantum yield of 11.5% in the NIR-II region is developed. NIR-IIb fluorescence imaging of blood vessels and deeply-located intestinal tract of live mice based on organic dyes is achieved with high clarity and enhanced signal-to-background ratio. We hope this study will inspire further development on the evolution of pure organic NIR-IIb dyes for bio-imaging. Light has limited penetration depth in vivo which has led to increasing interest in NIR-II fluorophores. Here, the authors report on the design and testing of an organic aggregation induced emission fluorophore with high quantum yield and demonstrate imaging of vasculature and intestines in live mice.

Fluorescent RNAs (FRs), aptamers that bind and activate fluorescent dyes, have been used to image abundant cellular RNA species. However, limitations such as low brightness and limited availability of dye/aptamer combinations with different spectral characteristics have limited use of these tools in live mammalian cells and in vivo. Here, we develop Peppers, a series of monomeric, bright and stable FRs with a broad range of emission maxima spanning from cyan to red. Peppers allow simple and robust imaging of diverse RNA species in live cells with minimal perturbation of the target RNA’s transcription, localization and translation. Quantification of the levels of proteins and their messenger RNAs in single cells suggests that translation is governed by normal enzyme kinetics but with marked heterogeneity. We further show that Peppers can be used for imaging genomic loci with CRISPR display, for real-time tracking of protein–RNA tethering, and for super-resolution imaging. We believe these FRs will be useful tools for live imaging of cellular RNAs.

Expanding the palette of fluorescent dyes is vital to push the frontier of biological imaging. Although rhodamine dyes remain the premier type of small-molecule fluorophore owing to their bioavailability and brightness, variants excited with far-red or near-infrared light suffer from poor performance due to their propensity to adopt a lipophilic, nonfluorescent form. We report a framework for rationalizing rhodamine behavior in biological environments and a general chemical modification for rhodamines that optimizes long-wavelength variants and enables facile functionalization with different chemical groups. This strategy yields red-shifted ‘Janelia Fluor’ (JF) dyes useful for biological imaging experiments in cells and in vivo. A general tuning strategy is introduced for improving the utility of rhodamines for biological imaging applications. The strategy yielded bright, versatile and bioavailable far-red and near-infrared ‘Janelia Fluor’ dyes.