Optical recordings of organellar membrane potentials and the components of membrane conductance in lysosomes

The eukaryotic cell is highly compartmentalized with organelles. Owing to their function in transporting metabolites, metabolic intermediates and byproducts of metabolic activity, organelles are important players in the orchestration of cellular function. Recent advances in optical methods for interrogating the different aspects of organellar activity promise to revolutionize our ability to dissect cellular processes with unprecedented detail. The transport activity of organelles is usually coupled to the transport of charged species; therefore, it is not only associated with the metabolic landscape but also entangled with membrane potentials. In this context, the targeted expression of fluorescent probes for interrogating organellar membrane potential (Ψorg) emerges as a powerful approach, offering less-invasive conditions and technical simplicity to interrogate cellular signalling and metabolism. Different research groups have made remarkable progress in adapting a variety of optical methods for measuring and monitoring Ψorg. These approaches include using potentiometric dyes, genetically encoded voltage indicators, hybrid fluorescence resonance energy transfer sensors and photoinduced electron transfer systems. These studies have provided consistent values for the resting potential of single-membrane organelles, such as lysosomes, the Golgi and the endoplasmic reticulum. We can foresee the use of dynamic measurements of Ψorg to study fundamental problems in organellar physiology that are linked to serious cellular disorders. Here, we present an overview of the available techniques, a survey of the resting membrane potential of internal membranes and, finally, an open-source mathematical model useful to interpret and interrogate membrane-bound structures of small volume by using the lysosome as an example.

An innovative fluorescent probe based on dicyanoisoflurone derivatives for differential detection of Hg2+ and Cu2+ and its applications in bacteria, cell imaging and food analysis

BACKGROUND

Heavy metal pollution has become one of the world's most important environmental pollution, especially Hg2+ is enriched, it is easy to enter the human body through the food chain, bind to the sulfhydryl group in the protein, cause mercury poisoning. Traditional methods for detecting Hg2+ have obvious drawbacks, such as poor selectivity and long detection time. Fluorescence detection has attracted attention because of its good sensitivity and specificity detection ability. In previously reported probes for detecting Hg2+, Cu2+ often interferes. Therefore, it is of great practical significance to synthesize a fluorescent probe that can distinguish between Hg2+ and Cu2+.

RESULTS

We have successfully synthesized the probe DFS, a fluorescent probe that can differentially detect Hg2+ and Cu2+, and the probe DFS has good selectivity and anti-interference ability for Hg2+ and Cu2+. The fluorescence intensity at 530 nm increased rapidly when Hg2+ was detected; during the Cu2+ detection, the fluorescence intensity at 636 nm gradually decreased, fluorescence quenching occurred, and the detection limits of Hg2+ and Cu2+ were 7.29 × 10-9 M and 2.13 × 10-9 M, respectively. Through biological experiments, it was found that probe DFS can complete the fluorescence imaging of Hg2+ and Cu2+ in Staphylococcus aureus and HUVEC cells, which has certain research value in the field of environmental monitoring and microbiology, and the probe DFS has low cytotoxicity, so it also has broad application prospects in the field of biological imaging. In addition, the probe DFS also has good applicability for Hg2+ and Cu2+ detection in actual samples.

SIGNIFICANCE AND NOVELTY

This is a fluorescent probe that can distinguish between Hg2+ and Cu2+, the fluorescence emission peak appears at 530 nm when Hg2+ is detected; when detecting Cu2+, fluorescence quenching occurs at 636 nm, the fluorescence emission peak distance between Hg2+ and Cu2+ differs by 106 nm. This reduces mutual interference between Hg2+ and Cu2+ during detection, it provides a new idea for the detection of Hg2+ and Cu2+.

An innovative fluorescent probe for the detection of cyanide - enhanced sensitivity by controlling its electrostatic potential and suitable for applications such as cell imaging and food analysis

As cyanide is a huge hazard to the environment and human health, the study of the method of detecting low concentrations of cyanide is of great significance. In general, materials with strong positive electrostatic properties can use electrostatic attraction to enrich anions in the water near the materials, then realize rapid detection of low concentration anions by fluorescent probes. In this paper, fluorescent probes PI-S, PI-I and PI-N with cyanide-specific recognition and different charges were synthesized to study the relationship between the charge effect of probes and the sensing sensitivity. Through the zeta potential test and the calculation of the surface electrostatic potential, the positive electricity of PI-S, PI-I and PI-N gradually increased, the ΔG < 0 of the adsorption process gradually decreased, CN- could be aggregated to the vicinity of probes. As a result, the detection limit of the probe was gradually reduced from 1.07 × 10-6 to 5.03 × 10-8 M, the sensitivity was significantly enhanced. Therefore, this is expected to be a new strategy to improve the sensitivity of anion probes by increasing the positive electricity of molecules. In addition, PI-N has good anti-interference ability, short response time and certain application value in cell imaging and identification of endogenous cyanide in food.

Visualization of microcystin-LR and sulfides in plateau lakes

In eutrophic water bodies, sulfides are closely related to the growth of cyanobacteria and the production of microcystin-LR (MC-LR). To date, the underlying interaction mechanism between a sulfides and MC-LR remains controversial. Thus, visually presenting the distribution characteristics of sulfides and MC-LR in contaminated water is crucial. Here, we propose a novel and expeditious practical approach, utilizing fluorescence probe technology, to assess the distribution characteristics of MC-LR and sulfur in natural lakes. We have developed novel probes, pib2, to detect HSO3- and HS-, and pib18, to simultaneously identify MC-LR and sulfides. Through correlation analysis of fluorescence data and physicochemical indicators at sampling points, it is found that fluorescence data has good correlation with sulfides and MC-LR, and speculated that pib2 and pib18 may be able to detect sulfides and MC-LR in lakes. Using this method, we rapidly obtained the distribution of MC-LR and sulfur in Qilu and Erhai Lakes. Notably, for the first time, we rapidly displayed the distributions of sulfides and MC-LR across lakes by the fluorescent probe technology.

Investigating the molecular weight distribution of atmospheric water-soluble brown carbon using high-performance size exclusion chromatography coupled with diode array and fluorescence detectors

Atmospheric brown carbon (BrC) contain amounts of organic species, but their molecular weight (MW) distributions is still poorly understood. This study applied high-performance size exclusion chromatography (HPSEC) coupled with a diode array detector (DAD) and fluorescence detector (FLD) to characterize the MW distributions of typical chromophores and fluorophores within water-soluble BrC. The investigation focused on the spring season, encompassing both typical urban and rural aerosols. Our results showed that chromophores (at 254 and 365 nm), and humic-like and protein-like fluorophores identified by excitation-emission matrix parallel factor analysis (EEM-PARAFAC) within BrC were broadly distributed along the MW continuum (∼50-20,000 Da). This suggests that BrC mainly comprises complex chromophores and fluorophores with heterogeneous molecular sizes. High-MW (HMW, >1 kDa) species (66%-74%) dominated the chromophores at 254 and 365 nm. However, the latter chromophores were enriched with more HMW species. This result suggested that the HMW chromophores might contribute more to BrC absorption at longer wavelengths. The PARAFAC-derived fluorescent components also exhibited different MW distributions. Three humic-like substances (HULIS) were all dominated by HMW fractions (51%-74%), but protein-like fluorescent component (PLOM) enriched low-MW (LMW, <1 kDa) species (60%-66%). Furthermore, the molecular size (i.e., weight-averaged and number-averaged MW) and the ratios between HMW and LMW species decreased in the order highly-oxygenated HULIS > less-oxygenated HULIS > PLOM, indicating that the fluorophores with longer Em were generally related to larger MW. To our knowledge, this is the first report on the molecular size of individual fluorescent components within aerosol BrC. The results obtained here enhanced our knowledge of heterogeneous composition, complex physicochemical properties, and potential atmospheric fates of aerosol BrC.

Quantitative assessment of lipophilic membrane dye-based labelling of extracellular vesicles by nano-flow cytometry

Although lipophilic membrane dyes (LMDs) or probes (LMPs) are widely used to label extracellular vesicles (EVs) for detection and purification, their labelling performance has not been systematically characterized. Through concurrent side scattering and fluorescence detection of single EVs as small as 40 nm in diameter by a laboratory-built nano-flow cytometer (nFCM), present study identified that (1) PKH67 and PKH26 could maximally label ∼60%-80% of EVs isolated from the conditioned cell culture medium (purity of ∼88%) and ∼40%-70% of PFP-EVs (purity of ∼73%); (2) excessive PKH26 could cause damage to the EV structure; (3) di-8-ANEPPS and high concentration of DiI could achieve efficient and uniform labelling of EVs with nearly 100% labelling efficiency for di-8-ANEPPS and 70%-100% for DiI; (4) all the four tested LMDs can aggregate and form micelles that exhibit comparable side scatter and fluorescence intensity with those of labelled EVs and thus hardly be differentiate from each other; (5) as the LMD concentration went up, the particle number of self-aggregates increased while the fluorescence intensity of aggregates remained constant; (6) PKH67 and PKH26 tend to form more aggregated micelles than di-8-ANEPPS and DiI, and the effect of LMD self-aggregation can be negligible at optimal staining conditions. (7) All the four tested LMDs can label almost all the very-low-density lipoprotein (VLDL) particles, indicating potential confounding factor in plasma-EV labelling. Besides, it was discovered that DSPE-PEG2000 -biotin can only label ∼50% of plasma-EVs. The number of LMP inserted into the membrane of single EVs was measured for the first time and it was confirmed that membrane labelling by lipophilic dyes did not interfere with the immunophenotyping of EVs. nFCM provides a unique perspective for a better understanding of EV labelling by LMD/LMP.

A dicyanoisophorone-based ICT fluorescent probe for the detection of Hg2+ in water/food sample analysis and live cell imaging

Mercury ions are notoriously difficult to biodegradable, and its abnormal bioaccumulation in the human body through the food chain can cause various diseases. Therefore, the quantitative and real-time detection of Hg²⁺ is very extremely important. Herein, we have brilliant designed and synthesized (E)-O-(4-(2-(3-(dicyanomethylene)-5,5-dimethylcyclohex-1-en-1-yl)vinyl)phenyl) O-phenyl carbonothioate (ICM-Hg) as a selective fluorescent probe for Hg²⁺ detection in real samples and intracellular staining. ICM-Hg displayed high specificity toward Hg²⁺ by activating the intramolecular charge transfer (ICT) process, resulting in distinguished color change from colorless to bright yellow along with noticeable switch on yellow fluorescence emission. The fluorescent intensity of ICM-Hg at 585 nm shows a well linear relationship in the range of Hg²⁺ concentration (0-45 μM), and the detection of limit for Hg²⁺ is calculated to be 231 nM. Promisingly, ICM-Hg can efficiently detect Hg²⁺ in real samples including tap water, tea, shrimp, and crab with quantitative recovery as well as the intracellular fluorescence imaging.

Beer-derived nitrogen, phosphorus co-doped carbon quantum dots: Highly selective on-off-on fluorescent probes for the detection of ascorbic acid in fruits

A rapid, facile and ultrasensitive fluorescence sensing system based on beer-derived nitrogen, phosphorus co-doped carbon quantum dots (N, P-CQDs) for the detection of ascorbic acid (AA) in fruits was proposed. N, P-CQDs were successfully synthesized by one-step hydrothermal method, which afforded a high quantum yield (21.7 %), and showed the fluorescence with a maximum emission wavelength of 450 nm at an excitation wavelength of 370 nm. Further, N, P-CQDs were employed as an efficient sensor for ultrasensitive Fe³⁺-detection at concentrations ranging from 1-20 µM and 100-300 µM, respectively. N, P-CQDs@Fe³⁺ showed a high sensitivity and selectivity for AA detection. A linear response range for AA was obtained from 1 to 200 µM with limit of detection of 0.84 µM was obtained for AA. The result of MTT test showed that N, P-CQDs exhibit low toxicity, providing fast, accurate and less toxic route for testing AA in the food analysis fields.

Visual and quantitative monitoring of thiophenol by a novel deep-red emitting fluorescent probe in environmental and biological systems

Detection of highly toxic thiophenols in biological or environmental systems is of great importance. Therefore, fast, reliable, and sensitive probes are needed to detect thiophenols. Herein, a novel triphenylamine conjugated dicyanoisophorone-based near infrared fluorescence probe is reported to determine trace thiophenol (PhSH) levels. The probe demonstrates a distinct "turn-on" fluorescence response to thiophenol among the tested analytes and its quantum yield (Φ) increases from 0.011 to 0.142. It has low cytotoxicity with cell viability of 90-100% up to 10.0 μM of the probe, a strong anti-interference capability, a large Stokes shift (150 nm), and a fast response time (<1 min). In addition, the probe exhibits a good linear response to PhSH over the range from 0 to 15.0 μM with a detection limit of 32.3 nM (R² = 0.9978). The detection process is also confirmed through HPLC. The practical applicability of the probe is proved by a smartphone platform, TLC kit, plant tissue imaging, soil assay, tap, and lake water analysis with good recovery values (92.3-117%), and concentration-dependent live cell bioimaging PhSH from 5.0 to 15.0 μM. Therefore, the present probe is a robust candidate for monitoring PhSH levels in biological and environmental systems.

Luminescent Pyrene-based Schiff base Receptor for Hazardous Mercury(II) Detection Demonstrated by Cell Imaging and Test Strip

Qualitative and quantitative analysis of mercury at concentration levels as low as parts per billion (ppb) is a basic and practical concern. The vast majority of research in this field has centered on the development of potent chemosensor to monitor mercuric (Hg²⁺) ions. Mercury exists in three oxidation states, + 2, + 1 and 0, all of which are highly poisonous. In this study, (N¹E,N²E)-N¹,N²-bis(pyrene-1-ylmethylene)benzene-1,2-diamine (PAPM), a novel photoluminescent sensor based on pyrene platform was synthesized. Over the tested metal ions (Cd²⁺, Co²⁺, Cu²⁺, Mg²⁺, Mn²⁺, Ni²⁺, K⁺, Na⁺, Zn²⁺, Sr²⁺, Pb²⁺, Al³⁺, Cr³⁺ and Fe³⁺) the sensor responds only to Hg²⁺ by showing high selectivity and sensitivity. After treatment with mercuric ions at room temperature, the luminescence intensity of probe was quenched at 456 nm. The quenching of fluorescence intensity of probe upon addition of mercury is due to the effect of "turn-off" chelation enhanced quenching (CHEQ) by the formation of 1:1 complex. The ESI-MS spectrum and the Job's experimental results confirm the formation of 1:1 complex between PAPM and Hg²⁺. The detection limit and association constant of sensor for mercury is computed using fluorescence titration data and were found to be 9.0 × 10^-8 M and 1.29 × 10⁵ M^-1 respectively. The practical application of sensor towards recognition of mercury(II) ions was explored through economically viable test strips and also using cell imaging studies.

Plastibodies for multiplexed detection and sorting of microplastic particles in high-throughput

Sensitive high-throughput analytic methodologies are needed to quantify microplastic particles (MPs) and thereby enable routine monitoring of MPs to ultimately secure animal, human, and environmental health. Here we report a multiplexed analytical and flow cytometry-based high-throughput methodology to quantify MPs in aqueous suspensions. The developed analytic MPs-quantification platform provides a sensitive as well as high-throughput detection of MPs that relies on the material binding peptide Liquid Chromatography Peak I (LCI) conjugated to Alexa-fluorophores (LCI_F16C-AF488, LCI_F16C-AF594, and LCI_F16C-AF647). These fluorescent material-binding peptides (also termed plastibodies) were used to fluorescently label polystyrene MPs, whereas Alexa-fluorophores alone exhibited a negligible background fluorescence. Mixtures of polystyrene MPs that varied in size (500 nm to 5 μm) and varied in labeled populations were analyzed and sorted into distinct populations reaching sorting efficiencies >90 % for 1 × 10⁶ sorted events. Finally, a multiplexed quantification and sorting with up to three plastibodies was successfully achieved to validate that the combination of plastibodies and flow cytometry is a powerful and generally applicable methodology for multiplexed analysis, quantification, and sorting of microplastic particles.

Complementary DNA Significantly Enhancing Signal Response and Sensitivity of a Molecular Beacon Probe to Aflatoxin B1

This paper reported an improved molecular beacon method for the rapid detection of aflatoxin B1 (AFB1), a natural mycotoxin with severe carcinogenicity. With the assistance of a complementary DNA (cDNA) chain, the molecular beacon which consists of a DNA aptamer flanked by FAM and BHQ1 displayed a larger fluorescent response to AFB1, contributing to the sensitive detection of AFB1. Upon optimization of some key experimental factors, rapid detection of AFB1 ranging from 1 nM to 3 μM, within 20 min, was realized by using this method. A limit of detection (LoD) of 1 nM was obtained, which was lower than the LoD (8 nM) obtained without cDNA assistance. This aptamer-based molecular beacon detection method showed advantages in easy operation, rapid analysis and larger signal response. Good specificity and anti-interference ability were demonstrated. This method showed potential in real-sample analysis.

A novel peptide-based relay fluorescent probe with a large Stokes shift for detection of Hg2+ and S2- in 100 % aqueous medium and living cells: Visual detection via test strips and smartphone

Herein, a novel relay peptide-based fluorescent probe DGRK was synthesized via solid phase peptide synthesis (SPPS) technology. DGRK exhibited excellent water-solubility, good stability, remarkably large Stokes shift (230 nm) and high selectivity response to Hg²⁺ with a non-fluorescence complex DGRK-Hg²⁺ formation via a 1:1 binding mode. Further studies indicated that the DGRK-Hg²⁺ complex could act as a secondary probe for rapidly and sequentially detecting S^2- based on fluorescent "off-on" response, and without interference from a range of anions. The limit of detection (LOD) for Hg²⁺ and S^2- were calculated to be 33.6 nM and 60.9 nM, respectively. In addition, The reversibility of interaction of confirmed that the continuous and reversible recognition behavior of Hg²⁺ and S^2- by the probe DGRK, and could be cycled more than 5 times. In addition, DGRK could be successfully applied to the fluorescence imaging of Hg²⁺ and S^2- in two living cells based on excellent cells permeability and low cytotoxicity. Meanwhile, DGRK was successfully used to create the low-cost and portable test strips for visual detection and rapid analysis under 365 nm UV lamp, and the test strips combined with a smartphone (RGB color) was successfully applied to the semi-quantitative analysis and monitoring of dynamic changes of Hg²⁺ levels.

Highly selective and multicolor ultrasensitive assay of dipicolinic acid: The integration of terbium(III) and gold nanocluster

A novel multicolor fluorescent nano-probe based on the hybridization of Tb³⁺ ion with gold nanoclusters (Au NCs) was synthesized to monitor and on-site visual assay of 2,6-pyridinedicarboxylic acid (DPA), a biomarker of bacterial spores. DPA can replace the water molecule in the center of Tb³⁺ and strongly coordinate with Tb³⁺ based on the analyte-triggered antenna effect. Simultaneously, the red fluorescence of Au NCs is not influenced after addition of DPA and can be used as steady inside fluorescence reference channel to measure background noise. On this basis, the multicolor fluorescence nano-probe based on Tb³⁺-doped Au NCs for fast analysis of DPA was fabricated. The linear range of this method is 0 to 12.5 μM and the limit of detection is 3.4 nM, which is well below the quantity of DPA concentration of 60 μM released by the spore transmission dose of anthrax infection. The proposed multicolor fluorescence nano-probe was successfully detecting DPA in actual sample with good sensitivity and specificity. In addition, the visual paper-based nano-probe is designed to detect DPA by using the color scanning application of smart phone. This developed platform possesses abroad application prospects with advantages of effective, convenient carrying, simple operation, good selectivity and repeatability.

New method for morphological identification and simultaneous quantification of multiple tetracyclines by a white fluorescent probe

The threat of tetracycline antibiotics to the environment and human health is attracting widespread attention. The development of morphological analysis and quantitative techniques of multiple tetracyclines is of great significance for the evaluation of biochemical toxicity, wide-spectrum antibacterial property and degradation cycle between different tetracyclines. In this study, the white fluorescent Eu/Tb@CDs was synthesized and applied successfully to the identification and detection of the most widely used tetracycline antibiotics (tetracycline (TC), oxytetracycline (OC), chlortetracycline (CC) and doxycycline (DC)) with detection limits all below 1 nM. For the actual water samples with coexistence of the above 4 tetracyclines, their simultaneous morphology identification and accurate quantitative detection can also be realized through simple spectrometric measurement. In addition, the selective and competitive experiments have been carried out on the pollutants widely present in water, and the results have also confirmed that other pollutants could not interfere with the detection of the above 4 tetracyclines. It is undeniable that this work will conveniently and visually reveal the existence information and geographical distribution characteristics of different tetracycline antibiotics in the environment and their action mechanism on organisms.

Comparative Two-Dimensional Fluorescence Gel Electrophoresis

Two-dimensional comparative fluorescence gel electrophoresis (CoFGE) uses an internal standard to increase the reproducibility of coordinate assignment for protein spots visualized on 2D polyacrylamide gels. This is particularly important for samples that need to be compared without the availability of replicates and thus cannot be studied using differential gel electrophoresis (DIGE). CoFGE corrects for gel-to-gel variability by co-running with the sample proteome a standardized marker grid of 80-100 nodes, which is formed by a set of purified proteins. Differentiating of reference and analyte is possible by the use of two fluorescent dyes. Variations in the y-dimension (molecular weight) are corrected by the marker grid. For the optional control of the x-dimension (pI), azo-dyes can be used. Experiments are possible in both vertical and horizontal (h) electrophoresis devices, but hCoFGE is much easier to perform. The CoFGE experimental principle can additionally be used for protein quantification. For data analysis, commercial software has been adapted.

DIGE Analysis of Fish Tissues

Two-dimensional difference gel electrophoresis (2D-DIGE) appears to be especially useful in quantitative approaches, allowing the co-separation of proteins of control samples and proteins of treated/disease samples on the same gel, eliminating gel-to-gel variability. The principle of 2D-DIGE is to label proteins prior to isoelectric focusing and use three spectrally resolvable fluorescent dyes, allowing the independent labeling of control and experimental samples. This procedure makes it possible to reduce the number of gels in an experiment, allowing the accurate and reproducible quantification of multiple samples. 2D-DIGE has been found to be an excellent methodical tool in several areas of fish research, including environmental pollution and toxicology, the mechanisms of development and disorders, reproduction, nutrition, evolution, and ecology.

Imidazo[1,2-a]pyridine based small organic fluorescent molecules for selective detection of nerve agents simulants

A fused heterocyclic ESIPT imidazo[1,2-a]pyridine-based probes for colorimetric and fluorometric detection of nerve agents simulant sarin (DCP) and tabun (DCNP) are reported. The probes (5b, 6a & 6b) were found to be highly sensitive and selective for the detection of DCNP and DCP at a micromolar concentration within seconds with no observed interference from other various types of analytes. The LOD for 6b towards DCP was found to be 0.6 µM with a linear range from 0 to 8 µM. The low-cost portable cellulose paper strip fabricated with probe 6b for real-time detection of DCP in the gas phase and spiked water has been developed. The paper strip product was found effective in detecting the presence of DCP in water and vapor state with substantial color changes which could be easily observed by the naked eye and under a handheld UV lamp at a wavelength of 365 nm.

Labeling Microplastics with Fluorescent Dyes for Detection, Recovery, and Degradation Experiments

Staining microplastics (MPs) for fluorescence detection has been widely applied in MP analyses. However, there is a lack of standardized staining procedures and conditions, with different researchers using different dye concentrations, solvents, incubation times, and staining temperatures. Moreover, with the limited types and morphologies of commercially available MPs, a simple and optimized approach to making fluorescent MPs is needed. In this study, 4 different textile dyes, along with Nile red dye for comparison, are used to stain 17 different polymers under various conditions to optimize the staining procedure. The MPs included both virgin and naturally weathered polymers with different sizes and shapes (e.g., fragments, fibers, foams, pellets, beads). We show that the strongest fluorescence intensity occurred with aqueous staining at 70 °C for 3 h with a dye concentration of 5 mg/mL, 55 mg/mL, and 2 µg/mL for iDye dyes, Rit dyes, and Nile red, respectively. Red fluorescent signals are stronger and thus preferred over green ones. The staining procedure did not significantly alter the surface, mass, and chemical characteristics of the particles, based on FTIR and stereomicroscopy. Stained MPs were spiked into freshwater, saltwater, a sediment slurry, and wastewater-activated sludge; even after several days, the recovered particles are still strongly fluoresced. The approach described herein for producing customized fluorescent MPs and quantifying MPs in laboratory-controlled experiments is both straightforward and simple.

Portuino-A Novel Portable Low-Cost Arduino-Based Photo- and Fluorimeter

A novel portable low-cost Arduino-controlled photo- and fluorimeter for on-site measurements has been developed. The device uses LEDs as a light source and a phototransistor as a light sensor. The circuit is based on the discharge of a capacitor with the photocurrent from the phototransistor. Validation experiments for absorbance measurements were performed by measuring protein concentration using the Bradford method and measuring phosphate ions in water using a commercial test kit. The emission light of the excited fluorescent dyes rhodamine 6G and calcofluor white was measured to validate the usability of the device as a fluorescence photometer. In all validation experiments, similar correlation coefficients and limit of detection could be achieved with the portable photo- and fluorimeter and a laboratory spectrometer and fluorimeter. Real sample analysis was performed, measuring phosphate concentration in freshwater and concentration of green fluorescent protein, extracted from Escherichia coli.

A ratiometric fluorescent probe for detection of γ-glutamyl transpeptidase in blood serum and living cells

γ-Glutamyl transpeptidase (GGT) is one of the biomarker of cancer, hepatitis, and numerous other diseases. The accurate analysis of GGT is useful for the early diagnosis of these diseases. In this work, Probe 1, a ratiometric fluorescent probe based on 2,3,5,6-tetrafluoroterephthalonitrile, was designed for GGT detection. The results indicated that Probe 1 can sensitively and selectively detect GGT in phosphate buffered solution and complex biological systems (e.g., blood serum). Furthermore, Probe 1 has been successfully applied for ratiometric imaging of GGT in cancer cells and normal cells.

A gold-silver bimetallic nanocluster-based fluorescent probe for cysteine detection in milk and apple

Noble metal nanoclusters have attracted much attention due to their excellent optical properties. In the present work, a silver-doped gold-based bimetallic nanoclusters (Au/Ag NCs) were reasonably designed and prepared through a one-pot method by using 5-mercapto-1-tetrazolea-acetic acid sodium salt (MTAS) as a protector and capping agent. In comparison with the monometallic nanoclusters, Ag-doped metallic nanoclusters show better performance. The particle size of the MTAS-Au/Ag NCs is slightly larger than that of the undoped Au NCs by about 1.86 ± 0.5 nm, and the MTAS-Au/Ag NCs exhibit an emission peak at 635 nm with a quantum yield (QY) of 3.05%. The presence of cysteine (Cys) induces efficient quenching of the photoluminescence of the obtained Au/Ag NCs, achieving the sensitive detection of Cys with a detection limit of 16 nM. The fluorescence quenching rate of the nano fluorescent probe has a linear relationship with the cysteine concentration. Under the best detection conditions, the linear range for Cys detection with MTAS-Au/Ag NCs as a probe is 0.05-25.0 μM. Moreover, this probe has been successfully applied to the analysis of Cys in milk and apples, and a satisfactory recovery rate has been obtained, indicating the effectiveness and reliability of the sensor system for the detection of actual samples.

Light-absorption and fluorescence fingerprinting characteristics of water and methanol soluble organic compounds in PM2.5 in cold regions of Northeast China

High-performance liquid chromatography-size exclusion chromatography and excitation-emission matrix (EEM) fluorescence spectroscopy were used to analyze the seasonal variations and potential sources of molecular weight (MW) separated light-absorbing chromophores and fluorophores of water-soluble organic compounds (WSOC) and methanol-soluble organic compounds (MSOC) in PM_2.5 in cold areas of northern China. The results showed that the light-absorbing organics in MSOC had larger weight-average MW (M_w) (3.19 kDa) and number-average MW (M_n) (1.13 kDa) compared with WSOC (M_w: 1.41 kDa, M_n: 0.692 kDa). The light-absorption of organics showed a trend of winter>spring>autumn>summer and increased on air pollution days. Three fluorescent components including humic-like, protein-like, and terrestrial humic-like components in WSOC were extracted by parallel factor analysis (PARAFAC). Fluorophores in WSOC were dominated by humic-like and terrestrial humic-like components (67.7%). Three fluorescent components extracted from MSOC were low oxidation humic-like, polycyclic aromatic hydrocarbon (PAH)-like, and protein-like components respectively. It is worth noting that compared with WSOC, MSOC may have a higher human health risk due to the presence of PAH-like components. The combination of PARAFAC and self-organizing map had the potential to identify potential sources of fluorophores. It provided a new perspective for comprehensively exploring the characteristics of fluorophores in aerosols. This study provided a reference for further understanding the chemical composition and optical properties of organic aerosols in the cold regions of northern China.

Highly sensitive fluorescent detection of EDIL3 overexpressed exosomes for the diagnosis of triple-negative breast cancer

EDIL3 is a strong and highly accurate diagnostic marker for breast cancer, meanwhile, EDIL3 overexpressed exosomes are novel biomarkers for the early diagnosis of triple-negative breast cancer (TNBC). Here, we proposed a fluorescent detection method for EDIL3 overexpressed exosomes, which is simple and sensitive. Basically, we utilized a magnetic nanospheres (MNS) based liquid sandwich immunoassay strategy. MNS were modified with CD63 aptamers, which can immunologically bound to the CD63 protein on the surface of exosomes. Alexa Fluor 647 labeled anti-EDIL3 antibodies (Anti-EDIL3/AF647) were used as the fluorescent probes to recognize the EDIL3 on exosomes derived from a TNBC cell line (MDA-MB-231). With the target TNBC exosomes present, sandwich structures containing MNS, exosomes and fluorescent probes were formed. After magnetic purification, optical super resolution imaging of the products was conducted to check the specificity of the assay. In addition, fluorescence signals of the products were detected to quantitatively analyze the EDIL3 overexpressed exosomes. The linear range was found to be 7.78 × 10¹to 7.78× 10⁶particlesμl^-1. The detection limit was approximately 10 particlesμl^-1. The feasibility of the method for the detection of exosomes in complex biological samples was also demonstrated. Such a simple and sensitive detection method for EDIL3 overexpressed exosomes holds a great potential in clinical diagnosis of TNBC.

Imidazolium-Modified Bispyrene-Based Fluorescent Aggregates for Discrimination of Multiple Anions in Aqueous Solution

A great number of anions exist in biological systems and natural environment, and are highly relevant to human health and environment quality. It is necessary to develop simple and effective sensors to differentiate and identify those similar or different anions. Here, an imidazolium-modified bispyrene-based fluorescent amphiphilic probe DPyDIM was synthesized and its aggregates were applied to detect and discriminate various anions. The fluorescent aggregates exhibit ratiometric responses to different types of anions. Moreover, the ratiometric responses to different types of anions are featured with multiple-wavelength cross-reactivity. The collection of fluorescence variation at four typical wavelengths can generate distinct recognition patterns to specific anions. The heat map and principal component analysis results verify that this single fluorescent sensor system can effectively and sensitively identify 16 kinds of anions that belong to phosphorus-containing, sulfur-containing anions, and anionic surfactants. The cross-reactive sensing of the amphiphilic fluorescent aggregates was attributed to the different influences on the aggregation behaviors of the probes by different anions. The present work provides a promising strategy for effective detection and discrimination of multiple anions by employing dynamic fluorescent aggregates as a sensing platform.

A fluorescent organic nanoparticles-based sensor synthesized through hydrothermal process and its application in sensing Hg2+ of real samples and fast visual detection

The fluorescent organic nanoparticles (FONs)-based sensor has been attracting great attention in recent years. There are still big challenges in the preparation and application of FONs-based sensor. In this study, a FONs-based sensor was designed and developed through facile hydrothermal process using 3-perylenecarboxaldehyde (PlCA) as the fluorophore and L-methionine (Met) as the recognition site for mercury ions. According to the experimental results, the fluorescence intensity of the as-prepared PlCA-M would decrease when adding Hg²⁺ and the mechanism was extrapolated to be photoinduced electron transfer inducing by specific coordination interaction. The acquired PlCA-M-based sensor was used to monitor Hg²⁺ in several real samples (environmental water, tea, and apple) with the limit of detection being 60 nM. Remarkably, a visual detection device based on FONs, SDS-PAAG (sodium dodecyl sulfate polyacrylamide gel) @PlCA-M was firstly constructed and successfully used to Hg²⁺ semi-quantitation by naked eyes. In addition, the acquired FONs was applied into imaging tool for security information detection and identified as solid-state luminescent material for the first time.

A highly selective turn-on fluorescence probe with large Stokes shift for detection of palladium and its applications in environment water and living cells

Nowadays, palladium has been widely used in many fields, which facilitates all aspects of our life. However, it may cause water and soil pollution and bring irreversible damage to the environment and organisms. Developing a fluorescence probe for rapid, highly sensitive and selective detection of palladium is still a poser. In this work, we designed and synthesized a novel fluorescence probe (RHS) for specific detection of palladium. Based on Pd⁰-mediated Tsuji-Trost reaction, the fluorescence probe was constructed by a rhodol derivative as thefluorophore and an allyl carbonate moiety as the specific palladium reactive site. The probe displayed excellent properties for detecting palladium, such as high selectivity and sensitivity, rapid response (20 min) and large Stokes shift (155 nm). The detection limit was determined to be as low as 0.140 μM with a linear range from 20 to 80 μM. After addition of palladium in RHS solution, the color of the solution turned from yellow to blue, indicating palladium could be monitored by the naked eyes. Moreover, probe RHS was successfully applied to palladium detection in environmental water samples. Importantly, with low cytotoxicity and good biocompatibility, the probe could monitor palladium in living cells.

Nanomolar Nitric Oxide Concentrations in Living Cells Measured by Means of Fluorescence Correlation Spectroscopy

Measurement of the nitric oxide (NO) concentration in living cells in the physiological nanomolar range is crucial in understanding NO biochemical functions, as well as in characterizing the efficiency and kinetics of NO delivery by NO-releasing drugs. Here, we show that fluorescence correlation spectroscopy (FCS) is perfectly suited for these purposes, due to its sensitivity, selectivity, and spatial resolution. Using the fluorescent indicators, diaminofluoresceins (DAFs), and FCS, we measured the NO concentrations in NO-producing living human primary endothelial cells, as well as NO delivery kinetics, by an external NO donor to the immortal human epithelial living cells. Due to the high spatial resolution of FCS, the NO concentration in different parts of the cells were also measured. The detection of nitric oxide by means of diaminofluoresceins is much more efficient and faster in living cells than in PBS solutions, even though the conversion to the fluorescent form is a multi-step reaction.

Generative adversarial network enables rapid and robust fluorescence lifetime image analysis in live cells

Fluorescence lifetime imaging microscopy (FLIM) is a powerful tool to quantify molecular compositions and study molecular states in complex cellular environment as the lifetime readings are not biased by fluorophore concentration or excitation power. However, the current methods to generate FLIM images are either computationally intensive or unreliable when the number of photons acquired at each pixel is low. Here we introduce a new deep learning-based method termed flimGANE (fluorescence lifetime imaging based on Generative Adversarial Network Estimation) that can rapidly generate accurate and high-quality FLIM images even in the photon-starved conditions. We demonstrated our model is up to 2,800 times faster than the gold standard time-domain maximum likelihood estimation (TD_MLE) and that flimGANE provides a more accurate analysis of low-photon-count histograms in barcode identification, cellular structure visualization, Förster resonance energy transfer characterization, and metabolic state analysis in live cells. With its advantages in speed and reliability, flimGANE is particularly useful in fundamental biological research and clinical applications, where high-speed analysis is critical.

Simultaneous Monitoring of pH and Chloride (Cl-) in Brain Slices of Transgenic Mice

Optosensorics is the direction of research possessing the possibility of non-invasive monitoring of the concentration of intracellular ions or activity of intracellular components using specific biosensors. In recent years, genetically encoded proteins have been used as effective optosensory means. These probes possess fluorophore groups capable of changing fluorescence when interacting with certain ions or molecules. For monitoring of intracellular concentrations of chloride ([Cl-]i) and hydrogen ([H+] i) the construct, called ClopHensor, which consists of a H+- and Cl--sensitive variant of the enhanced green fluorescent protein (E2GFP) fused with a monomeric red fluorescent protein (mDsRed) has been proposed. We recently developed a line of transgenic mice expressing ClopHensor in neurons and obtained the map of its expression in different areas of the brain. The purpose of this study was to examine the effectiveness of transgenic mice expressing ClopHensor for estimation of [H+]i and [Cl-]i concentrations in neurons of brain slices. We performed simultaneous monitoring of [H+]i and [Cl-]i under different experimental conditions including changing of external concentrations of ions (Ca2+, Cl-, K+, Na+) and synaptic stimulation of Shaffer's collaterals of hippocampal slices. The results obtained illuminate different pathways of regulation of Cl- and pH equilibrium in neurons and demonstrate that transgenic mice expressing ClopHensor represent a reliable tool for non-invasive simultaneous monitoring of intracellular Cl- and pH.

Fluorescent whitening agents in Baiyangdian Lake in North China: Analysis, occurrence, distribution and ecological risk assessment

Fluorescent whitening agents (FWAs) are very important chemical additives that are widely applied in the industrial production field. The history of global FWA production and use spans more than 60 years, but the environmental fate of FWAs has been less reported in the public literature and most studies predate 2000; in addition, the studied FWAs were still limited to FWA71 and FWA351. In this study, the occurrence and distribution of 9 commonly used FWAs in a lake in North China were reported for the first time. We found that 6 target FWAs were prevalent in the lake, and the concentration levels were usually at the ng L^-1 level. Decreasing FWA levels with increasing distance from the estuary area were observed in summer. FWA135, FWA185, and FWA367, the most detected 3 FWAs, with the ecological risk at high levels, and ΣRQ >10 were obtained from all the investigated samples, suggesting that all the sampling sites could be considered with certain ecological risk for aquatic life. As a category of heavily and widely used dyes, FWAs in environmental media have been ignored for a long time. Substantial additional research needs to be conducted to determine the environmental behavior and ecological toxicology of FWAs.

Visualizing hypochlorous acid production by human neutrophils with fluorescent graphene quantum dots

In living organisms, redox reactions play a crucial role in the progression of disorders accompanied by the overproduction of reactive oxygen and reactive chlorine species, such as hydrogen peroxide and hypochlorous acid, respectively. We demonstrate that green fluorescence graphene quantum dots (GQDs) can be employed for revealing the presence of the hypochlorous acid in aqueous solutions and cellular systems. Hypochlorous acid modifies the oxygen-containing groups of the GQD, predominantly opens epoxide ring C-O-C, forms excessive C=O bonds and damages the carbonic core of GQDs. These changes, which depend on the concentration of the hypochlorous acid and exposure time, manifest themselves in the absorbance and fluorescence spectra of the GQD, and in the fluorescence lifetime. We also show that the GQD fluorescence is not affected by hydrogen peroxide. This finding makes GQDs a promising sensing agent for selective detecting reactive chlorine species produced by neutrophils. Neutrophils actively accumulate GQDs allowing to visualize cells and to examine the redox processes via GQDs fluorescence. At high concentrations GQDs induce neutrophil activation and myeloperoxidase release, leading to the disruption of GQD structure by the produced hypochlorous acid. This makes the GQDs a biodegradable material suitable for various biomedical applications.

Combining dense and sparse labeling in optical DNA mapping

Optical DNA mapping (ODM) is based on fluorescent labeling, stretching and imaging of single DNA molecules to obtain sequence-specific fluorescence profiles, DNA barcodes. These barcodes can be mapped to theoretical counterparts obtained from DNA reference sequences, which in turn allow for DNA identification in complex samples and for detecting structural changes in individual DNA molecules. There are several types of DNA labeling schemes for ODM and for each labeling type one or several types of match scoring methods are used. By combining the information from multiple labeling schemes one can potentially improve mapping confidence; however, combining match scores from different labeling assays has not been implemented yet. In this study, we introduce two theoretical methods for dealing with analysis of DNA molecules with multiple label types. In our first method, we convert the alignment scores, given as output from the different assays, into p-values using carefully crafted null models. We then combine the p-values for different label types using standard methods to obtain a combined match score and an associated combined p-value. In the second method, we use a block bootstrap approach to check for the uniqueness of a match to a database for all barcodes matching with a combined p-value below a predefined threshold. For obtaining experimental dual-labeled DNA barcodes, we introduce a novel assay where we cut plasmid DNA molecules from bacteria with restriction enzymes and the cut sites serve as sequence-specific markers, which together with barcodes obtained using the established competitive binding labeling method, form a dual-labeled barcode. All experimental data in this study originates from this assay, but we point out that our theoretical framework can be used to combine data from all kinds of available optical DNA mapping assays. We test our multiple labeling frameworks on barcodes from two different plasmids and synthetically generated barcodes (combined competitive-binding- and nick-labeling). It is demonstrated that by simultaneously using the information from all label types, we can substantially increase the significance when we match experimental barcodes to a database consisting of theoretical barcodes for all sequenced plasmids.

DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications

DNA molecular combing is a technique that stretches thousands of long individual DNA molecules (up to 10 Mbp) into a parallel configuration on surface. It has previously been proposed to sequence these molecules by synthesis. However, this approach poses two critical challenges: 1-Combed DNA molecules are overstretched and therefore a nonoptimal substrate for polymerase extension. 2-The combing surface sterically impedes full enzymatic access to the DNA backbone. Here, we introduce a novel approach that attaches thousands of molecules to a removable surface, with a tunable stretching factor. Next, we dissolve portions of the surface, leaving the DNA molecules suspended as 'bridges'. We demonstrate that the suspended molecules are enzymatically accessible, and we have used an enzyme to incorporate labeled nucleotides, as predicted by the specific molecular sequence. Our results suggest that this novel platform is a promising candidate to achieve high-throughput sequencing of Mbp-long molecules, which could have additional genomic applications, such as the study of other protein-DNA interactions.

Renal-Clearable Molecular Probe for Near-Infrared Fluorescence Imaging and Urinalysis of SARS-CoV-2

Despite the importance of rapid and accurate detection of SARS-CoV-2 in controlling the COVID-19 pandemic, current diagnostic methods are static and unable to distinguish between viable/nonviable virus or directly reflect viral replication activity. Real-time imaging of protease activity specific to SARS-CoV-2 can overcome these issues but remains lacking. Herein, we report a near-infrared fluorescence (NIRF) activatable molecular probe (SARS-CyCD) for detection of SARS-CoV-2 protease in living mice. The probe comprises a hemicyanine fluorophore caged with a protease peptide substrate and a cyclodextrin unit, which function as an NIRF signaling moiety and a renal-clearable enabler, respectively. The peptide substrate of SARS-CyCD can be specifically cleaved by SARS-CoV-2 main protease (Mpro), resulting in NIRF signal activation and liberation of the renal-clearable fluorescent fragment (CyCD). Such a design not only allows sensitive detection of Mpro in the lungs of living mice after intratracheal administration but also permits optical urinalysis of SARS-CoV-2 infection. Thus, this study presents an in vivo sensor that holds potential in preclinical high-throughput drug screening and clinical diagnostics for respiratory viral infections.

Renal-Clearable Molecular Probe for Near-Infrared Fluorescence Imaging and Urinalysis of SARS-CoV-2

Despite the importance of rapid and accurate detection of SARS-CoV-2 in controlling the COVID-19 pandemic, current diagnostic methods are static and unable to distinguish between viable/nonviable virus or directly reflect viral replication activity. Real-time imaging of protease activity specific to SARS-CoV-2 can overcome these issues but remains lacking. Herein, we report a near-infrared fluorescence (NIRF) activatable molecular probe (SARS-CyCD) for detection of SARS-CoV-2 protease in living mice. The probe comprises a hemicyanine fluorophore caged with a protease peptide substrate and a cyclodextrin unit, which function as an NIRF signaling moiety and a renal-clearable enabler, respectively. The peptide substrate of SARS-CyCD can be specifically cleaved by SARS-CoV-2 main protease (M^pro), resulting in NIRF signal activation and liberation of the renal-clearable fluorescent fragment (CyCD). Such a design not only allows sensitive detection of M^pro in the lungs of living mice after intratracheal administration but also permits optical urinalysis of SARS-CoV-2 infection. Thus, this study presents an in vivo sensor that holds potential in preclinical high-throughput drug screening and clinical diagnostics for respiratory viral infections.

Diffusion MRI and anatomic tracing in the same brain reveal common failure modes of tractography

Anatomic tracing is recognized as a critical source of knowledge on brain circuitry that can be used to assess the accuracy of diffusion MRI (dMRI) tractography. However, most prior studies that have performed such assessments have used dMRI and tracer data from different brains and/or have been limited in the scope of dMRI analysis methods allowed by the data. In this work, we perform a quantitative, voxel-wise comparison of dMRI tractography and anatomic tracing data in the same macaque brain. An ex vivo dMRI acquisition with high angular resolution and high maximum b-value allows us to compare a range of q-space sampling, orientation reconstruction, and tractography strategies. The availability of tracing in the same brain allows us to localize the sources of tractography errors and to identify axonal configurations that lead to such errors consistently, across dMRI acquisition and analysis strategies. We find that these common failure modes involve geometries such as branching or turning, which cannot be modeled well by crossing fibers. We also find that the default thresholds that are commonly used in tractography correspond to rather conservative, low-sensitivity operating points. While deterministic tractography tends to have higher sensitivity than probabilistic tractography in that very conservative threshold regime, the latter outperforms the former as the threshold is relaxed to avoid missing true anatomical connections. On the other hand, the q-space sampling scheme and maximum b-value have less of an impact on accuracy. Finally, using scans from a set of additional macaque brains, we show that there is enough inter-individual variability to warrant caution when dMRI and tracer data come from different animals, as is often the case in the tractography validation literature. Taken together, our results provide insights on the limitations of current tractography methods and on the critical role that anatomic tracing can play in identifying potential avenues for improvement.

Detection of circulating genetically abnormal cells using 4-color fluorescence in situ hybridization for the early detection of lung cancer

PURPOSE

Available biomarkers lack sensitivity for an early lung cancer. Circulating genetically abnormal cells (CACs) occur early in tumorigenesis. To determine the diagnostic value of CACs in blood detected by 4-color fluorescence in situ hybridization (FISH) for lung cancer.

METHODS

This was a prospective study of patients with pulmonary nodules ≤ 30 mm detected between 10/2019 and 01/2020 at four tertiary hospitals in China. All patients underwent a pathological examination of lung nodules found by imaging and were grouped as malignant and benign. CACs were detected by 4-color FISH. Patients were divided into the training and validation cohorts. Receiver operating characteristics analysis was used to analyze the diagnosis value of CACs.

RESULTS

A total of 205 participants were enrolled. Using a cut-off value of ≥ 3, blood CACs achieved areas under the curve (AUCs) of 0.887, 0.823, and 0.823 for lung cancer in the training and validation cohorts, and all patients, respectively. CACs had high diagnostic values across all tumor sizes and imaging lesion types. CACs were decreased after surgery (median, 4 vs. 1, P < 0.001) in the validation set. The CAC status between blood and tissues was highly consistent (kappa = 0.909, P < 0.001). The AUC of CAC (0.823) was higher than that of CEA (0.478), SCC (0.516), NSE (0.506), ProGRP (0.519), and CYFRA21-1 (0.535) (all P < 0.001).

CONCLUSION

CACs might have a high value for the early diagnosis of lung cancer. These findings might need to be validated in future studies. Evidence suggested homology in genetic aberrations between the CACs and the tumor cells.

Engineering Electromagnetic Hot-Spots in Nanoparticle Cluster Arrays on Reflective Substrates for Highly Sensitive Detection of (Bio)molecular Analytes

Intense electromagnetic (EM) hot-spots arising at the junctions or gaps in plasmonic nanoparticle assemblies can drive ultrahigh sensitivity in molecular detection by surface-enhanced spectroscopies. Harnessing this potential however requires access to the confined physical space at the EM hot-spots, which is a challenge for larger analytes such as biomolecules. Here, we demonstrate self-assembly derived gold nanoparticle cluster arrays (NCAs) on gold substrates exhibiting controlled interparticle (<1 nm wide) and intercluster (<10 nm wide) hot-spots as highly promising in this direction. Sensitivity of the NCAs toward detection of small (<1 nm) or large (protein-receptor interactions) analytes in surface-enhanced Raman and metal-enhanced fluorescence assays is found to be strongly impacted by the size of the cluster and the presence of reflective substrates. Experiments supported by numerical simulations attribute the higher sensitivity to higher EM field enhancements at the hot-spots, as well as greater analyte leverage over EM hot-spots. The best-performing arrays could push the sensitivity down to picomolar detection limits for sub-nanometric organic analytes as well as large protein analytes. The investigation paves the way for rational design of plasmonic biosensors and highlights the unique capabilities of a molecular self-assembly approach toward catering to this objective.

Visual and quantitative detection of E. coli O157:H7 by coupling immunomagnetic separation and quantum dot-based paper strip

Simple and visual quantitative detection of foodborne pathogens can effectively reduce the outbreaks of foodborne diseases. Herein, we developed a simple and sensitive quantum dot (QD)-based paper device for visual and quantitative detection of Escherichia coli (E. coli) O157:H7 based on immunomagnetic separation and nanoparticle dissolution-triggered signal amplification. In this study, E. coli O157:H7 was magnetically separated and labeled with silver nanoparticles (AgNPs), and the AgNP labels can be converted into millions of Ag ions, which subsequently quench the fluorescence of QDs in the paper strip, which along with the readout can be visualized and quantified by the change in length of fluorescent quenched band. Owing to the high capture efficiency and effective signal amplification, as low as 500 cfu mL^-1 of E. coli O157:H7 could be easily detected by naked eyes. Furthermore, this novel platform was successfully applied to detect E. coli O157:H7 in spiked milk samples with good accuracy, indicating its potential in the detection of foodborne pathogens in real samples.

The effect of amisulpride, olanzapine, quetiapine, and aripiprazole single administration on c-Fos expression in vasopressinergic and oxytocinergic neurons of the rat hypothalamic paraventricular nucleus

Antipsychotics, including amisulpride (AMI), quetiapine (QUE), aripiprazole (ARI), and olanzapine (OLA), are used to treat mental illnesses associated with psychotic symptoms. The effect of these drugs on c-Fos expression in vasopressinergic (AVP) and oxytocinergic (OXY) neurons was studied in the hypothalamic paraventricular nucleus (PVN) of rats. The presence of c-Fos in AVP and OXY perikarya was investigated in seven PVN cells segregations: the anterior (Ant), dorsal cup (Dc), wing-shaped (Wi), periventricular zone (Pe), circle-shaped core (Co) and shell of core (Sh), and the posterior (pPVN) after an acute treatment with AMI-20 mg/kg, QUE-15 mg/kg, ARI-10 mg/kg, and OLA-5 mg/kg/bw in rats. Ninety min after treatments, the animals were sacrificed by transcardial perfusion with fixative and the PVN area sliced into 35 μm thick coronal sections for immunohistochemistry. The c-Fos was processed by avidin-biotin-peroxidase complex intensified with nickel-enhanced 3,3'-diaminobenzidine tetrahydrochloride. Visualization of AVP- and OXY-synthesizing neurons was achieved by a fluorescent marker Alexa Flour 568. The c-Fos-AVP and c-Fos-OXY colocalizations were evaluated from c-Fos stained sections merged with AVP or OXY ones. AMI, QUE, ARI, and OLA, single administration distinctly increased the c-Fos expression in each of the PVN cells segregations. QUE induced the highest magnitude of activation of AVP and OXY neurons, while OLA and AMI had only moderate effects. Incontestable variabilities detected in c-Fos expression in PVN AVP and OXY neurons extend the knowledge of selected antipsychotics extra-striatal actions and may also be helpful in a presumption of their possible functional impact.

3D positioning of tagged DNA loci by widefield and super-resolution fluorescence imaging of fixed yeast nuclei

This protocol describes how to culture, image, and determine the nuclear position of a fluorescently tagged DNA locus in the 3D nucleoplasm of fixed Saccharomyces cerevisiae cells. Here, we propose a manual scoring method based on widefield images and an automated method based on 3D-SIM images. Yeast culture conditions have to be followed meticulously to get the best biological response in a given environment. For complete details on the use and execution of this protocol, please refer to Forey et al. (2020).

Design and synthesis of highly fluorescent and stable fullerene nanoparticles as probes for folic acid detection and targeted cancer cell imaging

Rational design and construction of fullerene derivatives play significant roles in the development of applications for sensing, marking and imaging in biomedical fields. In the present work, a novel type of C₆₀ fluorescent nanoparticle (C₆₀ FNP) was synthesized by a combination of thiol-ene chemistry and modification with folic acid (FA). The as-prepared C₆₀ FNPs exhibited intense blue luminescence with a relatively high quantum yield of 26%, which is higher than that of any other reported fluorescent fullerene-based nanomaterial. Moreover, they revealed superior photobleaching resistance under constant UV lamp illumination for 5 h and excellent photostablity after 9 months of storage in water. Due to the mutual hydrogen bond interaction, the obtained C₆₀ FNPs were capable of acting as a sensitive and specific probe for FA detection and quantification, with a liner range of 0 to 80 μM and a detection limit of 0.24 μM. Satisfactory recoveries (95.4%-105.2%) were obtained from a series of actual samples, further confirming the feasibility of this nanoprobe. Additionally, taking advantage of the FA moiety, the C₆₀ FNPs had easy access to penetrate into cancer cells with higher expression levels of folate receptors, thereby achieving the function of targeted cellular imaging.

Pitfalls in RET Fusion Detection Using Break-Apart FISH Probes in Papillary Thyroid Carcinoma

OBJECTIVE

A standardized procedure of fused REarranged during Transfection (RET) gene detection using fluorescence in situ hybridization (FISH) remains to be established in papillary thyroid carcinoma (PTC). Our purpose was to investigate false-negative and false-positive events and their FISH signal characteristics.

METHODS

A total of 111 PTC cases were analyzed using break-apart FISH probes for RET status evaluation. All FISH results were validated using fusion-induced asymmetric transcription assay (FIATA)-based reverse transcription droplet digital PCR (RT-ddPCR). Then, suspected RET-positive cases were tested using quantitative reverse transcription-PCR (RT-qPCR), followed by next-generation sequencing (NGS) for recognizing fusion variants.

RESULTS

Thirty RET+ cases were revealed, including 20 CCDC6 (exon 1)-RET (exon 12), 6 NCOA4 (exon 8)-RET (exon 12), 1 NCOA4 (exon 7)-RET (exon 12), 1 CCDC186 (exon 7)-RET (exon 12), 1 ERC1 (exon 12)-RET (exon 12) and 1 SPECC1L (exon 9)-RET (exon 12) tumors. All RET fusion cases occurred in the BRAF- population, with a prevalence of 41.7% (30/72). Four cases of 8% to 13% (cutoff was 7.6%) dominant isolated 3' green (IG) FISH signals were RET-. One FISH- case with isolated 5' red (IR) signals with 94% abnormal tumor cells was demonstrated to be positive, harboring the NCOA4 (exon 7)-RET (exon 12) variant. Compared with RET fusions characterized by dominant break-apart signals with 29% to 100% aberrant cells, RET + with dominant IG-signal patterns all showed more frequent FISH+ cells (84%-92%). RET+ PTC with a break-apart signal pattern was more frequently found in unifocal lesions than in multifocal/bilateral tumors (P = 0.049).

CONCLUSIONS

A false-positive or false-negative event may exist for RET status detection in PTCs using the traditional FISH scoring method with break-apart probes.

Ratiometric pH sensing by fluorescence resonance energy transfer-based hybrid semiconducting polymer dots in living cells

Intracellular pH plays a significant role in all cell activities. Due to their precise imaging capabilities, fluorescent probes have attracted much attention for the investigation of pH-regulated processes. Detecting intracellular pH values with high throughput is critical for cell research and applications. In this work, hybrid semiconducting polymer dots (Pdots) were developed and characterized and were applied for cell imaging and exclusive ratiometric sensing of intracellular pH values. The reported Pdots were prepared by blending a synthesized block polymer (P_OMF) and a semiconducting polymer poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEHPPV) to construct a fluorescence resonance energy transfer system for ratiometric sensing. Pdots showed many advantages, including high brightness, excellent photostability and biocompatibility, giving the pH probe high sensitivity and good stability. Our results proved the capability of P_OMF-MEHPPV Pdots for the detection of pH in living cells.

Protocol for synthesis and use of a turn-on fluorescent probe for quantifying labile Zn2+ in the Golgi apparatus in live cells

Quantitative analysis using a turn-on fluorescent probe is inherently difficult due to the dependency of the fluorescence intensity on the probe concentration. To overcome this limitation, we developed an in situ quantification method using a turn-on fluorescent probe and a standard fluorophore, which are colocalized by protein tag technology. This protocol describes the synthesis of a Zn²⁺ probe, named ZnDA-1H, and the procedure to quantify the labile Zn²⁺ concentration in the Golgi of live HeLa cells by confocal fluorescence microscopy.

For complete details on the use and execution of this protocol, please refer to Kowada et al. (2020).

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Protocol for organic synthesis of turn-on Zn²⁺ fluorescent probe, ZnDA-1H

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ZnDA-1H is less pH sensitive and suitable for detecting labile Zn²⁺ in the Golgi

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Protocol for Zn²⁺ quantification method in live cells by confocal microscopy

Mobility shift-based electrophoresis coupled with fluorescent detection enables real-time enzyme analysis of carbohydrate sulfatase activity

Sulfated carbohydrate metabolism is a fundamental process, which occurs in all domains of life. Carbohydrate sulfatases are enzymes that remove sulfate groups from carbohydrates and are essential to the depolymerisation of complex polysaccharides. Despite their biological importance, carbohydrate sulfatases are poorly studied and challenges remain in accurately assessing the enzymatic activity, specificity and kinetic parameters. Most notably, the separation of desulfated products from sulfated substrates is currently a time-consuming process. In this paper, we describe the development of rapid capillary electrophoresis coupled to substrate fluorescence detection as a high-throughput and facile means of analysing carbohydrate sulfatase activity. The approach has utility for the determination of both kinetic and inhibition parameters and is based on existing microfluidic technology coupled to a new synthetic fluorescent 6S-GlcNAc carbohydrate substrate. Furthermore, we compare this technique, in terms of both time and resources, to high-performance anion exchange chromatography and NMR-based methods, which are the two current 'gold standards' for enzymatic carbohydrate sulfation analysis. Our study clearly demonstrates the advantages of mobility shift assays for the quantification of near real-time carbohydrate desulfation by purified sulfatases, and will support the search for small molecule inhibitors of these disease-associated enzymes.

Highly stable organic photothermal agent based on near-infrared-II fluorophores for tumor treatment

BACKGROUND

The aim to develop a highly stable near-infrared (NIR) photoinduced tumor therapy agent stems from its considerable potential for biological application. Due to its long wavelength, biological imaging exhibits a high signal-to-background ratio, deep tissue penetration and maximum permissible light power, which can minimize damage to an organism during photoinduced tumor therapy.

RESULTS

A class of stable NIR-II fluorophores (NIR998, NIR1028, NIR980, NIR1030, and NIR1028-S) based on aza-boron-dipyrromethene (aza-BODIPY) dyes with donor-acceptor-donor structures have been rationally designed and synthesized by harnessing the steric relaxation effect and intramolecular photoinduced electron transfer (IPET). These fluorophores exhibit an intense range of NIR-II emission, large Stokes shift (≥ 100 nm), excellent photothermal conversion performance, and superior stability against photobleaching. Among the NIR-II fluorophores, NIR998 possesses better NIR-II emission and photothermal conversion performance. NIR998 nanoparticles (NIR998 NPs) can be encapsulated by liposomes. NIR998 NPs show superior stability in the presence of light, heat, and reactive oxygen nitrogen species than that of indocyanine green NPs, as well as a higher photothermal conversion ability (η = 50.5%) compared to other photothermal agents. Finally, under the guidance of photothermal imaging, NIR998 NPs have been proven to effectively eliminate tumors via their excellent photothermal conversion performance while presenting negligible cytotoxicity.

CONCLUSIONS

Utilizing IPET and the steric relaxation effect can effectively induce NIR-II emission of aza-BODIPY dyes. Stable NIR998 NPs have excellent photothermal conversion performance and negligible dark cytotoxicity, so they have the potential to act as photothermal agents in biological applications.

An improved staining method of cell cycle analysis with Sybr Green I for fungi: Cryptococcus neoformans and Saccharomyces cerevisiae

Cryptococcus neoformans is a pathogenic fungus which causes millions of deaths and infections, especially threatening immunocompromised individuals. During the development of new drugs, the ubiquitination has been found to play an important role in the regulation of the virulence and cell cycle of this fungus. Based on this mechanism, ubiquitination-related mutant strains exhibiting cell cycle arrest have been established for drug development for the fungus. However, flow cytometry detection of the cell cycle in fungi is generally difficult because the thick cell wall and capsule of fungi generally contribute to a nonspecific signal of cytometry. In this study, an improved method, derived from Saccharomyces cerevisiae assays, is developed to specifically stain C. neoformans, in whose cell cycle the G1 and G2 peaks are separated enough to be allowed for cell cycle analysis. As a result, the improved method facilitates the detection of the alterations in the cell cycle of C. neoformans with a mutation that results in cell cycle arrest, which distinctly delays the cell division of C. neoformans. Thus, the improved method reported here provides detailed technical information regarding assays on C. neoformans and, more importantly, offers a solution for assessing the cell cycle in other fungi in the future. Abbreviation: PI: propidium iodide.

Customized optical mapping by CRISPR-Cas9 mediated DNA labeling with multiple sgRNAs

Whole-genome mapping technologies have been developed as a complementary tool to provide scaffolds for genome assembly and structural variation analysis (1,2). We recently introduced a novel DNA labeling strategy based on a CRISPR-Cas9 genome editing system, which can target any 20bp sequences. The labeling strategy is specifically useful in targeting repetitive sequences, and sequences not accessible to other labeling methods. In this report, we present customized mapping strategies that extend the applications of CRISPR-Cas9 DNA labeling. We first design a CRISPR-Cas9 labeling strategy to interrogate and differentiate the single allele differences in NGG protospacer adjacent motifs (PAM sequence). Combined with sequence motif labeling, we can pinpoint the single-base differences in highly conserved sequences. In the second strategy, we design mapping patterns across a genome by selecting sets of specific single-guide RNAs (sgRNAs) for labeling multiple loci of a genomic region or a whole genome. By developing and optimizing a single tube synthesis of multiple sgRNAs, we demonstrate the utility of CRISPR-Cas9 mapping with 162 sgRNAs targeting the 2Mb Haemophilus influenzae chromosome. These CRISPR-Cas9 mapping approaches could be particularly useful for applications in defining long-distance haplotypes and pinpointing the breakpoints in large structural variants in complex genomes and microbial mixtures.