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.

Ferrous sulfate efficiently kills Vibrio parahaemolyticus and protects salmon sashimi from its contamination.

The primary seafood-borne pathogen Vibrio parahaemolyticus seriously threats the health of consumers preferring raw-fish products, becoming a global concern in food safety. In the present study, we found ferrous sulfate (FeSO4), a nutritional iron supplement, could efficiently induce the death of V. parahaemolyticus. Further, the bactericidal mechanisms of FeSO4 were explored. With a fluorescent probe of Fe2+, a significant influx of Fe2+ was determined in V. parahaemolyticus exposed to FeSO4, and the addition of an intracellular Fe2+ chelator was able to block the cell death. This suggested that cell death in V. parahaemolyticus induced by FeSO4 was dependent on the influx of Fe2+. It was intriguing that we did not observe the eruption of reactive oxygen species (ROS) and lipid hydroperoxides by Fe2+, but the application of liproxstatin-1 (a ferroptosis inhibitor) significantly modified the occurrence of cell death in V. parahaemolyticus. These results suggested FeSO4-induced cell death in V. parahaemolyticus be a ferroptosis differing from that in mammalian cells. Through transcriptome analysis, it was discovered that the exposure of FeSO4 disturbed considerable amounts of gene expression in V. parahaemolyticus including those involved in protein metabolism, amide biosynthesis, two-component system, amino acid degradation, carbon metabolism, citrate cycle, pyruvate metabolism, oxidative phosphorylation, and so on. These data suggested that FeSO4 was a pleiotropic antimicrobial agent against V. parahaemolyticus. Notably, FeSO4 was able to eliminate V. parahaemolyticus in salmon sashimi as well, without affecting the color, texture, shearing force, and sensory characteristics of salmon sashimi. Taken together, our results deciphered a unique ferroptosis in V. parahaemolyticus by FeSO4, and highlighted its potential in raw-fish products to control V. parahaemolyticus.

A simple "turn-on" fluorescence sensor for salicylaldehyde skeleton based on switch of PET-AIE effect.

The selective detection of salicylaldehyde skeleton is of great significance in phytochemistry and biological research but rarely reported. In this research, a simple and highly selective "turn-on" fluorescence sensor (CDB-Am) for salicylaldehyde skeleton was developed based on switch of photoinduced electron transfer (PET) and aggregation-induced emission (AIE). CDB-Am bearing amino-cyanodistyrene structure responded to salicylaldehyde in the range of 3.1 to 40 µM with a detection limit of 0.94 µM. The sensing process of formation of Schiff-base adduct CDB-SA was confirmed by 1H NMR, MS, and FT-IR spectra, revealing that a recovered AIE property accounted for the turn-on fluorescence response of CDB-Am and the intramolecular hydrogen bonding played a crucial role in the disruption of PET process. This sensing ability was successfully applied for both fluorescence qualitative test of salicylaldehyde skeleton on TLC analysis and quantitative detection of salicylaldehyde skeleton with good accuracy in the root bark of Periploca sepium, suggesting the extensive applications in phytochemistry and traditional Chinese herbal medicine. Furthermore, CDB-Am exhibited the first excellent fluorescence imaging ability in detecting salicylaldehyde skeleton in a living system. This work supplied a new strategy of preparing a novel "turn-on" fluorescence probe for detecting salicylaldehyde skeleton in complex environments and living bodies.

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.

Two- and Three-Dimensional Spectrofluorimetric Qualitative Analysis of Selected Vegetable Oils for Biomedical Applications.

Vegetable oils obtained from different plants are known for their beneficial effects on prophylaxis and supportive treatment of a great deal of inflammatory-mediated conditions. Their wide range of saturated and unsaturated fatty acids, and the presence of other ingredients (e.g., tocopherols, chlorophylls), provide them with anti-inflammatory, antioxidant and anticancer properties, which are worth being exploited. In this study, we have carried out the spectrofluorometric analysis of selected vegetable oils, namely apricot (Prunus armeniaca) kernel oil; blueberry (Vaccinium spp.) seed oil; argan (Argania spinosa) nut oil; kiwi (Actinidia deliciosa) seed oil; grape (Vitis vinifera) seed oil; evening primrose (Oenothera biennis) oil and meadowfoam (Limnanthes alba) seed oil, with the purpose to detect their fluorescent ingredients for further identification and bioactivity comparison. The obtained two- (2D) and three-dimensional (3D) emission spectra offered a complete description of the fluorescent components of the mixture and revealed different features for studied oils.

Labelled chemical probes for demonstrating direct target engagement in living systems.

Demonstrating target engagement in living systems can help drive successful drug discovery. Target engagement and occupancy studies in cells confirm direct binding of a ligand to its intended target protein and provide the binding affinity. Combined with biomarkers to measure the functional consequences of target engagement, these experiments can increase confidence in the relationship between in vitro pharmacology and observed biological effects. In this review, we focus on chemically and radioactively labelled probes as key reagents for performing such experiments. Using recent examples, we examine how the labelled probes have been employed in combination with unlabelled ligands to quantify target engagement in cells and in animals. Finally, we consider future developments of this emerging methodology.

Transient Gene Expression as a Tool to Monitor and Manipulate the Levels of Acidic Phospholipids in Plant Cells.

Anionic phospholipids represent only minor fraction of cell membranes lipids but they are critically important for many membrane-related processes, including membrane identity, charge, shape, the generation of second messengers, and the recruitment of peripheral proteins. The main anionic phospholipids of the plasma membrane are phosphoinositides phosphatidylinositol 4-phosphate (PI4P), phosphatidylinositol 4,5-bisphosphate (PI4,5P2), phosphatidylserine (PS), and phosphatidic acid (PA). Recent insights in the understanding of the nature of protein-phospholipid interactions enabled the design of genetically encoded fluorescent molecular probes that can interact with various phospholipids in a specific manner allowing their imaging in live cells. Here, we describe the use of transiently transformed plant cells to study phospholipid-dependent membrane recruitment.

Selective recognition of c-MYC Pu22 G-quadruplex by a fluorescent probe.

Nucleic acid mimics of fluorescent proteins can be valuable tools to locate and image functional biomolecules in cells. Stacking between the internal G-quartet, formed in the mimics, and the exogenous fluorophore probes constitutes the basis for fluorescence emission. The precision of recognition depends upon probes selectively targeting the specific G-quadruplex in the mimics. However, the design of probes recognizing a G-quadruplex with high selectivity in vitro and in vivo remains a challenge. Through structure-based screening and optimization, we identified a light-up fluorescent probe, 9CI that selectively recognizes c-MYC Pu22 G-quadruplex both in vitro and ex vivo. Upon binding, the biocompatible probe emits both blue and green fluorescence with the excitation at 405 nm. With 9CI and c-MYC Pu22 G-quadruplex complex as the fluorescent response core, a DNA mimic of fluorescent proteins was constructed, which succeeded in locating a functional aptamer on the cellular periphery. The recognition mechanism analysis suggested the high selectivity and strong fluorescence response was attributed to the entire recognition process consisting of the kinetic match, dynamic interaction, and the final stacking. This study implies both the single stacking state and the dynamic recognition process are crucial for designing fluorescent probes or ligands with high selectivity for a specific G-quadruplex structure.

Isolation of Vacuoles from the Leaves of the Medicinal Plant Catharanthus roseus.

The isolation of vacuoles is an essential step to unravel the important and complex functions of this organelle in plant physiology. Here, we describe a method for the isolation of vacuoles from Catharanthus roseus leaves involving a simple procedure for the isolation of protoplasts, and the application of a controlled osmotic/thermal shock to the naked cells, leading to the release of intact vacuoles, which are subsequently purified by density gradient centrifugation. The purity of the isolated intact vacuoles is assayed by microscopy, western blotting, and measurement of vacuolar (V)-H+-ATPase hydrolytic activity. Finally, membrane functionality and integrity is evaluated by measuring the generation of a transtonoplast pH gradient by the V-H+-ATPase and the V-H+-pyrophosphatase, also producing further information on vacuole purity.

Screening of Chemical Dyes in Traditional Chinese Medicine by HPTLC-MS.

It has been uncovered that chemical dyes are illegally used in traditional Chinese medicines to brighten color and cover up inferiority, which threaten the safety of patients. In the present study, an HPTLC-MS method was developed for the effective screening of 11 chemical dyes (Sudan I, II, III, and IV; 808 Scarlet; Sudan Red 7B; malachite green; Basic Orange 2; auramine; Orange II; and erythrosine) in traditional Chinese medicine (TCM) raw materials and Chinese patent medicines. Firstly, unwashed HPTLC plates were chosen by comparing the background signals of the TLC plates used directly and prewashed with analytical grade and HPLC grade solvents. Twice developments were conducted to isolate chemical dyes of different polarity. Possible adulterants were preliminarily identified by comparing Rf values and in situ UV-Vis spectra with those of the references. Further confirmation was conducted by tandem MS analysis via an elution head-based TLC-MS interface. Sudan I and IV, 808 Scarlet, and Orange II were successfully detected in eight batches of TCM. The proposed method could be applied as a reliable technology for the screening of chemical dyes in TCM.

A Practical and High-Affinity Fluorescent Probe for Uridine Diphosphate Glucuronosyltransferase 1A1: A Good Surrogate for Bilirubin.

This study aimed to develop a practical and high-affinity fluorescent probe for uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1), a key conjugative enzyme responsible for the elimination and detoxification of many potentially harmful compounds. Several substrates derived from N-butyl-4-phenyl-1,8-naphthalimide were designed and synthesized on the basis of the substrate preference of UGT1A1 and the principle of photoinduced electron transfer (PET). Following the preliminary screening, substrate 2 was found with a high specificity and high affinity toward UGT1A1, while such biotransformation brought remarkable changes in fluorescence emission. Both inhibition kinetic analyses and molecular docking simulations demonstrated that 2 could bind on UGT1A1 at the same ligand-binding site as bilirubin. Furthermore, this newly developed probe was successfully used for sensing UGT1A1 activities and the high-throughput screening of UGT1A1 modulators in complex biological samples. In conclusion, a practical and high-affinity fluorescent probe for UGT1A1 was designed and well-characterized, which could serve as a good surrogate for bilirubin to investigate UGT1A1-ligand interactions.

Vascular Imaging of Matrix Metalloproteinase Activity as an Informative Preclinical Biomarker of Drug-induced Vascular Injury.

Lack of biomarkers specific to and either predictive or diagnostic of drug-induced vascular injury (DIVI) continues to be a major obstacle during drug development. Biomarkers derived from physiologic responses to vessel injury, such as inflammation and vascular remodeling, could make good candidates; however, they characteristically lack specificity for vasculature. We evaluated whether vascular remodeling-associated protease activity, as well as changes to vessel permeability resulting from DIVI, could be visualized ex vivo in affected vessels, thereby allowing for visual monitoring of the pathology to address specificity. We found that visualization of matrix metalloproteinase activation accompanied by increased vascular leakage in the mesentery of rats treated with agents known to induce vascular injury correlated well with incidence and severity of histopathological findings and associated inflammation as well as with circulating levels of tissue inhibitors of metalloproteinase 1 and neutrophil gelatinase-associated lipocalin. The weight of evidence approach reported here shows promise as a composite DIVI preclinical tool by means of complementing noninvasive monitoring of circulating biomarkers of inflammation with direct imaging of affected vasculature and thus lending specificity to its interpretation. These findings are supportive of a potential strategy that relies on translational imaging tools in conjunction with circulating biomarker data for high-specificity monitoring of VI both preclinically and clinically.

Construction of Protein-Based Biosensors Using Ligand-Directed Chemistry for Detecting Analyte Binding.

Protein-based fluorescent biosensors are powerful tools for quantitative detection of biomolecules or drugs with high sensitivity under physiological conditions. However, conventional methods for construction of biosensors require structural data with high resolution or amino acid sequence information in most cases, which hampers applicability of this method to structurally complicated receptor proteins. To sidestep such limitations, we recently developed a new method that employs ligand-directed chemistry coupled with a bimolecular fluorescence quenching and recovery system, which enabled the conversion of various kinds of membrane-bound receptors to "turn-on" type fluorescent sensors. Here, we describe a protocol for construction of "turn-on" type fluorescent biosensors based on the GABAA receptor which permits quantitative analysis of the ligand affinity.

Phototheranostic nanoplatform based on a single cyanine dye for image-guided combinatorial phototherapy.

This study represents a novel phototheranostic nanoplatform based on the near-infrared (NIR) heptamethine cyanine dye, IR775, which is capable of concurrent real-time fluorescence imaging and cancer eradication with combinatorial phototherapy. To achieve water solubility and enhance tumor delivery, the hydrophobic IR775 dye was loaded into a biocompatible polymeric nanoparticle with a diameter of ~40nm and slightly negative surface charge (-2.34mV). The nanoparticle-encapsulated hydrophobic IR775 dye (IR775-NP) is characterized by an enhanced fluorescence quantum yield (16%) when compared to the water soluble analogs such as ICG (2.7%) and IR783 (8%). Furthermore, the developed IR-775-NP efficiently generates both heat and reactive oxygen species under NIR light irradiation, eradicating cancer cells in vitro. Finally, animal studies revealed that the IR775-NP accumulates in cancer tumors after systemic administration, efficiently delineates them with NIR fluorescence signal and completely eradicates chemo resistant cancer tissue after a single dose of combinatorial phototherapy.

Bioorthogonal Probes for the Study of MDM2-p53 Inhibitors in Cells and Development of High-Content Screening Assays for Drug Discovery.

To study the behavior of MDM2-p53 inhibitors in a disease-relevant cellular model, we have developed and validated a set of bioorthogonal probes that can be fluorescently labeled in cells and used in high-content screening assays. By using automated image analysis with single-cell resolution, we could visualize the intracellular target binding of compounds by co-localization and quantify target upregulation upon MDM2-p53 inhibition in an osteosarcoma model. Additionally, we developed a high-throughput assay to quantify target occupancy of non-tagged MDM2-p53 inhibitors by competition and to identify novel chemical matter. This approach could be expanded to other targets for lead discovery applications.

A direct assay of butyrylcholinesterase activity using a fluorescent substrate.

In this study, we report a direct fluorometric assay for butyrylcholinesterase (BChE) activity and screening of its inhibitor, using a fluorescent substrate. 2-(2-(5,6-Dimethoxy-1,3-dioxoisoindolin-2-yl)acetoxy)-N,N,N-trimethylethan-1-ammonium iodide (1) was hydrolyzed by BChE, and its fluorescence was quenched by an intramolecular photoinduced electron transfer process. The resulting change in fluorescence provided a facile method for real-time BChE activity testing. Remarkably, 1 was selectively hydrolyzed by BChE, even in the presence of excess acetylcholinesterase, thereby facilitating the specific monitoring of BChE activity. This assay method is also useful for screening potential BChE inhibitors. Given its simplicity, selectivity, and higher assay speed, this method may be extended to high-throughput screening of BChE inhibitors and relevant drug discovery.

Development of propidium iodide as a fluorescence probe for the on-line screening of non-specific DNA-intercalators in Fufang Banbianlian Injection.

Fufang Banbianlian Injection (FBI) has been widely used as an anti-inflammatory and anti-tumor prescription. To understand the relationships between its bioactive ingredients and pharmacological efficacies, our previous study has been successfully identified some DNA-binding compounds in FBI using an established on-line screening system, in which 4',6-diamidino-2-phenylindole (DAPI) was developed as a probe. However, DAPI can be only used to screen ATT-specific DNA minor groove binders, leaving the potential active intercalators unknown in FBI. As a continuation of our studies on FBI, here we present a sensitive analytical method for rapid identification and evaluation of DNA-intercalators using propidium iodide (PI) as a fluorescent probe. We have firstly established the technique of high-performance liquid chromatography-diode-array detector-multistage mass spectrometry-deoxyribonucleic acid-propidium iodide-fluorescence detector (HPLC-DAD-MS(n)-DNA-PI-FLD) system. As a result, 38 of 58 previously identified compounds in FBI were DNA-intercalation active. Interestingly, all previously reported DNA-binders also showed intercalative activities, suggesting they are dual-mode DNA-binders. Quantitative study showed that flavonoid glycosides and chlorogenic acids were the main active compounds in FBI, and displayed similar DNA-binding ability using either DAPI or PI. In addition, 13 active compounds were used to establish the structure-activity relationships. In this study, PI was developed into an on-line method for identifying DNA-intercalators for the first time, and thus it will be a useful high-throughput screening technique for other related samples.

Preparation of Quenchbodies by protein transamination reaction.

Quenchbody (Q-body) is an antibody fragment labeled with fluorescent dye(s), which functions as a biosensor via the antigen-dependent removal of the quenching effect on fluorophores. It is based on the principle that the fluorescence of the dye(s) attached to the antibody N-terminal region is quenched primarily by the tryptophan residues present in the variable regions, and this quenching is released when the antigen binds to the antibody, resulting in increased fluorescence intensity. Hence Q-body is utilized in various immunoassays for the rapid and sensitive detection of analytes. So far, Q-bodies have been prepared by using a cell-free translation system or by combining Escherichia coli expression and post-labeling steps. However, the above methods need antibody gene cloning, and are time-consuming. In this study, we report a novel approach to prepare Q-bodies by protein N-terminal transamination. We used the antigen-binding fragment (Fab) of an antibody against the bone-Gla-protein (BGP), a biomarker for bone diseases, which was expressed in E. coli. The purified Fab was treated with Rapoport's salt to convert the amino group at the N-terminus to a ketone group, which in turn was allowed to react with fluorescent probes that have aminooxy or hydrazide groups, to prepare a Q-body. The Q-body prepared by this method could detect the BGP-C7 antigen at concentrations as low as 10 nM. Since the approach can label the protein N-terminus directly, it could be applied for preparing Q-bodies from natural antibodies and for the rapid screening of high-performance Q-bodies.

Study of the influence of over-the-counter vitamin supplement intake on urine fluorescence to optimize cancer detection by fluorescence cystoscopy.

Fluorescence cystoscopy (FC) efficiently enhances the detection and improves the therapeutic management of early bladder cancer. During an FC, about 150 ml of water is needed to inflate the bladder. The water is quickly diluted by urine which can be fluorescent. If this bladder washout fluid (BWF) becomes fluorescent, the FC images are frequently degraded. Unfortunately, it is unclear which elements of the diet may contribute to this background fluorescence. We propose to start this exploration with over-the-counter (OTC) vitamin supplements. To this end, we measured excitation­emission matrices of urine samples and the kinetics of modifications of urine fluorescence obtained from nine healthy volunteers before, during, and after intake of a commercially available OTC vitamin supplement. The pharmacokinetics shows that the BWF fluorescence values reach a maximum 8 to 10 h after vitamin intake. They decrease in the half-day that follows and reach values close to baseline ~1 day afterward. Based on these results, we conclude that, in order to avoid degradations of fluorescence images, it is likely best that the intake of OTC vitamin supplements be avoided during the week preceding an FC.

Perihematomal Cellular Injury Is Reduced by Trans-sodium Crocetinate in a Model of Intracerebral Hemorrhage.

The carotenoid compound trans-sodium crocetinate (TSC) has been shown to increase oxygenation in various tissues, including the brain. Notably, TSC can enhance oxygenation under conditions of reduced blood flow, thus attenuating the depth of an ischemic challenge. This study examined the impact of TSC on neuronal loss in an animal model of intracerebral hemorrhage (ICH). Utilizing a rat model of collagenase injection, TSC was shown to reduce perihematomal cellular loss after ICH, as assessed by Fluoro-Jade B staining in tissue sections. This is the first evidence demonstrating that TSC is capable of limiting hemorrhagic injury to neurons in the brain. The finding supports the concept that TSC may represent a candidate therapeutic for early intervention regardless of whether a stroke is hemorrhagic or ischemic in nature.