A machine learning-assisted fluorescent sensor array utilizing silver nanoclusters for coffee discrimination.

Coffee is a globally consumed commodity of substantial commercial significance. In this study, we constructed a fluorescent sensor array based on two types of polymer templated silver nanoclusters (AgNCs) for the detection of organic acids and coffees. The nanoclusters exhibited different interactions with organic acids and generated unique fluorescence response patterns. By employing principal component analysis (PCA) and random forest (RF) algorithms, the sensor array exhibited good qualitative and quantitative capabilities for organic acids. Then the sensor array was used to distinguish coffees with different processing methods or roast degrees and the recognition accuracy achieved 100%. It could also successfully identify 40 coffee samples from 12 geographical origins. Moreover, it demonstrated another satisfactory performance for the classification of pure coffee samples with their binary and ternary mixtures or other beverages. In summary, we present a novel method for detecting and identifying multiple coffees, which has considerable potential in applications such as quality control and identification of fake blended coffees.

Knockdown of BUB1B Inhibits the Proliferation, Migration, and Invasion of Colorectal Cancer by Regulating the JNK/c-Jun Signaling Pathway.

Background: Colorectal cancer (CRC) ranks as the third most common cancer, accounting for a significant number of cancer-related deaths worldwide every year. Yet, the molecular mechanisms responsible for the progression of this malignancy are not fully understood. Numerous studies indicate that BUB1 mitotic checkpoint serine/threonine kinase B (BUB1B) plays a role in the progression of various malignant tumors. However, the specific biological functions and the detailed mechanisms of how BUB1B influences CRC are still not completely known. This study aimed to explore the expression and role of BUB1B in CRC. Materials and Methods: To achieve this, the expression levels of BUB1B in human CRC tissues and cell lines were examined using real-time polymerase chain reaction and Western blotting. The role and associated mechanisms of BUB1B in CRC cell progression were assessed both in vitro and in vivo using RNA interference. Results: The findings of this study revealed an elevated expression of BUB1B in both CRC tissues and cell lines. The silencing of BUB1B in CRC cell lines notably inhibited cell proliferation, migration, and invasion, leading to cell cycle arrest and apoptosis. In addition, the knockdown of BUB1B inhibited the JNK/c-Jun signaling pathway, increased the expression of proapoptotic proteins, and decreased the expression of antiapoptotic proteins. The effects of BUB1B knockdown on CRC cell progression were reversed by the JNK activator PAF(C-16). Conclusions: In summary, the suppression of BUB1B hindered malignant tumor progression and heightened apoptosis and cell cycle arrest in CRC cells via the JNK/c-Jun pathway. Importantly, the removal of BUB1B expression curtailed tumor growth in human CRC xenografts in nude mice, suggesting its potential as a promising therapeutic target for CRC patients. ClinicalTrials.gov ID: No.2019 K-C086.

Genetically encoded fluorescence lifetime biosensors: overview, advances, and opportunities.

Genetically encoded biosensors based on fluorescent proteins (FPs) are powerful tools for tracking analytes and cellular events with high spatial and temporal resolution in living cells and organisms. Compared with intensiometric readout and ratiometric readout, fluorescence lifetime readout provides absolute measurements, independent of the biosensor expression level and instruments. Thus, genetically encoded fluorescence lifetime biosensors play a vital role in facilitating accurate quantitative assessments within intricate biological systems. In this review, we first provide a concise description of the categorization and working mechanism of genetically encoded fluorescence lifetime biosensors. Subsequently, we elaborate on the combination of the fluorescence lifetime imaging technique and lifetime analysis methods with fluorescence lifetime biosensors, followed by their application in monitoring the dynamics of environment parameters, analytes and cellular events. Finally, we discuss worthwhile considerations for the design, optimization and development of fluorescence lifetime-based biosensors from three representative cases.

Photoluminescent gold nanoclusters as two-photon excited ratiometric pH sensor and photoactivated peroxidase.

A two-photon excited ratiometric fluorescent pH sensor is reported by combining L-cysteine-protected AuNCs (Cys@AuNCs) with fluorescein isothiocyanate (FITC). Cys@AuNCs were synthesized through a one-step self-reduction route and showed pH-responsive photoluminescence at 650 nm. Benefiting from the opposite pH response of Cys@AuNCs and FITC, the fluorescence ratio (F515 nm/F650 nm) of FITC&Cys@AuNCs provided a large dynamic range of 200-fold for pH measurement in the response interval of pH 5.0-8.0. Based on the excellent two-photon absorption coefficient of Cys@AuNCs, the sensor was expected to achieve sensitive quantitation of pH in living cells under two-photon excitation. In addition, colorimetric biosensing based on enzyme-like metal nanoclusters has attracted wide attention due to their low-cost, simplicity, and practicality. It is crucial to develop high catalytic activity nanozyme from the viewpoint of practical application. The synthesized Cys@AuNCs exhibited excellent photoactivated peroxidase-like activity with high substrate affinity and catalytic reaction rate, promising for rapid colorimetric biosensing of field analysis and the control of catalytic reactions by photostimulation.

Tree-based machine learning models assisted fluorescent sensor array for detection of metal ions based on silver nanocluster probe.

The growing concern over heavy metal pollution and its impact on the environment and human health has led to a proliferation of research on the detection and differentiation of heavy metal ions. A novel fluorescent sensor array utilizing only one single Ag-nanoclusters (Ag NCs) was developed for the efficient detection of six metal ions. The Ag NCs probe was prepared by using poly(methyl vinyl ether-alt-maleic acid) (PMVEM) as the ligand and has different fluorescence properties in water and dimethyl sulfoxide (DMSO). The interaction between metal ions and Ag NCs resulted in a characteristic fluorescence variation pattern which was subsequently analyzed using various tree-based machine learning models. We have compared different combinations of classification models and pre-processing methods of which the K-Nearest Neighbors Classifier with the first five linear discriminants has the highest accuracy. Through the integration of concentration models within a tree-based pipeline optimization framework, six unique concentration regression models were selected for each metal ion. In addition, the developed sensor array could identify metal ions in binary mixtures. And it still kept high accuracy for the classification of six target metal ions in river water. In conclusion, the proposed framework was found to be effective in the detection of heavy metal ions in environmental samples, thus providing a promising approach for addressing heavy metal pollution.

Ultrafast Förster resonance energy transfer from tyrosine to tryptophan in monellin: potential intrinsic spectroscopic ruler.

Ultrafast Förster Resonance Energy Transfer (FRET) between tyrosine (Tyr) and tryptophan (Trp) residues in the protein monellin has been investigated using picosecond and femtosecond time-resolved fluorescence spectroscopy. Decay associated spectra (DAS) and time-resolved emission spectra (TRES) taken with the different excitation wavelengths of 275, 290 and 295 nm were constructed via global analysis. At two of those three excitation loci (275 and 290 nm), earmarks of energy transfer from Tyr to Trp in monellin are seen, and particularly when the excitation is 275 nm, the energy transfer between Tyr and Trp clearly changes the signature emission DAS shape to that indicating excited state reaction (especially on the red side of fluorescence emission, near 380 nm). Those FRET signatures may overlap with the conventional signatory DAS in heterogeneous systems. When overlap and addition occur between FRET type DAS and "full positive" QSSQ (quasi-static self-quenching), mixed DAS shapes will emerge that still show "positive blue side and negative red sides", just with zero crossing shifted. In addition, excitation decay associated spectra (EDAS) taken with the different emission wavelengths of 330, 350 and 370 nm were constructed. In the study of protein dynamics, ultrafast FRET between Tyr and Trp could provide a basis for an intrinsic (non-perturbing) "spectroscopic ruler", potentially a powerful tool to detect even slight changes in protein structures.

Ultrafast Electron Transfer Dynamics of Organic Polymer Nanoparticles with Graphene Oxide.

We prepared organic polymer poly-3-hexylthiophene (p3ht) nanoparticles (NPs) and graphene oxide (GO)/reduced graphene oxide (RGO) composites p3ht NPs-GO/RGO by using the reprecipitation method. We demonstrated that GO/RGO could improve the ordering and planarity of p3ht chains as well as the formation of p3ht NPs, and confirmed the effects of GO/RGO on the fluorescence and carrier transport dynamics of p3ht NPs by using femtosecond fluorescence upconversion and transient absorption (TA) techniques. Ultrafast electron transfer (∼1 ps) between GO/RGO and p3ht NPs quenched the fluorescence of p3ht NPs, indicating excellent properties of p3ht NPs-GO/RGO as the charge transfer complexes. Efficient electron transfer may promote the applications of p3ht NPs-GO/RGO composites in organic polymer solar cells and photocatalysis. Moreover, RGO had stronger interfacial interactions and more matched conduction band energy levels with p3ht NPs than GO did, which implied that p3ht NPs-RGO might have greater application values than p3ht NPs-GO.

A novel fluorescent sensor array to identify Baijiu based on the single gold nanocluster probe.

Baijiu occupies a vital position in Chinese food and China's market. Strict evaluation of Baijiu is highly demanded. In this study, we constructed a novel fluorescent sensor array based on the single glutathione-protected gold nanoclusters (AuNCs) probe for the detection of organic acids and Baijiu. The fluorescence of AuNCs was simply modulated by three metal ions (Cu2+, Mn2+, and Ag+), and formed new complexes as sensing elements. These four sensing elements responded variously to nine organic acids, and further chemometric analysis results allowed for the classification and quantification of acids. Moreover, the sensor array successfully identified 21 Baijiu samples of different brands among 11 aroma types. It could also distinguish Baijiu of different qualities as well as pure Baijiu from its adulterations and showed high selectivity among multiple interfering drinks. The results demonstrated that the AuNCs-based sensor array has considerable potential for quality monitoring of Baijiu.

Ultrafast Förster resonance energy transfer between tyrosine and tryptophan: potential contributions to protein-water dynamics measurements.

Ultrafast Förster Resonance Energy Transfer (FRET) between Tyrosine (Tyr, Y) and Tryptophan (Trp, W) in the model peptides Trp-(Pro)n-Tyr (WPnY) has been investigated using a femtosecond up-conversion spectrophotofluorometer. The ultrafast energy transfer process (<100 ps) in short peptides (WY, WPY and WP2Y) has been resolved. In fact, this FRET rate is found to be mixed with the rates of solvent relaxation (SR), ultrafast population decay (QSSQ) and other lifetime components. To further dissect and analyze the FRET, a spectral working model is constructed, and the contribution of a FRET lifetime is separated by reconciling the shapes of decay associated spectra (DAS). Surprisingly, FRET efficiency did not decrease monotonically with the growth of the peptide chain (as expected) but increased first and then decreased. The highest FRET efficiency occurred in peptide WPY. The kinetic results have been accompanied with molecular dynamics simulations that reconcile and explain this strange phenomenon: due to the strong interaction between amino acids, the distance between the donor and receptor in peptide WPY is actually closest, resulting in the fastest FRET. In addition, the FRET lifetimes (τcal) were estimated within the molecular dynamics simulations, and they were consistent with the lifetimes (τexp) separated out by the experimental measurements and the DAS working model. This benchmark study has implications for both previous and future studies of protein ultrafast dynamics. The approach taken can be generalized for the study of proximate tyrosine and tryptophan in proteins and it suggests spectral strategies for extracting mixed rates in other complex FRET problems.

Ultrafast Excited-State Dynamics of Thiazole Orange.

Thiazole orange (TO), an asymmetric cyanine dye, has been widely used in biomolecular detection and imaging of DNA/ RNA in gels, due to its unique fluorogenic behavior: fluorescence of free dye in aqueous solution is very weak but emission can be significantly enhanced in nucleic-acid-bound dye. Herein we describe the ultrafast excited-state dynamics of free TO in aqueous solution by exploiting both a femtosecond upconversion spectrophotofluorometer and a picosecond time-correlated single-photon counting (TCSPC) apparatus. For the first time, the fluorescence lifetime of TO monomer in water was found to be ∼1 ps, mixed with concurrent solvent relaxation (which was confirmed by the experimental results of TO in DMSO). Even at moderate concentration, this lifetime has an amplitude (a measure of molecular fraction) that significantly dominates other lifetimes, and this is the origin of weak steady state fluorescence of free TO in water. We also found a novel slower decay component around 34 ps. Interestingly and in addition, the lifetime component on the 30-40 ps timescale was also found in TO-γ-Cyclodextrin (CD) complexes. The fraction of this component increased with the addition of γ-CD. Cyclodextrin has been reported to promote the aggregation of TO. Thus, although a very coincidental match of this time constant by one for a torsional process within the cavity can not be ruled out, we ascribe the shared 30-40 ps component to the lifetime of a highly quenched TO dimer experiencing intra-and inter-molecular rearrangement.

Raman Fiber Photometry for Understanding Mitochondrial Superoxide Burst and Extracellular Calcium Ion Influx upon Acute Hypoxia in the Brain of Freely Moving Animals.

Developing a novel tool capable of real-time monitoring and simultaneous quantitation of multiple molecules in mitochondria across the whole brain of freely moving animals is the key bottleneck for understanding the physiological and pathological roles that mitochondria play in the brain events. Here we built a Raman fiber photometry, and created a highly selective non-metallic Raman probe based on the triple-recognition strategies of chemical reaction, charge transfer, and characteristic fingerprint peaks, for tracking and simultaneous quantitation of mitochondrial O2.- , Ca2+ and pH at the same location in six brain regions of free-moving animal upon hypoxia. It was found that mitochondrial O2.- , Ca2+ and pH changed from superficial to deep brain regions upon hypoxia. It was discovered that hypoxia-induced mitochondrial O2.- burst was regulated by ASIC1a, leading to mitochondrial Ca2+ overload and acidification. Furthermore, we found the overload of mitochondrial Ca2+ was mostly attributed to the influx of extracellular Ca2+ .

Targeting of MAD2L1 by miR-515-5p involves the regulation of cell cycle arrest and apoptosis of colorectal cancer cells.

Although many previous studies have found that the mitotic arrest deficient 2-like 1 (MAD2L1) protein contributes to the proliferation of colorectal cancer (CRC) cells, but the upstream mechanism of MAD2L1 is still largely elusive. This study aimed to explore the microRNAs (miRNAs) upstream of MAD2L1 to improve our understanding of the mechanism of the MAD2L1 gene in CRC. The upstream target miRNAs (miR-515-5p) of MAD2L1 were predicted by the online databases miRWalk, miRDIP, and TargetScan. Quantitative real-time PCR (qRT-PCR) was used to detect the expression level of miR-515-5p in human CRC tissues. The targeting relationship between miR-515-5p and MAD2L1 was tested by dual luciferase reporter gene assays. The effects of miR-515-5p on the biological behaviors of CRC cells by regulating MAD2L1 expression were verified by qRT-PCR, western blot, Cell Counting Kit-8, and flow cytometry. The results showed that miR-515-5p was a highly reliable upstream miRNA of the MAD2L1 gene. As an upstream target miRNA of MAD2L1, miR-515-5p was lowly expression in CRC tissues. The overexpression of miR-515-5p could inhibit the proliferation of CRC cells and induce cell cycle arrest at the G1 phase leading to cell apoptosis. However, MAD2L1 gene overexpression could reverse the effects of miR-515-5p overexpression on the biological behaviors of CRC cells above. This study illustrated that miR-515-5p can inhibit proliferation and induce G1 phase arrest leading to apoptosis in CRC cells. The mechanism underlying this phenomenon may be related to the negative targeted regulation of MAD2L1.

Copper nanoclusters-based fluorescent sensor array to identify metal ions and dissolved organic matter.

In recent years, the prevention and control of water pollution has received extensive attention. There is a need to develop simple and effective strategies for the rapid detection of metal ions and dissolved organic matter (DOM) in order to improve water quality. To this end, the first copper nanoclusters (CuNCs)-based fluorescent sensor array was done to identify 12 metal ions (Pb2+, Fe3+, Cu2+, Cd2+, Cr3+, Co2+, Ni2+, Zn2+, Ag+, Fe2+, Hg2+, and Al3+) and DOM (humic substances, lipids, fatty acids, amino acids, and lignans). The results revealed that CuNCs that were synthesized with polyethyleneimine (PEI), histidine (His), and glutathione (GSH) exhibited different binding abilities to metal ions and DOM. These unique fluorescence responses were analyzed using principal component analysis (PCA) and linear discriminant analysis (LDA) to identify metal ions and DOM in the buffer. The aforementioned 12 metal ions were classified at a limit concentration of 1.5 µM. Moreover, quantification of metal ions was achieved even at a low concentration of 0.83 µM (Zn2+). This array also worked well in the recognition of metal ions in tap water as well as distinguishing riverine and seawater samples of different regions, which was of great significance in environmental monitoring.

Recent Development of Fluorescent Light-Up RNA Aptamers.

Technologies for RNA imaging in live cells play an important role in understanding the function and regulatory process of RNAs. One approach for genetically encoded fluorescent RNA imaging involves fluorescent light-up aptamers (FLAPs), which are short RNA sequences that can bind cognate fluorogens and activate their fluorescence greatly. Over the past few years, FLAPs have emerged as genetically encoded RNA-based fluorescent biosensors for the cellular imaging and detection of various targets of interest. In this review, we first give a brief overview of the development of the current FLAPs based on various fluorogens. Then we further discuss on the photocycles of the reversibly photoswitching properties in FLAPs and their photostability. Finally, we focus on the applications of FLAPs as genetically encoded RNA-based fluorescent biosensors in biosensing and bioimaging, including RNA, non-nucleic acid molecules, metal ions imaging and quantitative imaging. Their design strategies and recent cellular applications are emphasized and summarized in detail.

Unravelling the role of charge transfer state during ultrafast intersystem crossing in compact organic chromophores.

When organic electron donor (D) and acceptor (A) chromophores are linked together, an electron transfer (ET) state can take place. When a short bridge such as one Sigma bond is used to link the donor and the acceptor, complete charge separation is difficult to access and one usually observes an intramolecular charge transfer (CT) state instead. Due to the inevitable coupling between the donor and the acceptor in compact organic chromophores, the most common decay pathway for the CT state is charge recombination, which may lead to a distinct longer wavelength fluorescence emission or non-radiative dissipation of the excited state energy. However, recent studies have shown that unique excited state dynamics can be observed when the CT state is involved during both forward and backward intersystem crossing (ISC) from singlet excited states to triplet excited states in organic chromophores. Analysis of the mechanism for ISC involving the CT state has received much attention over the last decade. In this perspective, we present a collection of molecular design rationales, spectroscopy and theoretical investigations that provide insights into the mechanism of the ISC involving the CT state in compact organic chromophores. We hope that this perspective will prove beneficial for researchers to design novel compact organic chromophores with a predictable ISC property for future biochemical and optoelectronic applications.

Colorimetric detection of water content in organic solvents via a smartphone with fluorescent Ag nanoclusters.

We detected the water content in ethanol and dimethyl sulfoxide (DMSO) solvents via a smartphone with the help of fluorescent Ag nanoclusters (Ag NCs). The Ag NCs intrinsically have two emission peaks, among which the long-wavelength emission intensified with decreasing water content due to the aggregation induced emission enhancement (AIEE) effect, but in contrast the short-wavelength emission was relatively insensitive to water content. This fact makes the Ag NCs an ideal colorimetric indicator of water content in organic solvents. A smartphone was applied to take pictures of Ag NC samples and read the R, G, and B values from the images. When the water content increased from 20% to 55% in ethanol, the G/B values displayed a good linear relationship with the water content, and a limit of detection (LOD) of 4.48% was achieved. Moreover, good consistency was observed when the colorimetric fluorescent Ag NCs were applied to detect water content in real samples such as white wine and medical alcohol. These studies demonstrated a convenient and practical method for the detection of water content via a smartphone.

LncRNA SNHG15 Knockdown Protects Against OGD/R-Induced Neuron Injury by Downregulating TP53INP1 Expression via Binding to miR-455-3p.

Cerebral ischemia-reperfusion (I/R) injury is the common symptom of ischemic stroke, which poses a heavy burden to human health. Long non-coding RNA (lncRNA) is indicated to be a critical regulator in cerebral ischemia. This study aims to reveal the effects of lncRNA small nucleolar RNA host gene 15 (SNHG15) on oxygen-glucose deprivation and reoxygenation (OGD/R)-induced neuron injury and underlying mechanism. The expression levels of SNHG15, microRNA-455-3p (miR-455-3p) and tumour protein p53 inducible nuclear protein 1 (TP53INP1) mRNA were determined by quantitative real time polymerase chain reaction in P12 cells. The protein levels of TP53INP1, cleaved caspase-3, caspase-3, B-cell lymphoma-2 and BCL2-associated x protein (Bax) were detected by western blot in P12 cells. Cell viability and apoptosis were revealed by cell counting kit-8 assay and flow cytometry analysis, respectively, in P12 cells. Caspase-3 activity, the levels of tumor necrosis factor-α and interleukin-1ß and the production of reactive oxygen species (ROS) were severally determined by caspase-3 activity assay, Enzyme-linked immunosorbent assay and ROS detection assay in P12 cells. The binding relationship between miR-455-3p and SNHG15 or TP53INP1 was predicted by starbase online database, and identified by dual-luciferase reporter, RNA pull-down or RNA immunoprecipitation assay. SNHG15 expression and the mRNA and protein levels of TP53INP1 were dramatically upregulated, while miR-455-3p expression was apparently downregulated in OGD/R-induced PC12 cells. SNHG15 silencing hindered the effects of OGD/R treatment on cell viability, apoptosis, inflammation and oxidative in PC12 cells; however, these impacts were restored after miR-455-3p inhibitor transfection. Additionally, SNHG15 acted as a sponge of miR-455-3p and miR-455-3p bound to TP53INP1. SNHG15 contributed to OGD/R-induced neuron injury by regulating miR-455-3p/TP53INP1 axis, which provided a novel insight to study lncRNA-directed therapy in ischemia stoke.

Ultrafast Fluorescence Spectroscopy via Upconversion and Its Applications in Biophysics.

In this review, the experimental set-up and functional characteristics of single-wavelength and broad-band femtosecond upconversion spectrophotofluorometers developed in our laboratory are described. We discuss applications of this technique to biophysical problems, such as ultrafast fluorescence quenching and solvation dynamics of tryptophan, peptides, proteins, reduced nicotinamide adenine dinucleotide (NADH), and nucleic acids. In the tryptophan dynamics field, especially for proteins, two types of solvation dynamics on different time scales have been well explored: ~1 ps for bulk water, and tens of picoseconds for "biological water", a term that combines effects of water and macromolecule dynamics. In addition, some proteins also show quasi-static self-quenching (QSSQ) phenomena. Interestingly, in our more recent work, we also find that similar mixtures of quenching and solvation dynamics occur for the metabolic cofactor NADH. In this review, we add a brief overview of the emerging development of fluorescent RNA aptamers and their potential application to live cell imaging, while noting how ultrafast measurement may speed their optimization.

Synthesis of highly stable fluorescent poly(methacrylic acid-co-itaconic)-protected silver nanoclusters and sensitive detection of Cu2.

Stable fluorescent silver nanoclusters (AgNCs) were synthesized through one-step UV photoreduction using the multiple carboxyl copolymer poly(methacrylic acid-co-itaconic acid) P(MAA-co-IA) as a novel template. The fluorescence lifetime and the quantum yield of the obtained AgNCs were 1.84 ns and 8.9% in an aqueous solution, respectively. Owing to the multiple carboxyls of the protective P(MAA-co-IA) template, the obtained AgNCs have excellent advantages such as good dispersity, and high stability, which make them suitable for highly sensitive and selective detection of Cu2+ by fluorescence quenching. A good linear relationship exists between the degree of fluorescence quenching for silver nanoclusters and Cu2+ concentration ranging from 0 to 10 µM. The limit of detection (LOD) is 6.36 nM. The result implies that the as-synthesized AgNCs show great potential in the analysis field.

One-Step Room-Temperature Synthesis of Metal(IV) Carboxylate Metal-Organic Frameworks.

Room-temperature syntheses of metal-organic frameworks (MOFs) are of interest to meet the demand of the sustainable chemistry and are a pre-requisite for the incorporation of functional compounds in water-stable MOFs. However, only few routes under ambient conditions have been reported to produce metal(IV)-based MOFs. Reported here is a new versatile one-step synthesis of a series of highly porous M6 -oxocluster-based MOFs (M=Zr, Hf, Ce) at room temperature, including 8- or 12-connected micro/mesoporous solids with different functionalized organic ligands. The compounds show varying degrees of defects, particularly for 12-connected phases, while maintaining the chemical stability of the parent MOFs. Proposed here are first insights into in situ kinetics observations for efficient MOF preparation. Remarkably, the synthesis has a high space-time yield and also provides the possibility to tune the particle size, therefore paving the way for their practical use.