Signal-Amplified Detection of the Tumor Biomarker FEN1 Based on Cleavage-Induced Ligation of a Dumbbell DNA Probe and Rolling Circle Amplification.

Flap endonuclease 1 (FEN1), an endogenous nuclease with the ability to cleave the 5' overhang of branched dsDNA, is of significance in DNA replication and repair. The overexpression of FEN1 is common in cancer because of the ubiquitous upregulation of DNA replication; thus, FEN1 has been recognized as a potential biomarker in oncological investigations. However, few analytical methods targeting FEN1 with high sensitivity and simplicity have been developed. This work developed a signal-amplified detection of FEN1 based on the cleavage-induced ligation of a dumbbell DNA probe and rolling circle amplification (RCA). A flapped dumbbell DNA probe (FDP) was rationally designed with a FEN1 cleavable flap at the 5' end. The cleavage generated a nick site with juxtaposed 5' phosphate and 3' hydroxyl ends, which were linkable by T4 DNA ligase to form a closed dumbbell DNA probe (CDP) with a circular conformation. The CDP functioned as a template for RCA, which produced abundant DNA that could be probed using SYBR Green I. The highly sensitive detection of FEN1 with a limit of detection of 15 fM was achieved, and this method showed high specificity, which enabled the quantification of FEN1 in real samples. The inhibitory effects of chemicals on FEN1 were also evaluated. This study represents the first attempt to develop an FEN1 assay that involves signal amplification, and the novel biosensor method enriches the tools for FEN1-based diagnostics.

Demodulation technique for 3-D tip clearance measurements based on output signals from optical fiber probe with three two-circle coaxial optical fiber bundles.

In this work, we propose a new demodulation technique for three-dimensional (3-D) tip clearance measurements using the output signals acquired from three two-circle coaxial optical fiber bundles. This technique is based on the ratio of the difference in the signal intensities between any two sensing units of the optical fiber probe, and we derived the demodulation equations using the second-order Taylor expansion for a three-variable function. We verified the feasibility of the demodulation technique by experiments and demodulation error curves, which indicates that the method is viable for 3-D tip clearance measurements.

Optical-fiber-based dynamic measurement system for 3D tip clearance of rotating blades.

This paper proposes a dynamic model for measuring the 3D tip clearance of rotating blades using an isosceles-right-triangle sensing structure consisting of three identical two-circle coaxial optical fiber bundles and a demodulation approach using the ratios of difference signals between any two bundles based on the Taylor expansion principle. The dynamic system comprising the optical fiber probe, hardware circuits, and measurement software is designed and established according to the characteristics of dynamic sensing signals. Finally, the feasibility of the system for the dynamic measurement of 3D tip clearance is experimentally verified using the simulated blades of a rotor test bench.

Output characteristics of two-circle coaxial optical fiber bundle with regard to three-dimensional tip clearance.

A two-circle coaxial optical fiber bundle is a type of optical sensor which has been widely used in non-contact radial displacement measurement applications. This paper has focused on output characteristics of a two-circle coaxial optical fiber bundle used as a measurement unit in a probe designed to measure a three-dimensional tip clearance. First, a model that could calculate intensity point-by-point on each receiving fiber with a simplified algorithm of overlap area was established, an aperture angle compensation algorithm was then proposed to improve the performance of the model. In order to test the reliability of the model, an experiment was done with different three-dimensional displacement of the reflector. Comparison between experimental and simulation results indicates the model built in this article could better describe how three-dimensional displacement of reflector affects the output of the bundle than previous studies.

Supramolecular Nanotubules as a Catalytic Regulator for Palladium Cations: Applications in Selective Catalysis.

Despite the recent development of highly efficient and stable metal catalysts, conferral of regulatory characteristics to the catalytic reaction in heterogeneous systems remains a challenge. Novel supramolecular nanotubules were prepared by alternative stacking from trimeric macrocycles, which was found to be able to coordinate with Pd cations. The Pd complexes exhibited a high catalytic performance for C-C coupling reaction. Notably, the tubular catalyst was observed to be controlled by supramolecular reversible assembly and showed superior heterogeneous catalytic activity, which was maintained for a number of cycles or reuse under an aerobic environment. Furthermore, the supramolecular catalyst showed unprecedented selectivity for the multifunctional coupling reaction and was able to serve as a new constructor of asymmetrical compounds.

Postamplifying Cas12a Activation through Hybridization Chain Reaction-Triggered Fluorescent Nanocluster Formation for Ultrasensitive Nucleic Acid Detection.

CRISPR/Cas12a-based biosensing is advancing rapidly; however, achieving sensitive and cost-effective reporting of Cas12a activation remains a challenge. In response, we have developed a label-free system capable of postamplifying Cas12a activation by integrating hybridization chain reaction (HCR) and DNA-copper nanoclusters (DNA-CuNCs). The trans-cleavage of Cas12a triggers a silenced HCR, leading to the in situ assembly of fluorescent DNA-CuNCs, allowing for the turn-on reporting of Cas12a activation. Without preamplification, this assay can detect DNA with a detection limit of 5 fM. Furthermore, when coupled with preamplification, the system achieves exceptional sensitivity, detecting the monkeypox virus (MPXV) plasmid at 1 copy in human serum. In a MPXV pseudovirus-based validation test, the obtained results are in agreement with those obtained by qPCR, reinforcing the robustness of this method. Our study represents the first effort to manipulate DNA-CuNC formation on HCR for highly sensitive and cost-effective reporting of Cas12a, resulting in an efficient synthetic biology-enabled sensing platform for biosafety applications.

Functional nucleic acids in glycobiology: A versatile tool in the analysis of disease-related carbohydrates and glycoconjugates.

As significant components of the organism, carbohydrates and glycoconjugates play indispensable roles in energy supply, cell signaling, immune modulation, and tumor cell invasion, and function as biomarkers since aberrance of them has been proved to be associated with the emergence and development of certain diseases. Functional nucleic acids (FNAs) have properties including easy-to-synthesize, good stability, good biocompatibility, low cost, and high programmability, they have attracted significant research attention and been incorporated into biosensors for detecting disease-related carbohydrates and glycoconjugates. This review summarizes the construction strategies and biosensing applications of FNAs-based biosensors in glycobiology in terms of target recognition and signal transduction. By illustrating the mechanisms and comparing the performances, the challenges and development opportunities in this area have been critically elaborated. We believe that this review will provide a better understanding of the role of FNAs in the analysis of disease-related carbohydrates and glycoconjugates, and inspire further discovery in fields that include glycobiology, chemical biology, clinical diagnosis, and drug development.

Methodologies in visualizing the activation of CRISPR/Cas: The last mile in developing CRISPR-Based diagnostics and biosensing - A review.

CRISPR/Cas-based analytical procedures have revolutionized the sensing platform to fulfill the requirements of the current era in terms of sensitivity, selectivity, robustness, user-friendly feature, and cost-effectiveness for the detection of nucleic acid as well as non-nucleic acid analytes. Molecular target monitoring and transduction of the signals is a crucial prerequisite for precise molecular sensing tools. Besides, the reporting systems have become the last milestone for fabricating Cas-based molecular probes to visualize the activation of CRISPR/Cas enzymes. In this review, we have highlighted various CRISPR/Cas reporters, their mechanisms, sensing strategies, merits, and demerits. Moreover, signal transducers, i.e. fluorescent, colorimetric, and electrochemical, have also been discussed in detail along with various sensing strategies to generate recordable signals. It was concluded that there is still a need to overcome issues offered by the reported sensing devices, such as off-target effect, target sequence limitation, multiplexed quantitative detection, the influence of the inhibitor, and reaction kinetic constraint. Additionally, it is required to make them available for commercial use by validating their stability, robustness, safety profile in an off-lab environment as most of the probes have been tested in the controlled atmosphere of the laboratories. We believe that this novel critical interpretation and summary will assist the researchers in designing and validating new CRISPR/Cas reporters and probes for practical applications on a commercial scale.

A DNA-Cu nanocluster and exonuclease I integrated label-free reporting system for CRISPR/Cas12a-based SARS-CoV-2 detection with minimized background signals.

CRISPR-driven biosensing is developing rapidly, but current studies mostly adopt dye-labeled ssDNA as the signal reporter, which is costly and unstable. Herein, we developed a label-free and low-background reporter for CRISPR/Cas12a signaling by integrating DNA-templated copper nanoclusters (DNA-CuNCs) and exonuclease I (EXO I). The template of the DNA-CuNCs was rationally designed as a ds-/ss-DNA hybrid, ensuring that after a quick and nonpersistent cut of Cas12a, a majority of the template can be digested by EXO I. Based on this novel reporter, a biosensor termed CRISPR-CNS (cost-effective, nimble, and sensitive copper nanocluster sensor integrating CRISPR) was developed. Due to the high signal-to-background ratio of our proposed reporter, CRISPR-CNS shows excellent performances for nucleic acid detection, yielding a detection limit of 20 copies for SARS-CoV-2 RNA. Considering its facile synthesis, robust fluorescence, effective cost, and good sensitivity, this combination shall serve as a highly potential output for CRISPR-based point-of-care testing.

Visual category representations in the infant brain.

Visual categorization is a human core cognitive capacity1,2 that depends on the development of visual category representations in the infant brain.3,4,5,6,7 However, the exact nature of infant visual category representations and their relationship to the corresponding adult form remains unknown.8 Our results clarify the nature of visual category representations from electroencephalography (EEG) data in 6- to 8-month-old infants and their developmental trajectory toward adult maturity in the key characteristics of temporal dynamics,2,9 representational format,10,11,12 and spectral properties.13,14 Temporal dynamics change from slowly emerging, developing representations in infants to quickly emerging, complex representations in adults. Despite those differences, infants and adults already partly share visual category representations. The format of infants' representations is visual features of low to intermediate complexity, whereas adults' representations also encode high-complexity features. Theta band activity contributes to visual category representations in infants, and these representations are shifted to the alpha/beta band in adults. Together, we reveal the developmental neural basis of visual categorization in humans, show how information transmission channels change in development, and demonstrate the power of advanced multivariate analysis techniques in infant EEG research for theory building in developmental cognitive science.

Accumulation of Heterocyclic Amines and Advanced Glycation End Products in Various Processing Stages of Plant-Based Burgers by UHPLC-MS/MS.

The accumulation of heterocyclic amines (HAs) and advanced glycation end products (AGEs) during different processing stages was investigated in commercial raw materials to plant-based hamburger meats (PBHMs). Principal component analysis (PCA) was performed to explore the difference between the samples of each processing stage. The total free HA level accumulated from 4.74-6.63 ng/g in raw plant proteins to 5.81-20.23 ng/g in textured vegetable proteins after extrusion. The concentration of MeAαC increased from 29.23 ± 3.50 to 59.44 ± 0.26 ng/g, resulting in an accumulation of the total protein-bound HAs after cooking at 160 °C for 6 min, but the MeAαC content decreased to 42.26 ± 0.11 ng/g when the heating duration was prolonged to 12 min. An evident accumulation of AGEs was observed during the thermal home-processing of PBHM. The total levels for all HAs were 381.30 and 160.30 ng/g in roast beef patty (RBP) and PBHM, respectively, with RBP having a better amino acid composition pattern. These results may reveal the target processing stage, which should be paid attention to for the inhibition of Maillard reaction derivative harmful products (MRDHPs) in plant-based meat products.

Advancing sensing technology with CRISPR: From the detection of nucleic acids to a broad range of analytes - A review.

The CRISPR/Cas technology, derived from an adaptive immune system in bacteria, has been awarded the Nobel Prize in Chemistry in 2020 for its success in gene editing. Increasing reports reveal that CRISPR/Cas technology has a wide scope of applications and it could be incorporated into biosensors for detecting critical analytes. CRISPR-powered biosensors have attracted significant research interest due to their advantages including high accuracy, good specificity, rapid response, and superior integrity. Now the CRISPR technology is not only admirable in nucleic acid monitoring, but also promising for other kinds of biomarkers' detection, including metal ions, small molecules, peptides, and proteins. Therefore, it is of great worth to explore the prospect, and summarize the strategies in applying CRISPR technology for the recognition of a broad range of targets. In this review, we summarized the strategies of CRISPR biosensing for non-nucleic-acid analytes, the latest development of nucleic acid detection, and proposed the challenges and outlook of CRISPR-powered biosensors.

DNA nanotechnology: A recent advancement in the monitoring of microcystin-LR.

The Microcystin-Leucine-Arginine (MC-LR) is the most toxic and widely distributed microcystin, which originates from cyanobacteria produced by water eutrophication. The MC-LR has deleterious effects on the aquatic lives and agriculture, and this highly toxic chemical could severely endanger human health when the polluted food was intaken. Therefore, the monitoring of MC-LR is of vital importance in the fields including environment, food, and public health. Utilizing the complementary base pairing between DNA molecules, DNA nanotechnology can realize the programmable and predictable regulation of DNA molecules. In analytical applications, DNA nanotechnology can be used to detect targets via target-induced conformation change and the nano-assemblies of nucleic acids. Compared with the conventional analytical technologies, DNA nanotechnology has the advantages of sensitive, versatile, and high potential in real-time and on-site applications. According to the molecular basis for recognizing MC-LR, the strategies of applying DNA nanotechnology in the MC-LR monitoring are divided into two categories in this review: DNA as a recognition element and DNA-assisted signal processing. This paper introduces state-of-the-art analytical methods for the detection of MC-LR based on DNA nanotechnology and provides critical perspectives on the challenges and development in this field.

Fluorometric detection of cancer marker FEN1 based on double-flapped dumbbell DNA nanoprobe functionalized with silver nanoclusters.

Flap endonuclease 1 (FEN1), a ubiquitous enzyme involved in DNA repair and replication, is overexpressed in highly proliferative cancer cells. FEN1 has been recognized as a promising diagnostic marker of cancers; however, very few analytical techniques have been developed for the convenient detection of FEN1. To realize the simplified quantification of FEN1, we developed a FEN1-responsive fluorescent nanoprobe based on DNA-silver nanoclusters (DNA-AgNCs). The nanoprobe was rationally designed with a double-flapped dumbbell conformation, where its 5' flap was produced with DNA-AgNCs, and the 3' flap was elongated by a guanine-rich enhancer sequence (GRS). Rigidified by the DNA scaffold, DNA-AgNCs and the GRS are in close proximity, resulting in high fluorescence because of the GRS-induced activation of DNA-AgNCs. Upon the addition of FEN1, the 5' flap of the nanoprobe is cleaved due to the structure-specific endonuclease activity of FEN1. This cleavage released the DNA-AgNCs from the nanoprobe, broke the proximity between DNA-AgNCs and the GRS, and caused decreased fluorescence. This nanoprobe can be applied in the sensitive detection of FEN1 with a detection limit of 40 fM, and it showed high specificity for the monitoring of FEN1 in clinical samples. As the first attempt to develop biosensors targeting FEN1 based on DNA-AgNCs, this work provided a potent platform for monitoring FEN1 and screening FEN1 inhibitors.

Visual Imagery and Perception Share Neural Representations in the Alpha Frequency Band.

To behave adaptively with sufficient flexibility, biological organisms must cognize beyond immediate reaction to a physically present stimulus. For this, humans use visual mental imagery [1, 2], the ability to conjure up a vivid internal experience from memory that stands in for the percept of the stimulus. Visually imagined contents subjectively mimic perceived contents, suggesting that imagery and perception share common neural mechanisms. Using multivariate pattern analysis on human electroencephalography (EEG) data, we compared the oscillatory time courses of mental imagery and perception of objects. We found that representations shared between imagery and perception emerged specifically in the alpha frequency band. These representations were present in posterior, but not anterior, electrodes, suggesting an origin in parieto-occipital cortex. Comparison of the shared representations to computational models using representational similarity analysis revealed a relationship to later layers of deep neural networks trained on object representations, but not auditory or semantic models, suggesting representations of complex visual features as the basis of commonality. Together, our results identify and characterize alpha oscillations as a cortical signature of representations shared between visual mental imagery and perception.

Emotional arousal elicited by irrelevant stimuli affects event-related potentials (ERPs) during response inhibition.

Previous event-related potential (ERP) studies using the Go/Nogo task have indicated that response inhibition is influenced by the arousal elicited by emotional stimuli, when those stimuli are relevant to response selection of Go and Nogo trials. Due to stimulus and task design issues, however, it is uncertain whether response inhibition is affected by emotional valence or arousal, when emotional stimuli are irrelevant to response selection. Therefore, the present study aimed to re-investigate this issue by circumventing limitations of previous research. To address this issue, thirty-one young adults (16 females and 15 males) were required to make motor responses to frequently-presented faces of one sex (Go trials) and to inhibit responses to less-frequently presented faces of the opposite sex (Nogo trials). Crucially, the faces were superimposed onto positive, negative and neutral pictures. The pictures were presented in a randomized order. The arousal values between positive and negative pictures were highly matched. Results showed that Nogo faces elicited smaller N2 but larger P3a amplitudes, when the faces were associated with positive and negative pictures as compared to neutral pictures. These findings suggest that response inhibition is influenced by emotional arousal, when emotional stimuli are irrelevant to response selection. Additionally, for Go faces, results showed smaller N2 but larger P3a amplitudes within negative pictures as compared to neutral and positive pictures, suggesting a role of emotional valence elicited by irrelevant stimuli on response execution.

Intelligent Mesoporous Materials for Selective Adsorption and Mechanical Release of Organic Pollutants from Water.

Despite recent advances in the porous materials for efficient removal of dissolved organic pollutants from water, the regeneration of porous characteristics for reuse with preventing secondary contamination remains a challenge. Here, novel supramolecular absorbents with hydrophobic pore are prepared by the self-assembly of propeller-shaped aromatic amphiphiles. The assembly of folded propeller provides a mesoporous environment within aromatic segments, which is suitable for the removal of organic pollutants from waste water. The removal efficiency is found to be 92% and 90% for ethinyl oestradiol (Eo) and bisphenol A (BPA). Notably, the folded architecture of propeller is observed to be flattened by the salt addition, which results in the strong π-π interaction driving the porous materials closed and forms solid fibers. It is found that most of the removed pollutants are spontaneously released by the dynamic porous assembly, and subsequent dialysis triggers the porous materials to be recovered.