Unmodificated stepless regulation of CRISPR/Cas12a multi-performance.

As CRISPR technology is promoted to more fine-divided molecular biology applications, its inherent performance finds it increasingly difficult to cope with diverse needs in these different fields, and how to more accurately control the performance has become a key issue to develop CRISPR technology to a new stage. Herein, we propose a CRISPR/Cas12a regulation strategy based on the powerful programmability of nucleic acid nanotechnology. Unlike previous difficult and rigid regulation of core components Cas nuclease and crRNA, only a simple switch of different external RNA accessories is required to change the reaction kinetics or thermodynamics, thereby finely and almost steplessly regulating multi-performance of CRISPR/Cas12a including activity, speed, specificity, compatibility, programmability and sensitivity. In particular, the significantly improved specificity is expected to mark advance the accuracy of molecular detection and the safety of gene editing. In addition, this strategy was applied to regulate the delayed activation of Cas12a, overcoming the compatibility problem of the one-pot assay without any physical separation or external stimulation, and demonstrating great potential for fine-grained control of CRISPR. This simple but powerful CRISPR regulation strategy without any component modification has pioneering flexibility and versatility, and will unlock the potential for deeper applications of CRISPR technology in many finely divided fields.

AND Logic-Gate-Based Dual-Locking Probe System for the Sensitive Detection of microRNA and APE1.

MicroRNA (miRNA) and apurinic/apyrimidinic endonuclease 1 (APE1) have been reported to be closely associated with cancers, making them potential crucial biomarkers and therapeutic targets. However, focusing on the detection of a single target is not conducive to the diagnosis and prognosis assessment of diseases. In this study, an AND logic-gate-based dual-locking hairpin-mediated catalytic hairpin assembly (DL-CHA) was developed for sensitive and specific detection of microRNA and APE1. By addition of a lock to each of the hairpins, with APE1 and microRNA serving as keys, fluorescence signals could only be detected in the presence of simultaneous stimulation by APE1 and miRNA-224. This indicated that the biosensor could operate as an AND logic gate. DL-CHA exhibited advantages such as a low background, rapid response, and high logic capability. Therefore, the biosensor serves as a novel approach to cancer diagnosis with significant potential applications.

DNA-based molecular classifiers for the profiling of gene expression signatures.

Although gene expression signatures offer tremendous potential in diseases diagnostic and prognostic, but massive gene expression signatures caused challenges for experimental detection and computational analysis in clinical setting. Here, we introduce a universal DNA-based molecular classifier for profiling gene expression signatures and generating immediate diagnostic outcomes. The molecular classifier begins with feature transformation, a modular and programmable strategy was used to capture relative relationships of low-concentration RNAs and convert them to general coding inputs. Then, competitive inhibition of the DNA catalytic reaction enables strict weight assignment for different inputs according to their importance, followed by summation, annihilation and reporting to accurately implement the mathematical model of the classifier. We validated the entire workflow by utilizing miRNA expression levels for the diagnosis of hepatocellular carcinoma (HCC) in clinical samples with an accuracy 85.7%. The results demonstrate the molecular classifier provides a universal solution to explore the correlation between gene expression patterns and disease diagnostics, monitoring, and prognosis, and supports personalized healthcare in primary care.

H/D Exchange Coupled with 2H-labeled Stable Isotope-Assisted Metabolomics Discover Transformation Products of Contaminants of Emerging Concern.

Stable isotope-assisted metabolomics (SIAM) is a powerful tool for discovering transformation products (TPs) of contaminants. Nevertheless, the high cost or lack of isotope-labeled analytes limits its application. In-house H/D (hydrogen/deuterium) exchange reactions enable direct 2H labeling to target analytes with favorable reaction conditions, providing intuitive and easy-to-handle approaches for environmentally relevant laboratories to obtain cost-effective 2H-labeled contaminants of emerging concern (CECs). We first combined the use of in-house H/D exchange and 2H-SIAM to discover potential TPs of 6PPD (N-1,3-dimethylbutyl-N'-phenyl-p-phenylenediamine), providing a new strategy for finding TPs of CECs. 6PPD-d9 was obtained by in-house H/D exchange with favorable reaction conditions, and the impurities were carefully studied. Incomplete deuteride, for instance, 6PPD-d8 in this study, constitutes a major part of the impurities. Nevertheless, it has few adverse effects on the 2H-SIAM pipeline in discovering TPs of 6PPD. The 2H-SIAM pipeline annotated 9 TPs of 6PPD, and commercial standards further confirmed the annotated 6PPDQ (2-anilino-5-(4-methylpentan-2-ylamino)cyclohexa-2,5-diene-1,4-dione) and PPPD (N-phenyl-p-phenylenediamine). Additionally, a possible new formation mechanism for 6PPDQ was proposed, highlighting the performance of the strategy. In summary, this study highlighted a new strategy for discovering the TPs of CECs and broadening the application of SIAM in environmental studies.

A Spatially Controlled Proximity Split Tweezer Switch for Enhanced DNA Circuit Construction and Multifunctional Transduction.

DNA strand displacement reactions are vital for constructing intricate nucleic acid circuits, owing to their programmability and predictability. However, the scarcity of effective methods for eliminating circuit leakages has hampered the construction of circuits with increased complexity. Herein, a versatile strategy is developed that relies on a spatially controlled proximity split tweezer (PST) switch to transduce the biomolecular signals into the independent oligonucleotides. Leveraging the double-stranded rigidity of the tweezer works synergistically with the hindering effect of the hairpin lock, effectively minimizing circuit leakage compared with sequence-level methods. In addition, the freely designed output strand is independent of the target binding sequence, allowing the PST switch conformation to be modulated by nucleic acids, small molecules, and proteins, exhibiting remarkable adaptability to a wide range of targets. Using this platform, established logical operations between different types of targets for multifunctional transduction are successfully established. Most importantly, the platform can be directly coupled with DNA catalytic circuits to further enhance transduction performance. The uniqueness of this platform lies in its design straightforwardness, flexibility, scalable intricacy, and system compatibility. These attributes pave a broad path toward nucleic acid-based development of sophisticated transduction networks, making them widely applied in basic science research and biomedical applications.

VARAdb: a comprehensive variation annotation database for human.

With the study of human diseases and biological processes increasing, a large number of non-coding variants have been identified and facilitated. The rapid accumulation of genetic and epigenomic information has resulted in an urgent need to collect and process data to explore the regulation of non-coding variants. Here, we developed a comprehensive variation annotation database for human (VARAdb, http://www.licpathway.net/VARAdb/), which specifically considers non-coding variants. VARAdb provides annotation information for 577,283,813 variations and novel variants, prioritizes variations based on scores using nine annotation categories, and supports pathway downstream analysis. Importantly, VARAdb integrates a large amount of genetic and epigenomic data into five annotation sections, which include 'Variation information', 'Regulatory information', 'Related genes', 'Chromatin accessibility' and 'Chromatin interaction'. The detailed annotation information consists of motif changes, risk SNPs, LD SNPs, eQTLs, clinical variant-drug-gene pairs, sequence conservation, somatic mutations, enhancers, super enhancers, promoters, transcription factors, chromatin states, histone modifications, chromatin accessibility regions and chromatin interactions. This database is a user-friendly interface to query, browse and visualize variations and related annotation information. VARAdb is a useful resource for selecting potential functional variations and interpreting their effects on human diseases and biological processes.

ATACdb: a comprehensive human chromatin accessibility database.

Accessible chromatin is a highly informative structural feature for identifying regulatory elements, which provides a large amount of information about transcriptional activity and gene regulatory mechanisms. Human ATAC-seq datasets are accumulating rapidly, prompting an urgent need to comprehensively collect and effectively process these data. We developed a comprehensive human chromatin accessibility database (ATACdb, http://www.licpathway.net/ATACdb), with the aim of providing a large amount of publicly available resources on human chromatin accessibility data, and to annotate and illustrate potential roles in a tissue/cell type-specific manner. The current version of ATACdb documented a total of 52 078 883 regions from over 1400 ATAC-seq samples. These samples have been manually curated from over 2200 chromatin accessibility samples from NCBI GEO/SRA. To make these datasets more accessible to the research community, ATACdb provides a quality assurance process including four quality control (QC) metrics. ATACdb provides detailed (epi)genetic annotations in chromatin accessibility regions, including super-enhancers, typical enhancers, transcription factors (TFs), common single-nucleotide polymorphisms (SNPs), risk SNPs, eQTLs, LD SNPs, methylations, chromatin interactions and TADs. Especially, ATACdb provides accurate inference of TF footprints within chromatin accessibility regions. ATACdb is a powerful platform that provides the most comprehensive accessible chromatin data, QC, TF footprint and various other annotations.

Denoising of BOTDR Dynamic Strain Measurement Using Convolutional Neural Networks.

The Brillouin optical time domain reflectometry (BOTDR) system measures the distributed strain and temperature information along the optic fibre by detecting the Brillouin gain spectra (BGS) and finding the Brillouin frequency shift profiles. By introducing small gain stimulated Brillouin scattering (SBS), dynamic measurement using BOTDR can be realized, but the performance is limited due to the noise of the detected information. An image denoising method using the convolutional neural network (CNN) is applied to the derived Brillouin gain spectrum images to enhance the performance of the Brillouin frequency shift detection and the strain vibration measurement of the BOTDR system. By reducing the noise of the BGS images along the length of the fibre under test with different network depths and epoch numbers, smaller frequency uncertainties are obtained, and the sine-fitting R-squared values of the detected strain vibration profiles are also higher. The Brillouin frequency uncertainty is improved by 24% and the sine-fitting R-squared value of the obtained strain vibration profile is enhanced to 0.739, with eight layers of total depth and 200 epochs.

Neutrophil/lymphocyte, platelet/lymphocyte, monocyte/lymphocyte ratios and systemic immune-inflammation index in patients with depression.

BACKGROUND: Evidence suggest immunity abnormalities and inflammation might play an important role in the pathophysiology of depression. This study explored the relationship between inflammation and depression using neutrophil-to-lymphocyte ratio (NLR), monocyte-to-lymphocyte ratio (MLR), platelet-to-lymphocyte ratio (PLR), and systemic immune-inflammation index (SII) as inflammatory markers. METHODS: We collected the full blood count results of 239 patients with depression and 241 healthy controls. Patients were divided into three diagnostic subtype groups: severe depressive disorder with psychotic symptoms, severe depressive disorder without psychotic symptoms, and moderate depressive disorder. We analyzed the Participants' neutrophil (NEU), lymphocyte (LYM), monocyte (MON), and platelet (PLT) counts, compared the differences in NLR, MLR, PLR and SII, and explored the relationships between depression and these indicators. RESULTS: There were significant differences in PLT, MON, NEU, MLR, and SII among the four groups. MON and MLR were significantly higher in three groups of depressive disorders. SII was significantly increased in two severe depressive disorder groups, while the SII in the moderate depressive disorder group showed an increasing trend. CONCLUSION: Increased MON, MLR and SII, as signs of inflammatory response, were not different among three subtypes of depressive disorders, and may be biological indictors of depressive disorders (Tab. 1, Ref. 17). Text in PDF www.elis.sk Keywords: depression, neutrophil-to-lymphocyte ratio (NLR), monocyte-to-lymphocyte ratio (MLR), platelet-to-lymphocyte ratio (PLR), systemic immune-inflammation index (SII).

Photoresponsive Solid Nanochannels Membranes: Design and Applications.

Light stimuli have notable advantages over other environmental stimuli, such as more precise spatial and temporal regulation, and the ability to serve as an energy source to power the system. In nature, photoresponsive nanochannels are important components of organisms, with examples including the rhodopsin channels in optic nerve cells and photoresponsive protein channels in the photosynthesis system of plants. Inspired by biological channels, scientists have constructed various photoresponsive, smart solid-state nanochannels membranes for a range of applications. In this review, the methods and applications of photosensitive nanochannels membranes are summarized. The authors believe that this review will inspire researchers to further develop multifunctional artificial nanochannels for applications in the fields of biosensors, stimuli-responsive smart devices, and nanofluidic devices, among others.

HiFreSP: A novel high-frequency sub-pathway mining approach to identify robust prognostic gene signatures.

With the increasing awareness of heterogeneity in cancers, better prediction of cancer prognosis is much needed for more personalized treatment. Recently, extensive efforts have been made to explore the variations in gene expression for better prognosis. However, the prognostic gene signatures predicted by most existing methods have little robustness among different datasets of the same cancer. To improve the robustness of the gene signatures, we propose a novel high-frequency sub-pathways mining approach (HiFreSP), integrating a randomization strategy with gene interaction pathways. We identified a six-gene signature (CCND1, CSF3R, E2F2, JUP, RARA and TCF7) in esophageal squamous cell carcinoma (ESCC) by HiFreSP. This signature displayed a strong ability to predict the clinical outcome of ESCC patients in two independent datasets (log-rank test, P = 0.0045 and 0.0087). To further show the predictive performance of HiFreSP, we applied it to two other cancers: pancreatic adenocarcinoma and breast cancer. The identified signatures show high predictive power in all testing datasets of the two cancers. Furthermore, compared with the two popular prognosis signature predicting methods, the least absolute shrinkage and selection operator penalized Cox proportional hazards model and the random survival forest, HiFreSP showed better predictive accuracy and generalization across all testing datasets of the above three cancers. Lastly, we applied HiFreSP to 8137 patients involving 20 cancer types in the TCGA database and found high-frequency prognosis-associated pathways in many cancers. Taken together, HiFreSP shows higher prognostic capability and greater robustness, and the identified signatures provide clinical guidance for cancer prognosis. HiFreSP is freely available via GitHub: https://github.com/chunquanlipathway/HiFreSP.

ENdb: a manually curated database of experimentally supported enhancers for human and mouse.

Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, are highly associated with human disease and biological processes. Although some enhancer databases have been published, most only focus on enhancers identified by high-throughput experimental techniques. Therefore, it is highly desirable to construct a comprehensive resource of manually curated enhancers and their related information based on low-throughput experimental evidences. Here, we established a comprehensive manually-curated enhancer database for human and mouse, which provides a resource for experimentally supported enhancers, and to annotate the detailed information of enhancers. The current release of ENdb documents 737 experimentally validated enhancers and their related information, including 384 target genes, 263 TFs, 110 diseases and 153 functions in human and mouse. Moreover, the enhancer-related information was supported by experimental evidences, such as RNAi, in vitro knockdown, western blotting, qRT-PCR, luciferase reporter assay, chromatin conformation capture (3C) and chromosome conformation capture-on-chip (4C) assays. ENdb provides a user-friendly interface to query, browse and visualize the detailed information of enhancers. The database is available at http://www.licpathway.net/ENdb.

Colorimetric assay based on peroxidase-like activity of dodecyl trimethylammonium bromide-tetramethyl zinc (4-pyridinyl) porphyrin for detection of organophosphorus pesticides.

A simple and sensitive colorimetric assay for detecting organophosphorus pesticides (OPs) was developed based on 3,3',5,5'-tetramethylbenzidine (TMB)/hydrogen peroxide (H2O2)/dodecyl trimethylammonium bromide (DTAB)-tetramethyl zinc (4-pyridinyl) porphyrin (ZnTPyP). In this system, based on the peroxidase-like activity of DTAB-ZnTPyP, H2O2 decomposes to produce hydroxyl radicals, which oxidize TMB, resulting in blue oxidation products. The OPs (trichlorfon, dichlorvos, and thimet) were first combined with DTAB-ZnTPyP through electrostatic interactions. The OPs caused a decrease in the peroxidase-like activity of DTAB-ZnTPyP due to spatial site blocking. At the same time, π-interactions occurred between them, and these interactions also inhibited the oxidation of TMB (652 nm), thus making the detection of OPs possible. The limits of detection for trichlorfon, dichlorvos, and thimet were 0.25, 1.02, and 0.66 µg/L, respectively, and the corresponding linear ranges were 1-35, 5-45, and 1-40 µg/L, respectively. Moreover, the assay was successfully used to determine OPs in cabbage, apple, soil, and traditional Chinese medicine samples (the recovery ratios were 91.8-109.8%), showing a great promising potential for detecting OPs also in other complex samples.

Neutrophil/lymphocyte, platelet/lymphocyte and monocyte/lymphocyte ratios in schizophrenia.

OBJECTIVE: Neutrophil-to-lymphocyte ratio (NLR), monocyte-to-lymphocyte ratio (MLR), and platelet-to-lymphocyte ratio (PLR) have been used as markers of inflammation in mental illness. However, these indices have not been widely used in schizophrenia research in Chinese participants. Our aim was to use these ratios to explore the relationship between schizophrenia and inflammation. METHODS: In this retrospective cross-sectional study, we collected total blood cell counts of 549 patients with schizophrenia and 930 healthy controls at Beijing Huilongguan Hospital in October 2019. We analyzed the subjects' platelet, lymphocyte, monocyte, and neutrophil counts; compared the calculated NLR, MLR, and PLR between patients and healthy controls; and evaluated the correlations with age and gender. RESULTS: Platelet and lymphocyte counts were significantly lower, while NLR and MLR were significantly higher, in patients with schizophrenia compared to healthy controls. Additionally, monocyte count, lymphocyte count, MLR, and NLR were different between male and female subjects. CONCLUSION: This study supports the inflammatory hypothesis of schizophrenia in the Chinese population.

SEdb: a comprehensive human super-enhancer database.

Super-enhancers are important for controlling and defining the expression of cell-specific genes. With research on human disease and biological processes, human H3K27ac ChIP-seq datasets are accumulating rapidly, creating the urgent need to collect and process these data comprehensively and efficiently. More importantly, many studies showed that super-enhancer-associated single nucleotide polymorphisms (SNPs) and transcription factors (TFs) strongly influence human disease and biological processes. Here, we developed a comprehensive human super-enhancer database (SEdb, http://www.licpathway.net/sedb) that aimed to provide a large number of available resources on human super-enhancers. The database was annotated with potential functions of super-enhancers in the gene regulation. The current version of SEdb documented a total of 331 601 super-enhancers from 542 samples. Especially, unlike existing super-enhancer databases, we manually curated and classified 410 available H3K27ac samples from >2000 ChIP-seq samples from NCBI GEO/SRA. Furthermore, SEdb provides detailed genetic and epigenetic annotation information on super-enhancers. Information includes common SNPs, motif changes, expression quantitative trait locus (eQTL), risk SNPs, transcription factor binding sites (TFBSs), CRISPR/Cas9 target sites and Dnase I hypersensitivity sites (DHSs) for in-depth analyses of super-enhancers. SEdb will help elucidate super-enhancer-related functions and find potential biological effects.

Three New Hydroxyphenylacetic Acid Derivatives and A New Alkaloid from Endophytic Fungus Mortierella sp. in Epimedium acuminatum Franch. and Their Antibacterial Activity.

Three new hydroxyphenylacetic acid derivatives, stachylines E-G (1-3), and a new alkaloid, mortieridinone (4), along with six known compounds (5-10), were isolated from endophytic fungus Mortierella sp. in Epimedium acuminatum Franch. Their structures were determined by their spectroscopic analyses and by comparison with the literature data. Compounds 7 and 10 showed selective antibacterial activity against tested multidrug-resistant bacteria with minimum inhibitory concentration (MIC) values ranging from 25 to 3.13 µg/mL.

Cytotoxicity of CdTe quantum dots with different surface coatings against yeast Saccharomyces cerevisiae.

Cadmium (Cd)-based QDs are well studied owing to their excellent optical properties. The applications of Cd-based QDs in biomedical filed, however, is hindered by its inherent toxicity. In this study, to overcome the inherent toxicity of heavy metals, CdTe QDs were encapsulated with different shells (NAC, MPA and GSH) to reduce the leakage of Cd from the core. We studied the cytotoxicity of the three kinds of CdTe QDs on S. cerevisiae by spectroscopic, electrochemical, microscopic methods and microcalorimetric technique. Results showed that toxicity of CdTe QDs increased with the augment of QD concentration. According to the values of IC50 ((GSH-CdTe QDs (15.3 nmol/L) < MPA-CdTe QDs (56.2 nmol/L) < NAC-CdTe QDs (89.8 nmol/L)), the most toxic one is GSH-CdTe QDs, followed by MPA-CdTe QDs, then NAC-CdTe QDs. The coatings have contribution to their toxicity. The three kinds of QDs with the similar shape (sphere) can enter the cell by the clathrin-mediated endocytosis and lead to the different impairments. The mechanism of cytotoxicity is due to the release of Cd2+ leading elevation of intracellular reactive oxygen species (ROS), which damage mitochondria. The clathrin-mediated endocytosis is a significant factor in determining the toxicity of CdTe QDs.

The Optimal Length of Hospitalization for Functional Recovery of Schizophrenia Patients, a Real-World Study in Chinese People.

This study investigated the relationship between the activities of daily living and the length of hospitalization to determine the optimal length of hospitalization for patients with schizophrenia. We collected information from all schizophrenia patients discharged in Peking University Huilongguan Clinical Medical School from January 1, 2015 to December 31, 2015. A total of 1967 patients were enrolled in this study. The Chinese version of the modified Barthel index (MBI-C) was used to assess patients' actual performance on activities of daily living. We used the paired samples t-test to compare MBI-C scores at admission and discharge and performed correlation analysis to find the trend of MBI-C change with length of hospitalization. The average length of hospitalization was 73.3 ± 42.2 days. There were significant differences between the MBI-C scores at the time of discharge from hospital compared with those at the time of admission to the hospital (93.4 ± 11.2 vs. 88.7 ± 11.8; P < 0.001). Taking the length of hospitalization as the grouping boundary value, the correlation analysis of the subgroup found that below a minimum of 20 days, the improvement in the MBI-C scores increased with the increase of length of hospitalization, and above a maximum of 50 days, the improvement in the MBI-C scores decreased with the increase of length of hospitalization. The optimal length of hospitalization for patients with schizophrenia may lie between 20 and 50 days, with regard to the recovery of daily living function.

Application of Fiber Bragg Grating Acoustic Emission Sensors in Thin Polymer-Bonded Explosives.

Fiber Bragg grating (FBG) acoustic emission (AE) sensors have been used in many applications. In this paper, based on an FBG AE sensor, the sensing principle of the interaction between the AE wave and the sensor is introduced. Then, the directionality of the FBG AE sensor on the surface of a thin polymer-bonded explosive (PBX) material is studied. Finally, the time coefficient location method is proposed to correct the AE time detected by the FBG AE sensor, thereby improving the accuracy of location experiments.

Novel Fiber-Optic Ring Acoustic Emission Sensor.

Acoustic emission technology has been applied to many fields for many years. However, the conventional piezoelectric acoustic emission sensors cannot be used in extreme environments, such as those with heavy electromagnetic interference, high pressure, or strong corrosion. In this paper, a novel fiber-optic ring acoustic emission sensor is proposed. The sensor exhibits high sensitivity, anti-electromagnetic interference, and corrosion resistance. First, the principle of a novel fiber-optic ring sensor is introduced. Different from piezoelectric and other fiber acoustic emission sensors, this novel sensor includes both a sensing skeleton and a sensing fiber. Second, a heterodyne interferometric demodulating method is presented. In addition, a fiber-optic ring sensor acoustic emission system is built based on this method. Finally, fiber-optic ring acoustic emission experiments are performed. The novel fiber-optic ring sensor is glued onto the surface of an aluminum plate. The 150 kHz standard continuous sinusoidal signals and broken lead signals are successfully detected by the novel fiber-optic ring acoustic emission sensor. In addition, comparison to the piezoelectric acoustic emission sensor is performed, which shows the availability and reliability of the novel fiber-optic ring acoustic emission sensor. In the future, this novel fiber-optic ring acoustic emission sensor will provide a new route to acoustic emission detection in harsh environments.