dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data.

The last 18 months, or more, have seen a profound shift in our global experience, with many of us navigating a once-in-100-year pandemic. To date, COVID-19 remains a life-threatening pandemic with little to no targeted therapeutic recourse. The discovery of novel antiviral agents, such as vaccines and drugs, can provide therapeutic solutions to save human beings from severe infections; however, there is no specifically effective antiviral treatment confirmed for now. Thus, great attention has been paid to the use of natural or artificial antimicrobial peptides (AMPs) as these compounds are widely regarded as promising solutions for the treatment of harmful microorganisms. Given the biological significance of AMPs, it was obvious that there was a significant need for a single platform for identifying and engaging with AMP data. This led to the creation of the dbAMP platform that provides comprehensive information about AMPs and facilitates their investigation and analysis. To date, the dbAMP has accumulated 26 447 AMPs and 2262 antimicrobial proteins from 3044 organisms using both database integration and manual curation of >4579 articles. In addition, dbAMP facilitates the evaluation of AMP structures using I-TASSER for automated protein structure prediction and structure-based functional annotation, providing predictive structure information for clinical drug development. Next-generation sequencing (NGS) and third-generation sequencing have been applied to generate large-scale sequencing reads from various environments, enabling greatly improved analysis of genome structure. In this update, we launch an efficient online tool that can effectively identify AMPs from genome/metagenome and proteome data of all species in a short period. In conclusion, these improvements promote the dbAMP as one of the most abundant and comprehensively annotated resources for AMPs. The updated dbAMP is now freely accessible at http://awi.cuhk.edu.cn/dbAMP.

dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications.

Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version. Due to the increasing number of studies on the mechanism of PTMs in the past few years, a great deal of upstream regulatory proteins of PTM substrate sites have been revealed. The updated dbPTM thus collates regulatory information from databases and literature, and merges them into a protein-protein interaction network. To enhance the understanding of the association between PTMs and molecular functions/cellular processes, the functional annotations of PTMs are curated and integrated into the database. In addition, the existing PTM-related resources, including annotation databases and prediction tools are also renewed. Overall, in this update, we would like to provide users with the most abundant data and comprehensive annotations on PTMs of proteins. The updated dbPTM is now freely accessible at https://awi.cuhk.edu.cn/dbPTM/.

Prediction of the mechanisms of action of Qutan Huoxue decoction in non-alcoholic steatohepatitis (NASH): a network pharmacology study and experimental validation.

CONTEXT: Qutan Huoxue decoction (QTHX) is used to treat non-alcoholic steatohepatitis (NASH) with good efficacy in the clinic. However, the mechanism is not clear yet. OBJECTIVE: This study investigates the mechanism of QTHX in the treatment of NASH. MATERIALS AND METHODS: Potential pathways of QTHX were predicted by network pharmacology. Fourty Sprague Dawley (SD) rats (half normal diet, half high-fat diet) were fed six to eight weeks, primary hepatocytes and Kupffer cells were extracted and co-cultured by the 0.4-micron trans well culture system. Then, the normal co-cultured cells were treated by normal serum, the NASH co-cultured cells were treated with various concentrations of QTHX-containing serum (0, 5, 7.5 or 10 µg/mL) for 24 h. The expression of targets were measured with Activity Fluorometric Assay, Western blot and PCR assay. RESULTS: Network pharmacology indicated that liver-protective effect of QTHX was associated with its anti-inflammation response, oxidative stress, and lipid receptor signalling. 10 µg/mL QTHX significantly reduced the inflammation response and lipid levels in primary hepatocytes (ALT: 46.43 ± 2.76 U/L, AST: 13.96 ± 1.08 U/L, TG: 0.25 ± 0.01 mmol/L, TC: 0.14 ± 0.05 mmol/L), comparing with 0 µg/mL NASH group (ALT: 148 ± 9.22 U/L, AST: 53.02 ± 2.30 U/L, TG: 0.74 ± 0.07 mmol/L, TC: 0.91 ± 0.07 mmol/L) (p < 0.01). Meanwhile, QTHX increased expression of SOCS1 and decreased expression of TLR4, Myd88, NF-κB. CONCLUSIONS: The study suggested that QTHX treats NASH in rats by activating the SCOS1/NF-κB/TLR4 pathway, suggesting QTHX could be further developed as a potential liver-protecting agent.

Genome­wide association study and genomic prediction for growth traits in yellow-plumage chicken using genotyping-by-sequencing.

BACKGROUND: Growth traits are of great importance for poultry breeding and production and have been the topic of extensive investigation, with many quantitative trait loci (QTL) detected. However, due to their complex genetic background, few causative genes have been confirmed and the underlying molecular mechanisms remain unclear, thus limiting our understanding of QTL and their potential use for the genetic improvement of poultry. Therefore, deciphering the genetic architecture is a promising avenue for optimising genomic prediction strategies and exploiting genomic information for commercial breeding. The objectives of this study were to: (1) conduct a genome-wide association study to identify key genetic factors and explore the polygenicity of chicken growth traits; (2) investigate the efficiency of genomic prediction in broilers; and (3) evaluate genomic predictions that harness genomic features. RESULTS: We identified five significant QTL, including one on chromosome 4 with major effects and four on chromosomes 1, 2, 17, and 27 with minor effects, accounting for 14.5 to 34.1% and 0.2 to 2.6% of the genomic additive genetic variance, respectively, and 23.3 to 46.7% and 0.6 to 4.5% of the observed predictive accuracy of breeding values, respectively. Further analysis showed that the QTL with minor effects collectively had a considerable influence, reflecting the polygenicity of the genetic background. The accuracy of genomic best linear unbiased predictions (BLUP) was improved by 22.0 to 70.3% compared to that of the conventional pedigree-based BLUP model. The genomic feature BLUP model further improved the observed prediction accuracy by 13.8 to 15.2% compared to the genomic BLUP model. CONCLUSIONS: A major QTL and four minor QTL were identified for growth traits; the remaining variance was due to QTL effects that were too small to be detected. The genomic BLUP and genomic feature BLUP models yielded considerably higher prediction accuracy compared to the pedigree-based BLUP model. This study revealed the polygenicity of growth traits in yellow-plumage chickens and demonstrated that the predictive ability can be greatly improved by using genomic information and related features.

Influence of weight management on the prognosis of steatohepatitis in chronic hepatitis B patients during antiviral treatment.

BACKGROUND: Although concomitant nonalcoholic steatohepatitis (NASH) is common in chronic hepatitis B (CHB), the impact of viral factors on NASH and the outcome of CHB patients concomitant with NASH remain unclear. We aimed to investigate the outcomes of NASH in CHB patients receiving antiviral treatment. METHODS: In the post-hoc analysis of a multicenter trial, naïve CHB patients receiving 72-week entecavir treatment were enrolled. We evaluated the biochemical, viral and histopathological responses of these patients. The histopathological features of NASH were also evaluated, using paired liver biopsies at baseline and week 72. RESULTS: A total of 1000 CHB patients were finally enrolled for analysis, with 18.2% of whom fulfilling the criteria of NASH. A total of 727 patients completed entecavir antiviral treatment and received the second biopsy. Serum HBeAg loss, HBeAg seroconversion and HBV-DNA undetectable rates were similar between patients with or without NASH (P > 0.05). Among patients with NASH, the hepatic steatosis, ballooning, lobular inflammation scores and fibrosis stages all improved during follow-up (all P < 0.001), 46% (63/136) achieved NASH resolution. Patients with baseline body mass index (BMI) ≥ 23 kg/m2 (Asian criteria) [odds ratio (OR): 0.414; 95% confidence interval (95% CI): 0.190-0.899; P = 0.012] and weight gain (OR: 0.187; 95% CI: 0.050-0.693; P = 0.026) were less likely to have NASH resolution. Among patients without NASH at baseline, 22 (3.7%) developed NASH. Baseline BMI ≥ 23 kg/m2 (OR: 12.506; 95% CI: 2.813-55.606; P = 0.001) and weight gain (OR: 5.126; 95% CI: 1.674-15.694; P = 0.005) were predictors of incident NASH. CONCLUSIONS: Lower BMI and weight reduction but not virologic factors determine NASH resolution in CHB. The value of weight management in CHB patients during antiviral treatment deserves further evaluation.

ViTT: Vision Transformer Tracker.

This paper presents a new model for multi-object tracking (MOT) with a transformer. MOT is a spatiotemporal correlation task among interest objects and one of the crucial technologies of multi-unmanned aerial vehicles (Multi-UAV). The transformer is a self-attentional codec architecture that has been successfully used in natural language processing and is emerging in computer vision. This study proposes the Vision Transformer Tracker (ViTT), which uses a transformer encoder as the backbone and takes images directly as input. Compared with convolution networks, it can model global context at every encoder layer from the beginning, which addresses the challenges of occlusion and complex scenarios. The model simultaneously outputs object locations and corresponding appearance embeddings in a shared network through multi-task learning. Our work demonstrates the superiority and effectiveness of transformer-based networks in complex computer vision tasks and paves the way for applying the pure transformer in MOT. We evaluated the proposed model on the MOT16 dataset, achieving 65.7% MOTA, and obtained a competitive result compared with other typical multi-object trackers.

Statistic Experience Based Adaptive One-Shot Detector (EAO) for Camera Sensing System.

Object detection in a camera sensing system has been addressed by researchers in the field of image processing. Highly-developed techniques provide researchers with great opportunities to recognize objects by applying different algorithms. This paper proposes an object recognition model, named Statistic Experience-based Adaptive One-shot Detector (EAO), based on convolutional neural network. The proposed model makes use of spectral clustering to make detection dataset, generates prior boxes for object bounding and assigns prior boxes based on multi-resolution. The model is constructed and trained for improving the detection precision and the processing speed. Experiments are conducted on classical images datasets while the results demonstrate the superiority of EAO in terms of effectiveness and efficiency. Working performance of the EAO is verified by comparing it to several state-of-the-art approaches, which makes it a promising method for the development of the camera sensing technique.

Hierarchical mesoporous TiO2/starch-based microparticles used as an efficient and reusable adsorbent for removal of water-soluble dye.

The widespread use of organic dyes in various industrial applications, driven by rapid industrialization, has become a significant environmental concern. Thus, highly efficient and reusable adsorbent for removal of pollutant dyes have gained increasing attention in water treatment. In this study, we present TiO2 nanoparticle-embedded mesoporous starch-based microparticle (TiO2@MSMP) with hierarchical rose-like structure were synthesis by using acetone precipitation of short-chain glucan (SCG) obtained from waxy maize starch. The resulting TiO2@MSMP exhibits an A-type crystalline polymorph and mean particle size of approximately 2 µm, displaying a type IV adsorption isotherm with a mean pore diameter of 19 nm and an average surface area of 12.34 m2/g. The adsorption ability of TiO2@MSMP towards methyl orange (MO) and crystal violet (CV) were 85.8 mg/g and 103.8 mg/g, respectively. The reusability of TiO2@MSMP was achieved by UV irradiation, which resulted in photodegradation of the adsorbed dye over 80 % while maintaining good absorption ability and structural stability during the recycling process. Given its cost-effectiveness, high adsorption capacity, and excellent reusability, TiO2@MSMP holds promise as an effective and environmentally friendly adsorbent with significant potential for removing dyes from aqueous solutions and purifying water.

Facile Synthesis of Multifunctional Mesoporous Starch-Based Microparticle for Effective Hemostasis and Wound Healing.

Uncontrolled hemorrhage and infection are the principal causes of mortality associated with trauma in both military and civilian medical settings. Modified starch granules have emerged as a safe hemostatic agent for irregular and noncompressible wounds, but their performance is constrained by limited hemostasis efficiency and modest antibacterial activity. This study reported a directed self-assembly approach for a multifunctional mesoporous starch-based microparticle loaded with chitosan and calcium ions (Ca@MSMP) used for rapid hemostasis and wound healing. Directed self-assembly of uniform Ca@MSMP with a hierarchical hollow structure in the presence of chitosan was confirmed by scanning electron microscopy (SEM) analysis and pore structure analysis. The resulting Ca@MSMP exhibited a well-defined spherical shape and uniform size of 1 µm and demonstrated excellent antibacterial activity (>95%) without hemolytic activity. Importantly, Ca@MSMP enhanced blood coagulation and platelet aggregation via the synergistic effect of rapid calcium release and chitosan-mediated electrostatic interactions, leading to a significant decrease in blood loss and reduction in hemostasis time in rat tail amputation and liver injury models. In comparative analyses, Ca@MSMP significantly outperformed the commercial hemostatic agent Quickclean, notably enhancing the healing of full-thickness skin wounds in vivo by effectively preventing infection. These results underscore the potential of this innovative hemostatic material in diverse clinical scenarios, offering effective solutions for the management of bleeding in wounds that are irregularly shaped and noncompressible.

Calcium Doped NASICON Electrolyte with Graphite Coating for Stable All-solid-state Sodium Metal Batteries.

All-solid-state sodium metal batteries face the challenges of low ionic conductivity of solid electrolytes and poor wettability towards metallic Na anode. Herein, Na3Zr2Si2PO12 solid electrolyte is doped with Ca2+, obtaining a high ionic conductivity of 2.09×10-3 S cm-1 with low electronic conductivity of 1.43×10-8 S cm-1 at room temperature, which could accelerate Na+ transportation and suppress sodium dendrite growth. Meanwhile, a graphite-based interface layer is coated on Na3.4Zr1.8Ca0.2Si2PO12 (Na3.4Zr1.8Ca0.2Si2PO12-G) in order to improve the solid-solid contact between solid electrolyte and Na anode, realizing a uniform current distribution and smooth Na metal plating/stripping, and thus achieving a triple higher critical current density of 3.5 mA cm-2 compared with that of Na3.4Zr1.8Ca0.2Si2PO12. In addition, the assembled Na3V2(PO4)3/Na3.4Zr1.8Ca0.2Si2PO12-G/Na all-solid-state battery exhibits excellent electrochemical performances with a reversible capacity of 81.47 mAh g-1 at 1 C and capacity retention of 97.75 % after 500 cycles.

Evaluate the clinical efficacy of traditional Chinese Medicine as the neoadjuvant treatment in reducing the incidence of hepatocellular carcinoma in patients with hepatitis B-related cirrhosis: A systematic review and meta-analysis.

Background: Traditional Chinese Medicine (TCM), has been used for hepatocellular carcinoma (HCC) at every therapeutic stage, even before tumor formation. However, the efficacy of TCM in reducing the incidence of HCC in patients with chronic hepatitis B-related cirrhosis remains unclear. This study aims to address this gap. Methods: Publications were collected from PubMed, EMBASE, Cochrane Library, Web of Science, CNKI, Sino Med, VIP, and Wan Fang Databases. Relative risk (RR) was calculated with a 95 % confidence interval (CI). Heterogeneity was assessed. The Cochrane Collaboration's tool was used to assess the risk of bias. Results: 10 studies with 2702 patients showed that the combination therapy significantly reduced the incidence of HCC in patients with post-hepatitis B cirrhosis at 1, 3, and 5 years. However, the preventive effects of TCM were in compensated cirrhosis, but not the decompensated cirrhosis. Furthermore, TCM correlated with improved liver function and enhanced virological response. Conclusion: Combination therapy with TCM demonstrated the certain potential in reducing the incidence of HCC in patients with hepatitis B cirrhosis. This is attrinuted to the improvement of liver function and enhancement of the viral response. However, the efficacy of TCM in the field still needs more high-quality RCTs to provide stronger evidence in the future.

Short-chain glucan self-assembly for green synthesis of functional biomaterials: Mechanism, synthesis, and microstructural control.

Short-chain glucan (SCG) is a linear homopolymer containing 10 to 50 glucose units linked with α(1,4) glycosidic bonds. With its abundant, low-cost, nontoxic, biodegradable/biocompatible nature, self-assembled SCG particles (SSC) have emerged as functional biomaterials, which have recently attracted tremendous attentions in various fields. SCG self-assembly occurs through the spontaneous association of molecules under equilibrium conditions into stable and structurally well-defined nanoscale or micrometer-scale aggregates, which is governed by various intermolecular non-covalent interactions, including hydrogen-bonding, electrostatic, hydrophobic, and van der Waals. With precise and effective control of the self-assembly process of SSC, its structural modulation and function integration can be expected. Thus, we convinced that SCG self-assembly could provide an effective means of developing starch-based functional biomaterials with beneficial health properties and wide application in food industries. In this review, we provide an overview of recent advances in the green approach for the self-assembly of SSC, as well as the influence of thermodynamic and kinetic factors on its morphology and physicochemical properties. We highlight recent contributions to developing strategies for the construction of SSC with increasing complexity and functionality that are suitable for a variety of food applications. Finally, we briefly outline our perspectives and discuss the challenges in the field.

Serum metabolic profile and metabolome genome-wide association study in chicken.

BACKGROUND: Chickens provide globally important livestock products. Understanding the genetic and molecular mechanisms underpinning chicken economic traits is crucial for improving their selective breeding. Influenced by a combination of genetic and environmental factors, metabolites are the ultimate expression of physiological processes and can provide key insights into livestock economic traits. However, the serum metabolite profile and genetic architecture of the metabolome in chickens have not been well studied. RESULTS: Here, comprehensive metabolome detection was performed using non-targeted LC-MS/MS on serum from a chicken advanced intercross line (AIL). In total, 7,191 metabolites were used to construct a chicken serum metabolomics dataset and to comprehensively characterize the serum metabolism of the chicken AIL population. Regulatory loci affecting metabolites were identified in a metabolome genome-wide association study (mGWAS). There were 10,061 significant SNPs associated with 253 metabolites that were widely distributed across the entire chicken genome. Many functional genes affect metabolite synthesis, metabolism, and regulation. We highlight the key roles of TDH and AASS in amino acids, and ABCB1 and CD36 in lipids. CONCLUSIONS: We constructed a chicken serum metabolite dataset containing 7,191 metabolites to provide a reference for future chicken metabolome characterization work. Meanwhile, we used mGWAS to analyze the genetic basis of chicken metabolic traits and metabolites and to improve chicken breeding.

Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits.

The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However, epigenetic information, such as a bird-specific chromatin accessibility atlas, is currently lacking for the thousands of bird species currently described. The major genomic difference between birds and mammals is their shorter introns and intergenic distances, which seriously hinders the use of humans and mice as a reference for studying the function of important regulatory regions in birds. In this study, using chicken as a model bird species, we systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) samples across 11 tissues. An average of 50 796 open chromatin regions were identified per sample, cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence-specific transcription factors and direct regulation of adjacent functional genes. By integrating data from genome-wide association studies, our results suggest that chicken body weight is driven by different regulatory variants active in growth-relevant tissues. We propose CAB39L (active in the duodenum), RCBTB1 (muscle and liver), and novel long non-coding RNA ENSGALG00000053256 (bone) as candidate genes regulating chicken body weight. Overall, this study demonstrates the value of epigenetic data in fine-mapping functional variants and provides a compendium of resources for further research on the epigenetics and evolution of birds and mammals.

Impact of solvent polarity on the morphology, physicochemical properties, and digestibility of A-type resistant starch particles.

Resistant starch particles (RSP) formed by antisolvent precipitation method has attracted much attention as a functional food ingredient having beneficial effects on obesity and diabetes. However, the effect of solvent polarity on the physicochemical properties and digestibility of RSP remains unclear. Here, n-propanol, isopropanol, acetone, and ethanol were employed as antisolvents to prepare RSP. The width and length of the resulting RSP decreased from 0.87 µm to 0.59 µm and from 2.56 µm to 1.31 µm, respectively, upon increasing the solvent polarity, while dramatically decreasing their crystallinity and the gelatinization enthalpy from 80.5% to 62.3% and from 67.9 ± 14.4 J/g to 41.5 ± 8.3 J/g, respectively, suggesting that solvent polarity is critical factor determining morphology, crystallinity, and thermostability of RSP. Furthermore, the level of resistant starch in RSP was found to be inversely proportional to the degree of solvent polarity, which would provide a useful means for modulating the digestibility of RSP.

Recent Advances in Biosensor Development for the Detection of Viral Particles in Foods: A Comprehensive Review.

Viral foodborne diseases cause serious harm to human health and the economy. Rapid, accurate, and convenient approaches for detecting foodborne viruses are crucial for preventing diseases. Biosensors integrating electrochemical and optical properties of nanomaterials have emerged as effective tools for the detection of viruses in foods. However, they still face several challenges, including substantial sample preparation and relatively poor sensitivity due to complex food matrices, which limit their field applications. Hence, the purpose of this review is to provide an overview of recent advances in biosensing techniques, including electrochemical, SERS-based, and colorimetric biosensors, for detecting viral particles in food samples, with emerging techniques for extraction/concentration of virus particles from food samples. Moreover, the principle, design, and advantages/disadvantages of each biosensing method are comprehensively described. This review covers the recent development of rapid and sensitive biosensors that can be used as new standards for monitoring food safety and food quality in the food industry.

Traditional Chinese medicine combined with radiofrequency ablation improves primary liver cancer outcomes: A systematic review with meta-analysis.

Background & aims: Traditional Chinese medicine and radiofrequency ablation are becoming increasingly important in the treatment of primary liver cancer. However, the clinical outcome of traditional Chinese medicine plus radiofrequency ablation is contentious. This study aimed to conduct a meta-analysis of randomized controlled clinical trials to address this gap. Methods: Short-term efficacy, alpha-fetoprotein level, immune function, liver function, and quality of life outcomes in patients with primary liver cancer treated with Chinese herbal medicine adjuvant radiofrequency ablation were systematically reviewed. Results: Eighteen randomized controlled clinical trials with 1488 patients with primary liver cancer were included. The combination treatment significantly increased the objective remission rate and quality of patient survival compared to the control group. Combination treatment significantly improved immunity and liver function factors, including CD3, CD4, CD4/CD8, alanine aminotransferase, aspartate aminotransferase, total bilirubin, and albumin levels. However, there were no statistical differences in CD8 levels across treatments. Trial sequential analysis showed that the cumulative Z-curve of the Objective response rate crossed the conventional and test sequence monitoring boundaries; however, it did not cross the required information size line. Conclusions: Traditional Chinese medicine combined with radiofrequency ablation for primary liver cancer can effectively reduce alpha-fetoprotein and improve clinical efficacy, immune function, liver function, as well as the quality of life.

Identification of a novel ANK1 mutation in a Chinese family with hereditary spherocytosis: A case report.

The present study describes the clinical profile and ankyrin 1 (ANK1) mutation status of a Chinese family with hereditary spherocytosis (HS). A young male patient (proband) was diagnosed with HS after presenting with anaemia and jaundice. The Coombs test was negative and spherocytes were found in peripheral blood smears. Magnetic resonance imaging showed splenomegaly and splenic iron depositions. The red blood cell osmotic fragility test was positive. The eosin-5'-maleimide binding test showed reduced mean channel fluorescence. Whole-exome sequencing revealed a novel ANK1 mutation (c.4707G>A), resulting in a nonsense mutation (p.Trp1569*). The patient's father, paternal aunt and paternal grandmother exhibited comparable clinical symptoms and Sanger sequencing confirmed the same mutation in these family members. To the best of our knowledge, an HS pedigree with this novel ANK1 nonsense mutation has not been previously reported. At the same time, the unique clinical presentation of this pedigree helps our understanding of the heterogeneity of clinical manifestations of HS.

A review of nucleic acid-based detection methods for foodborne viruses: Sample pretreatment and detection techniques.

Viruses are major pathogens that cause food poisoning when ingested via contaminated food and water. Therefore, the development of foodborne virus detection technologies that can be applied throughout the food distribution chain is essential for food safety. A common nucleic acid-based detection method is polymerase chain reaction (PCR), which has become the gold standard for monitoring food contamination by viruses due to its high sensitivity, and availability of commercial kits. However, PCR-based methods are labor intensive and time consuming, and are vulnerable to inhibitors that may be present in food samples. In addition, the methods are restricted with regard to site of analysis due to the requirement of expensive and large equipment for sophisticated temperature regulation and signal analysis procedures. To overcome these limitations, optical and electrical readout biosensors based on nucleic acid isothermal amplification technology and nanomaterials have emerged as alternatives for nucleic acid-based detection of foodborne viruses. Biosensors are promising portable detection tools owing to their easy integration into compact platforms and ability to be operated on-site. However, the complexity of food components necessitates the inclusion of tedious preprocessing steps, and the lack of stability studies on residual food components further restricts the practical application of biosensors as a universal detection method. Here, we summarize the latest advances in nucleic acid-based strategies for the detection of foodborne viruses, including PCR-based and isothermal amplification-based methods, gene amplification-free methods, as well as food pretreatment methods. The principles, strengths/disadvantages, and performance of each method, problems to be solved, and future prospects for the development of a universal detection method are discussed.

Transcription-wide impact by RESCUE-induced off-target single-nucleotide variants in mammalian cells.

RNA base editing is a promising tool in precise molecular therapy. Currently, there are two widely used RNA base editors, REPAIR and RESCUE. REPAIR only facilitates A-to-I conversions, while RESCUE performs both A-to-I and C-to-U conversions. Thus, RESCUE can generate twice the number of mutations compared to REPAIR. However, transcription-wide impact due to RESCUE-induced off-target single-nucleotide variants (SNVs) is not fully appreciated. Therefore, to determine the off-target effects of RESCUE-mediated editing, we employed transcription-wide sequencing on cells edited by RESCUE. The SNVs showed different off-target effects on mRNA, circRNA, lncRNA, and miRNA expression patterns and their interacting networks. Our results illustrate the transcription-wide impact of RESCUE-induced off-target SNVs and highlight the need for careful characterization of the off-target impact by this editing platform.