Site-Specific Radical Alkylation of Aryl Cyanide: Visible-Light, Photoredox-Catalyzed, Three-Component Arylalkylation of [1.1.1]Propellane

We report herein a three-component radical arylalkylation of [1.1.1]propellane toward the synthesis of aryl-substituted bicyclo[1.1.1]pentane derivatives. The use of electron-deficient aryl cyanide as an aryl group source not only reduces the energy barrier of the arylation of the nucleophilic alkyl radical species, but also suppresses the electrophilic Friedel-Crafts alkylation process, enabling the present site-selective arylalkylation.

A rapid on-site visualization platform based on RPA coupled with CRISPR-Cas12a for the detection of genetically modified papaya 'Huanong No.1'

The Papaya ringspot virus (PRSV)-resistant genetically modified (GM) papaya 'Huanong No.1' has been certified as safe for consumption and widely planted in China for about 18 years. To protect consumers' rights and facilitate government supervision and monitoring, it is necessary to establish a simple, rapid, and specific detection method for 'Huanong No.1'. Herein, we developed a platform based on recombinase polymerase amplification (RPA) coupled with CRISPR-Cas12a for the detection of 'Huanong No.1'. The RPA-CRISPR-Cas12a platform was found to have high specificity, with amplification signals only present in 'Huanong No.1'. Additionally, the platform was highly sensitive, with a limit of detection (LOD) of approximately 20 copies. The detection process was fast and could be completed in less than 1 h. This novel platform enables the rapid on-site visualization detection of 'Huanong No.1', eliminating dependence on laboratory conditions and specialized instruments, and can serve as a technical reference for the rapid detection of other GM plants.

Resolving 3D genomic landscape of CD4+ T cells in the peripheral blood of patients with psoriasis

A precise regulation of gene expression depends on the accuracy of the three-dimensional (3D) structure of chromatin; however, the effects of 3D genome on gene expression in psoriasis remain unknown. In this study, we conducted Hi-C and RNA-seq on CD4+ T cells collected from five psoriasis patients and three healthy controls, and constructed a comprehensive 3D chromatin interaction map to delineate the genomic hierarchies including A/B compartments, topologically associated domains (TADs), and chromatin loops. Then, the specific super-enhancers (SEs) related to psoriasis were identified by Hi-C and H3K27ac ChIP-seq data. Subsequently, comprehensive analyses were carried out on the differentially expressed genes that are associated with altered TADs, loops and SEs in psoriasis. Lastly, we screened the candidate target genes and examined the potential functional single nucleotide polymorphism in psoriasis affected by disruptions of the spatial organization. This paper provides a comprehensive reference for examining the 3D genome interactions in psoriasis and elucidating the interplay between spatial organization disruption and gene regulation. We hope our findings can help clarify the mechanisms underlying the pathogenesis of psoriasis and shed light on the role of 3D genomic structure, therefore informing potential therapeutic approaches.

The significance of CD16+ monocytes in the occurrence and development of chronic thromboembolic pulmonary hypertension: insights from single-cell RNA sequencing

Background

Chronic thromboembolic pulmonary hypertension (CTEPH) is a serious pulmonary vascular disease characterized by residual thrombi in the pulmonary arteries and distal pulmonary microvascular remodeling. The pathogenesis of CTEPH remains unclear, but many factors such as inflammation, immunity, coagulation and angiogenesis may be involved. Monocytes are important immune cells that can differentiate into macrophages and dendritic cells and play an important role in thrombus formation. However, the distribution, gene expression profile and differentiation trajectory of monocyte subsets in CTEPH patients have not been systematically studied. This study aims to reveal the characteristics and functions of monocytes in CTEPH patients using single-cell sequencing technology, and to provide new insights for the diagnosis and treatment of CTEPH.

Methods

Single-cell RNA sequencing (scRNA-seq) were performed to analyze the transcriptomic features of peripheral blood mononuclear cells (PBMCs) from healthy controls, CTEPH patients and the tissues from CTEPH patients after the pulmonary endarterectomy (PEA). We established a CTEPH rat model with chronic pulmonary embolism caused by repeated injection of autologous thrombi through a central venous catheter, and used flow cytometry to detect the proportion changes of monocyte subsets in CTEPH patients and CTEPH rat model. We also observed the infiltration degree of macrophage subsets in thrombus tissue and their differentiation relationship with peripheral blood monocyte subsets by immunofluorescence staining.

Results

The results showed that the monocyte subsets in peripheral blood of CTEPH patients changed significantly, especially the proportion of CD16+ monocyte subset increased. This monocyte subset had unique functional features at the transcriptomic level, involving processes such as cell adhesion, T cell activation, coagulation response and platelet activation, which may play an important role in pulmonary artery thrombus formation and pulmonary artery intimal remodeling. In addition, we also found that the macrophage subsets in pulmonary endarterectomy tissue of CTEPH patients showed pro-inflammatory and lipid metabolism reprogramming features, which may be related to the persistence and insolubility of pulmonary artery thrombi and the development of pulmonary hypertension. Finally, we also observed that CD16+ monocyte subset in peripheral blood of CTEPH patients may be recruited to pulmonary artery intimal tissue and differentiate into macrophage subset with high expression of IL-1β, participating in disease progression.

Conclusion

CD16+ monocytes subset had significant gene expression changes in CTEPH patients, related to platelet activation, coagulation response and inflammatory response. And we also found that these cells could migrate to the thrombus and differentiate into macrophages with high expression of IL-1β involved in CTEPH disease progression. We believe that CD16+ monocytes are important participants in CTEPH and potential therapeutic targets.

Accuracy of 11 intraocular lens calculation formulas in shallow anterior chamber eyes

PURPOSE

To evaluate the performance of intraocular lens (IOL) calculation formulas and the effect of anterior chamber depth (ACD), axial length (AL) and lens thickness (LT) on the prediction accuracy in shallow ACD eyes.

METHODS

This retrospective, consecutive case-series study included 648 eyes of 648 patients with an ACD < 3.0 mm who underwent phacoemulsification and IOL implantation. Eleven formulas were evaluated: Barrett Universal II (BUII), Emmetropia Verifying Optical (EVO) 2.0, Hill-Radial Basis Function (RBF) 3.0, Hoffer QST, Kane, Olsen, Pearl-DGS and traditional formulas (Haigis, Hoffer Q, Holladay 1 and SRK/T). Subgroup analysis was performed based on ACD, AL and LT.

RESULTS

Overall, the Hoffer QST and Kane showed no systematic bias. The Kane, EVO 2.0, Hill-RBF 3.0 and Hoffer QST had relatively lower mean absolute error and higher percentages of prediction error within ±0.5 D. For the ACD of 2.5-3.0 mm and AL < 22.0 mm subgroup, the Pearl-DGS exhibited the lowest MAE (0.45 D) and MedAE (0.41 D). Most formulas had a significant myopic bias (-0.43 to -0.18 D, p < 0.05) in the LT < 4.3 mm subgroup and a significant hyperopic bias (0.09-0.29 D, p < 0.05) in the LT ≥ 5.1 mm subgroup.

CONCLUSION

The Kane and Hoffer QST were recommended for shallow ACD eyes. In eyes with an ACD between 2.5 and 3.0 mm and a short AL, the Pearl-DGS showed excellent performance. Clinicians need to fine-tune the target refraction according to LT in shallow ACD eyes.

Correction of axial length measurement error by IOLMaster 700 could improve refractive prediction accuracy in silicone oil-filled eyes

PURPOSE

To determine whether correcting the axial length (AL) measurement error of the IOLMaster 700 could improve the refractive prediction accuracy in silicone oil-filled eyes.

METHODS

This study included 265 cataract patients (265 eyes) with silicone oil tamponade who were scheduled for phacoemulsification with intraocular lens (IOL) implantation. The performances of various formulas, including Barrett Universal II, Emmetropia Verifying Optical, Hoffer-QST, Kane, Ladas Super Formula, Pearl-DGS, Radial Basis Function and traditional formulas (Haigis, Hoffer Q, Holladay 1 and SRK/T), were evaluated. The refractive prediction errors (PE) calculated with measured AL (ALmeas) and corrected AL with silicone oil adjustment (SOAL) were compared. Subgroup analysis was performed based on the ALmeas (<23 mm; 23-26 mm; ≥26 mm).

RESULTS

Using SOAL significantly reduced the hyperopic PE of formulas when compared to ALmeas (-0.05 to 0.17 D vs 0.15 to 0.38 D, p < 0.001). After applying AL correction, all formulas showed a lower mean absolute PE (0.47-0.57 D vs 0.50-0.69 D). The percentage of eyes within ±1.0 D of PE increased from 84.91%-88.68% to 89.81%-91.32% for new formulas and from 78.11%-83.40% to 85.66%-88.68% for traditional formulas, with the use of SOAL. Subgroup analysis showed that the majority of formulas with SOAL in prediction accuracy for eyes with an AL ≥26 mm (p < 0.05).

CONCLUSIONS

The refractive prediction accuracy in silicone oil-filled eyes was improved by correcting the AL measurement error of the IOLMaster 700, especially for long eyes.

Development of a novel Cas13a/Cas12a-mediated 'one-pot' dual detection assay for genetically modified crops

INTRODUCTION

Genetically modified (GM) crops have been widely cultivated across the world and the development of rapid, ultrasensitive, visual multiplex detection platforms that are suitable for field deployment is critical for GM organism regulation.

OBJECTIVE

In this study, we developed a novel one-pot system, termed MR-DCA (Multiplex RPA and Dual CRISPR assay), for the simultaneous detection of CaMV35S and NOS genetic targets in GM crops. This innovative approach combined Multiplex RPA (recombinase polymerase amplification) with the Dual CRISPR (clustered regularly interspaced short palindromic repeat) assay technique, to provide a streamlined and efficient method for GM crop detection.

METHODS

The RPA reaction used for amplification CaMV35S and NOS targets was contained in the tube base, while the dual CRISPR enzymes were placed in the tube cap. Following centrifugation, the dual CRISPR (Cas13a/Cas12a) detection system was initiated. Fluorescence visualization was used to measure CaMV35S through the FAM channel and NOS through the HEX channel. When using lateral flow strips, CaMV35S was detected using rabbit anti-digoxin (blue line), whilst NOS was identified using anti-mouse FITC (red line). Line intensity was quantified using Image J and depicted graphically.

RESULTS

Detection of the targets was completed in 35 min, with a limit of detection as low as 20 copies. In addition, two analysis systems were developed and they performed well in the MR-DCA assay. In an analysis of 24 blind samples from GM crops with a wide genomic range, MR-DCA gave consistent results with the quantitative PCR method, which indicated high accuracy, applicability and semi-quantitative ability.

CONCLUSION

The development of MR-DCA represents a significant advancement in the field of GM detection, offering a rapid, sensitive and portable method for multiple target detection that can be used in resource-limited environments.

A platform for precise quantification of gene editing products based on microfluidic chip-based digital PCR

The new generation of gene editing technologies, primarily based on CRISPR/Cas9 and its derivatives, allows for more precise editing of organisms. However, when the editing efficiency is low, only a small fraction of gene fragments is edited, leaving behind minimal traces and making it difficult to detect and evaluate the editing effects. Although a series of technologies and methods have been developed, they lack the ability for precise quantification and quantitative analysis of these products. Digital polymerase chain reaction (dPCR) offers advantages such as high precision and sensitivity, making it suitable for absolute quantification of nucleic acid samples. In the present study, we developed a novel platform for precise quantification of gene editing products based on microfluidic chip-based dPCR. The results indicated that our assay accurately identified different types of edited samples within a variety of different types, including more complex genomic crops such as tetraploid rapeseed and soybean (highly repetitive sequence). The sensitivity of this detection platform was as low as 8.14 copies per μL, with a detection limit of 0.1%. These results demonstrated the superior performance of the platform, including high sensitivity, low detection limit, and wide applicability, enabling precise quantification and assessment of gene editing efficiency. In conclusion, microfluidic chip-based dPCR was used as a powerful tool for precise quantification and assessment of gene editing products.

Fibroblast: A Novel Target for Autoimmune and Inflammatory Skin Diseases Therapeutics

Fibroblasts are crucial components of the skin structure. They were traditionally believed to maintain the skin's structure by producing extracellular matrix and other elements. Recent research illuminated that fibroblasts can respond to external stimuli and exhibit diverse functions, such as the secretion of pro-inflammatory factors, adipogenesis, and antigen presentation, exhibiting remarkable heterogeneity and plasticity. This revelation positions fibroblasts as active contributors to the pathogenesis of skin diseases, challenging the traditional perspective that views fibroblasts solely as structural entities. Based on their diverse functions, fibroblasts can be categorized into six subtypes: pro-inflammatory fibroblasts, myofibroblasts, adipogenic fibroblasts, angiogenic fibroblasts, mesenchymal fibroblasts, and antigen-presenting fibroblasts. Cytokines, metabolism, and epigenetics regulate functional abnormalities in fibroblasts. The dynamic changes fibroblasts exhibit in different diseases and disease states warrant a comprehensive discussion. We focus on dermal fibroblasts' aberrant manifestations and pivotal roles in inflammatory and autoimmune skin diseases, including psoriasis, vitiligo, lupus erythematosus, scleroderma, and atopic dermatitis, and propose targeting aberrantly activated fibroblasts as a potential therapeutic strategy for inflammatory and autoimmune skin diseases.

B and N Codoped Cellulose-Supported Ag-/Bi-Doped Mo(S,O)3 Trimetallic Sulfo-Oxide Catalyst for Photocatalytic H2 Evolution Reaction and 4-Nitrophenol Reduction

Cellulose plays a significant role in designing efficient and stable cellulose-based metallic catalysts, owing to its surface functionalities. Its hydroxyl groups are used as anchor sites for the nucleation and growth of metallic nanoparticles and, as a result, improve the stability and catalytic activity. Meanwhile, cellulose is also amenable to surface modifications to be more suitable for incorporating and stabilizing metallic nanoparticles. Herein, the Ag-/Bi-doped Mo(S,O)3 trimetallic sulfo-oxide anchored on B and N codoped cellulose (B-N-C) synthesized by a facile approach showed excellent stability and catalytic activity for PHER at 573.28 μmol/h H2 with 25 mg of catalyst under visible light, and 92.3% of the 4-nitrophenol (4-NP) reduction was achieved within 135 min by in situ-generated protons. In addition to B and N codoping, our use of the calcination method for B-N-C preparation further increases the structural disorders and defects, which act as anchoring sites for Ag-/Bi-doped Mo(S,O)3 nanoparticles. The Ag-/Bi-doped Mo(S,O)3@B-N-C surface active site also stimulates H2O molecule adsorption and activation kinetics and reduces the photogenerated charge carrier's recombination rate. The Mo4+ → Mo6+ electron hopping transport and the O 2p and Bi 6s orbital overlap facilitate the fast electron transfer by enhancing the electron's lifetime and photoinduced charge carrier mobility, respectively. In addition to acting as a support, B-N-C provides a highly conductive network that enhances charge transport, and the relocated electron in B-N-C activates the H2O molecule, which enables Ag-/Bi-doped Mo(S,O)3@B-N-C to have appreciable PHER performance.

Molecular behavior of silicone adhesive at buried polymer interface studied by molecular dynamics simulation and sum frequency generation vibrational spectroscopy

Silicones have excellent material properties and are used extensively in many applications, ranging from adhesives and lubricants to electrical insulation. To ensure strong adhesion of silicone adhesives to a wide variety of substrates, silane-based adhesion promotors are typically blended into the silicone adhesive formulation. However, little is known at the molecular level about the true silane adhesion promotion mechanism, which limits the ability to develop even more effective adhesion promoters. To understand the adhesion promotion mechanism of silane molecules at the molecular level, this study has used sum frequency generation vibrational spectroscopy (SFG) to determine the behavior of (3-glycidoxypropyl)trimethoxy silane (γ-GPS) at the buried interface between poly(ethylene terephthalate) (PET) and a bulk silicone adhesive. To complement and extend the SFG results, atomistic molecular dynamics (MD) simulations were applied to investigate molecular behavior and interfacial interaction of γ-GPS at the silicone/PET interface. Free energy computations were used to study the γ-GPS interaction in the sample system and determine the γ-GPS interfacial segregation mechanism. Both experiments and simulations consistently show that γ-GPS molecules prefer to segregate at the interface between PET and PDMS. The methoxy groups on γ-GPS molecules orient toward the PDMS polymer phase. The consistent picture of interfacial structure emerging from both simulation and experiment provides enhanced insight on how γ-GPS behaves in the silicone - PET system and illustrates why γ-GPS could improve the adhesion of silicone adhesive, leading to further understanding of silicone adhesion mechanisms useful in the design of silicone adhesives with improved performance.

Quantifying Chemical Reactions and Interfacial Properties at Buried Polymer/Polymer Interfaces

Maleic anhydride (MAH)-modified polymers are used as tie layers for binding dissimilar polymers in multilayer polymer films. The MAH chemistry which promotes adhesion is well characterized in the bulk; however, only recently has the interfacial chemistry been studied. Sum frequency generation vibrational spectroscopy (SFG) is an interfacial spectroscopy technique which provides detailed information on interfacial chemical reactions, species, and molecular orientations and has been essential for characterizing the MAH chemistry in both nylon and ethyl vinyl alcohol copolymer (EVOH) model systems and coextruded multilayer films. Here, we further characterize the interfacial chemistry between MAH-modified polyethylene tie layers and both EVOH and nylon by investigating the model systems over a range of MAH concentrations. We can detect the interfacial chemical reaction products between MAH and the barrier layer at MAH concentrations of ≥0.022 wt % for nylon and ≥0.077 wt % for EVOH. Additionally, from the concentration-dependent reaction reactant/product SFG peak positions and the product imide or ester/acid C═O group tilt angles extracted from the polarization-dependent SFG spectra, we quantitatively observe concentration-dependent changes to both the interfacial chemistry and interfacial structure. The interfacial chemistry and molecular orientation as a function of MAH concentration are well correlated with the adhesion strength, providing important quantitative information for the future design of MAH-modified tie layers for a variety of important applications.

Group 3 innate lymphoid cells promotes Th17 cells differentiation in rheumatoid arthritis

OBJECTIVES

To investigate the correlation between innate lymphoid cell (ILC) subsets with T-helper (Th) cells and to explore the effect of ILCs on T cells in rheumatoid arthritis (RA).

METHODS

We analysed the frequencies of ILC subsets in RA patients with varying disease activity and their correlation with Th cell subsets. We further investigated this correlation in various organs of collagen-induced arthritis (CIA) mice. The effects of ILCs on CD4+ T cells were determined by in vitro cell co-culture experiments.

RESULTS

ILCs were less frequent in RA patients than in healthy controls, with higher levels of group 3 ILCs (ILC3s) in RA (p<0.05). ILC3s correlated positively with Th1 and Th17 cells in RA peripheral blood (p<0.05). In the peripheral blood, spleen, and lymph nodes of CIA, ILC3s decreased and then increased during arthritis progression. ILC3s correlated positively with Th1 and Th17 cells in the spleen and lymph nodes of CIA (p<0.05). NKp46+ ILC3s in the spleen positively correlated with Th1 and Th17 cells (p<0.05). Under Th17 cell differentiation conditions, co-culturing CIA-derived ILC3s directly with naive CD4+ T cells promoted Th17 differentiation and increased IL-17 secretion. However, co-culturing through a transwell insert impeded Th17 differentiation without affecting IL-17 secretion.

CONCLUSIONS

ILC3s positively correlated with Th1 and Th17 cells in RA. In CIA, the frequencies of ILC3s changed with disease development and showed a positive correlation with Th1 and Th17 cells. ILC3s may facilitate the differentiation of Th17 cells through direct cell-cell contact.

Effect of Posterior Keratometry on the Accuracy of 10 Intraocular Lens Calculation Formulas: Standard Keratometry versus Total Keratometry

PURPOSE

To investigate the effect of posterior keratometry (PK) on the accuracy of 10 intraocular lens (IOL) power calculation formulas using standard keratometry (K) and total keratometry (TK).

METHODS

This is a retrospective consecutive case-series study. The IOL power was calculated using K and TK measured by IOLMaster 700 in 6 new-generation formulas (Barrett Universal II, Emmetropia Verifying Optical (EVO) 2.0, RBF Calculator 3.0, Hoffer QST, Kane, and Ladas Super Formula) and 4 traditional formulas (Haigis, Hoffer Q, Holladay 1, and SRK/T). The arithmetic prediction error (PE) and mean absolute PE (MAE) were evaluated. The locally-weighted scatterplot smoothing was performed to assess the relationship between PE and PK.

RESULTS

A total of 576 patients (576 eyes) who underwent cataract surgery were included. Compared with using K, all formulas using TK showed a hyperopic shift in the whole group. Specifically, for eyes with PK exceeding -5.90 D, all formulas using TK exhibited a hyperopic shift (all P < 0.001), while eyes with PK less than -5.90 D showed a myopic shift (all P < 0.001). The MAE of new-generation formulas calculated with TK and K showed no statistical differences, while the MAE of traditional formulas with TK was larger (TK: 0.34 ~ 0.43 D; K: 0.33 ~ 0.42 D, all P < 0.05).

CONCLUSIONS

The prediction bias of formulas with TK increased as PK deviated from -5.90 D. TK did not improve the prediction accuracy of new-generation formulas, and even performed worse in traditional formulas.

Limosilactobacillus reuteri peptidoglycan alleviates aflatoxin B1-induced toxicity through adsorbing toxins and improving growth, antioxidant status, immunity and liver pathological changes in chicks

1. The objective of this study was to investigate the protective effects of a peptidoglycan produced by Limosilactobacillus reuteri against aflatoxin B1 (AFB1) induced toxicity in vitro and in vivo in broiler chicks.2. Toxin adsorption experiments were carried out firstly in vitro. These experiments indicated that the absorption efficiency of the peptidoglycan for AFB1 was 64.3-75.9%.3. In the in vivo experiments, Hy-Line Brown chicks were fed a diet containing AFB1 at 71.43 µg/kg with and without peptidoglycan supplementation at concentrations of 100, 200, or 300 g/kg feed from 0-42 d of age.4. The peptidoglycan supplementation in AFB1-contaminated diets resulted in significant improvements in terms of average daily gain, feed intake, feed conversion ratio, white blood cell count, haemoglobin content, glutathione peroxidase activity, immunoglobulin (Ig) A, IgG, IgM and Newcastle disease virus antibody titres (p < 0.05) and diminished liver steatosis.5. In conclusion, peptidoglycan supplementation alleviated AFB1-induced toxicity through adsorbing toxins and improving growth performance, antioxidant ability, immunity and liver pathological changes in chicks. The optimal supplemental dose was 200 mg/kg in feed.

[A multicenter study on the accuracy of PAX1/JAM3 dual genes methylation testing for screening cervical cancer]

Objective: To explore the value of cervical cytologic DNA methylation for screening cervical cancer. Methods: This study was a prospective multicenter study conducted from May to October 2022 in Peking Union Medical College Hospital, Zhejiang Provincial People's Hospital, and the Second Affiliated Hospital of Zhejiang University School of Medicine. Women who accepted opportunistic cervical cancer screening in gynecological outpatient clinics were subjected to liquid-based thin-layer cytology testing (TCT), high-risk human papillomavirus (hrHPV) DNA testing and PAX1/JAM3 dual-genes methylation testing (PAX1m/JAM3m). Colposcopy evaluation and biopsy were offered to women according to current guidelines. The accuracies of various testing methods and their combinations were compared based on histological diagnosis. Results: A total of 1 184 samples diagnosed by histopathology were included in this study, consisting of 541 cases (45.7%) of benign cervical tissue or chronic cervicitis, 273 (23.1%) of cervical intraepithelial neoplasia (CIN) 1, 168 (14.2%) of CIN2, 140 (11.8%) of CIN3, and 62 (5.2%) of cervical cancer. The sensitivity and specificity of PAX1m/JAM3m testing for detecting CIN2 or more severe lesions (CIN2+) were 74.1% and 95.9%, respectively. The sensitivity and specificity of PAX1m/JAM3m testing for detecting CIN3+were 87.6% and 86.8%, respectively. Receiver operating characteristic curve analysis showed that, for detecting CIN3+, the area under curve of PAX1m/JAM3m testing (0.872, 95%CI: 0.847-0.897) was significantly superior to TCT testing (0.580, 95%CI: 0.551-0.610) or hrHPV testing (0.503, 95%CI: 0.479-0.515) (all P values<0.05). Conclusions: The PAX1m/JAM3m test in cervical exfoliated cells has excellent accuracy for the diagnosis of both CIN2+and CIN3+, which is superior to traditional screening protocols and screening strategies.

Novel CRISPR/SpRY system for rapid detection of CRISPR/Cas-mediated gene editing in rice

The gene editing technology represented by clustered rule-interspersed short palindromic repeats (CRISPR)/Cas9 has developed as a common tool in the field of biotechnology. Many gene-edited products in plant varieties have recently been commercialized. However, the rapid on-site visual detection of gene-edited products without instrumentation remains challenging. This study aimed to develop a novel and efficient method, termed the CRISPR/SpRY detection platform, for the rapid screening of CRISPR/Cas9-induced mutants based on CRISPR/SpRY-mediated in vitro cleavage using rice (Oryza sativa L.) samples genetically edited at the TGW locus as an example. We designed the workflow of the CRISPR/SpRY detection platform and conducted a feasibility assessment. Subsequently, we optimized the reaction system of CRISPR/SpRY, and developed a one-pot CRISPR/SpRY assay by integrating recombinase polymerase amplification (RPA). The sensitivity of the method was further verified using recombinant plasmids. The proposed method successfully identified various types of mutations, including insertions, deletions (indels), and nucleotide substitutions, with excellent sensitivity. Finally, the applicability of this method was validated using different rice samples. The entire process was completed in less than an hour, with a limit of detection as low as 1%. Compared with previous methods, our approach is simple to operate, instrumentation-free, cost-effective, and time-efficient. The primary significance lies in the liberation of our developed system from the limitations imposed using protospacer adjacent motif sequences. This expands the scope and versatility of the CRISPR-based detection platform, making it a promising and groundbreaking platform for detecting mutations induced by gene editing.

Oxygen enhances antiviral innate immunity through maintenance of EGLN1-catalyzed proline hydroxylation of IRF3

Oxygen is essential for aerobic organisms, but little is known about its role in antiviral immunity. Here, we report that during responses to viral infection, hypoxic conditions repress antiviral-responsive genes independently of HIF signaling. EGLN1 is identified as a key mediator of the oxygen enhancement of antiviral innate immune responses. Under sufficient oxygen conditions, EGLN1 retains its prolyl hydroxylase activity to catalyze the hydroxylation of IRF3 at proline 10. This modification enhances IRF3 phosphorylation, dimerization and nuclear translocation, leading to subsequent IRF3 activation. Furthermore, mice and zebrafish with Egln1 deletion, treatment with the EGLN inhibitor FG4592, or mice carrying an Irf3 P10A mutation are more susceptible to viral infections. These findings not only reveal a direct link between oxygen and antiviral responses, but also provide insight into the mechanisms by which oxygen regulates innate immunity.

Dual modifying of MAVS at lysine 7 by SIRT3-catalyzed deacetylation and SIRT5-catalyzed desuccinylation orchestrates antiviral innate immunity

To effectively protect the host from viral infection while avoiding excessive immunopathology, the innate immune response must be tightly controlled. However, the precise regulation of antiviral innate immunity and the underlying mechanisms remain unclear. Here, we find that sirtuin3 (SIRT3) interacts with mitochondrial antiviral signaling protein (MAVS) to catalyze MAVS deacetylation at lysine residue 7 (K7), which promotes MAVS aggregation, as well as TANK-binding kinase I and IRF3 phosphorylation, resulting in increased MAVS activation and enhanced type I interferon signaling. Consistent with these findings, loss of Sirt3 in mice and zebrafish renders them more susceptible to viral infection compared to their wild-type (WT) siblings. However, Sirt3 and Sirt5 double-deficient mice exhibit the same viral susceptibility as their WT littermates, suggesting that loss of Sirt5 in Sirt3-deficient mice may counteract the increased viral susceptibility displayed in Sirt3-deficient mice. Thus, we not only demonstrate that SIRT3 positively regulates antiviral immunity in vitro and in vivo, likely via MAVS, but also uncover a previously unrecognized mechanism by which SIRT3 acts as an accelerator and SIRT5 as a brake to orchestrate antiviral innate immunity.

[Research progress on the effect of hepatitis B virus DNA integration on antiviral therapy]

Hepatitis B virus (HBV) DNA integration occurs during the reverse transcription process of HBV replication, which develops in the early stages of HBV infection and accompanies the entire disease course. The integration of HBV DNA is detrimental to the attainment of clinical cure goals and also raises the risk of developing liver cancer. Theoretically, nucleos(t)ide analogs can reduce the synthesis of new double-stranded linear DNA, but there is no clearance function for hepatocytes that have already integrated HBV. Therefore, patients with serum HBV DNA-negative conversions still have the risk of developing liver cancer. As an immunomodulatory drug, interferon can not only inhibit viral replication but also inhibit or even eliminate existing clonally amplified hepatocytes carrying integrated HBV DNA fragments. However, there are currently few studies on the effects of nucleos(t)ide analogues and interferon therapy on HBV DNA integration. Thus, large-scale clinical studies are urgently needed for further clarification.

PCR Independent Strategy-Based Biosensors for RNA Detection

RNA is an important information and functional molecule. It can respond to the regulation of life processes and is also a key molecule in gene expression and regulation. Therefore, RNA detection technology has been widely used in many fields, especially in disease diagnosis, medical research, genetic engineering and other fields. However, the current RT-qPCR for RNA detection is complex, costly and requires the support of professional technicians, resulting in it not having great potential for rapid application in the field. PCR-free techniques are the most attractive alternative. They are a low-cost, simple operation method and do not require the support of large instruments, providing a new concept for the development of new RNA detection methods. This article reviews current PCR-free methods, overviews reported RNA biosensors based on electrochemistry, SPR, microfluidics, nanomaterials and CRISPR, and discusses their challenges and future research prospects in RNA detection.

A PAM-Free One-Step Asymmetric RPA and CRISPR/Cas12b Combined Assay (OAR-CRISPR) for Rapid and Ultrasensitive DNA Detection

Current research endeavors have focused on the combination of various isothermal nucleic acid amplification methods with CRISPR/Cas systems, aiming to establish a more sensitive and reliable molecular diagnostic approach. Nevertheless, most assays adopt a two-step procedure, complicating manual operations and heightening the risk of contamination. Efforts to amalgamate both assays into a single-step procedure have faced challenges due to their inherent incompatibility. Furthermore, the presence of the protospacer adjacent motif (PAM) motif (e.g., TTN or TTTN) in the target double-strand DNA (dsDNA) is an essential prerequisite for the activation of the Cas12-based method. This requirement imposes constraints on crRNA selection. To overcome such limitations, we have developed a novel PAM-free one-step asymmetric recombinase polymerase amplification (RPA) coupled with a CRISPR/Cas12b assay (OAR-CRISPR). This method innovatively merges asymmetric RPA, generating single-stranded DNA (ssDNA) amenable to CRISPR RNA binding without the limitations of the PAM site. Importantly, the single-strand cleavage by PAM-free crRNA does not interfere with the RPA amplification process, significantly reducing the overall detection times. The OAR-CRISPR assay demonstrates sensitivity comparable to that of qPCR but achieves results in a quarter of the time required by the latter method. Additionally, our OAR-CRISPR assay allows the naked-eye detection of as few as 60 copies/μL DNA within 8 min. This innovation marks the first integration of an asymmetric RPA into one-step CRISPR-based assays. These advancements not only support the progression of one-step CRISPR/Cas12-based detection but also open new avenues for the development of detection methods capable of targeting a wide range of DNA targets.

[Effect of HBV DNA load on the safety and prognosis of systematic therapy in advanced hepatocellular carcinoma]

Objective: To study the effect of hepatitis B virus (HBV) infection on the occurrence of liver damage, HBV reactivation (HBVr) and the influence of HBVr on the prognosis of patients with advanced hepatocellular carcinoma (HCC) receiving systemic therapy. Methods: The clinical data of 403 patients with HBV-related HCC at the Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-Sen University et al, from July 2018 to December 2020 were collected. The incidence of liver damage and HBVr during systematic therapy, and the influence of HBVr on survival prognosis were analyzed. Results: Of the 403 patients, 89.1% were male (n=359), with a median age of 51 years (51.5±12.1). Before propensity score matching (PSM), the proportion of patients with cirrhosis, TNM and advanced BCLC stage was higher in high HBV-DNA (baseline HBV-DNA>1000 U/ml, n=147) group comparing with the low HBV-DNA (baseline HBV DNA≤1000 u/ml, n=256) group (P<0.05). There was no significant difference in baseline indexes between the two groups after PSM. In 290 patients after PSM, there was no significant difference in the incidence of liver damage and HBVr between high HBV-DNA group and low HBV-DNA group (P>0.05). Survival analysis was performed on 169 patients with survival data, the median overall survival (OS) was found to be 11.49 months (95%CI: 7.77-12.89) and 16.65 months (95%CI: 10.54-21.99, P=0.008) in the high and low HBV-DNA groups, respectively. And median progression-free survival (PFS) was 7.41 months (95%CI: 5.06-8.67) and 10.55 months (95%CI: 6.72-13.54, P=0.038), respectively, with a statistically significant difference. There were no differences in overall survival (OS) and progression-free survival (PFS) between patients with and without HBVr and those with or without liver damage (P>0.05). Conclusions: HBV-DNA levels above 1 000 U/ml before systemic therapy do not increase the risk of liver damage or HBVr during systemic therapy in patients with HBV-related hepatocellular carcinoma, and such patients can safely receive systemic therapy.