Antifungal mechanism of cell-free supernatant produced by Trichoderma virens and its efficacy for the control of pear Valsa canker.

Introduction: Pear Valsa canker, caused by Valsa pyri (V. pyri), poses a major threat to pear production. We aimed to assess the effectiveness of the cell-free supernatant (CFS) produced by Trichoderma virens (T. virens) to control the development of pear Valsa canker and reveal the inhibitory mechanism against the pathogenic fungi. Results: Using morphological characteristics and phylogenetic analysis, the pathogen G1H was identified as V. pyri, and the biocontrol fungus WJ561 was identified as Trichoderma virens. CFS derived from WJ561 exhibited strong inhibition of mycelial growth and was capable of reducing the pathogenicity of V. pyri on pear leaves and twigs. Scanning electron microscopy (SEM) observations revealed deformations and shrinkages in the fungal hyphae treated with CFS. The CFS also destroyed the hyphal membranes leading to the leakage of cellular contents and an increase in the malondialdehyde (MDA) content. Additionally, CFS significantly inhibited the activities of catalase (CAT) and superoxide dismutase (SOD), and downregulated the expression of antioxidant defense-related genes in V. pyri, causing the accumulation of reactive oxygen species (ROS). Artesunate, identified as the main component in CFS by liquid chromatograph-mass spectrometry (LC-MS), exhibited antifungal activity against V. pyri. Conclusion: Our findings demonstrate the promising potential of T. virens and its CFS in controlling pear Valsa canker. The primary inhibitory mechanism of CFS involves multiple processes, including membrane damage and negatively affecting enzymatic detoxification pathways, consequently leading to hyphal oxidative damage of V. pyri. This study lays a theoretical foundation for the utilization of T. virens to control V. pyri in practical production.

Identification and validation of a novel predictive signature based on hepatocyte-specific genes in hepatocellular carcinoma by integrated analysis of single-cell and bulk RNA sequencing.

BACKGROUND: Hepatocellular carcinoma represents a significant global burden in terms of cancer-related mortality, posing a substantial risk to human health. Despite the availability of various treatment modalities, the overall survival rates for patients with hepatocellular carcinoma remain suboptimal. The objective of this study was to explore the potential of novel biomarkers and to establish a novel predictive signature utilizing multiple transcriptome profiles. METHODS: The GSE115469 and CNP0000650 cohorts were utilized for single cell analysis and gene identification. The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) datasets were utilized in the development and evaluation of a predictive signature. The expressions of hepatocyte-specific genes were further validated using the GSE135631 cohort. Furthermore, immune infiltration results, immunotherapy response prediction, somatic mutation frequency, tumor mutation burden, and anticancer drug sensitivity were analyzed based on various risk scores. Subsequently, functional enrichment analysis was performed on the differential genes identified in the risk model. Moreover, we investigated the expression of particular genes in chronic liver diseases utilizing datasets GSE135251 and GSE142530. RESULTS: Our findings revealed hepatocyte-specific genes (ADH4, LCAT) with notable alterations during cell maturation and differentiation, leading to the development of a novel predictive signature. The analysis demonstrated the efficacy of the model in predicting outcomes, as evidenced by higher risk scores and poorer prognoses in the high-risk group. Additionally, a nomogram was devised to forecast the survival rates of patients at 1, 3, and 5 years. Our study demonstrated that the predictive model may play a role in modulating the immune microenvironment and impacting the anti-tumor immune response in hepatocellular carcinoma. The high-risk group exhibited a higher frequency of mutations and was more likely to benefit from immunotherapy as a treatment option. Additionally, we confirmed that the downregulation of hepatocyte-specific genes may indicate the progression of hepatocellular carcinoma and aid in the early diagnosis of the disease. CONCLUSION: Our research findings indicate that ADH4 and LCAT are genes that undergo significant changes during the differentiation of hepatocytes into cancer cells. Additionally, we have created a unique predictive signature based on genes specific to hepatocytes.

Evolution of Peritoneal Dialysis-Associated Peritonitis: Pathogen, Antibiotic Resistance, and the Impact of Lymphocyte Count on Treatment Outcomes.

Purpose: Antibiotic administration leads to alterations in pathogenic organisms and antibiotic resistance, posing a significant risk to peritoneal dialysis patients' health. This study aimed to investigate changes in the cause-specific peritonitis, pathogen profiles, antibiotic resistance, and the prognostic factors among patients with peritoneal dialysis-associated peritonitis (PDAP) at our center. Patients and Methods: We included 463 PDAP patients who attended Peking University Shenzhen Hospital between 2002 and 2023. We analyzed the effects of empirical treatment regimens with cefazolin and ceftazidime or gentamicin. Results: From 2002 to 2023, we observed that gram-positive staphylococci emerged as the primary causative agents, while the proportion of gram-negative bacillary, enteric peritonitis, and catheter-associated peritonitis decreased significantly. However, the overall cure rate for PDAP and gram-negative bacillary peritonitis declined significantly from 2014 to 2023. Notably, we observed no increase in antibiotic resistance associated with antibiotic drugs use. In addition, reduced lymphocyte counts due to the prevalence of 2019 coronavirus disease (COVID-19) emerged as an independent risk factor for treatment failure in cases of gram-negative bacillary peritonitis. Conclusion: We did not observe elevated antibiotic resistance in our center when employing empirical dosing strategies involving cefazolin, ceftazidime, or gentamicin. Additionally, we found that a decrease in lymphocyte count due to the COVID-19 epidemic was a significant risk factor for treatment failure in cases of gram-negative bacillary peritonitis at our center. This study provides a foundation for developing clinical treatment strategies for PDAP.

Effect of Modification Strategies on the Biological Activity of Peptides/Proteins.

Covalent attachment of biologically active peptides/proteins with functional moieties is an effective strategy to control their biodistribution, pharmacokinetics, enzymatic digestion, and toxicity. This review focuses on the characteristics of different modification strategies and their effects on the biological activity of peptides/proteins and illustrates their relevant applications and potential.

Red cell distribution width to albumin ratio predicts treatment failure in peritoneal dialysis-associated peritonitis.

BACKGROUND: This study aims to investigate the potential correlation between baseline red cell distribution width (RDW) to albumin ratio (RAR) levels and treatment failure in peritoneal dialysis-associated peritonitis (PDAP) patients. METHODS: A retrospective single-center study was conducted on 286 PDAP patients. Logistic regression and generalized estimation equation (GEE) analyses were employed to assess the relationship between RAR and treatment failure. RESULTS: RAR emerged as a robust predictor of treatment failure in PDAP patients. Elevated RAR levels were associated with an increased risk of treatment failure, exhibiting a linear relationship. Even after adjusting for demographic and clinical variables, this association remained statistically significant. ROC analysis revealed that RAR outperformed RDW and albumin individually in predicting PDAP prognosis. CONCLUSION: This study highlights RAR as a superior prognostic marker for treatment failure in PDAP patients, offering new insights into risk assessment and management strategies for this challenging condition.

Decreased Peripheral Blood Lymphocyte Count Predicts Poor Treatment Response in Peritoneal Dialysis-Associated Peritonitis.

Purpose: Peripheral blood lymphocyte counts is a pivotal parameter in assessing the host's immune response during maladies and the equilibrium of the immune system which has been found to correlate with various diseases progression and prognosis. However, there was no study on patients with peritoneal dialysis-associated peritonitis (PDAP). We sought to investigate the prognostic value of baseline peripheral blood lymphocyte count in PDAP patients. Patients and methods: This retrospective study analyzed data from 286 PDAP patients over nine years. Episodes were categorized according to the tertiles of peripheral blood lymphocyte counts (Very Low Lymphocyte Count (VLLC) Group, <0.72×106/L; Low Lymphocyte Count (LLC) Group, 0.72-1.11×106/L; Normal Lymphocyte Count (NLC) Group, ≥ 1.11×106/L). Demographic, laboratory, and infection-related variables were analyzed. Cox regression and generalized estimating equation (GEE) models were used to estimate the association between lymphocyte counts and PDAP treatment failure, which included PD catheter removal and death. Results: After adjusting for other potential predictors, decreased lymphocyte counts exhibited an incremental relationship with the risk of treatment failure. The VLLC group indicated a 270% (95% CI, 1.168-6.247, P=0.020) and 273% (95% CI, 1.028-7.269, P=0.044) increased venture of treatment failure in Cox regression and GEE analyses, respectively, compared with the NLC group. As a continuous variable, the restricted cubic spline showed a linear negative correlation between lymphocyte counts and the treatment failure risk (P for overall = 0.026). The multivariate model C (combined lymphocyte count with baseline age, sex, dialysis age, Charlson Comorbidity index (CCI), etiology of kidney failure, hemoglobin, albumin, total bilirubin and infection type) showed an area under the curve of 0.824 (95% CI, 0.767-0.881, P=0.001) for the prediction of treatment failure. Conclusion: Lower lymphocyte counts are linked to increased PDAP treatment failure risk. This highlights lymphocyte count's potential as a prognostic indicator for PDAP.

Association of Different Total Bilirubin Levels with Prognosis of Peritoneal Dialysis-Associated Peritonitis.

Background and Objectives: Peritoneal dialysis-associated peritonitis (PDAP) poses significant challenges in peritoneal dialysis (PD) patient management and outcomes. Total bilirubin has gained attention due to its antioxidant and immunomodulatory properties. However, its relationship with PDAP prognosis remains underexplored. Materials and Methods: We conducted a retrospective single-center study involving 243 PDAP patients stratified into tertile-based groups according to total bilirubin levels. The association between total bilirubin levels and treatment failure risk was investigated through statistical analyses and restricted cubic spline curve analysis. Results: Our analysis revealed a non-linear correlation between total bilirubin levels and PDAP treatment failure risk. At total bilirubin levels below 8.24 µmol/L, a protective effect was observed, while levels exceeding this threshold heightened the risk of treatment failure. Conclusions: This study unveils a dual role of total bilirubin in PDAP prognosis. Below a certain threshold, it confers protection, while higher levels exacerbate the risk of treatment failure. These findings emphasize the need for further investigation in larger, multicenter prospective studies to validate and elucidate the mechanisms behind bilirubin's impact on PDAP, potentially guiding the development of targeted therapeutic strategies.

Self-Assembly Nanostructure Induced by Regulation of G-Quadruplex DNA Topology via a Reduction-Sensitive Azobenzene Ligand on Cells.

The control of DNA assembly systems on cells has increasingly shown great importance for precisely targeted therapies. Here, we report a controllable DNA self-assembly system based on the regulation of G-quadruplex DNA topology by a reduction-sensitive azobenzene ligand. Specifically, three azobenzene multiamines are developed, and AzoDiTren is identified as the best G4 binder, which displays high affinity and specificity for G4 DNA. Moreover, the reduction-sensitive nature of the azobenzene scaffold allows AzoDiTren to induce a complete change of the G4 topology in a tissue-specific manner, even at high metal cation concentrations. On this basis, the AzoDiTren-induced G4 conformational switch achieves control of the self-assembly of G4-functionalized DNAs on cells. This strategy enables the regulation of G4 and DNA self-assembly by the bioreductant-responsive ligand.

Effect of Mini-PEGs Modification on the Enzymatic Digestion of D-Amino Acid-Containing Peptides under the Action of PROK.

It was previously reported that D-amino acid-containing peptides exhibited the ability to resist enzymatic hydrolysis. This study investigated the influence of mini-PEGs modification on enzymatic hydrolysis ability of D-amino acid-containing peptides. The results showed that PEGylation promoted enzymatic hydrolysis of the D-amino acid-containing peptide, especially, the cleavage rate of the D-amino acid-containing peptide 6-w with PEG3 modification at the N-ends was up to 17 times higher in the presence of proteinase K (PROK) compared to those without PEG3 modification. Moreover, analysis of the enzymatic cleavage sites demonstrated a similar cleavage pattern of the PEGylated D-amino acid-containing peptide to that of the unmodified peptide. The computational simulations further showed that the enhanced enzymatic hydrolysis ability can be attributed to the strong interaction between PROK and the peptide after PEG3 modification and the resulting formation of a mature catalytic triad structure.

Benzalkonium Chloride and Benzethonium Chloride Effectively Reduce Spore Germination of Ginger Soft Rot Pathogens: Fusarium solani and Fusarium oxysporum.

Ginger soft rot is a serious soil-borne disease caused by Fusarium solani and Fusarium oxysporum, resulting in reduced crop yields. The application of common chemical fungicides is considered to be an effective method of sterilization, and therefore, they pose a serious threat to the environment and human health due to their high toxicity. Benzalkonium chloride (BAC) and benzethonium chloride (BEC) are two popular quaternary ammonium salts with a wide range of fungicidal effects. In this study, we investigated the fungicidal effects of BAC and BEC on soft rot disease of ginger as alternatives to common chemical fungicides. Two soft rot pathogens of ginger were successfully isolated from diseased ginger by using the spread plate method and sequenced as F. solani and F. oxysporum using the high-throughput fungal sequencing method. We investigated the fungicidal effects of BAC and BEC on F. solani and F. oxysporum, and we explored the antifungal mechanisms. Almost complete inactivation of spores of F. solani and F. oxysporum was observed at 100 mg/L fungicide concentration. Only a small amount of spore regrowth was observed after the inactivation treatment of spores of F. solani and F. oxysporum in soil, which proved that BAC and BEC have the potential to be used as an alternative to common chemical fungicides for soil disinfection of diseased ginger.

Replicative bypass studies of l-deoxyribonucleosides in Vitro and in E. coli cell.

L-nucleosides were the most important antiviral lead compounds because they can inhibit viral DNA polymerase and DNA synthesis of many viruses, whereas they may lead to mutations in DNA replication and cause genomic instability. In this study, we reported the replicative bypass of L-deoxynucleosides in recombinant DNA by restriction enzyme-mediated assays to examine their impact on DNA replication in vitro and in E. coli cells. The results showed that a template L-dC inhibited Taq DNA polymerase reaction, whereas it can be bypassed by Vent (exo-) DNA polymerase as well as in cell replication, inserting correct nucleotides opposite L-dC. L-dG can be bypassed by Taq DNA polymerase and in E. coli cells, maintaining insertion of correct incoming nucleotides, and L-dG induced mutagenic replication by Vent (exo-) DNA polymerase. In contrast, L-dA can induced mutagenic replication in vitro and in E. coli cells. MD simulations were performed to investigate how DNA polymerase affected replicative bypass and mutations when D-nucleosides replaced with L-nucleosides. This study will provide a basis for the ability to assess the cytotoxic and mutagenic properties of the L-nucleoside drugs.

Reversible On-Off Photoswitching of DNA Replication Using a Dumbbell Oligodeoxynucleotide.

In most organisms, DNA extension is highly regulated; however, most studies have focused on controlling the initiation of replication, and few have been done to control the regulation of DNA extension. In this study, we adopted a new strategy for azODNs to regulate DNA extension, which is based on azobenzene oligonucleotide chimeras regulated by substrate binding affinity, and the conformation of the chimera can be regulated by a light source with a light wavelength of 365 nm. The results showed that the primer was extended with Taq DNA polymerase after visible light treatment, and DNA extension could be effectively hindered with UV light treatment. We also verify the reversibility of the photoregulation of primer extension through photoswitching of dumbbell asODNs by alternate irradiation with UV and visible light. Our method has the advantages of fast and simple, green response and reversible operations, providing a new strategy for regulating gene replication.

Superelastic 3D Assembled Clay/Graphene Aerogels for Continuous Solar Desalination and Oil/Organic Solvent Absorption.

Superelastic, arbitrary-shaped, and 3D assembled clay/graphene aerogels (CGAs) are fabricated using commercial foam as sacrificial skeleton. The CGAs possess superelasticity under compressive strain of 95% and compressive stress of 0.09-0.23 MPa. The use of clay as skeletal support significantly reduces the use of graphene by 50%. The hydrophobic CGAs show high solvent absorption capacity of 186-519 times its own weight. Moreover, both the compression and combustion methods can be adopted for reusing the CGAs. In particular, it is demonstrated a design of 3D assembled hydrophilic CGA equipped with salt collection system for continuous solar desalination. Due to energy recovery and brine transport management promoted by this design, the 3D assembled CGA system exhibits an extremely high evaporation rate of 4.11 kg m-2  h-1 and excellent salt-resistant property without salt precipitation even in 20 wt% brine for continuous 36 h illumination (1 kW m-2 ), which is the best reported result from the solar desalination devices. More importantly, salts can be collected conveniently by squeezing and drying the solution out of the salt collection system. The work provides new insights into the design of 3D assembled CGAs and advances their applications in continuous solar desalination and efficient oil/organic solvent adsorption.

Major Advances in Emerging Degrader Technologies.

Recently, degrader technologies have attracted increasing interest in the academic field and the pharmaceuticals industry. As one of the degrader technologies, proteolysis-targeting chimeras (PROTACs) have emerged as an attractive pharmaceutical development approach due to their catalytic ability to degrade numerous undruggable disease-causing proteins. Despite the remarkable progress, many aspects of traditional PROTACs still remain elusive. Its expansion could lead to PROTACs with new paradigm. Currently, many reviews focused on the design and optimization strategies through summarizing classical PROTACs, application in diseases and prospect of PROTACs. In this review, we categorize various emerging PROTACs ranging from simply modified classical PROTACs to atypical PROTACs such as nucleic acid-based PROTACs, and we put more emphasis on molecular design of PROTACs with different strategies. Furthermore, we summarize alternatives of PROTACs as lysosome-targeting chimeras (LYTACs) and macroautophagy degradation targeting chimeras (MADTACs) based on different degradation mechanism despite of lysosomal pathway. Beyond these protein degraders, targeting RNA degradation with the potential for cancer and virus therapeutics has been discussed. In doing so, we provide our perspective on the potential development or concerns of each degrader technology. Overall, we hope this review will offer a better mechanistic understanding of emerging degraders and prove as useful guide for the development of the coming degrader technologies.

Washed microbiota transplantation reduces serum uric acid levels in patients with hyperuricaemia.

BACKGROUND: Previous studies have found that hyperuricaemia (HUA) is closely related to intestinal flora imbalance. AIM: The current study investigated the effects and safety of washed microbiota transplantation (WMT) on serum uric acid (SUA) levels in different populations. METHODS: A total of 144 patients who received WMT from July 2016 to April 2020 in the First Affiliated Hospital of Guangdong Pharmaceutical University and had SUA data before treatment were selected. Changes in SUA levels before and after treatment were retrospectively reviewed based on short-term and mid-term effects of WMT regimens. SUA levels measured in the last test within 3 mo after the first WMT represented the short-term effect, and SUA levels measured in the last test within 3-6 mo after the first WMT represented the mid-term effect. The patients were divided into an HUA group (SUA > 416 µM) and a normal uric acid (NUA) group (SUA ≥ 202 µM to ≤ 416 µM) based on pretreatment SUA levels. RESULTS: Average short-term SUA levels in the HUA group decreased after WMT (481.00 ± 99.85 vs 546.81 ± 109.64 µM, n = 32, P < 0.05) in 25/32 patients and returned to normal in 10/32 patients. The short-term level of SUA reduction after treatment moderately correlated with SUA levels before treatment (r = 0.549, R² = 0.300, P < 0.05). Average SUA levels decreased after the first and second courses of WMT (469.74 ± 97.68 vs 540.00 ± 107.16 µM, n = 35, and 465.57 ± 88.88 vs 513.19 ± 78.14 µM, n = 21, P < 0.05). Short-term and mid-term SUA levels after WMT and SUA levels after the first, second and third courses of WMT were similar to the levels before WMT in the NUA group (P > 0.05). Only 1/144 patients developed mild diarrhea after WMT. CONCLUSION: WMT reduces short-term SUA levels in patients with HUA with mild side effects but has no obvious effect on SUA levels in patients with NUA.

Redox manipulation of enzyme activity through physiologically active molecule.

The effective utility of physiologically active molecules is crucial in numerous biological processes. However, the regulation of enzyme functions through active substances remains challenging at present. Here, glutathione (GSH), produced in cells, was used to modulate the catalytic activity of thrombin without external stimulus. It was found that high concentrations of GSH was more conducive to initiate the cleavage of compound AzoDiTAB in the range of concentration used to mimic the difference between cancer and normal cells, which has practical implications for targeting cancel cells since GSH is overexpressed in cancer cells. Importantly, GSH treatment caused the deformation of G4 structure by cleaving AzoDiTAB and thus triggered the transition of thrombin from being free to be inhibited in complex biological systems. This work would open up a new route for the specific manipulation of enzyme-catalyzed systems in cancer cells.

Migration mechanism and risk assessment of chlorinated paraffins in highly polluted Ya'Er lake area, China.

Chlorinated paraffins (CPs), a type of toxic and persistent organic substances, can persist in environmental media for a long time and have adverse effects on human health. Thus, it is of great importance to investigate the accumulation and environmental behavior of CPs in industrial areas. In this study, farmland soil, water, and sediment core samples from abandoned oxidation ponds used by three chemical plants to treat wastewater over the past 38 years were investigated in detail. Results show that the concentration of CPs in sediments varied significantly with the water flow direction. The oxidation pond closest to a sewage outlet had the highest concentrations of short-chain chlorinated paraffin (SCCPs) and medium-chain chlorinated paraffin (MCCPs), within the ranges of 44.0-6.21 × 104 ng/g dw (mean 9.32 × 103 ng/g dw) and 143-1.30 × 106 ng/g dw (mean 1.22 × 105 ng/g dw), respectively. However, in the oxidation pond farthest from the sewage outlet, CP concentrations in sediments were significantly reduced, with ∑SCCPs and ∑MCCPs concentrations ranging from N.D.-249 ng/g dw (mean 66.8 ng/g dw) and N.D.-222 ng/g dw (mean 34.0 ng/g dw), respectively. Moreover, MCCP level in the water was below the detection limit, while the concentration of SCCP ranged from 41.0 to 1.53 × 103 ng/L (mean 267 ng/L). Finally, a remarkable spatial trend and specific congener distribution were observed in the sediment test results. The horizontal and vertical distributions of the sediments indicate that short-chain (C10-11) and low-chlorinated (Cl6-7) homologs are more likely to migrate deeper or farther away from the pollution source.

Dissipation, residue, dietary, and ecological risk assessment of atrazine in apples, grapes, tea, and their soil.

Atrazine is one of the most used herbicides in China. It is a persistent organic pollutant but has been widely used on Chinese farmlands for a long time. To assess its dietary and ecological risks to human and environment, in this study, atrazine residues were extracted with acetonitrile and then plant samples were detected with gas chromatography coupled with mass spectrometry (GC-MS) and soil samples were determined with gas chromatography coupled with nitrogen-phosphorus detector (GC-NPD). The limit of quantification (LOQ) of the method was 0.01 mg/kg for all matrices. The recoveries ranged from 82.0 to 105.4% for plant samples and 75.6 to 85.6% for soil samples. The final residues of atrazine in all plant samples were lower than LOQ. Dietary risk assessment suggested that under good agricultural practices (GAP) conditions, intake of atrazine from apples, grapes, and tea would exhibit an acceptably low health risk on consumers. However, the final residues of atrazine in soil samples were <0.01-9.2 mg/kg, and the half-lives were 2.0-9.1 days. Based on the species sensitivity distribution (SSD) model, the potential affected fraction (PAF) of atrazine in soil samples ranges from 0.01 to 65.8%. Atrazine residues in 43.1% soil samples were higher than 0.11 mg/kg, which was the hazardous concentration for 5% of species (HC5) of atrazine in soil. These results suggested that the ecological risks of atrazine in apples, grapes, and tea garden soil would exhibit a high risk on environmental species even under the same GAP conditions. This study could provide guidance for comprehensive risk assessment of atrazine properly used in apple, grape, and tea gardens.

Ferrocene-based conjugated microporous polymer and its multiwalled carbon nanotube composite for direct photocatalytic benzene hydroxylation to phenol.

Ferrocene is used as a catalytically active site and building block to construct a new conjugated microporous polymer (CMP), named Fc-POP. A corresponding carbon nanotube composite (CNTs@Fc-POP) with tubular structure was obtained through the π-π interaction between multi-walled carbon nanotubes (MWCNTs) and reactive molecules. This innovative modification method of carbon nanotubes provides a way to construct functionalized carbon materials. The two materials can achieve high conversion and selectivity of benzene hydroxylation to phenol under light irradiation using hydrogen peroxide (H2O2) as an oxidant. Due to the synergistic effect between the carbon nanotubes and the ferrocene group, the incorporation of MWCNTs can improve the yield of phenol significantly. This work explores a new photocatalystic system and expands the related photocatalytic application of CNTs.