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1.
New Phytol ; 2024 Jul 29.
Article in English | MEDLINE | ID: mdl-39073209

ABSTRACT

Mycorrhizal associations are key mutualisms that shape the structure of forest communities and multiple ecosystem functions. However, we lack a framework for predicting the varying dominance of distinct mycorrhizal associations in an integrated proxy of multifunctionality across ecosystems. Here, we used the datasets containing diversity of mycorrhizal associations and 18 ecosystem processes related to supporting, provisioning, and regulating services to examine how the dominance of ectomycorrhiza (EcM) associations affects ecosystem multifunctionality in subtropical mountain forests in Southwest China. Meanwhile, we synthesized the prevalence of EcM-dominant effects on ecosystem functioning in forest biomes. Our results demonstrated that elevation significantly modified the distributions of EcM trees and fungal dominance, which in turn influenced multiple functions simultaneously. Multifunctionality increased with increasing proportion of EcM associations, supporting the ectomycorrhizal-dominance hypothesis. Meanwhile, we observed that the impacts of EcM dominance on individual ecosystem functions exhibited different relationships among forest biomes. Our findings highlight the importance of ectomycorrhizal dominance in regulating multifunctionality in subtropical forests. However, this ectomycorrhizal feedback in shaping ecosystem functions cannot necessarily be generalized across forests. Therefore, we argue that the predictions for ecosystem multifunctionality in response to the shifts of mycorrhizal composition could vary across space and time.

2.
Toxins (Basel) ; 16(7)2024 Jul 15.
Article in English | MEDLINE | ID: mdl-39057959

ABSTRACT

Tenuazonic acid (TeA), usually found in cereals, fruits, vegetables, oil crops, and their products, was classified as one of the highest public health problems by EFSA as early as 2011, but it has still not been regulated by legislation due to the limited toxicological profile. Moreover, it has been reported that the coexistence of TeA and patulin (PAT) has been found in certain agricultural products; however, there are no available data about the combined toxicity. Considering that the gastrointestinal tract is the physiological barrier of the body, it would be the first target site at which exogenous substances interact with the body. Thus, we assessed the combined toxicity (cell viability, ROS, CAT, and ATP) in Caco-2 cells using mathematical modeling (Chou-Talalay) and explored mechanisms using non-targeted metabolomics and molecular biology methods. It revealed that the co-exposure of TeA + PAT (12.5 µg/mL + 0.5 µg/mL) can induce enhanced toxic effects and more severe oxidative stress. Mechanistically, the lipid and amino acid metabolisms and PI3K/AKT/FOXO signaling pathways were mainly involved in the TeA + PAT-induced synergistic toxic effects. Our study not only enriches the scientific basis for the development of regulatory policies but also provides potential targets and treatment options for alleviating toxicities.


Subject(s)
Cell Survival , Drug Synergism , Metabolome , Oxidative Stress , Patulin , Tenuazonic Acid , Caco-2 Cells , Patulin/toxicity , Humans , Tenuazonic Acid/toxicity , Tenuazonic Acid/metabolism , Metabolome/drug effects , Oxidative Stress/drug effects , Cell Survival/drug effects , Reactive Oxygen Species/metabolism , Signal Transduction/drug effects
3.
Toxicon ; 247: 107850, 2024 Aug 28.
Article in English | MEDLINE | ID: mdl-38971137

ABSTRACT

BACKGROUND: Enterobacter cloacae insecticidal proteins have been reported to kill Galleria mellonella larvae through affecting their midgut microbiome. However, the mechanisms involved remain unclear. Here we aim to investigate how the insecticidal proteins act on the midgut Duox-ROS system and microbial community of G. mellonella larvae. METHODS: Reverse transcription qPCR and fluorescence probes were utilized to assess the Duox expression levels and to evaluate quantitative changes of the ROS levels. Sequencing of the 16S rRNA gene sequences of the midgut bacteria of G. mellonella larvae was conducted for further analyses of bacterial diversity, composition, and abundance. RESULTS: After the injection of the insecticidal proteins, the Duox expression levels first increased within 28 h, then dramatically peaked at 36 h, and slowly decreased thereafter. Simultaneously, the ROS levels increased significantly at 36 h, peaked at 48 h, and rapidly declined to the normal level at 60 h. Responsive to the change of the ROS levels, the structure of the midgut microbial community was altered substantially, compared to that of the untreated larvae. The relative abundance of Enterobacteriaceae and other specific pathogenic bacteria increased significantly, whereas that of Lactobacillus decreased sharply. Importantly, notable shifts were observed in the crucial midgut predicted metabolic functions, including membrane transportation, carbohydrate metabolism, and amino acid metabolism. CONCLUSION: Insecticidal proteins of E. cloacae kill G. mellonella larvae mainly through generation of high oxidative stress, alterations of the midgut microbial community and function, and damage to the physiological functions. These findings provide insights into the inhibition mechanism of E. cloacae insecticidal proteins to G. mellonella larvae.


Subject(s)
Enterobacter cloacae , Gastrointestinal Microbiome , Larva , Moths , Reactive Oxygen Species , Animals , Larva/microbiology , Moths/microbiology , Gastrointestinal Microbiome/drug effects , Reactive Oxygen Species/metabolism , Insecticides , Bacterial Proteins , RNA, Ribosomal, 16S , Dual Oxidases
4.
FEMS Microbiol Lett ; 3712024 Jan 09.
Article in English | MEDLINE | ID: mdl-38982336

ABSTRACT

The extensive use of chemical pesticides, such as herbicides, has resulted in significant environmental pollution. Microbial degradation represents a crucial approach for managing this pesticide-associated pollution, with enrichment culturing serving as a method for isolating pesticide-degrading microorganisms. However, the efficiency of this strategy is limited, often yielding only a few isolated strains. In this study, a new mineral salt medium (MSM) was developed, and a high-throughput method was used for screening pendimethalin-degrading bacteria by measuring the bacterial growth in the MSM. The utilization of this method resulted in the isolation of 56 pendimethalin-degrading bacteria from approximately 2000 bacterial strains, including 37 Bacillus spp., 10 Alcaligenes spp., 5 Pseudomonas spp., and other 4 strains identified for the first time as pendimethalin-degrading strains. This method may hold promise not only for isolating bacterial strains capable of degrading other pesticides but also for facilitating the utilization of the substantial bacterial strains stored in bacterial banks.


Subject(s)
Aniline Compounds , Bacteria , Herbicides , High-Throughput Screening Assays , Aniline Compounds/metabolism , Bacteria/metabolism , Bacteria/isolation & purification , Bacteria/classification , Bacteria/genetics , Bacteria/growth & development , Herbicides/metabolism , High-Throughput Screening Assays/methods , Biodegradation, Environmental , Culture Media/chemistry
5.
Int J Biol Macromol ; 277(Pt 1): 134015, 2024 Jul 20.
Article in English | MEDLINE | ID: mdl-39038566

ABSTRACT

Nanocellulose has been favored as one of the most promising sustainable nanomaterials, due to its competitive advantages and superior performances such as hydrophilicity, renewability, biodegradability, biocompatibility, tunable surface features, excellent mechanical strength, and high specific surface area. Based on the above properties of nanocellulose and the advantages of hydrogels such as high water absorption, adsorption, porosity and structural adjustability, nanocellulose based hydrogels integrating the benefits of both have attracted extensive attention as promising materials in various fields. In this review, the main fabrication strategies of nanocellulose based hydrogels are initially discussed in terms of different crosslinking methods. Then, the typical properties of nanocellulose based hydrogels are comprehensively summarized, including porous structure, swelling ability, adsorption, mechanical, self-healing, smart response performances. Especially, relying on these properties, the general application of nanocellulose based hydrogels in food field is also discussed, mainly including food packaging, food detection, nutrient embedding delivery, 3D food printing, and enzyme immobilization. Finally, the safety of nanocellulose based hydrogel is summarized, and the current challenges and future perspectives of nanocellulose based hydrogels are put forward.

6.
Inorg Chem ; 63(29): 13197-13201, 2024 Jul 22.
Article in English | MEDLINE | ID: mdl-38975741

ABSTRACT

Nonlinear optical (NLO) crystals are widely used in various fields. The introduction of lone-pair cations is regarded as an effective strategy to explore NLO crystals. In this work, two novel lead phosphite halides, centrosymmetric Pb6(HPO3)(H2PO3)Cl9 and noncentrosymmetric Pb6(HPO3)2Br8(H2O)·H2O, were obtained via a hydrothermal method. Pb6(HPO3)(H2PO3)Cl9 is the first reported lone-pair metal phosphite with two kinds of phosphite groups (HPO32- and H2PO3-) and Pb6(HPO3)2Br8(H2O)·H2O is the first inorganic NLO phosphite halide with a phase-matchable SHG effect of 1.02 × KDP. In addition, the Pb-centered polyhedral units of PbOCl4, PbOCl6, PbO2Cl5, PbO2Br5, PbOBr6, and PbO3(H2O)Br3 in these two structures have never been reported before. An in-depth study on the structure-property relationship of the two compounds with halogen substitution is also performed.

7.
Adv Healthc Mater ; : e2400290, 2024 Jul 17.
Article in English | MEDLINE | ID: mdl-39021323

ABSTRACT

Molecularly imprinted polymers (MIPs) show significant promise as effective alternatives to antibodies in disease diagnosis and therapy. However, the challenging process of screening extensive libraries of monomer combinations and synthesis conditions to identify formulations with enhanced selectivity and affinity presents a notable time constraint. The need for expedient methods becomes clear in accelerating the strategic development of MIPs tailored for precise molecular recognition purposes. In this study, an innovative high-throughput screening methodology designed to identify the optimal MIP formulation for targeting tumors is presented. Employing a microtiter plate format, over 100 polymer syntheses are conducted, incorporating diverse combinations of functional monomers. Evaluation of binding performance utilizes fluorescence-based assays, focusing on an epitope of the epidermal growth factor receptor (EGFR). Through this meticulously structured screening process, synthesis conditions that produced MIP nanoparticles exhibiting substantial specificity for EGFR targeting (KD = 10-12 m) are identified. These "bionic antibodies" demonstrate selective recognition of cancer cells in whole blood samples, even at concentrations as low as 5 cells mL-1. Further validation through fluorescent imaging confirms the tumor-specific localization of the MIPs in vivo. This highly efficient screening approach facilitates the strategic synthesis of imprinted polymers functioning as precision bioprobes.

8.
Int Immunopharmacol ; 139: 112668, 2024 Jul 14.
Article in English | MEDLINE | ID: mdl-39008938

ABSTRACT

Sepsis-associated acute kidney injury (SA-AKI) is one of common critical illnesses with high morbidity and mortality. At present, effective therapeutic drugs for SA-AKI are remain lacking. SKLB023 is a synthetic small-molecule compound which exerts potent anti-inflammatory effects in our previous studies. Here, this study aimed to characterize the protective effect of SKLB023 on SA-AKI and explore its underlying mechanism. The SA-AKI experimental models have been established by cecum ligation/puncture (CLP) and lipopolysaccharide (LPS) injection in male C57BL/6J mice. SKLB023 was administered by gavage (50 or 25 mg/kg in CLP model and 50 mg/kg in LPS model) daily 3 days in advance and 30 min earlier on the day of modeling. Our results confirmed SKLB023 treatment could improve the survival of SA-AKI mice and ameliorate renal pathological injury, inflammation, and apoptosis in the two types of septic AKI mice. Mechanically, SKLB023 deceased the expression of TLR4 in LPS-triggered renal tubular epithelial cells, and inhibited the activation of downstream pathways including NF-κB and MAPK pathways. Our study suggested that SKLB023 is expected to be a potential drug for the prevention and treatment of septic AKI.

9.
J Ethnopharmacol ; 334: 118533, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38971347

ABSTRACT

ETHNOPHARMACOLOGICAL RELEVANCE: Flos Chrysanthemi Indici (FCI), the flower of Chrysanthemum Indicum L., is a popular traditional Chinese medicine (TCM) for treatment of inflammatory diseases in China. FCI is also a functional food, and is widely used as herbal tea for clearing heat and detoxicating. AIM OF THE STUDY: To explore quality control markers of FCI based on the optimal harvest period. MATERIALS AND METHODS: First, UPLC-Q-TOF/MS based untargeted metabolomics was applied to explore the chemical profiles of FCIs collected at bud stages (BS), initial stages (IS), full bloom stages (FS) and eventual stages (ES) from eight cultivated regions in China. Subsequently, lipopolysaccharide (LPS)-induced RAW264.7 cell inflammatory model and carrageenan-induced rat paw edema model were used to confirm the anti-inflammatory effect of FCIs collected at IS/FS. Then, UPLC-PDA targeted metabolomics was used to quantitatively analyze 9 constituents with anti-inflammatory activity (7 flavonoids and 2 phenolic acids) changed significantly (VIP > 4) during flowering stages. Finally, ROC curves combined with PCA analysis based on the variation of 9 active constituents in FCIs from different flowering stages were applied to screen the quality markers of FCI. RESULTS: FCIs at IS/FS had almost same chemical characteristics, but quite different from those at BS and ES. A total of 32 constituents in FCIs including flavonoids and phenolic acids were changed during flowering development. Most of the varied constituents had the highest or higher contents at IS/FS compared with those at ES, indicating that the optimal harvest period of FCI should be at IS/FS. FCI extract could effectively suppress nitric oxide (NO) production in LPS-induced RAW264.7 cells and regulate the abnormal levels of cytokines and PGE2 in carrageenan-induced paw edema model rat. The results of quantitatively analysis revealed that the variation trends of phenolic acids and flavonoids in FCIs were different during flowering development, but most of them had higher contents at IS/FS than those at ES in all FCIs collected from eight cultivated regions, except one sample from Anhui. Finally, linarin, luteolin, apigenin and 3,5-dicaffeoylquinic acid were selected as the Q-markers based on the contribution of their AUC values in ROC and clustering of PCA analysis. CONCLUSIONS: Our study demonstrates the optimal harvest period of FCI and specifies the multi-constituents Q-markers of FCI based on the influence of growth progression on the active constituents using untargeted/targeted metabolomics. The findings not only greatly increase the utilization rate of FCI resources and improve quality control of FCI products, but also offer new strategy to identify the Q-markers of FCI.

10.
Anal Chem ; 96(28): 11326-11333, 2024 Jul 16.
Article in English | MEDLINE | ID: mdl-38953527

ABSTRACT

Herein, the aptamer-antibody sandwich module was first introduced to accurately recognize a low molecular weight compound (mycotoxin). Impressively, compared with the large steric hindrance of a traditional dual-antibody module, the aptamer-antibody sandwich with low Gibbs free energy and a low dissociation constant has high recognition efficiency; thus, it could reduce false positives and false negatives caused by a dual-antibody module. As a proof of concept, a sensitive electrochemiluminescence (ECL) biosensor was constructed for detecting mycotoxin zearalenone (ZEN) based on an aptamer-antibody sandwich as a biological recognition element and porous ZnO nanosheets (Zn NSs) supported Cu nanoclusters (Cu NCs) as the signal transduction element, in which the antibody was modified on the vertex of a tetrahedral DNA nanostructure (TDN) with a rigid structure to increase the kinetics of target recognition for promoting the detection sensitivity. Moreover, the Cu NCs/Zn NSs exhibited an excellent ECL response that was attributed to the aggregation-induced ECL enhancement through electrostatic interactions. The sensing platform achieved trace detection of ZEN with a low detection limit of 0.31 fg/mL, far beyond that of the enzyme-linked immunosorbent assay (ELISA, the current rapid detection method) and high-performance liquid chromatography (HPLC, the national standard detection method). The strategy has great application potential in food analysis, environmental monitoring, and clinical diagnosis.


Subject(s)
Aptamers, Nucleotide , Biosensing Techniques , Electrochemical Techniques , Zearalenone , Aptamers, Nucleotide/chemistry , Biosensing Techniques/methods , Zearalenone/analysis , Zearalenone/immunology , Electrochemical Techniques/methods , Copper/chemistry , Limit of Detection , Antibodies/chemistry , Antibodies/immunology , Luminescent Measurements/methods , Zinc Oxide/chemistry , Molecular Weight
11.
Proc Natl Acad Sci U S A ; 121(30): e2404164121, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-39012823

ABSTRACT

The development of advanced neural modulation techniques is crucial to neuroscience research and neuroengineering applications. Recently, optical-based, nongenetic modulation approaches have been actively investigated to remotely interrogate the nervous system with high precision. Here, we show that a thin-film, silicon (Si)-based diode device is capable to bidirectionally regulate in vitro and in vivo neural activities upon adjusted illumination. When exposed to high-power and short-pulsed light, the Si diode generates photothermal effects, evoking neuron depolarization and enhancing intracellular calcium dynamics. Conversely, low-power and long-pulsed light on the Si diode hyperpolarizes neurons and reduces calcium activities. Furthermore, the Si diode film mounted on the brain of living mice can activate or suppress cortical activities under varied irradiation conditions. The presented material and device strategies reveal an innovated optoelectronic interface for precise neural modulations.


Subject(s)
Neurons , Optogenetics , Silicon , Animals , Silicon/chemistry , Neurons/physiology , Mice , Optogenetics/methods , Calcium/metabolism , Light , Brain/physiology
12.
Biomater Sci ; 2024 Jul 12.
Article in English | MEDLINE | ID: mdl-38993162

ABSTRACT

With the increasing research and deepening understanding of the glioblastoma (GBM) tumour microenvironment (TME), novel and more effective therapeutic strategies have been proposed. The GBM TME involves intricate interactions between tumour and non-tumour cells, promoting tumour progression. Key therapeutic goals for GBM treatment include improving the immunosuppressive microenvironment, enhancing the cytotoxicity of immune cells against tumours, and inhibiting tumour growth and proliferation. Consequently, remodeling the GBM TME using nanotechnology has emerged as a promising approach. Nanoparticle-based drug delivery enables targeted delivery, thereby improving treatment specificity, facilitating combination therapies, and optimizing drug metabolism. This review provides an overview of the GBM TME and discusses the methods of remodeling the GBM TME using nanotechnology. Specifically, it explores the application of nanotechnology in ameliorating immune cell immunosuppression, inducing immunogenic cell death, stimulating, and recruiting immune cells, regulating tumour metabolism, and modulating the crosstalk between tumours and other cells.

13.
Chem Commun (Camb) ; 2024 Jul 11.
Article in English | MEDLINE | ID: mdl-38990518

ABSTRACT

The industrial separation of hydrocarbons relies on distillation. Organic solvent nanofiltration can provide an energy-efficient alternative. We prepared high performance organosiloxane membranes for fractionation of heavy aromatics. They achieved a high permeance up to 0.13 L m-2 h-1 bar-1, with a rejection rate of 88.7% for hydrocarbons with five aromatic rings.

14.
J Transl Med ; 22(1): 605, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38951874

ABSTRACT

BACKGROUND: Uveal melanoma (UM), the most common adult intraocular tumor, is characterized by high malignancy and poor prognosis in advanced stages. Angiogenesis is critical for UM development, however, not only the role of vascular endothelial dysfunction in UM remains unknown, but also their analysis at the single-cell level has been lacking. A comprehensive analysis is essential to clarify the role of the endothelium in the development of UM. METHODS: By using single-cell RNA transcriptomics data of 11 cases of primary and liver metastasis UM, we analyzed the endothelial cell status. In addition, we analyzed and validated ECs in the in vitro model and collected clinical specimens. Subsequently, we explored the impact of endothelial dysfunction on UM cell migration and explored the mechanisms responsible for the endothelial cell abnormalities and the reasons for their peripheral effects. RESULTS: UM metastasis has a significantly higher percentage of vascular endothelial cells compared to in situ tumors, and endothelial cells in metastasis show significant senescence. Senescent endothelial cells in metastatic tumors showed significant Krüppel-like factor 4 (KLF4) upregulation, overexpression of KLF4 in normal endothelial cells induced senescence, and knockdown of KLF4 in senescent endothelium inhibited senescence, suggesting that KLF4 is a driver gene for endothelial senescence. KLF4-induced endothelial senescence drove tumor cell migration through a senescence-associated secretory phenotype (SASP), of which the most important component of the effector was CXCL12 (C-X-C motif chemokine ligand 12), and participated in the composition of the immunosuppressive microenvironment. CONCLUSION: This study provides an undesirable insight of senescent endothelial cells in promoting UM metastasis.


Subject(s)
Cell Movement , Cellular Senescence , Endothelial Cells , Kruppel-Like Factor 4 , Liver Neoplasms , Melanoma , Single-Cell Analysis , Uveal Neoplasms , Humans , Uveal Neoplasms/pathology , Uveal Neoplasms/genetics , Melanoma/pathology , Melanoma/genetics , Liver Neoplasms/pathology , Liver Neoplasms/secondary , Liver Neoplasms/genetics , Endothelial Cells/metabolism , Endothelial Cells/pathology , Kruppel-Like Transcription Factors/metabolism , Kruppel-Like Transcription Factors/genetics , Cell Line, Tumor , Chemokine CXCL12/metabolism , Chemokine CXCL12/genetics , Gene Expression Regulation, Neoplastic , Female , Male
15.
Eur J Radiol ; 178: 111619, 2024 Jul 14.
Article in English | MEDLINE | ID: mdl-39024666

ABSTRACT

OBJECTIVES: This study aims to analyze the efficacy of transcatheter arterial chemoembolization (TACE) combined with radiofrequency ablation (RFA), microwave ablation (MWA), and cryoablation (CA) in hepatocellular carcinoma (HCC). METHODS: A retrospective analysis was conducted on 632 patients with HCC at Barcelona Clinic Liver Cancer Staging (BCLC) System stages 0, A, and B from Beijing You'an Hospital affiliated with Capital Medical University. The primary outcomes analyzed were overall survival (OS) and progression-free survival (PFS), while the secondary outcomes included one-, three-, and five-year OS rates among different groups. RESULTS: The median follow-up period for 632 cases identified with HCC was 52.1 months (range: 3-162 months), while 127 patients died during follow-up. The one-, three-, and five-year OS rates were 97.1 %, 89.5 %, and 80.4 %, respectively. Moreover, the one-, three-, and five-year PFS rates were 58.1 %, 29.3 %, and 19.8 %, respectively. Multivariate analysis revealed that the BCLC stages and complete ablation were independent predictors of OS and PFS (all p < 0.05). Subgroup analysis showed no difference in OS rate among TACE-RFA, TACE-MWA, and TACE-CA groups, but TACE-CA showed better efficacy in improving the PFS rate (all p < 0.05). CONCLUSIONS: The combination of TACE and ablation is effective in early-stage HCC and BCLC stage B. Complete ablation and BCLC stages are significant prognostic factors for PFS and OS. Further research, including randomized controlled trials, is needed to validate these findings.

16.
Biomater Sci ; 2024 Jul 22.
Article in English | MEDLINE | ID: mdl-39034872

ABSTRACT

Renal ischemia/reperfusion injury (RIRI) is an inevitable complication following kidney transplantation surgery, accompanied by the generation of a large amount of free radicals. A cascade of events including oxidative stress, extreme inflammation, cellular apoptosis, and thrombosis disrupts the microenvironment of renal cells and the hematological system, ultimately leading to the development of acute kidney injury (AKI). The current research primarily focuses on reducing inflammation and mitigating damage to renal cells through antioxidative approaches. However, studies on simultaneously modulating the renal hematologic system remain unreported. Herein, potent and novel drug-loaded nanomicelles can be efficiently self-assembled with magnolol (MG) and ebselen (EBS) by π-π conjugation, hydrophobic action and the surfactant properties of Tween-80. The ultrasmall MG/EBS nanomicelles (average particle size: 10-25 nm) not only fully preserve the activity of both drugs, but also greatly enhance drug utilization (encapsulation rates: MG: 90.1%; EBS: 49.3%) and reduce drug toxicity. Furthermore, EBS, as a glutathione peroxidase mimic and NO catalyst, combines with the multifunctional MG to scavenge free radicals and hydroperoxides, significantly inhibiting inflammation and thrombosis while effectively preventing apoptosis of vascular endothelial cells and renal tubular epithelial cells. This study provides a new strategy and theoretical foundation for the simultaneous regulation of kidney cells and blood microenvironment stability.

17.
Bioinform Adv ; 4(1): vbae086, 2024.
Article in English | MEDLINE | ID: mdl-39027640

ABSTRACT

Motivation: Single-cell RNA sequencing (scRNA-seq) has become a valuable tool for studying cellular heterogeneity. However, the analysis of scRNA-seq data is challenging because of inherent noise and technical variability. Existing methods often struggle to simultaneously explore heterogeneity across cells, handle dropout events, and account for batch effects. These drawbacks call for a robust and comprehensive method that can address these challenges and provide accurate insights into heterogeneity at the single-cell level. Results: In this study, we introduce scVIC, an algorithm designed to account for variational inference, while simultaneously handling biological heterogeneity and batch effects at the single-cell level. scVIC explicitly models both biological heterogeneity and technical variability to learn cellular heterogeneity in a manner free from dropout events and the bias of batch effects. By leveraging variational inference, we provide a robust framework for inferring the parameters of scVIC. To test the performance of scVIC, we employed both simulated and biological scRNA-seq datasets, either including, or not, batch effects. scVIC was found to outperform other approaches because of its superior clustering ability and circumvention of the batch effects problem. Availability and implementation: The code of scVIC and replication for this study are available at https://github.com/HiBearME/scVIC/tree/v1.0.

18.
Acta Pharmacol Sin ; 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-39043969

ABSTRACT

Acute kidney injury (AKI) is a common disease, but lacking effective drug treatments. Chromodomain Y-like (CDYL) is a kind of chromodomain protein that has been implicated in transcription regulation of autosomal dominant polycystic kidney disease. Benzo[d]oxazol-2(3H)-one derivative (compound D03) is the first potent and selective small-molecule inhibitor of CDYL (KD = 0.5 µM). In this study, we investigated the expression of CDYL in three different models of cisplatin (Cis)-, lipopolysaccharide (LPS)- and ischemia/reperfusion injury (IRI)-induced AKI mice. By conducting RNA sequencing and difference analysis of kidney samples, we found that tubular CDYL was abnormally and highly expressed in injured kidneys of AKI patients and mice. Overexpression of CDYL in cisplatin-induced AKI mice aggravated tubular injury and pyroptosis via regulating fatty acid binding protein 4 (FABP4)-mediated reactive oxygen species production. Treatment of cisplatin-induced AKI mice with compound D03 (2.5 mg·kg-1·d-1, i.p.) effectively attenuated the kidney dysfunction, pathological damages and tubular pyroptosis without side effects on liver or kidney function and other tissue injuries. Collectively, this study has, for the first time, explored a novel aspect of CDYL for tubular epithelial cell pyroptosis in kidney injury, and confirmed that inhibition of CDYL might be a promising therapeutic strategy against AKI.

19.
Bioeng Transl Med ; 9(4): e10665, 2024 Jul.
Article in English | MEDLINE | ID: mdl-39036077

ABSTRACT

Synucleinopathies, including Parkinson's disease (PD), multiple system atrophy (MSA), and dementia with Lewy bodies (DLB), are neurodegenerative disorders caused by the accumulation of misfolded alpha-synuclein protein. Developing effective vaccines against synucleinopathies is challenging due to the difficulty of stimulating an immune-specific response against alpha-synuclein without causing harmful autoimmune reactions, selectively targeting only pathological forms of alpha-synuclein. Previous attempts using linear peptides and epitopes without control of the antigen structure failed in clinical trials. The immune system was unable to distinguish between native alpha-synuclein and its amyloid form. The prion domain of the fungal HET-s protein was selected as a scaffold to introduce select epitopes from the surface of alpha-synuclein fibrils. Four vaccine candidates were generated by introducing specific amino acid substitutions onto the surface of the scaffold protein. The approach successfully mimicked the stacking of the parallel in-register beta-sheet structure seen in alpha-synuclein fibrils. All vaccine candidates induced substantial levels of IgG antibodies that recognized pathological alpha-synuclein fibrils derived from a synucleinopathy mouse model. Furthermore, the antisera recognized pathological alpha-synuclein aggregates in brain lysates from patients who died from DLB, MSA, or PD, but did not recognize linear alpha-synuclein peptides. Our approach, based on the rational design of vaccines using the structure of alpha-synuclein amyloid fibrils and strict control over the exposed antigen structure used for immunization, as well as the ability to mimic aggregated alpha-synuclein, provides a promising avenue toward developing effective vaccines against alpha-synuclein fibrils.

20.
Natl Sci Rev ; 11(7): nwae003, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38883288

ABSTRACT

Focusing on the ternary hydrides, the new hope of Room-Temperature Superconductivity, this perspective delves into the research background, highlights current challenges, and illuminates promising avenues for future studies.

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