Search Results (92)

Plant fungal diseases remain a major threat to global agricultural production, necessitating eco-friendly and sustainable strategies. Conventional chemical fungicides often lead to the development of resistant pathogen strains and cause environmental contamination. Therefore, the development of biocontrol agents is particularly important. In this study, we identified Burkholderia stagnalis YJ-2 from the rhizosphere soil of Woodsia ilvensis as a promising biocontrol strain using 16S rRNA and whole-genome sequencing. This strain demonstrated broad-spectrum antifungal activity against plant fungal pathogens, with its bioactive extracts maintaining high stability across a temperature range of 25–100 °C and pH range of 2–12. We used in vitro assays to further show that the metabolites of B. stagnalis YJ-2 disrupted the hyphal morphology of Valsa mali, resulting in swelling, reduced branching, and increased pigmentation. Fluorescence labeling confirmed that B. stagnalis YJ-2 stably colonized the roots and stems of tomato and wheat plants. Furthermore, various formulations of microbial agents based on B. stagnalis YJ-2 were evaluated for their efficacy against plant pathogens. The seed-coating formulation notably protected tomato seedlings from Alternaria solani infection without affecting germination (p > 0.1), while the wettable powder exhibited significant control effects on early blight in tomatoes, with the preventive treatment showing better efficacy than the therapeutic treatment. Additionally, the B. stagnalis YJ-2 bone glue agent showed a substantial inhibitory effect on apple tree canker. Whole-genome analysis of B. stagnalis YJ-2 revealed a 7,705,355 bp genome (67.68% GC content) with 6858 coding genes and 20 secondary metabolite clusters, including three clusters (YJ-2_GM002015-YJ-2_GM002048, YJ-2_GM0020090-YJ-2_GM002133, and YJ-2_GM06534-YJ-2_GM006569) that are related to the antifungal activity of YJ-2 and are homologous to the biosynthetic gene clusters of known secondary metabolites, such as icosalide, ornibactin, and sinapigladioside. We further knocked out core biosynthetic genes of two secondary metabolic gene clusters and found that only the YJ-2_GM006534-YJ-2_GM006569 gene cluster had a corresponding function in two potential antifungal gene clusters. In contrast to the wild-type strain YJ-2, only deletion of the YJ-2_GM006563 gene reduced the antifungal activity of B. stagnalis YJ-2 by 8.79%. These findings highlight the biocontrol potential of B. stagnalis YJ-2, supporting a theoretical foundation for its development as a biocontrol agent against plant fungal diseases and thereby promoting sustainable agricultural disease management. Full article

Background: The global burden of obesity and type 2 diabetes mellitus is a significant contributor to mortality and disability in the modern world. In this regard, the modification of adipocyte metabolism has been identified as a promising approach to develop new genetic and cellular engineering therapeutics. In this study, we activate the expression of creatine kinase B (CKB), a key enzyme of a non-canonical futile cycle and the regulator of energy storage, to promote catabolic processes in mature adipocytes. Methods: The protein-coding sequence of CKB was amplified by PCR from Mus musculus brain mRNA. Lentiviral transduction was used to transfer the CKB sequence into mature adipocytes. Adipocyte metabolism was analyzed by radioisotope monitoring of labeled [3H]-2-deoxyglucose and [14C]-glucose. Confocal microscopy was applied to estimate lipid droplets morphology (BODIPY493/503 dye), mitochondrial membrane potential (JC-1 dye), and thermogenesis (ERthermAC dye). Results: After lentiviral delivery of the CKB-coding sequence, CKB mRNA level increased 75-fold and protein expression fivefold. CKB overexpression does not cause significant changes in lipid droplet morphology. Despite this, enhanced glucose uptake and reduced lipid synthesis under adrenergic stimulation are detected during CKB overexpression. CKB causes an increase in mitochondrial potential with no effect on thermogenesis in adipocytes. Conclusions: In this study, we have shown that CKB overexpression in mature adipocytes allows us to obtain adipocytes with high glucose uptake, potency of ATP synthesis, and suppressed lipogenesis. These genetically modified cells may potentially exhibit a favorable metabolic effect in the context of excessive nutrient utilization. Full article

Bacteria are ubiquitous in the environment and critical to human health and disease, yet only a small fraction can be identified through standard culture methods. Advances in next-generation sequencing techniques have improved bacterial identification, but these DNA-based methods cannot distinguish live bacteria from relic DNA. Recently, DNA-labeling dyes (e.g., 5-bromo-2′-deoxyuridine [BrdU] and propidium monoazide [PMA]) have been used to detect metabolically active bacteria in different sample types. Here, we compare BrdU and PMA in combination with 16SrRNA gene sequencing to characterize metabolically active bacteria in two different sample types: (1) manufactured products (n = 78; cigarettes, hookah, and little cigar) and (2) natural samples (n = 186; rainwater, soil, and produce). Metabolically active bacterial communities identified in BrdU-labeled samples had lower alpha diversity than that of PMA-treated and non-treated samples. Pseudomonas, Sphingomonas, Enterobacter, and Acinetobacter were observed in all the samples tested. Irrespective of sample type, Pseudomonas was predominant in BrdU-treated samples, while Acinetobacter was more abundant in non-treated samples compared to PMA-treated samples. We also observed that PMA-treated samples tend to overestimate the metabolically active bacterial fraction compared to BrdU-treated samples. Overall, our study highlights how different labeling techniques influence bacterial community analysis findings, underscoring the need for careful selection of labeling approaches when assessing environmental samples. Full article

Objectives: This research aims to explore the therapeutic potential of Bi-Qi capsules in the treatment of gout by identifying crucial drug targets through a multidimensional data analysis strategy. Methods: Bi-Qi capsule drug targets and differentially expressed genes (DEGs) of gout were derived from public databases, such as Swiss Target Prediction, STITCH, and the GEO database. Subsequently, the overlapped targets were analyzed to elucidate the potential therapeutic mechanism and to identify candidate targets of Bi-Qi capsules against gout. Next, Mendelian randomization (MR) analysis was employed to screen and explore the causal relationship between candidate targets and gout. Finally, single-cell RNA sequencing (scRNA-seq), gene set enrichment analysis (GSEA), transcription factor and ceRNA regulatory networks, and molecular docking were performed to validate the role of the crucial targets of Bi-Qi capsules in the treatment of gout. Results: A total of 46 candidate targets were identified, in which KCNA5, PTGS2, and TNF exhibited significant causal relationships with gout (p < 0.05) and were regarded as the crucial targets. Through scRNA-seq and gene labeling, crucial targets were found to be expressed in eighteen cell clusters and eight cell types, which are closely associated with carbohydrate metabolism, nerve conduction, and the innate immunity process. Bi-Qi capsule active compounds such as tanshinone IIA, strychnine, tanshinaldehyde, cryptotanshinone, tumulosic acid, and glycyrrhetic acid exhibit a better binding ability to crucial targets. Conclusions: The results not only elucidate the anti-gout mechanism of Bi-Qi capsules but also provide an insight into multi-target natural medication for metabolic disease treatment, which contributes to guiding the clinical application of Bi-Qi capsules in the future. Full article

Matrine, a quinoline alkaloid, possesses lipid-regulating effects, but the underlying mechanisms are rarely characterized in vivo. With a fat-accumulating Caenorhabditis elegans model, we show that matrine reduces the fat content and the DHS-3::GFP-labeled lipid droplets in high-glucose-diet N2 and transgenic LIU1 nematodes, respectively. Based on RNA-seq, this study demonstrates that a loss of AAK-2 function suppresses the fat-lowering effects of matrine, and the hyperactivated AAK-2 strain has a relatively lower fat content than N2. The involvement of NHR-49 in matrine’s fat-lowering effects further suggests that matrine impacts fat breakdown and storage via the AAK-2/NHR-49-governed pathway. Using the transgenic SJ4143 (ges-1::GFP(mit)) and VS10 (vha-6p::mRFP-PTS1), we show that matrine activates the AAK-2/NHR-49 pathway, coupling the alteration of mitochondrial and peroxisomal functions. Studies of aak-2 and nhr-49 mutants reveal that AAK-2 and NHR-49 modulate lipid metabolic homeostasis; meanwhile, matrine increases physical fitness and lifespan through activating the AAK-2/NHR-49 pathway in high-glucose-diet nematodes. Surprisingly, we found that β-amyloid (Aβ) induces lipid metabolic disorder in an Alzheimer’s disease (AD) C. elegans model, but matrine not only reduces Aβ aggregation but also alleviates Aβ-mediated lipid metabolic disorder. Our data suggest that matrine has promise as a fat-lowering agent, and also offer new insights into its therapeutic potential for AD. Full article

The respiratory epithelium maintains the barrier against inhaled harmful agents. When barrier failure occurs, as in several respiratory diseases, acute or chronic inflammation leading to destructive effects and exacerbations can occur. Macrolides are used to treat a spectrum of infections but are also known for off-label use. Some macrolides, particularly azithromycin (AZM), reduce exacerbations in chronic obstructive pulmonary disease (COPD), whereby its efficacy is thought to be due to its effects on inflammation and oxidative stress. In vitro data indicate that AZM reduces epithelial barrier failure, evidenced by increased transepithelial electrical resistance (TEER). Here, we compared the effects of macrolides on differentiation and barrier integrity in VA10 cells, a bronchial epithelial cell line for 14 and 21 days. Erythromycin, clarithromycin, roxithromycin, AZM, solithromycin, and tobramycin (an aminoglycoside) were analyzed using RNA sequencing, barrier integrity assays, and immunostaining to evaluate effects on the epithelium. All macrolides affected the gene expression of pathways involved in epithelial-to-mesenchymal transition, metabolism, and immunomodulation. Treatment with AZM, clarithromycin, and erythromycin raised TEER and induced phospholipid retention. AZM treatment was distinct in terms of enhancement of the epithelial barrier, retention of phospholipids, vesicle build-up, and its effect on gene sets related to keratinocyte differentiation and establishment of skin barrier. Full article

Background/Objectives: Deoxynivalenol (DON), known as vomitoxin, is one of the most common mycotoxins produced by Fusarium graminearum, with high detection rates in feed worldwide. Ferroptosis is a novel mode of cell death characterized by lipid peroxidation and the accumulation of reactive oxygen species. Although it has been demonstrated that DON can induce ferroptosis in the liver, the specific mechanisms and pathways are still unknown. The aim of this experiment was to investigate that DON can induce iron metabolism disorders in the livers of mice, thereby triggering ferroptosis and causing toxic damage to the liver. Methods: Male C57 mice were treated with DON at a 5 mg/kg BW concentration as an in vivo model. After sampling, organ coefficient monitoring, liver function test, histopathological analysis, liver Fe²⁺ content test, and oxidative stress-related indexes were performed. The mRNA and protein expression of Nrf2 and its downstream genes were also detected using a series of methods including quantitative real-time PCR, immunofluorescence double-labeling, and Western blotting analysis. Results: DON can cause damage to the liver of a mouse. Specifically, we found that mouse livers in the DON group exhibited pathological damage in cell necrosis, inflammatory infiltration, cytoplasmic vacuolization, elevated relative liver weight, and significant changes in liver function indexes. Meanwhile, the substantial reduction in the levels of glutathione (GSH), catalase (CAT), superoxide dismutase (SOD), and total antioxidant capacity (T-AOC) in the DON group indicated that DON also caused oxidative stress in the liver. Notably, DON exposure increased the levels of Fe²⁺ and Malondialdehyde (MDA) in the liver, which provides strong evidence for the occurrence of iron metabolism and ferroptosis disorders. Most importantly, mRNA and protein expression of Nrf2, an important pathway for iron metabolism and ferroptosis, along with its downstream genes, heme oxygenase (HO-1), quinone oxidoreductase (NQO1), glutathione peroxidase (GPX4), and solute carrier gene (SLC7a11), were significantly inhibited in the DON group. Conclusions: Based on our results, the Nrf2 pathway is closely associated with DON-induced iron metabolism disorders and ferroptosis in mouse livers, suggesting that maintaining hepatic iron homeostasis and activating the Nrf2 pathway may be a potential target for mitigating DON hepatotoxicity in the future. Full article

T cells play a crucial role in the immune system by identifying and eliminating tumor cells. Malignant cancer cells can hijack mitochondria (MT) from nearby T cells, affecting their metabolism and weakening their immune functions. This phenomenon, observed through co-culture systems and fluorescent labeling, has been further explored with the development of the MERCI algorithm, which predicts T cell MT hijacking in cancer cells using single-cell RNA (scRNA) sequencing data. However, MERCI is limited by its reliance on a linear model and its inability to handle data sparsity. To address these challenges, we introduce MitoR, a computational algorithm using a Poisson–Gamma mixture model to predict T cell MT hijacking from tumor scRNA data. In performance comparisons, MitoR demonstrated improved performance compared to MERCI’s on gold-standard benchmark datasets scRNA-bench1 (top AUROC: 0.761, top accuracy: 0.769) and scRNA-bench2 (top AUROC: 0.730, top accuracy: 0.733). Additionally, MitoR showed an average 4.14% increase in AUROC and an average 3.86% increase in accuracy over MERCI in all rank strategies and simulated datasets. Finally, MitoR revealed T cell MT hijacking events in two real-world tumor datasets (basal cell carcinoma and esophageal squamous-cell carcinoma), highlighting their role in tumor immune evasion. Full article

Small non-coding RNAs play a pivotal role in regulating various metabolic processes in both prokaryotic and eukaryotic organisms. However, knowledge about small RNAs (sRNAs) in Streptomyces clavuligerus (S. clavuligerus) is scarce. This study aimed to use cutting-edge bioinformatics tools and a compendium of RNA-seq data to predict the potential coding of sRNAs that might be present in the genome of S. clavuligerus ATCC 27064. In the genome of S. clavuligerus, 606 intergenic regions (IGRs) are conserved, and 272 possess a highly thermodynamically stable and conserved secondary structure, indicating the presence of non-coding RNA in these regions. The transcriptome assembly of S. clavuligerus showed that the genome is completely functional, as all the annotated genes are expressed under the conditions analyzed. From this assembly, transcripts originating from IGRs were labeled as putative sRNAs, and their differential expression during the growth curve of S. clavuligerus for clavulanic acid (CA) production was established. The interactome of these differentially expressed (DE) RNAs displayed the sRNAs as global regulators, as they can have multiple mRNA targets. The functional annotation of the target genes of DE sRNAs demonstrated that they are directly involved in secondary metabolite production. Specifically, two sRNA have the genes of the biosynthetic gene cluster of CA as targets. Thus, these molecules add an additional layer to the regulatory cascade for CA biosynthesis, and we propose them as targets for metabolic engineering to increase CA production. Full article

Transcriptome analysis in single cells, enabled by single-cell RNA sequencing, has become a prevalent approach in biomedical research, ranging from investigations of gene regulation to the characterization of tissue organization. Over the past decade, advances in single-cell RNA sequencing technology, including its underlying chemistry, have significantly enhanced its performance, marking notable improvements in methodology. A recent development in the field, which integrates RNA metabolic labeling with single-cell RNA sequencing, has enabled the profiling of temporal transcriptomes in individual cells, offering new insights into dynamic biological processes involving RNA kinetics and cell fate determination. In this review, we explore the chemical principles and design improvements that have enhanced single-molecule capture efficiency, improved RNA quantification accuracy, and increased cellular throughput in single-cell transcriptome analysis. We also illustrate the concept of RNA metabolic labeling for detecting newly synthesized transcripts and summarize recent advancements that enable single-cell temporal transcriptome analysis. Additionally, we examine data analysis strategies for the precise quantification of newly synthesized transcripts and highlight key applications of transcriptome and temporal transcriptome analyses in single cells. Full article

Background: The relationship between consuming Thai desserts—predominantly composed of carbohydrates—and gut microbiome profiles remains unclear. This study aimed to evaluate the effects of consuming various Thai desserts with different GI values on the gut microbiomes of healthy volunteers. Methods: This open-label, parallel randomized clinical trial involved 30 healthy individuals aged 18 to 45 years. Participants were randomly assigned to one of three groups: Phetchaburi’s Custard Cake (192 g, low-GI group, n = 10), Saraburi’s Curry Puff (98 g, medium-GI group, n = 10), and Lampang’s Crispy Rice Cracker (68 g, high-GI group, n = 10), each consumed alongside their standard breakfast. Fecal samples were collected at baseline and 24 h post-intervention for metagenomic analysis of gut microbiome profiles using 16S rRNA gene sequencing. Results: After 24 h, distinct trends in the relative abundance of various gut microbiota were observed among the dessert groups. In the high-GI dessert group, the abundance of Collinsella and Bifidobacterium decreased compared to the low- and medium-GI groups, while Roseburia and Ruminococcus showed slight increases. Correlation analysis revealed a significant negative relationship between sugar intake and Lactobacillus abundance in the medium- and high-GI groups, but not in the low-GI group. Additionally, a moderately negative association was observed between Akkermansia abundance and sugar intake in the high-GI group. These bacteria are implicated in energy metabolism and insulin regulation. LEfSe analysis identified Porphyromonadaceae and Porphyromonas as core microbiota in the low-GI group, whereas Klebsiella was enriched in the high-GI group, with no predominant bacteria identified in the medium-GI group. Conclusions: The findings suggest that Thai desserts with varying GI levels can influence specific gut bacteria, though these effects may be temporary. Full article

In this study, “Longjia (LJ)” and “Yangpao (YP)”exhibited higher contents of major nutrients compared to “Niangqing (NQ)” walnuts. The combination of transcriptome and proteome by RNA sequencing and isotope labeling for relative and absolute quantification techniques provides new insights into the molecular mechanisms underlying the nutritional quality of the three walnut species. A total of 4146 genes and 139 proteins showed differential expression levels in the three comparison groups. Combined transcriptome and proteome analyses revealed that these genes and proteins were mainly enriched in signaling pathways such as fatty acid biosynthesis, protein processing in endoplasmic reticulum, and amino acid metabolism, revealing their relationship with the nutritional quality of walnut kernels. This study identified key genes and proteins associated with nutrient metabolism and accumulation in walnut kernels, provided transcriptomic and proteomic information on the molecular mechanisms of nutrient differences in walnut kernels, and contributed to the elucidation of the mechanisms of nutrient differences and the selection and breeding of high-quality walnut seedlings. Full article

This study aimed to assess the fermentation characteristics, bacterial community structure, co-occurrence networks, and their predicted functionality and pathogenic risk in high-moisture Italian ryegrass (IR; Lolium multiflorum Lam.) silage. The IR harvested at heading stage (208 g dry matter (DM)/kg fresh weight) was spontaneously ensiled in plastic silos (10 L scale). Triplicated silos were opened after 1, 3, 7, 15, 30, and 60 days of fermentation, respectively. The bacterial community structure on days 3 and 60 were investigated using high-throughput sequencing technology, and 16S rRNA-gene predicted functionality and phenotypes were determined by PICRUSt2 and BugBase tools, respectively. After 60 days, the IR silage exhibited good ensiling characteristics indicated by large amounts of acetic acid (~58.7 g/kg DM) and lactic acid (~91.5 g/kg DM), relatively low pH (~4.20), acceptable levels of ammonia nitrogen (~87.0 g/kg total nitrogen), and trace amounts of butyric acid (~1.59 g/kg DM). Psychrobacter was prevalent in fresh IR, and Lactobacillus became the most predominant genus after 3 and 60 days. The ensilage process reduced the complexity of the bacterial community networks in IR silage. The bacterial functional pathways in fresh and ensilaged IR are primarily characterized by the metabolism of carbohydrate and amino acid. The pyruvate kinase and 1-phosphofructokinase were critical in promoting lactic acid fermentation. A greater (p < 0.01) abundance of the “potentially pathogenic” label was noticed in the bacterial communities of ensiled IR than fresh IR. Altogether, the findings indicated that the high-moisture IR silage exhibited good ensiling characteristics, but the potential for microbial contamination and pathogens still remained after ensiling. Full article

Ram sperm undergo a sequence of physiological and biochemical changes collectively termed as capacitation to perform oocyte fertilization. However, the protein changes induced by capacitation remain in need of further exploration. Thus, the present study investigated the comparative proteomic profiling in ram spermatozoa under non-capacitating (NC) and capacitating (CAP) conditions in vitro using a liquid chromatography–tandem mass spectrometry combined with tandem mass tag labeling strategy. As a results, 2050 proteins were identified and quantified; 348 of them were differentially abundant, with 280 of the proteins upregulated and 68 of the proteins downregulated between the CAP and NC spermatozoa, respectively. Functional enrichment analysis indicated that the differentially abundant proteins Prune Exopolyphosphatase 1, Galactose-1-Phosphate Uridylyltransferase, and ATP Citrate Lyase were strictly related to energy production and conversion, and Phosphoglycolate phosphatase, Glucosamine-6-Phosphate Deaminase 1 and 2 were related to metabolism, RNA processing, and vesicular transport pathways. Furthermore, the networks of protein–protein interaction indicated a strong interaction among these differential proteins in annotated pathways such as ubiquitin and transport metabolism. Our findings indicate that capacitation progress might be regulated through different pathways, providing insights into mechanisms involved in ram sperm capacitation and fertility. Full article

Unsaturated fatty acids (UFAs) in beef play a vital role in promoting human health. Long-chain fatty acyl-CoA synthase 1 (ACSL1) is a crucial gene for UFA synthesis in bovine adipocytes. To investigate the protein expression profile during UFA synthesis, we performed a proteomic analysis of bovine adipocytes by RNA interference and non-interference with ACSL1 using label-free techniques. A total of 3558 proteins were identified in both the NC and si-treated groups, of which 1428 were differentially expressed proteins (DEPs; fold change ≥ 1.2 or ≤ 0.83 and p-value < 0.05). The enrichment analysis of the DEPs revealed signaling pathways related to UFA synthesis or metabolism, including cAMP, oxytocin, fatty acid degradation, glycerol metabolism, insulin, and the regulation of lipolysis in adipocytes (p-value < 0.05). Furthermore, based on the enrichment analysis of the DEPs, we screened 50 DEPs that potentially influence the synthesis of UFAs and constructed an interaction network. Moreover, by integrating our previously published transcriptome data, this study established a regulatory network involving differentially expressed long non-coding RNAs (DELs), highlighting 21 DEPs and 13 DELs as key genes involved in UFA synthesis. These findings present potential candidate genes for further investigation into the molecular mechanisms underlying UFA synthesis in bovines, thereby offering insights to enhance the quality of beef and contribute to consumer health in future studies. Full article