Frontiers in Nutrition
·
2021
·
IF 6.576
Yang Ruopeng,Chen Xiu,Huang Qiang,Chen Chuying,Rengasamy Kannan R. R.,Chen Jinyin,Wan Chunpeng (Craig)
Penicillium digitatum is the most severe pathogen that infects citrus fruits during storage. It can cause fruit rot and bring significant economic losses. The continuous use of fungicides has resulted in the emergence of drug-resistant strains. Consequently, there is a need to develop naturally and efficiently antifungal fungicides. Natural antimicrobial agents such as clove oil, cinnamon oil, and thyme oil can be extracted from different plant parts. They exhibited broad-spectrum antimicrobial properties and have great potential in the food industry. Here, we exploit a novel cinnamaldehyde (CA), eugenol (EUG), or carvacrol (CAR) combination antifungal therapy and formulate it into nanoemulsion form to overcome lower solubility and instability of essential oil. In this study, the antifungal activity evaluation and transcriptional profile of Penicillium digitatum exposed to compound nanoemulsion were evaluated. Results showed that compound nanoemulsion had a striking inhibitory effect on P. digitatum in a dose-dependent manner. According to RNA-seq analysis, there were 2,169 differentially expressed genes (DEGs) between control and nanoemulsion-treated samples, including 1,028 downregulated and 1,141 upregulated genes. Gene Ontology (GO) analysis indicated that the DEGs were mainly involved in intracellular organelle parts of cell component: cellular respiration, proton transmembrane transport of biological process, and guanyl nucleotide-binding molecular function. KEGG analysis revealed that metabolic pathway, biosynthesis of secondary metabolites, and glyoxylate and dicarboxylate metabolism were the most highly enriched pathways for these DEGs. Taken together, we can conclude the promising antifungal activity of nanoemulsion with multiple action sites against P. digitatum. These outcomes would deepen our knowledge of the inhibitory mechanism from molecular aspects and exploit naturally, efficiently, and harmlessly antifungal agents in the citrus postharvest industry.
研究领域:
微生物学
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分子生物学
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植物病理学
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植病学
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食品科学
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PubMed
高影响因子
AQUATIC TOXICOLOGY
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2023
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IF 4.5
Xin Li,Weiwei Wang,Xuedong Wang,Huili Wang
Herein, we demonstrated that sublethal-dose exposure to triclosan (TCS) and triclocarban (TCC) triggered larval zebrafish immunotoxicity. Acute exposure to TCS induced significant increases in larval neutrophils and macrophages and a prominent decrease in thymic T cells. In contrast, three kinds of cells (neutrophils, macrophages, and thymic T cells) were significantly reduced under TCC exposure, suggesting that both TCS and TCC suppress thymus development and mature T-cell differentiation. TCC was confirmed to have more severe immunotoxicity than TCS. Using Illumina RNA-Seq, 581 and 738 differentially expressed genes (DEGs) were identified in the TCS and TCC treatments, respectively. GO function and KEGG pathway enrichment analyses revealed that the DEGs were not identical in terms of biological processes, cellular components and molecular functions, but were primarily involved in immune response. KEGG analysis showed that approximately 47% and 11% of DEGs were mainly enriched in the immune system of the TCC and TCS treatments, respectively. Protein-protein interaction (PPI) network analysis confirmed that the hub genes enriched in the immune-related pathways differed between TCS and TCC exposure. The hub genes were fynb, mapk12b, scarb1, pik3r2, prkg3, srfa, arhgef2, cldn15la , and cldn15lb in the TCS treatment, and plg, serping1, masp2, fgg, vtnb, mmp9, serpine1, il1b, sb:cb37 and stat3 in the TCC treatment. Molecular docking simulation demonstrated that both TCS and TCC were stably docked with their target hub genes, and that their target molecules for inducing immunotoxicity were different. The differential target molecules and action pathways induced by TCS and TCC exposure provide us with diagnostic targets and toxicological endpoints.
研究领域:
毒理学
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免疫学
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分子生物学
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生物信息学
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DOI
PubMed
高影响因子
Synthetic and Systems Biotechnology
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2025
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IF 4.4
Yixin Sun,Qi Sun,Tiantian Gao,Shumin Ren,Xiaomei Hu
Efficient cellulase production is essential for its application in green bioprocessing, yet the transcriptional regulation of cellulase biosynthesis in Talaromyces sp. remains largely uncharacterized. In this study, we elucidate the regulatory functions of TeXlnR and TeAmyR in Talaromyces endophyticus . Our results demonstrate that TeXlnR, as a potent transcriptional activator, enhances enzyme production by over 33 %. RNA-seq analysis shows that TeXlnR overexpression upregulates 33 cellulase genes and 11 hemicellulase genes, while concurrently repressing the expression of the transcription factor TeAmyR . Further investigation identified TeAmyR as a repressor of cellulase production in T. endophyticus . EMSA and yeast one-hybrid analyses confirmed the specific competitive binding of these two transcription factors to the promoter regions of cellulase genes eg5B and eg12A . TeXlnR both directly activates target gene transcription and indirectly promotes cellulase synthesis by downregulating TeAmyR expression to reduce its competitive binding to promoters. These findings provide direct evidence for competitive regulation by transcription factors in Talaromyces sp. and establish a theoretical foundation for the rational engineering of industrial strains with improved cellulase production.
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高影响因子
Frontiers in Microbiology
·
2022
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IF 6.064
Shi Zhihui,He Xiaoxian,Zhang Hailiang,Guo Xuena,Cheng Yanfei,Liu Xuelian,Wang Zhaoyue,He Xiuping
Carotenoids are unsaturated compounds with terpene groups. Among them, astaxanthin has strong antioxidant properties. It is widely used in aquaculture, food, medicine, and cosmetics with a broad market prospect. Phaffia rhodozyma is an important microorganism that synthesizes astaxanthin, but its wild strains have low pigment content, long growth cycle, and low fermentation temperature. Therefore, it is important to research the genetic improvement of the physiological and biochemical properties of P. rhodozyma. In this study, the atmospheric and room temperature plasma mutagenesis technology was adopted, through the functional evolution of the carotenoid production performance; then, through the comparative analysis of the genomics and transcriptomics of the wild strain and evolved strain, the key factor GST1 gene that affects carotenoid synthesis was discovered.
研究领域:
微生物学
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遗传学
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生物化学
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PubMed
高影响因子
FISH & SHELLFISH IMMUNOLOGY
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2019
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IF 3.298
Yafei Duan,Yun Wang,Dalin Xiong,Jiasong Zhang
The intestine is important for nutrition, metabolism and immunity. Succinate (SA) plays a vital role in the physiological homeostasis of animal intestines. However, the effects of dietary SA on the intestinal immunity and metabolism in shrimp are not clear. In this study, we investigated the immune and metabolic responses in the intestine of Litopenaeus vannamei that were fed diets consisting of different levels of SA: 0 g/kg (Con) and 10 g/kg (SA) for 56 days. The results from a RNA-seq analysis identified 6005 differentially expressed genes (DEGs), including 2728 upregulated genes and 3277 downregulated genes, which were grouped into 312 pathways. The DEGs were most enriched in pathways related to protein synthesis and amino acid metabolism , including “ribosome”, “aminoacyl-tRNA biosynthesis”, “pyrimidine metabolism”, and “arginine and proline metabolism”; additionally, carbohydrate and lipid metabolism pathways were also activated. A large number of immune-related genes were associated with mucus barrier modification, antimicrobial activity , pathogen attachment and recognition, antioxidant activity , and apoptosis. The expression patterns of several candidate genes involved in the immune response and nutrition metabolism were detected by qPCR. This study provides insight into the transcriptomic modulating mechanisms associated with intestinal immunity and the metabolism of L. vannamei in response to the intake of dietary SA.
研究领域:
水产养殖学
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分子生物学
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营养学
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DOI
PubMed
高影响因子
CHEMICO-BIOLOGICAL INTERACTIONS
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2023
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IF 5.1
Hongzhou Lin,Huihui Chen,Rengcheng Qian,Guoqi Tang,Yinjuan Ding,Yalan Jiang,Congde Chen,Dexuan Wang,Maoping Chu,Xiaoling Guo
Background Nephrotic syndrome (NS) is a chronic kidney disease mainly caused by impaired podocytes, ultimately resulting in massive proteinuria or even end-stage renal disease (ESRD). Methods The objective of this study was to explore the potential pathogenesis of NS caused by podocyte injury, and further explore the underlying mechanism through data mining , bioinformatics analysis, and experimental verification. The integrated analyses including Seurat, CellChat, gene ontology (GO), and molecular docking were performed based on the single-cell RNA-seq data (scRNA-seq). The adriamycin (ADR)-induced podocyte injury model in vitro was established to conduct the experimental verification for bioinformatics analysis results through western blot and real-time quantitative PCR (RT-qPCR). Results The results of bioinformatics analysis revealed that the bone morphogenetic protein (BMP) signaling pathway was involved in the podocyte-to-podocyte communication, which plays a crucial role in podocyte injury. The expression of BMP7 was significantly increased in ADR-induced podocytes through activating the Adenosine-monophosphate activated-protein kinase/Mammalian target of rapamycin (AMPK/mTOR) mediated autophagy pathway, and these findings were confirmed by in vitro experiments. Conclusion This study first demonstrated that BMP7 participated in ADR-induced podocyte injury. The BMP7/AMPK/mTOR mediated autophagy pathway may play a crucial role in podocyte injury, which may be the potential therapeutic target for NS patients.
研究领域:
肾病学
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分子生物学
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生物信息学
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DOI
PubMed
高影响因子
JOURNAL OF NANOBIOTECHNOLOGY
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2024
·Vol. 22
·期 1
·1-21
·
IF 10.6
Xu Wenhao,Ye Shiqi,Liu Wangrui,Guo Huaqi,Zhang Linhui,Wei Shiyin,Anwaier Aihetaimujiang,Chang Kun,Malafaia Guilherme,Zhang Hailiang,Ye Dingwei,Wei Gang
In recent years, the environmental health issue of microplastics has aroused an increasingly significant concern. Some studies suggested that exposure to polystyrene microplastics (PS-MPs) may lead to renal inflammation and oxidative stress in animals. However, little is known about the essential effects of PS-MPs with high-fat diet (HFD) on renal development and microenvironment. In this study, we provided the single-cell transcriptomic landscape of the kidney microenvironment induced by PS-MPs and HFD in mouse models by unbiased single-cell RNA sequencing (scRNA-seq). The kidney injury cell atlases in mice were evaluated after continued PS-MPs exposure, or HFD treated for 35 days. Results showed that PS-MPs plus HFD treatment aggravated the kidney injury and profibrotic microenvironment, reshaping mouse kidney cellular components. First, we found that PS-MPs plus HFD treatment acted on extracellular matrix organization of renal epithelial cells, specifically the proximal and distal convoluted tubule cells, to inhibit renal development and induce ROS-driven carcinogenesis. Second, PS-MPs plus HFD treatment induced activated PI3K-Akt, MAPK, and IL-17 signaling pathways in endothelial cells. Besides, PS-MPs plus HFD treatment markedly increased the proportions of CD8 + effector T cells and proliferating T cells. Notably, mononuclear phagocytes exhibited substantial remodeling and enriched in oxidative phosphorylation and chemical carcinogenesis pathways after PS-MPs plus HFD treatment, typified by alterations tissue-resident M2-like PF4 + macrophages. Multispectral immunofluorescence and immunohistochemistry identified PF4 + macrophages in clear cell renal cell carcinoma (ccRCC) and adjacent normal tissues, indicating that activate PF4 + macrophages might regulate the profibrotic and pro-tumorigenic microenvironment after renal injury. In conclusion, this study first systematically revealed molecular variation of renal cells and immune cells in mice kidney microenvironment induced by PS-MPs and HFD with the scRNA-seq approach, which provided a molecular basis for decoding the effects of PS-MPs on genitourinary injury and understanding their potential profibrotic and carcinogenesis in mammals. Graphical Abstract
研究领域:
环境健康
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分子生物学
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免疫学
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肾病学
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癌症研究
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DOI
PubMed
高影响因子
Frontiers in Pharmacology
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2025
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IF 4.8
Miao Li,Na Gao,Lei Xu,Peng Ge,Nan Jiang,Yuhong Shang
Background: The natural compound paeonol exhibits therapeutic promise against cervical carcinoma, though its precise molecular mechanisms remain undefined.Methods: First, we treated human cervical cancer (HeLa) cells with different concentrations of paeonol. Cellular proliferation and apoptotic responses were evaluated via cell-counting kit 8 (CCK8) assays and flow cytometric analysis. Subsequent transcriptomic profiling employed RNA sequencing coupled with alternative splicing assessment to detect differentially expressed genes (DEGs). Protein interaction networks were established for pivotal DEGs, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment investigations. Clinical data pertinent to cervical cancer were retrieved from The Cancer Genome Atlas (TCGA). Prognostic model development incorporated Kaplan–Meier survival estimation, Least Absolute Shrinkage and Selection Operator (LASSO) regression, alongside univariate and multivariate COX proportional hazards analyses, with model accuracy subsequently assessed. Finally, Quantitative reverse transcription polymerase chain reaction (qRT-PCR) validated DEG expression.Results: Paeonol treatment suppressed proliferation while inducing apoptosis in HeLa cells. Transcriptomic and splicing analyses revealed 12 critical DEGs: NLRP1, FN1, NQO2, NREP, B4GALNT1, ANK3, FAM219A, ODF3B, MAPK15, EPGN, MUC1, and MEG3. Enrichment analyses indicated these DEGs principally associate with inflammatory processes and the biological regulation of cellular proliferation and apoptotic death. Analysis of clinical outcomes in 197 TCGA patients demonstrated significantly enhanced five-year survival probability within the low-risk cohort. FN1, NQO2, and ODF3B were incorporated into a prognostic signature following LASSO regression. Univariate and multivariate COX analyses identified T stage, tumor grade, and differential expression of these three genes as significant outcome predictors; the resultant prognostic model exhibited robust accuracy. qRT-PCR results corroborated the RNA sequencing data concerning DEG expression patterns.Conclusion: Paeonol modulates HeLa cell proliferation and apoptosis through regulation of 12 key genes, including FN1. This activity involves governing inflammatory responses alongside cellular proliferation, migration, and differentiation processes. These findings offer a theoretical foundation supporting paeonol’s potential clinical utility in cervical cancer management.
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PubMed
高影响因子
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
·
2022
·Vol. 102
·期 10
·4054-4064
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IF 4.125
Xianxian Dong,Yin Wan,Yanru Chen,Xiaojiang Wu,Yulong Zhang,Mengfei Deng,Wenqin Cai,Xiaodan Wu,Guiming Fu
BACKGROUND Tannase is an enzyme produced by microbial fermentation and is widely used in the food industry; however, the molecular mechanism of tannase production by Aspergillus has not yet been studied. This study was conducted to reveal the differences in Aspergillus carbonarius tannase enzymatic characterization, secondary structures and molecular mechanisms after treatment of the strain with atmospheric and room temperature plasma (ARTP). RESULTS The results showed that the specific activity of tannase was improved by ARTP treatment, and it showed higher thermostability and tolerance to metal ions and additives. The enzymatic characterization and molecular docking results indicated that tannase had a higher affinity and catalytic rate with tannic acid as a substrate after ARTP treatment. In addition, the docking results indicated that Aspergillus tannases may catalyze tannic acid by forming two hydrogen-bonding networks with neighboring residues. RNA-seq analysis indicated that changes in steroid biosynthesis, glutathione metabolism, glycerolipid metabolism, oxidative phosphorylation pathway and mitogen-activated protein kinase signaling pathways might be crucial reasons for the high production of tannase. CONCLUSION ARTP enhanced the yield and properties of A. carbonarius tannase by changing the enzyme structure and cell metabolism. This study provides a theoretical basis for elucidating the molecular mechanism underlying high production of Aspergillus tannases. © 2022 Society of Chemical Industry.
研究领域:
微生物学
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生物化学
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基因组学
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酶学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
FISH & SHELLFISH IMMUNOLOGY
·
2025
·
IF 3.9
Meiqin Mao,Zhixia Zhuang,Xiaoru Wang,Huabin Huang,Jiaonan Zhang,Jiaolin Zhang,Qingpi Yan
Pseudomonas plecoglossicida is a significant pathogen in aquaculture, capable of infecting various teleost fish and causing visceral white spot disease, which leads to substantial economic losses. The PhoP/PhoQ two-component system plays a central role in virulence regulation in Gram-negative bacteria; however, its specific function in P. plecoglossicida remains unclear. To elucidate the role of the phoP gene in the pathogenicity of this bacterium, we used hybrid grouper ( Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) as an infection model to compare the pathogenicity and host immune responses among the wild-type (NZBD9), phoP deletion (Δ phoP ), and complemented (C-Δ phoP ) strains. In artificial infection experiments, the Δ phoP strain exhibited significantly attenuated virulence, with an LD 50 value of 4.082 × 10 4 , which was 13.7 times higher than that of the wild-type strain. Furthermore, the deletion of phoP reduced bacterial load in the spleen and alleviated histopathological damage in the spleen, head kidney, and intestine. RNA-seq analysis of spleen tissue at 4 days post-infection identified 1768 differentially expressed genes (DEGs), including 704 up-regulated and 1064 down-regulated genes. GO and KEGG enrichment analyses revealed that these DEGs were primarily involved in immune-related processes and pathways, including TLR signaling, NF-κB activation, PI3K-Akt signaling, cytokine-cytokine receptor interaction, and cell adhesion molecules. Temporal expression profiling via qRT-PCR demonstrated that key immune genes (including tlr1, tlr5 , tlr13 , traf5 , nf-κb , mcp1 , cd3 , and il10 ) were generally down-regulated or exhibited delayed and weakened activation in Δ phoP -infected fish, indicating a subdued and dysregulated immune response. These results suggest that the phoP gene is essential for maintaining full virulence in P. plecoglossicida , modulating host immunity by suppressing critical inflammatory and immune signaling pathways. Our study provides novel insights into the role of the PhoP/PhoQ system in host–pathogen interactions and lays a theoretical foundation for developing targeted control strategies against P. plecoglossicida infection in aquaculture.
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DOI
PubMed
高影响因子
Foods
·
2022
·Vol. 11
·期 17
·2660
·
IF 5.561
Xiayu Liu,Xinxin Pang,Yansha Wu,Yajing Wu,Ying Shi,Xinglin Zhang,Qihe Chen
Mannosylerythritol lipids-A (MEL-A) is a novel biosurfactant with multiple biological effects. The synergistic antibacterial activity and mechanism of MEL-A and lactic acid (LA) againstListeria monocytogeneswere investigated. The synergistic effect resulted in a significant increase in the antibacterial rate compared to LA treatment alone. Genome-wide transcriptomic analysis was applied to deeply investigate the synergistic antibacterial mechanism. Gene Ontology (GO) enrichment analysis showed that the synergy between MEL-A and LA affected many potential cellular responses, including the sugar phosphotransferase system, carbohydrate transport, and ribosomes. KEGG enrichment analysis showed that the PTS system and ribosome-related pathways were significantly enriched. In addition, synergistic treatment affected locomotion and membrane-related cellular responses in GO enrichment analysis and carbohydrate metabolism and amino acid metabolism pathways in KEGG enrichment analysis compared to LA treatment alone. The accuracy of the transcriptome analysis results was verified by qPCR (R2= 0.9903). This study will provide new insights for the prevention and control ofL. monocytogenes.Keywords:Mannosylerythritol lipids-A (MEL-A);lactic acid;Listeria monocytogenes;RNA-Seq
研究领域:
微生物学
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分子生物学
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食品安全
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基因组学
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DOI
PubMed
高影响因子
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
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2025
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IF 4
Ruosheng Yang,Hongle Xu,Qinghao Liu,Lanlan Sun,Wangcang Su,Fei Xue,Renhai Wu
Pyroxasulfone has been widely used to control malignant weeds in wheat fields. However, differences in pyroxasulfone tolerance across wheat varieties warrant attention owing to their potential impact on food production security. In this study, 54 wheat varieties were collected for screening, and Yunong 922 with 6.01-fold higher tolerance than Zhengmai 1354 was identified. Ultra-performance liquid chromatography–mass spectrometry analysis revealed that Yunong 922 exhibited a significantly shorter degradation half-life of pyroxasulfone (5.03 days) than Zhengmai 1354 (7.02 days). The P450 inhibitor malathion and the glutathione S-transferase (GST) inhibitor NBD-Cl reduced the tolerance factor of Yunong 922 to pyroxasulfone from 6.01 to 1.44 and 1.16, respectively, with no significant difference in tolerance to pyroxasulfone compared with Zhengmai 1354. RNA-Seq transcriptome analysis was used to identify candidate genes that may confer metabolic tolerance to pyroxasulfone in wheat. Eight candidate genes (five P450 enzymes and three GSTs) exhibited significantly different expression levels between Yunong 922 and Zhengmai 1354, as validated by qRT–PCR. Pyroxasulfone tolerance in Yunong 922 is associated with the coordinated upregulation of CYP72A397 , CYP72A14 , and GSTDHAR1 , each contributing approximately 33.7 %, 32.6 %, and 33.7 % to the dominant principal component 1 that accounts for 88.7 % of the explained variance. These results revealed that the faster degradation of pyroxasulfone observed in Yunong 922 could be linked to the higher expression of P450s and GSTs, though this relationship remains to be confirmed. This study also offers valuable insights into mechanisms underlying crop tolerance and informs the development of herbicide management strategies.
研究领域:
植物学
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作物科学
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农业科学
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分子生物学
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遗传学
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生物化学
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PubMed
高影响因子
危险品化学品经营许可证（带存储）