Molecular mechanism of high‐production tannase of Aspergillus carbonarius NCUF M8 after ARTP mutagenesis: revealed by RNA ‐seq and molecular docking

2022 ◽  
Author(s):  
Xianxian Dong ◽  
Yin Wan ◽  
Yanru Chen ◽  
Xiaojiang Wu ◽  
Yulong Zhang ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Molecular Mechanism ◽  
Aspergillus Carbonarius ◽  
Rna Seq ◽  
Artp Mutagenesis ◽  
High Production

scholarly journals Tianma Formula Alleviates Dementia via ACER2-Mediated Sphingolipid Signaling Pathway Involving Aβ

2021 ◽  
Vol 2021 ◽  
pp. 1-20
Author(s):  
Haochang Lin ◽  
Sha Wu ◽  
Zhiying Weng ◽  
Hongyan Wang ◽  
Rui Shi ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Signaling Pathway ◽  
Molecular Mechanism ◽  
Sphingolipid Metabolism ◽  
Network Pharmacology ◽  
Rna Seq ◽  
C Elegans ◽  
Metabolism Pathway

Objective. To reveal the molecular mechanism of the antagonistic effect of traditional Chinese medicine Tianma formula (TF) on dementia including vascular dementia (VaD) and Alzheimer’s disease (AD) and to provide a scientific basis for the study of traditional Chinese medicine for prevention and treatment of dementia. Method. The TF was derived from the concerted application of traditional Chinese medicine. We detected the pharmacological effect of TF in VaD rats. The molecular mechanism of TF was examined by APP/PS1 mice in vivo, Caenorhabditis elegans (C. elegans) in vitro, ELISA, pathological assay via HE staining, and transcriptome. Based on RNA-seq analysis in VaD rats, the differentially expressed genes (DEGs) were identified and then verified by quantitative PCR (qPCR) and ELISA. The molecular mechanisms of TF on dementia were further confirmed by network pharmacology and molecular docking finally. Results. The Morris water maze showed that TF could improve the cognitive memory function of the VaD rats. The ELISA and histological analysis suggested that TF could protect the hippocampus via reducing tau and IL-6 levels and increasing SYN expression. Meanwhile, it could protect the neurological function by alleviating Aβ deposition in APP/PS1 mice and C. elegans. In the RNA-seq analysis, 3 sphingolipid metabolism pathway-related genes, ADORA3, FCER1G, and ACER2, and another 5 nerve-related genes in 45 key DEGs were identified, so it indicated that the protection mechanism of TF was mainly associated with the sphingolipid metabolism pathway. In the qPCR assay, compared with the model group, the mRNA expressions of the 8 genes mentioned above were upregulated, and these results were consistent with RNA-seq. The protein and mRNA levels of ACER2 were also upregulated. Also, the results of network pharmacology analysis and molecular docking were consistent with those of RNA-seq analysis. Conclusion. TF alleviates dementia by reducing Aβ deposition via the ACER2-mediated sphingolipid signaling pathway.

scholarly journals Molecular mechanism underlying the hypolipidemic effect of Shanmei Capsule based on network pharmacology and molecular docking

2021 ◽  
Vol 29 ◽  
pp. 239-256
Author(s):  
Qian Wang ◽  
Lijing Du ◽  
Jiana Hong ◽  
Zhenlin Chen ◽  
Huijian Liu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Molecular Mechanism ◽  
Kegg Pathway ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Signal Pathways ◽  
Hypolipidemic Effect ◽  
Active Ingredients ◽  
Pathway Enrichment

BACKGROUND: Shanmei Capsule is a famous preparation in China. However, the related mechanism of Shanmei Capsule against hyperlipidemia has yet to be revealed. OBJECTIVE: To elucidate underlying mechanism of Shanmei Capsule against hyperlipidemia through network pharmacology approach and molecular docking. METHODS: Active ingredients, targets of Shanmei Capsule as well as targets for hyperlipidemia were screened based on database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were performed via Database for Annotation, Visualization, and Integrated Discovery (DAVID) 6.8 database. Ingredient-target-disease-pathway network was visualized utilizing Cytoscape software and molecular docking was performed by Autodock Vina. RESULTS: Seventeen active ingredients in Shanmei Capsule were screened out with a closely connection with 34 hyperlipidemia-related targets. GO analysis revealed 40 biological processes, 5 cellular components and 29 molecular functions. A total of 15 signal pathways were enriched by KEGG pathway enrichment analysis. The docking results indicated that the binding activities of key ingredients for PPAR-α are equivalent to that of the positive drug lifibrate. CONCLUSIONS: The possible molecular mechanism mainly involved PPAR signaling pathway, Bile secretion and TNF signaling pathway via acting on MAPK8, PPARγ, MMP9, PPARα, FABP4 and NOS2 targets.

Molecular Mechanism of The Effect of Huanglian Jiedu Decoction On Ulcerative Colitis Based On Network Pharmacology And Molecular Docking

2021 ◽  
Author(s):  
Jing Yang ◽  
Chao-Tao Tang ◽  
Ruiri Jin ◽  
Bixia Liu ◽  
Peng Wang ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Molecular Docking ◽  
Molecular Mechanism ◽  
Target Genes ◽  
Signal Pathway ◽  
Intestinal Barrier Function ◽  
Network Pharmacology ◽  
Bioactive Components ◽  
Ppi Network ◽  
Active Components

Abstract Huanglian jiedu decoction (HLJDD) is a heat-clearing and detoxifying agent composed of four kinds of Chinese herbal medicine. Previous studies have shown that HLJDD can improve the inflammatory response of ulcerative colitis (UC) and maintain intestinal barrier function. However, its molecular mechanism is not completely clear. In this study, we verified the bioactive components (BCI) and potential targets of HLJDD in the treatment of UC by means of network pharmacology and molecular docking, and constructed the pharmacological network and PPI network. Then the core genes were enriched by GO and KEGG. Finally, the bioactive components were docked with the key targets to verify the binding ability between them. A total of 54 active components related to UC were identified. Ten genes are considered to be very important to PPI network. Functional analysis showed that these target genes were mainly involved in the regulation of cell response to different stimuli, IL-17 signal pathway and TNF signal pathway. The results of molecular docking showed that the active components of HLJDD had good affinity with Hub gene. This study systematically elucidates the "multi-component, multi-target, multi-pathway" mechanism of anti-UC with HLJDD for the first time, suggesting that HLJDD or its active components may be candidate drugs for the treatment of ulcerative colitis.

scholarly journals Transcriptome analysis of xa5-mediated resistance to bacterial leaf streak in rice (Oryza sativa L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xiaofang Xie ◽  
Zhiwei Chen ◽  
Binghui Zhang ◽  
Huazhong Guan ◽  
Yan Zheng ◽  
...  
Keyword(s):  
Cell Death ◽  
Molecular Mechanism ◽  
Oryza Sativa L ◽  
Blast Resistance ◽  
Rna Seq ◽  
Bacterial Leaf Streak ◽  
Wild Type ◽  
Cell Death Pathways ◽  
Rnai Line ◽  
Transgenic Lines

Abstract Bacterial leaf steak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a devastating disease in rice production. The resistance to BLS in rice is a quantitatively inherited trait, of which the molecular mechanism is still unclear. It has been proved that xa5, a recessive bacterial blast resistance gene, is the most possible candidate gene of the QTL qBlsr5a for BLS resistance. To study the molecular mechanism of xa5 function in BLS resistance, we created transgenic lines with RNAi of Xa5 (LOC_Os05g01710) and used RNA-seq to analyze the transcriptomes of a Xa5-RNAi line and the wild-type line at 9 h after inoculation with Xoc, with the mock inoculation as control. We found that Xa5-RNAi could (1) increase the resistance to BLS as expected from xa5; (2) alter (mainly up-regulate) the expression of hundreds of genes, most of which were related to disease resistance; and (3) greatly enhance the response of thousands of genes to Xoc infection, especially of the genes involved in cell death pathways. The results suggest that xa5 is the cause of BLS-resistance of QTL qBlsr5a and it displays BLS resistance effect probably mainly because of the enhanced response of the cell death-related genes to Xoc infection.

scholarly journals Transcriptome Analysis of a Jujube (Ziziphus Jujuba Mill.) Cultivar Response to Heat Stress

2021 ◽  
Author(s):  
Lei Yang ◽  
Juan Jin ◽  
Ding-yu Fan ◽  
Qing Hao ◽  
Jianxin Niu
Keyword(s):  
Gene Ontology ◽  
Heat Stress ◽  
Stress Response ◽  
Heat Resistance ◽  
Molecular Mechanism ◽  
Cdna Libraries ◽  
Biological Processes ◽  
Rna Seq ◽  
Ziziphus Jujuba ◽  
Growth And Reproduction

Abstract Background: Heat stress (HS) is a common stress and influences the growth and reproduction of plant species. We found and bred a putative heat-resistant jujube (Ziziphus jujuba Mill.) cultivar (JHR17) in previous study. Results: In the current study, we made the seedlings of ‘JHR17’ cultivar to be under HS (45°C) for 0, 1, 3, 5 and 7 days, respectively, and the leaf samples (HR0, HR1, HR3, HR5 and HR7) were collected accordingly. Fifteen cDNA libraries from ‘JHR17’ leaves were built with a transcriptome assay. The RNA sequencing (RNA-seq) and transcriptome comparisons were performed, and the results indicated that 1642, 4080, 5160 and 2119 differentially expressed genes (DEGs) were identified in HR1 vs. HR0, HR3 vs. HR0, HR5 vs. HR0 and HR7 vs. HR0, respectively. Gene Ontology (GO) analyses of the DEGs from these comparisons were implemented. Conclusion: It revealed that a series of biological processes, involved in stress response, photosynthesis and metabolism, were enriched successfully, suggesting that lowering or up-regulating these genes of processes might play important roles in response to HS. This study may contribute to understand the molecular mechanism of ‘JHR17’ cultivar response to HS, and be beneficial for developing jujube cultivars to improve heat resistance.

scholarly journals Transcriptomic Profiling of Cotton Leaves in Response to Cotton Aphid Attack

2019 ◽  
Author(s):  
Jianmin Zhang ◽  
Xiao Zhong ◽  
Pei Feng ◽  
Qiqi Ma ◽  
Qi Su ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Functional Annotation ◽  
Insect Pests ◽  
Aphis Gossypii ◽  
Rna Seq ◽  
Cotton Production ◽  
Cotton Aphid ◽  
Time Points ◽  
New Genes ◽  
Comparison Results

Abstract Main conclusion The molecular mechanism of the interaction between cotton and cotton aphids remains unclear currently. The RNA-Seq study of cotton leaves was performed in response to cotton aphid damage at different time points. The transcriptome analysis revealed that a lot of cotton gene transcripts were regulated by cotton aphid damage. Cotton aphids (Aphis gossypii Glover) are regarded as one of the most harmful insect pests for cotton production. They are usually capable of causing severe yield loss through sucking cotton liquids, secreting honeydews and transmitting plant viral diseases. However, the molecular mechanism of the interaction between cotton and cotton aphids remains unclear currently. Therefore, the RNA-Seq study of cotton leaves was performed in response to cotton aphid damage at different time points (0 h,6 h,12 h, 24 h, 48 h and 72 h). A total of 9, 103 new genes were identified, and 7, 510 of them were annotated functionally. Based on the comparison results, the gene expression was analyzed according to the expression amount of genes in different samples. 24,793 differentially expressed genes were authenticate in all and their functional annotation and enrichment analysis were conducted. Compared with 0 h (without aphid damage, CK), the amount of down-regulated DEGs was largely more than that of the up-regulated genes at different time points under cotton aphid attack except for 48h. As revealed by the functional annotation of DEGs, these genes were involved in all kinds of plant biological process, including various resistance to abiotic and biotic stress, hormone metabolism, signaling transduction and transcriptional regulation. These results established a firm foundation for the study of the molecular mechanism of the interaction between cotton and cotton aphids and would facilitate the development of plant aphid resistant cultivars.

scholarly journals The Study of Yin-Chen-Hao-Tang Preventing and Treating Alcoholic Fatty Liver Disease Through PPAR Signaling Pathway Based on Network Pharmacology and RNA-Seq Transcriptomics

2021 ◽  
Author(s):  
Yi-Wei Zhu ◽  
Du Li ◽  
Ting-Jie Ye ◽  
Feng-Jun Qiu ◽  
Xiao-Ling Wang ◽  
...  
Keyword(s):  
Liver Disease ◽  
Signaling Pathway ◽  
Molecular Mechanism ◽  
Liver Tissue ◽  
Network Pharmacology ◽  
Rna Seq ◽  
Alcoholic Fatty Liver ◽  
Ppar Signaling ◽  
Alcoholic Fatty Liver Disease ◽  
Alt Activity

Abstract Background: Alcoholic fatty liver disease (AFLD) is the first stage of the alcoholic liver disease course. Yin-Chen-Hao-Tang (YCHT) has a good clinical effect on the treatment of AFLD, but its molecular mechanism has not been elucidated. In this study, we tried to explore the molecular mechanism of YCHT in improving hepatocyte steatosis in AFLD mice through network pharmacology and RNA sequencing (RNA-Seq) transcriptomics. Methods: Network pharmacological methods were used to analyze the potential therapeutic signaling pathways and targets of YCHT on AFLD. Then, the AFLD mice model was induced and YCHT was administered concurrently. Liver injury was measured by serum alanine aminotransferase (ALT) activity and liver tissue H&E staining, and liver steatosis was determined by serum triglyceride (TG) level and liver tissue Oil Red staining. The molecular mechanism of YCHT on prevention and treatment of mice AFLD was investigated according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the differential expression genes data obtained by liver tissue RNA-Seq. Finally, the key signaling pathway and targets of YCHT on AFLD were verified in the ethanol-induced AFLD hepatocyte model by pathway inhibition experiments.Results: The results of network pharmacology analysis showed that YCHT may exert its pharmacological effect on AFLD through 312 potential targets which are involved in many signaling pathways including the PPAR signaling pathway. AFLD mice experiments results showed that YCHT markedly decreased mice serum ALT activity and serum TG levels. YCHT also significantly improved alcohol-induced hepatic injury and steatosis in mice livers. Furthermore, both KEGG analysis of RNA-Seq and AFLD hepatocyte model experiments showed that the PPAR signaling pathway should be the most relevant pathway of YCHT in the prevention and treatment of AFLD. YCHT could remarkably reduce the expression of PPARγ which is related to the lipogenesis pathway. YCHT also could increase the expression of PPARα which is related to the lipolysis pathway. Conclusions: Our study discovered that PPARγ and PPARα are the key targets and the PPAR signaling pathway is the main signaling pathway for YCHT to prevent and treat AFLD.

Sign in / Sign up

Export Citation Format

Share Document