scholarly journals Study of Terpenoid Synthesis and Prenyltransferase in Roots of Rehmannia glutinosa Based on iTRAQ Quantitative Proteomics

2021 ◽  
Vol 12 ◽  
Author(s):  
Peilei Chen ◽  
Xiaoyan Wei ◽  
Qianting Qi ◽  
Wenjing Jia ◽  
Mingwei Zhao ◽  
...  
Keyword(s):  
Tca Cycle ◽  
Maturation Stage ◽  
Rehmannia Glutinosa ◽  
Active Components ◽  
Kegg Pathways ◽  
Medicinal Value ◽  
Go Enrichment ◽  
Expansion Stage ◽  
Proteasome Pathway ◽  
Ggpp Synthase

Rehmannia glutinosa has important medicinal value; terpenoid is one of the main active components in R. glutinosa. In this study, iTRAQ technique was used to analyze the relative abundance of proteins in roots of R. glutinosa, and 6,752 reliable proteins were quantified. GO enrichment results indicated that most proteins were involved in metabolic process or cellular process, 57.63% proteins had catalytic activity, and 65.80% proteins were enriched in membrane-bounded organelle. In roots of R. glutinosa, there were 38 KEGG enrichments with significance, more DEPs were found in some pathways, especially the proteasome pathway and TCA cycle with 15.0% DEPs between elongation stage and expansion stage of roots. Furthermore, five KEGG pathways of terpenoid synthesis were found. Most prenyltransferases belong to FPP/GGPP synthase family, involved in terpenoid backbone biosynthesis, and all interacted with biotin carboxylase CAC2. Compared with that at the elongation stage, many prenyltransferases exhibited higher expression at the expansion stage or maturation stage of roots. In addition, eight FPP/GGPP synthase encoding genes were cloned from R. glutinosa, namely FPPS, FPPS1, GGPS, GGPS3, GGPS4, GGPS5, GPPS and GPPS2, introns were also found in FPPS, FPPS1, GGPS5 and GGPS2, and FPP/GPP synthases were more conservative in organisms, especially in viridiplantae, in which the co-occurrence of GPPS or GPPS2 was significantly higher in plants. Further analysis found that FPP/GGPP synthases of R. glutinosa were divided into three kinds, GGPS, GPPS and FPPS, and their gene expression was significantly diverse in different varieties, growth periods, or tissues of R. glutinosa. Compared with that of GGPS, the expression of GPPS and FPPS was much higher in R. glutinosa, especially at the expansion stage and maturation stage. Thus, the synthesis of terpenoids in roots of R. glutinosa is intricately regulated and needs to be further studied.

scholarly journals Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Songbai Yang ◽  
Xiaolong Zhou ◽  
Yue Pei ◽  
Han Wang ◽  
Ke He ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Hormone Secretion ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
The Novel ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Single Organism

Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P≤0.05, log2  Ratio≥1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.

scholarly journals Revealing the Therapeutic Uses of Garlic (Allium sativum) and Its Potential for Drug Discovery

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Azene Tesfaye
Keyword(s):  
Drug Development ◽  
Therapeutic Potential ◽  
Biologically Active ◽  
Human Diseases ◽  
Active Components ◽  
Runny Nose ◽  
Medicinal Value ◽  
Therapeutic Uses ◽  
Tract Disease ◽  
Chronic Fever

Background. Garlic is a common bulb vegetable that is used to flavor and flavor food. The plant contains biologically active components that contribute to its pharmacological properties. This paper attempts to examine the therapeutic uses and potential role in the drug development of garlic for various human diseases. Methods. To obtain crucial data and scientific knowledge about the therapeutic uses of garlic, systematic literature searches were conducted using key terms on well-known indexed platforms such as PubMed, Scopus, Web of Science, Medline, Embase, and popular search engines. Results. Garlic, which is utilized as a spice and flavoring ingredient, is found to have fundamental nutritional components. Carbohydrates, protein, fat, minerals, water, and vitamins are all found in abundance in this plant. The plant also has a high medicinal value and is used to cure a variety of human diseases. It has anti-inflammatory, rheumatological, ulcer inhibiting, anticholinergic, analgesic, antimicrobial, antistress, antidiabetes, anticancer, liver protection, anthelmintics, antioxidants, antifungal, and wound healing properties, as well as properties that help with asthma, arthritis, chronic fever, tuberculosis, runny nose, malaria, leprosy, skin discoloration, and itching, indigestion, colic, enlarged spleen, hemorrhoids, fistula, bone fracture, gout, urinary tract disease, diabetes, kidney stones, anemia, jaundice, epilepsy, cataract, and night blindness. Conclusions. The nutritional content of the plant is significant, and it has incredible therapeutic potential. The findings of this study are needed to investigate the therapeutic potential, as it may be a promising option for drug development.

scholarly journals RNA-Seq reveals differential expression profile and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio

2019 ◽  
Author(s):  
Madhu Sudhana Saddala ◽  
Anton Lennikov ◽  
Hu Huang
Keyword(s):  
Gene Expression ◽  
Retinal Degeneration ◽  
Expression Profile ◽  
Calcium Binding ◽  
Vision Loss ◽  
Gene Annotation ◽  
Insulin Signalling ◽  
Tca Cycle ◽  
Kegg Pathways ◽  
Insulin Signalling Pathway

Abstract Retinal degenerative diseases affect millions of people and are the leading cause of vision loss. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes that are involved in phototransduction, biosynthesis, folding of the rhodopsin molecule and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear. The molecular basis of the retinal pathologies defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we have analyzed the differential gene expression profile of retina from a wild-type zebrafish and pde6c mutant. The datasets were downloaded from the Sequence Read Archive (SRA), removed adaptors and unbiased bases and checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish and calculated gene expression. The differentially expressed genes (DEGs) were filtered based on the FDR (±4) and p-values (p<0.001). We performed gene annotation (Molecular function, biological process, cellular component), and functional pathways (KEGG pathway) for the DEGs. Our result showed that 216 up-regulated and 3527 down-regulated between normal and pde6c mutant zebrafish. These DEGs are involved in various KEGG pathways like Phototransduction (12 genes), mRNA surveillance pathway (17 genes), Phagosome (25 genes), Glycolysis / Gluconeogenesis (15 genes), Adrenergic signalling in cardiomyocytes (29 genes), Ribosome (20 genes), Citrate cycle (TCA cycle) (8 genes), Insulin signalling pathway (24 genes), Oxidative phosphorylation (20 genes) and RNA transport (22 genes) pathways respectively. Much more of all the pathways genes were down-regulated, but fewer genes were up-regulated in retina mutant of zebrafish. Our data strongly indicate that the among these genes, above mentioned pathways genes as well as calcium-binding proteins, neural damage proteins, peptidase proteins, immunological proteins, and apoptosis proteins are mostly involved in retinal and neural degeneration that cause abnormalities in photoreceptors or RPE cells.

scholarly journals Changes in mineral nutrition during fruit growth and development of ‘Seike’ and ‘Newhall’ navel orange as a guide for fertilization

2019 ◽  
Vol 41 (5) ◽  
Author(s):  
Xing-Zheng Fu ◽  
Xie Fa ◽  
Cao Li ◽  
Ling Li-Li ◽  
Chun Chang-Pin ◽  
...  
Keyword(s):  
Maturation Stage ◽  
Navel Orange ◽  
Fruit Pulp ◽  
Fruit Maturation ◽  
Timely Manner ◽  
Fruit Peel ◽  
Fruit Maturity ◽  
Expansion Stage ◽  
Micro Elements ◽  
Fruit Stage

Abstract Changes in the accumulation patterns of mineral nutrients at different development stages of fruit reflect the requirements of citrus trees for different nutrients, and this information provides an essential reference for rational fertilization. In this study, changes in the contents of 11 nutrients in the whole fruit, fruit pulp, and peel were studied during the whole developmental period of the fruit of ‘Seike’ and ‘Newhall’ navel oranges. We found that the two navel orange cultivars showed very similar changes in nutrients. Specifically, the N, P, Mg, S, Mn, and Zn contents were high in the young fruit stage (April), the K and Fe contents were high in the fruit expansion stage (July and August), and the Ca content was high in the fruit maturation stage (October). As the fruit developed, the N, P, Mg, S, Zn, and B contents decreased to the lowest levels at fruit maturity in November. In addition, the contents of N, P, K, Fe, Zn, and Cu were ranked as fruit pulp > whole fruit > peel, while Ca, Mn, and B contents were ranked as fruit peel > whole fruit > fruit pulp. N, P, K, and Mg accumulated in the fruit in June and July, in contrast to the June to September period for the micro-elements. During these accumulation periods, it is recommended that suitable fertilizers be applied in a timely manner.

scholarly journals A Study on the Mechanism of Milkvetch Root in the Treatment of Diabetic Nephropathy Based on Network Pharmacology

2020 ◽  
Vol 2020 ◽  
pp. 1-18
Author(s):  
Chunli Piao ◽  
Qi Zhang ◽  
De Jin ◽  
Li Wang ◽  
Cheng Tang ◽  
...  
Keyword(s):  
Diabetic Nephropathy ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Signaling Pathway ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Systems Pharmacology ◽  
Active Components ◽  
Kegg Pathways

Diabetic nephropathy (DN) is one of the most common complications of diabetes mellitus. Owing to its complicated pathogenesis, no satisfactory treatment strategies for DN are available. Milkvetch Root is a common traditional Chinese medicine (TCM) and has been extensively used to treat DN in clinical practice in China for many years. However, due to the complexity of botanical ingredients, the exact pharmacological mechanism of Milkvetch Root in treating DN has not been completely elucidated. The aim of this study was to explore the active components and potential mechanism of Milkvetch Root by using a systems pharmacology approach. First, the components and targets of Milkvetch Root were analyzed by using the Traditional Chinese Medicine Systems Pharmacology database. We found the common targets of Milkvetch Root and DN constructed a protein-protein interaction (PPI) network using STRING and screened the key targets via topological analysis. Enrichment of Gene Ontology (GO) pathways and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed. Subsequently, major hubs were identified and imported to the Database for Annotation, Visualization and Integrated Discovery for pathway enrichment analysis. The binding activity and targets of the active components of Milkvetch Root were verified by using the molecular docking software SYBYL. Finally, we found 20 active components in Milkvetch Root. Moreover, the enrichment analysis of GO and KEGG pathways suggested that AGE-RAGE signaling pathway, HIF-1 signaling pathway, PI3K-Akt signaling pathway, and TNF signaling pathway might be the key pathways for the treatment of DN; more importantly, 10 putative targets of Milkvetch Root (AKT1, VEGFA, IL-6, PPARG, CCL2, NOS3, SERPINE1, CRP, ICAM1, and SLC2A) were identified to be of great significance in regulating these biological processes and pathways. This study provides an important scientific basis for further elucidating the mechanism of Milkvetch Root in treating DN.

scholarly journals RNA seq analyses of chicken reveals biological pathways involved in acclimation into different geographical locations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Himansu Kumar ◽  
Hyojun Choo ◽  
Asankadyr U. Iskender ◽  
Krishnamoorthy Srikanth ◽  
Hana Kim ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Mapk Signaling ◽  
Climatic Conditions ◽  
Rna Seq ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Commercial Chicken ◽  
Pathways Analysis ◽  
Ppar Signaling ◽  
Transcriptome Expression

Abstract Transcriptome expression reflects genetic response in diverse conditions. In this study, RNA sequencing was utilized to profile multiple tissues such as liver, breast, caecum, and gizzard of Korean commercial chicken raised in Korea and Kyrgyzstan. We analyzed ten samples per tissue from each location to identify candidate genes which are involved in the adaptation of Korean commercial chicken to Kyrgyzstan. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, we found 315, 196, 167 and 198 genes in liver, breast, cecum, and gizzard respectively as differentially expressed between the two locations. GO enrichment analysis showed that these genes were highly enriched for cellular and metabolic processes, catalytic activity, and biological regulations. Similarly, KEGG pathways analysis indicated metabolic, PPAR signaling, FoxO, glycolysis/gluconeogenesis, biosynthesis, MAPK signaling, CAMs, citrate cycles pathways were differentially enriched. Enriched genes like TSKU, VTG1, SGK, CDK2 etc. in these pathways might be involved in acclimation of organisms into diverse climatic conditions. The qRT-PCR result also corroborated the RNA-Seq findings with R2 of 0.76, 0.80, 0.81, and 0.93 for liver, breast, caecum, and gizzard respectively. Our findings can improve the understanding of environmental acclimation process in chicken.

scholarly journals Virtual screening and network pharmacology-based synergistic mechanism identification of multiple components contained in Guanxin V against coronary artery disease

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Bo Liang ◽  
Xiao-Xiao Zhang ◽  
Ning Gu
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Virtual Screening ◽  
Molecular Mechanisms ◽  
Functional Enrichment ◽  
Network Pharmacology ◽  
Active Components ◽  
Kegg Pathways ◽  
Synergistic Mechanism ◽  
Artery Disease

Abstract Background Guanxin V (GXV), a traditional Chinese medicine (TCM), has been widely used to treat coronary artery disease (CAD) in clinical practice in China. However, research on the active components and underlying mechanisms of GXV in CAD is still scarce. Methods A virtual screening and network pharmacological approach was utilized for predicting the pharmacological mechanisms of GXV in CAD. The active compounds of GXV based on various TCM-related databases were selected and then the potential targets of these compounds were identified. Then, after the CAD targets were built through nine databases, a PPI network was constructed based on the matching GXV and CAD potential targets, and the hub targets were screened by MCODE. Moreover, Metascape was applied to GO and KEGG functional enrichment. Finally, HPLC fingerprints of GXV were established. Results A total of 119 active components and 121 potential targets shared between CAD and GXV were obtained. The results of functional enrichment indicated that several GO biological processes and KEGG pathways of GXV mostly participated in the therapeutic mechanisms. Furthermore, 7 hub MCODEs of GXV were collected as potential targets, implying the complex effects of GXV-mediated protection against CAD. Six specific chemicals were identified. Conclusion GXV could be employed for CAD through molecular mechanisms, involving complex interactions between multiple compounds and targets, as predicted by virtual screening and network pharmacology. Our study provides a new TCM for the treatment of CAD and deepens the understanding of the molecular mechanisms of GXV against CAD.

scholarly journals Reveals of New Candidate Active Components in Hemerocallis Radix and Its Anti-Depression Action of Mechanism Based on Network Pharmacology Approach

2020 ◽  
Vol 21 (5) ◽  
pp. 1868 ◽  
Author(s):  
Hsin-Yi Lin ◽  
Jen-Chieh Tsai ◽  
Lung-Yuan Wu ◽  
Wen-Huang Peng
Keyword(s):  
Network Pharmacology ◽  
Antidepressant Effect ◽  
Depression Symptoms ◽  
Active Components ◽  
Protein Protein Interaction ◽  
Pharmacological Mechanism ◽  
Go Enrichment ◽  
Therapeutic Mechanism ◽  
And Cluster Analysis ◽  
Depression Disorder

The global depression population is showing a significant increase. Hemerocallis fulva L. is a common Traditional Chinese Medicine (TCM). Its flower buds are known to have ability to clear away heat and dampness, detoxify, and relieve depression. Ancient TCM literature shows that its roots have a beneficial effect in calming the spirit and even the temper in order to reduce the feeling of melancholy. Therefore, it is inferred that the root of Hemerocallis fulva L. can be used as a therapeutic medicine for depression. This study aims to uncover the pharmacological mechanism of the antidepressant effect of Hemerocallis Radix (HR) through network pharmacology method. During the analysis, 11 active components were obtained and screened using ADME—absorption, distribution, metabolism, and excretion— method. Furthermore, 267 HR targets and 740 depressive disorder (DD) targets were gathered from various databases. Then protein–protein interaction (PPI) network of HR and DD targets were constructed and cluster analysis was applied to further explore the connection between the targets. In addition, gene ontology (GO) enrichment and pathway analysis was applied to further verify that the biological process related to the target protein is associated with the occurrence of depression disorder. In conclusion, the most important bioactive components—anthraquinone, kaempferol, and vanillic acid—can alleviate depression symptoms by regulating MAOA, MAOB, and ESR1. The proposed network pharmacology strategy provides an integrating method to explore the therapeutic mechanism of multi-component drugs on a systematic level.

scholarly journals Prognostic values and prospective pathway signaling of miR-126 in non-small cell lung cancer: a study based on gene expression omnibus and bioinformatics analysis

2020 ◽  
Author(s):  
Zichen Jiao ◽  
Ao Yu ◽  
Xiaofeng He ◽  
Yulong Xuan ◽  
He Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Gene Expression Omnibus ◽  
Data Sets ◽  
Hub Genes ◽  
Biological Regulation ◽  
Protein Protein Interaction ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Nsclc Patients

Abstract Objective MiRNAs are considered to be crucial for NSCLC’s initiation and development. MiRNAs have been widely identified in NSCLC. However, the role of miR-126 in NSCLC has not been fully explained.Methods miR-126 Expression in NSCLC was evaluated by analyzing the common data sets in Gene Expression Omnibus(GEO) database and reviewing former thesis papers. Three mRNA datasets, GSE18842, GSE19804 and GSE101929, from GEO to indentify the differentially expressed genes (DEG). We prognosed the target genes of hsa-miR-126-5p using TargetScan and analyzed the gene overlap between the target genes of miR-126 and DEG in NSCLC. Subsequently, we analyzed Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. We used STRING and Cytoscape to construct a protein-protein interaction (PPI) network, and analyzed the influence of HUB gene on the prognosis of NSCLC.Results A common pattern of mir-126 downregulation in NSCLC was identified in the literature review. A total of 187 DEGs were identified, both NSCLC-related and miR-126-related. Many DEGs are extendedly enriched in cell membranes, signal receptor binding, and biological regulation. Among the 10 main Hub genes analyzed by PPI, 4 HUB genes (NCAP-G,MELK,KIAA0101,TPX2) were obviously related to the poor recuperation of NSCLC patients. When these genes highly expressed, survival rate of NSCLC patients was low. Furthermore, we identified the recessive miR-126-related genes that may be involved in NSCLC, such as TPX2, HMMR, and ANLN through network analysis.Conclusion this study suggests that mir-126 is radical for the biological processing of NSCLC.

scholarly journals Analysis of the Active Components and Mechanism of Three Prescriptions in the Treatment of COVID-19 Via Network Pharmacology and Molecular Docking

2021 ◽  
Vol 16 (9) ◽  
pp. 1934578X2110477
Author(s):  
Fei Wang ◽  
Jia-Hui Chen ◽  
Bo Liu ◽  
Ting Zhang
Keyword(s):  
Molecular Docking ◽  
Binding Energies ◽  
Network Pharmacology ◽  
Active Components ◽  
Chinese Medicines ◽  
Protein Protein Interaction ◽  
Kegg Pathways ◽  
Ppi Networks ◽  
Infection And Inflammation ◽  
Analysis Platform

Purpose: Prescriptions of Han-Shi-Yu-Fei (HSYF), Han-Shi-Zu-Fei (HSZF), and Yi-Du-Bi-Fei (YDBF) were effective in treating COVID-19. Based on network pharmacology and molecular docking, overlapping Traditional Chinese medicines (TCMs), their active components, and core targets were explored in this study. Methods: First, the overlapping TCMs and their active components were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) by evaluating Oral Bioactivity (OB) and Drug Likeness (DL). The overlapping targets of potential components and COVID-19 were collected by SwissTargetPrediction, Gene Cards, and Venn 2.1.0 databases. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were analyzed via DAVID6.8.1 database. Through comprehensive analysis of the “prescriptions-TCMs-components” (P-T-C), “components-targets-pathways” (C-T-P) and “protein–protein interaction” (PPI) networks constructed by Cytoscape 3.7.1 software, the active components and core targets were obtained. Finally, the binding energies of these components with ACE2 and SARS-CoV-2 3CL were analyzed by AutDockTools-1.5.6 and PyMOL software. Results: In all, five overlapping TCMs, 40 potential active components, and 47 candidate targets were obtained and analyzed in these prescriptions. There were 288 GO entries ( P < 0.05), including 211 biological process (BP), 40 cell composition (CC), and 37 molecular function (MF) entries. Most of the 105 KEGG pathways ( P < 0.05) were involved with viral infection and inflammation. Through “PPI” and “C-T-P” networks, the core targets (EGFR, PTGS2, CDK2, GSK3B, PIK3R1, and MAPK3) and active components (Q27134551, acanthoside B, neohesperidin, and irisolidone) with high degrees were obtained. Molecular docking results showed that the above-mentioned four components could inhibit the binding of ACE2 and SARS-COV-2 3CL to protect against COVID-19. Conclusion: In this study, the active components and core targets of three prescriptions in the treatment of COVID-19 were elaborated by network pharmacology and molecular docking, providing a reference for their applications.

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