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1.
Article in Chinese | WPRIM | ID: wpr-939692

ABSTRACT

OBJECTIVE@#To screen differentially expressed gene (DEG) related to myelodysplastic syndrome (MDS) based on Gene Expression Omnibus (GEO) database, and explore the core genes and pathogenesis of MDS by analyzing the biological functions and related signaling pathways of DEG.@*METHODS@#The expression profiles of GSE4619, GSE19429, GSE58831 including MDS patients and normal controls were downloaded from GEO database. The gene expression analysis tool (GEO2R) of GEO database was used to screen DEG according to | log FC (fold change) |≥1 and P<0.01. David online database was used to annotate gene ontology function (GO). Metascape online database was used to enrich and analyze differential genes in Kyoto Encyclopedia of Genes and Genomes (KEGG). The protein-protein interaction network (PPI) was constructed by using STRING database. CytoHubba and Mcode plug-ins of Cytoscape were used to analyze the key gene clusters and hub genes. R language was used to diagnose hub genes and draw the ROC curve. GSEA enrichment analysis was performed on GSE19429 according to the expression of LEF1.@*RESULTS@#A total of 74 co-DEG were identified, including 14 up-regulated genes and 60 down regulated genes. GO enrichment analysis indicated that BP of down regulated genes was mainly enriched in the transcription and regulation of RNA polymerase II promoter, negative regulation of cell proliferation, and immune response. CC of down regulated genes was mainly enriched in the nucleus, transcription factor complexes, and adhesion spots. MF was mainly enriched in protein binding, DNA binding, and β-catenin binding. KEGG pathway was enriched in primary immunodeficiency, Hippo signaling pathway, cAMP signaling pathway, transcriptional mis-regulation in cancer and hematopoietic cell lineage. BP of up-regulated genes was mainly enriched in type I interferon signaling pathway and viral response. CC was mainly enriched in cytoplasm. MF was mainly enriched in RNA binding. Ten hub genes and three important gene clusters were screened by STRING database and Cytoscape software. The functions of the three key gene clusters were closely related to immune regulation. ROC analysis showed that the hub genes had a good diagnostic significance for MDS. GSEA analysis indicated that LEF1 may affect the normal function of hematopoietic stem cells by regulating inflammatory reaction, which further revealed the pathogenesis of MDS.@*CONCLUSION@#Bioinformatics can effectively screen the core genes and key signaling pathways of MDS, which provides a new strategy for the diagnosis and treatment of MDS.


Subject(s)
Computational Biology , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Gene Ontology , Humans , Myelodysplastic Syndromes/genetics
2.
Article in Chinese | WPRIM | ID: wpr-928064

ABSTRACT

This study explored the anticoagulant material basis and mechanism of Trichosanthis Semen and its shell and kernel based on spectrum-effect relationship-integrated molecular docking. High performance liquid chromatography(HPLC) fingerprints of Trichosanthis Semen and its shell and kernel were established. Prothrombin time(PT) and activated partial thromboplastin time(APTT) in mice in the low-and high-dose(5, 30 g·kg~(-1), respectively) Trichosanthis Semen, the shell, and kernel groups were determined as the coagulation markers. The spectrum-effect relationship and anticoagulant material basis of Trichosanthis Semen and its shell and kernel were analyzed with mean value calculation method of Deng's correlation degree(MATLAB) and the common effective component cluster was obtained. Then the common targets of the component cluster and coagulation were retrieved from TCMSP, Swiss-TargetPrediction, GenCLiP3, GeneCards, and DAVID, followed by Gene Ontology(GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment of the targets. The main anticoagulant molecular mechanism of the component cluster was verified by SYBYL-X 2.1.1. The spectrum-effect relationship of Trichosanthis Semen and its shell and kernel was in positive correlation with the dosage. The contribution of each component to anticoagulation was not the same, suggesting that the material basis for anticoagulation was different, but they have common effective components(i.e. common material basis), such as adenine(peak 3), uracil(peak 4), hypoxanthine(peak 6), xanthine(peak 9), and adenosine(peak 11). Network pharmacology showed that these components can act on multiple target proteins such as NOS3, KDR, and PTGS2, and exert anticoagulant effect through multiple pathways such as VEGF signaling pathway. They involved the biological functions such as proteolysis, cell component such as cytosol, and molecular functions. The results of molecular docking showed that the binding free energy of these components with NOS3(PDB ID: 1 D0 C), KDR(PDB ID: 5 AMN), and PTGS2(PDB ID: 4 COX) was ≤-5 kJ·mol~(-1), and the docking conformations were stable. Spectrum-effect relationship-integrated molecular docking can be used for the optimization, virtual screening, and verification of complex chemical and biological information of Chinese medicine. Trichosanthis Semen and its shell and kernel have the common material basis for anticoagulation and they exert the anticoagulant through multiple targets and pathways.


Subject(s)
Animals , Anticoagulants/pharmacology , Drugs, Chinese Herbal/pharmacology , Gene Ontology , Mice , Molecular Docking Simulation , Semen
3.
Int. braz. j. urol ; 47(4): 843-855, Jul.-Aug. 2021. tab, graf
Article in English | LILACS | ID: biblio-1286781

ABSTRACT

ABSTRACT Objective: Interstitial cystitis (IC)/bladder pain syndrome (BPS) is a chronic inflammatory disease that can cause bladder pain and accompanying symptoms, such as long-term urinary frequency and urgency. IC/BPS can be ulcerative or non-ulcerative. The aim of this study was to explore the core genes involved in the pathogenesis of ulcerative IC, and thus the potential biomarkers for clinical treatment. Materials and Methods: First, the gene expression dataset GSE11783 was downloaded using the Gene Expression Omnibus (GEO) database and analyzed using the limma package in R to identify differentially expressed genes (DEGs). Then, the Database for Annotation, Visualization and Integrated Discovery (DAVID) was used for Gene Ontology (GO) functional analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) was used for pathway enrichment analysis. Finally, the protein-protein interaction (PPI) network was constructed, and key modules and hub genes were determined using the STRING and Cytoscape software. The resulting key modules were then analyzed for tissue-specific gene expression using BioGPS. Results: A total of 216 up-regulated DEGs and 267 down-regulated genes were identified, and three key modules and nine hub genes were obtained. Conclusion: The core genes (CXCL8, CXCL1, IL6) obtained in this study may be potential biomarkers of interstitial cystitis with guiding significance for clinical treatment.


Subject(s)
Humans , Cystitis, Interstitial/genetics , Software , Gene Expression Profiling , Protein Interaction Maps/genetics , Gene Ontology
4.
Arch. latinoam. nutr ; 71(2): 138-148, jun. 2021. tab, graf
Article in English | LILACS, LIVECS | ID: biblio-1290912

ABSTRACT

Reflex-ontogeny and intestinal morphometrics were evaluated in Wistar rats whose mothers were fed on a high-fat diet during the perinatal period. Male pups (n=52) formed four experimental groups: NN (pups from mothers with lab chow diet during gestation and lactation); NH (pups from mothers with lab chow diet during pregnancy and high-fat in lactation); HH (pups from mothers with high-fat diet during gestation and lactation); HN (pups from mothers with high-fat diet during pregnancy and lab chow in lactation). The reflex ontogeny, the maturation of physical characteristics and parameters of somatic growth were evaluated during lactation. In addition, the body mass index (BMI), the specific rate of weight gain (SRWG), the Lee index, the weight of the brain and intestinal parameters were analyzed after weaning. High-fat diet during pregnancy (HH and HN groups) delayed the maturation of reflexes and physical characteristics. The high-fat diet affected somatic growth differently, reducing somatic growth parameters in the groups NH and HH and increasing in the HN group. The highest SRWG was found in group HN. SRWG and BMI were reduced in the groups NH and HH. The relative intestinal weight was reduced in the groups NH, HH and HN. The relative length of small intestine was longer in group HN than in group NN. The total height of the mucosa and size of the villous were lower in group HH than in group NN. In conclusion, high-fat diet promoted negative consequences for the development of the nervous and enteric systems of the offspring(AU)


Ontogenia refleja y morfometría intestinal fueron evaluados en crías de ratas Wistar que fueron alimentadas con una dieta alta en grasas durante el período perinatal. Los descendientes machos (n = 52) formaron cuatro grupos experimentales: NN (hijos de madres que utilizaron alimentos de laboratorio durante la gestación y la lactancia); NH (hijos de madres que comieron dieta de laboratorio durante el embarazo y dieta con un alto contenido de grasas en la lactancia); HH (hijos de madres con una dieta alta en grasas durante el embarazo y la lactancia); HN (hijos de madres que comieron una dieta alta en grasas durante el embarazo y comida de laboratorio durante la lactancia). La ontogenia refleja, la maduración de las características físicas y los parámetros de crecimiento somático durante la lactancia fueron evaluados. Además, el índice de masa corporal (IMC), la tasa específica de aumento de peso (SRWG), el índice de Lee, el peso cerebral y los parámetros intestinales fueron analizados después del destete. La dieta alta en grasas durante el embarazo (grupos HH y HN) retrasó la maduración de reflejos y características físicas. La dieta alta en grasas afectó el crecimiento somático de manera diferente, reduciendo los parámetros de crecimiento somático en los grupos NH y HH y aumentando en el grupo HN. El SRWG más grande se encontró en el grupo HN. El SRWG y el IMC se redujeron en los grupos NH y HH. El peso relativo intestinal se redujo en los grupos NH, HH y HN. La longitud relativa del intestino delgado fue mayor en el grupo HN que en el grupo NN. La altura total de la mucosa y el tamaño de las vellosidades fueron menores en el grupo HH que en el grupo NN. En conclusión, la dieta alta en grasas tuvo consecuencias negativas para el desarrollo de los sistemas nervioso y entérico de la prole(AU)


Subject(s)
Rats , Breast Feeding , Dietary Fats , Gene Ontology , Dietary Sugars , Chronic Disease , Obesity
5.
Electron. j. biotechnol ; 51: 8-16, May. 2021. tab, graf, ilus
Article in English | LILACS | ID: biblio-1343314

ABSTRACT

BACKGROUND: Myogenic regulatory factors (MRFs) such as MyoD, Myf6 and Myf5 play a vital role in the growth and development of muscles. Jeju Native Pig (JNP) is the top ranker in Korea amongst the indigenous livestock reared for meat purpose. Few studies covering transcript abundance of the MRFs and related to their co-expression with Pax7 in JNP have been conducted. Despite having better quality pork, JNP does not have a comparative growth rate with respect to western breeds. Therefore, the present study was designed with the objective to study the relative transcript levels of MRFs in the postnatal myogenesis of longissimus dorsi muscles in JNP and Berkshire breeds. RESULTS: Relative transcript levels were analyzed by qRT-PCR and blot expression analysis through Western blotting. Immunocytochemistry was performed to analyze their expressions at cellular levels. ToppCluster aided in the analysis of gene ontology of biological processes. The quantitative transcript levels of MyoD and Pax7 were significantly (P < 0.05) higher in Berkshire than in JNP. Myotube formation was observed under the co-expression of MyoD and Pax7. ToppCluster helped in the understanding of the linking of biological processes of the MRFs with the different signaling pathways. MyBPH had significantly (P < 0.05) high transcript levels during the chosen age groups in JNP than Berkshire. CONCLUSIONS: The current study can be helpful in understanding the genetic basis for myogenesis in postnatal stage. Moreover, it can act as stepping stone for the identification of marker genes related to body growth and meat quality in JNP.


Subject(s)
Animals , Swine , Myogenic Regulatory Factors/metabolism , Muscle Development/genetics , Immunohistochemistry , Genetic Markers , Blotting, Western , Myogenic Regulatory Factors/genetics , PAX7 Transcription Factor/metabolism , Real-Time Polymerase Chain Reaction , Gene Ontology , Pork Meat
6.
Braz. j. med. biol. res ; 54(11): e11372, 2021. tab, graf
Article in English | LILACS | ID: biblio-1339455

ABSTRACT

Immune-mediated inflammation plays a key role in the pathology of abdominal aortic aneurysm (AAA). We aimed to use a computational approach to profile the immune infiltration patterns and related core genes in AAA samples based on the overexpression of gene signatures. The microarray datasets of AAA and normal abdominal tissues were acquired from gene expression omnibus (GEO) database. We evaluated the composition of immune infiltrates through microenvironment cell populations (MCP)-counter. Weighted gene correlation network analysis (WGCNA) was employed to construct the co-expression network and extract gene information in the most relevant module. Functional and pathway enrichment analysis was performed and immune infiltration related core genes were screened. AAA tissues had a higher level of infiltration by cytotoxic lymphocytes, NK cells, T cells, fibroblasts, myeloid dendritic cells, and neutrophils than normal aorta. The red module was strongly correlated with the infiltrating levels of T cells and cytotoxic lymphocytes. Gene ontology (GO) and pathway analyses revealed that genes in the most relevant module were mainly enriched in T cell activation, regulation of lymphocyte activation, cytokine-cytokine receptor interaction, and chemokine signaling pathway, etc. The expression of GZMK, CCL5, GZMA, CD2, and EOMES showed significant correlations with cytotoxic lymphocytes, while CD247, CD2, CD6, RASGRP1, and CD48 expression were positively associated with T cell infiltration. In conclusion, we comprehensively analyzed profiles of infiltrated immune cells in AAA tissues and their associated marker genes. Our data may provide a novel clue to indicate the underlying molecular mechanisms of AAA formation in terms of immune infiltration.


Subject(s)
Humans , Aortic Aneurysm, Abdominal/genetics , Biomarkers , Gene Expression Profiling , Transcriptome , Gene Ontology
7.
Article in English | WPRIM | ID: wpr-922097

ABSTRACT

OBJECTIVE@#To investigate a Met-controlled allosteric module (AM) of neural generation as a potential therapeutic target for brain ischemia.@*METHODS@#We selected Markov clustering algorithm (MCL) to mine functional modules in the related target networks. According to the topological similarity, one functional module was predicted in the modules of baicalin (BA), jasminoidin (JA), cholic acid (CA), compared with I/R model modules. This functional module included three genes: Inppl1, Met and Dapk3 (IMD). By gene ontology enrichment analysis, biological process related to this functional module was obtained. This functional module participated in generation of neurons. Western blotting was applied to present the compound-dependent regulation of IMD. Co-immunoprecipitation was used to reveal the relationship among the three members. We used IF to determine the number of newborn neurons between compound treatment group and ischemia/reperfusion group. The expressions of vascular endothelial growth factor (VEGF) and matrix metalloproteinase 9 (MMP-9) were supposed to show the changing circumstances for neural generation under cerebral ischemia.@*RESULTS@#Significant reduction in infarction volume and pathological changes were shown in the compound treatment groups compared with the I/R model group (P<0.05). Three nodes in one novel module of IMD were found to exert diverse compound-dependent ischemic-specific excitatory regulatory activities. An anti-ischemic excitatory allosteric module (AM@*CONCLUSIONS@#AM


Subject(s)
Animals , Brain Ischemia/drug therapy , Gene Ontology , Gene Regulatory Networks , Rodentia , Vascular Endothelial Growth Factor A
8.
Neotrop. ichthyol ; 19(1): e200106, 2021. tab, graf, mapas, ilus
Article in English | LILACS, VETINDEX | ID: biblio-1154968

ABSTRACT

Two new species from the upper rio Tocantins basin are described in Knodus based on the traditional definition of the genus. The new species are distinguished from other congeners by meristic and morphometric characters, such as the number of cusps in the premaxillary and dentary teeth, the number of scale series between dorsal-fin origin and lateral line, the orbital diameter and the body depth. With the two new species, the number of endemic species in the upper rio Tocantins basin upstream of the mouth of the rio Paranã, rises to 53 (89 to the confluence with rio Araguaia). The existence of a meristic character that changes through ontogeny (allomery), viz. the number of scale series between dorsal-fin origin and lateral line, was detected in some species of Knodus through a regression analysis. Additionally, this paper describes an unambiguous, more informative and precise new method for counting vertebrae, which will enhance the efficacy of this trait in species comparisons.(AU)


Duas novas espécies do alto rio Tocantins são descritas em Knodus com base na definição tradicional do gênero. As novas espécies são distinguidas das demais congêneres por caracteres merísticos e morfométricos, tais como o número de cúspides nos dentes do pré-maxilar e do dentário, o número de séries de escamas entre a origem da nadadeira dorsal e a linha lateral, o diâmetro da órbita e a altura do corpo. Com as duas novas espécies, o número de espécies endêmicas na bacia do alto rio Tocantins, acima da barra do rio Paranã, sobe para 53 (89 até a confluência com o rio Araguaia). A existência de um caráter merístico que muda ao longo da ontogenia (alomeria), ou seja, o número de séries de escamas entre a origem da nadadeira dorsal e a linha lateral, foi detectado em algumas espécies de Knodus com uma análise de regressão. Adicionalmente, este artigo descreve um novo método não-ambíguo, mas informativo e mais preciso, para a contagem de vértebras, que aumentará a eficácia deste caráter em comparações entre espécies.(AU)


Subject(s)
Humans , Characidae , Gene Ontology , Gender Identity
9.
Article in Chinese | WPRIM | ID: wpr-921755

ABSTRACT

Microarray data of hippocampal tissue(HC) of the cognitively intact elderly(60-99 years old) were compared with those of the middle-aged and the young(20-59 years old) by bioinformatics techniques to initially screen out differentially expressed genes(DEGs) and then predict potential effective Chinese medicinals for the treatment of brain aging. The gene expression profile(accession: GSE11882) was downloaded from the Gene Expression Omnibus(GEO) and DEGs were screened based on R package. The key DEGs were identified by STRING, Cytoscape and the plug-in, followed by Gene Ontology(GO) term and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis. Then the key genes and the medical ontology information retrieval platform(Coremine Medical) were mapped against each other to single out the Chinese medicinals for the treatment of brain aging and construct the " Chinese medicinal-active constituent-target" network. Among the resultant 268 DEGs(246 down-regulated and 22 up-regulated), the 15 key genes were mainly involved in biological processes such as leukocyte migration, neutrophil activation, cell chemotaxis, microglia activation and response to external stimulus, and pathways such as inflammatory process, immune response, cytokine-cytokine receptor interaction, PI3 K-Akt signaling pathway, Rap1 signaling pathway, chemokine signaling pathway and Toll-like receptor signaling pathway. The potential effective Chinese medicinals were Notoginseng Radix et Rhizoma, Ginseng Radix et Rhizoma, Salviae Miltiorrhizae Radix et Rhizoma and Astragali Radix. The analysis of DEGs and key genes enhances the understanding of the mechanisms of brain aging. This study provides potential gene targets and ideas for the development of Chinese medicine for brain aging.


Subject(s)
Adult , Aged , Aged, 80 and over , Brain , China , Computational Biology , Gene Expression Profiling , Gene Ontology , Humans , Middle Aged , Transcriptome , Young Adult
10.
Article in Chinese | WPRIM | ID: wpr-921682

ABSTRACT

This study aims to predict the material basis and mechanism of Dachengqi Decoction in the treatment of sepsis based on network pharmacology. The chemical constituents and targets of Dachengqi Decoction were retrieved from TCMSP, UniPot and DrugBank and the targets for the treatment of sepsis from OMIM and GeneCards. The potential targets of Dachengqi Decoction for the treatment of sepsis were screened by OmicShare. STRING database and Cytoscape 3.7.2 were used to construct the Chinese medicinal-active component-target-disease, active component-key target-key pathway, and protein-protein interaction(PPT) networks. The gene ontology(GO) term enrichment analysis and Kyoto encyclopedia of genes and genomes(KEGG) pathway enrichment analysis were performed by DAVID(P<0.05). Finally, the animal experiment was conducted to verify some targets and pathways. A total of 40 active components and 157 targets of the Dachengqi Decoction, 2 407 targets for the treatment of sepsis, and 91 common targets of the prescription and the disease were also obtained. The key targets were prostaglandin G/H synthase 2(PTGS2), prostaglandin G/H synthase 1(PTGS1), protein kinase cAMP-dependent catalytic-α(PRKACA), coagulation factor 2 receptor(F2 R), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic gamma subunit(PIK3 CG), dipeptidyl peptidase 4(DPP4), etc. A total of 533 terms and 125 pathways were obtained for the 91 targets. The main terms were the response to drug, negative regulation of apoptotic process, positive regulation of nitric oxide biosynthetic process and lipopolysaccharide-mediated signaling pathway, and the pathways included pathways in cancer, hepatitis B, and phosphatidylinositol 3-kinase and protein kinase B(PI3 K/Akt) signaling pathway. The animal experiment confirmed that Dachengqi Decoction can down-regulate inflammatory cytokines interleukin-1β(IL-1β), IL-6 and tumor necrosis factor α(TNF-α)(P<0.01). It could also reduce the wet/dry weight ratio of lung tissue, the level of myeloperoxidase(MPO) and the phosphorylation of PI3 K and Akt(P<0.01). These results indicated that Dchengqi Decoction could act on inflammation-related targets and improve sepsis by inhibiting PI3 K/Akt signaling pathway. The animal experiment supported the predictions of network pharmacology. Dachengqi Decoction intervenes sepsis via multiple components, multiple targets, and multiple pathways. The result lays a foundation for further research on the mechanism of Dachengqi Decoction in the treatment of sepsis.


Subject(s)
Animals , Drugs, Chinese Herbal , Gene Ontology , Plant Extracts , Sepsis/genetics
11.
Chinese Medical Journal ; (24): 2322-2332, 2021.
Article in English | WPRIM | ID: wpr-921158

ABSTRACT

BACKGROUND@#Age-related macular degeneration (AMD) is the leading cause of vision loss worldwide. However, the mechanisms involved in the development and progression of AMD are poorly delineated. We aimed to explore the critical genes involved in the progression of AMD.@*METHODS@#The differentially expressed genes (DEGs) in AMD retinal pigment epithelial (RPE)/choroid tissues were identified using the microarray datasets GSE99248 and GSE125564, which were downloaded from the gene expression omnibus database. The overlapping DEGs from the two datasets were screened to identify DEG-related biological pathways using gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. The hub genes were identified from these DEGs through protein-protein interaction network analyses. The expression levels of hub genes were evaluated by quantitative real-time polymerase chain reaction following the induction of senescence in ARPE-19 with FK866. Following the identification of AMD-related key genes, the potential small molecule compounds targeting the key genes were predicted by PharmacoDB. Finally, a microRNA-gene interaction network was constructed.@*RESULTS@#Microarray analyses identified 174 DEGs in the AMD RPE compared to the healthy RPE samples. These DEGs were primarily enriched in the pathways involved in the regulation of DNA replication, cell cycle, and proteasome-mediated protein polyubiquitination. Among the top ten hub genes, HSP90AA1, CHEK1, PSMA4, PSMD4, and PSMD8 were upregulated in the senescent ARPE-19 cells. Additionally, the drugs targeting HSP90AA1, CHEK1, and PSMA4 were identified. We hypothesize that Hsa-miR-16-5p might target four out of the five key DEGs in the AMD RPE.@*CONCLUSIONS@#Based on our findings, HSP90AA1 is likely to be a central gene controlling the DNA replication and proteasome-mediated polyubiquitination during the RPE senescence observed in the progression of AMD. Targeting HSP90AA1, CHEK1, PSMA4, PSMD4, and/or PSMD8 genes through specific miRNAs or small molecules might potentially alleviate the progression of AMD through attenuating RPE senescence.


Subject(s)
DNA Replication , Gene Expression Profiling , Gene Ontology , Humans , Macular Degeneration/genetics , Proteasome Endopeptidase Complex
12.
Article in Chinese | WPRIM | ID: wpr-888039

ABSTRACT

The acupoint application of Euodiae Fructus at Yongquan(KI1) can significantly improve the sleep quality of patients with insomnia with berberine as the main effective component for the efficacy. Nineteen active compounds and 203 drug targets were screened out from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP). After comparison with GeneCards and Online Mendelian Inheritance in Man(OMIM), 24 common genes of diseases and drugs were obtained. STRING 11.0 was used to construct a protein-protein interaction(PPI) network of the overlapping genes, and Matthews correlation coefficient(MCC) was employed to screen the core genes, which were then subjected to enrichment analysis with gene ontology(GO) and Kyoto encyclopedia of genes and genomes(KEGG). The results revealed that the main compounds of Euodiae Fructus, such as berberine and rutaecarpine, participated in the biological processes(such as neurotransmitter receptor activity) by regulating C-reactive protein(CRP), estrogen receptor 1(ESR1), 5-hydroxytryptamine(5-HT) receptor, and interleukin-6(IL-6) to exert sedative, anxiolytic, and antidepressant effects. Sixty 4-week-old SPF mice were randomly divided into a control group, a model group, a positive drug(diazepam tablets) group, and low-, medium-, and high-dose berberine groups. Medication with corresponding drugs was performed for one week. The results demonstrated that berberine was potent in reducing the activities and standing times of mice, down-regulating the levels of CRP and IL-6 mRNA in the hypothalamus, and up-regulating the expression of 5-HT(P<0.01); however, no significant effect on ESR1 was observed. The network of Euodiae Fructus in treating insomnia was constructed by network pharmacology and verified by tests. The findings indicated that the therapeutic efficacy of Euodiae Fructus in treating insomnia was achieved by participating in multiple biological processes, such as neurotransmitter receptor activity, which provided a scientific basis for its clinical application.


Subject(s)
Animals , Databases, Genetic , Drugs, Chinese Herbal/pharmacology , Gene Ontology , Humans , Medicine, Chinese Traditional , Mice , Sleep Initiation and Maintenance Disorders/genetics
13.
Article in Chinese | WPRIM | ID: wpr-887935

ABSTRACT

This study used network pharmacology and molecular docking to study the mechanism of Bushen Culuan Formula in the treatment of infertility caused by polycystic ovary syndrome(PCOS). The active ingredients and potential drug targets of Bushen Cu-luan Decoction were obtained by searching the Traditional Chinese Medicine System Pharmacology(TCMSP) database, and the targets of PCOS by searching GeneCards. After the drug targets and disease targets were corrected by Uniprot, the intersection genes were obtained. STRING database and Cytoscape 3.7.2 were used for protein-protein interaction(PPI) analysis of the intersection genes. The ClueGO plug-in of Cytoscape 3.7.2 was employed to perform gene ontology(GO) enrichment and KEGG pathway enrichment for the intersection genes. Finally, molecular docking of the key active ingredients with the targets of Bushen Culuan Formula was performed using AutoDockVina and MGLtools. A total of 136 active ingredients and 314 drug targets of the decoction were obtained from TCMSP, and 136 disease targets from GeneCards. Finally, 49 drug-disease intersection genes were obtained. GO enrichment found that the genes were mainly involved in the regulation of muscle cell apoptosis, positive regulation of small molecule metabolism, core promoter binding, RNA polymerase Ⅱ regulation of pri-miRNA transcription, negative regulation of transmembrane transport and other biological functions. The enriched KEGG pathways mainly included MAPK, PI3 K-Akt, p53, and HIF-1 signaling pathways. The results of molecular docking showed that quercetin and PTGS2 can bind stably and interact through amino acid residues THR206, TRP387, ASN382, etc. This study preliminarily reveals the multi-component, multi-target, and multi-pathway mechanism of Bushen Culuan Formula in the treatment of PCOS-related infertility, which provides a basis for further research.


Subject(s)
Drugs, Chinese Herbal/pharmacology , Female , Gene Ontology , Humans , Medicine, Chinese Traditional , Molecular Docking Simulation , Polycystic Ovary Syndrome/genetics , Signal Transduction
14.
Investig. desar. ; 28(2): 125-146, July-Dec. 2020.
Article in Spanish | LILACS, COLNAL | ID: biblio-1346381

ABSTRACT

RESUMEN Las competencias laborales generales (CLG) como aspectos asociados a la productividad y la competitividad buscan la formación de personas que emprendan proyectos de vida que les posibilite desempeñarse con éxito en su quehacer laboral, por ello estas competencias preparan a los jóvenes en la responsabilidad de ser productivos para sí mismos y para los demás, en atención a los retos sociales, económicos, culturales y tecnológicos. Lo anterior exige el reconocimiento de bases epistémicas y ontológicas para la generación y el desarrollo de esa competencia. Este artículo realiza un acercamiento a estas bases y explica las relaciones ante el nuevo paradigma de la complejidad, brinda cuatro postulados en los que se explica por qué la formación en CLG exige una mirada no mecanicista, ni reduccionista, ni fragmentada, que permita comprender la formación y dar nuevas pistas ante las reducidas miradas de educación en los territorios.


ABSTRACT The General Job Competencies (GJC), as aspects associated with productivity and competitiveness, seek to train people to undertake life projects that enable them to perform successfully in their work tasks. For this reason, these competencies prepare young people in the responsibility of being productive for themselves and for others; taking into account social, economic, cultural, and technological challenges. This requires the recognition of epistemic and ontological bases for the generation and development of these competencies. This article makes an approach to these bases, explaining the relationships in the face of the new paradigm of complexity, and provides four postulates where it is explained why training at GJC requires a non-mechanistic, reductionist, or fragmented view that allows for an understanding of the training, and for giving new clues to the reduced views of education in the territories.


Subject(s)
Humans , Work , Workplace , Knowledge , Education , Systems Analysis , Projects , Gene Ontology
16.
Acta toxicol. argent ; 28(1): 5-12, Apr. 2020. graf
Article in English | LILACS | ID: biblio-1248663

ABSTRACT

Abstract In the 1960s, organochlorine compounds were responsible for the decline of birds of prey populations such as Haliaee- tus leucocephalus and Falco peregrinus. Pesticides similar to DDT cause bioaccumulation in birds, affecting their eggshell com- position and compromising their development. Using system biology tools, the goal of this study was to better comprehend how organochlorines act on birds. We performed a literature review, using the STITCH 5.0 platform, searching for the terms DDT and TCDD. The sub-networks were amplified in 100 interactions in STRING 10.5 and joined by the Cytoscape 3.4.0 Merge software, using the experimental animal model Gallus gallus. Clusterization, gene ontology, and centrality were the parameters evaluated in the resulting network. The resulting network had 1,417 interactions and 137 nodes. The clusterization indicated four clusters and the gene ontology pointed to biological processes related to cell signaling and morphological development. The centrality analysis indicated ESR1 and HSP90AB1 as hub/bottleneck proteins involved in the estrogen pathway and calcium transport. Therefore, it is possible that HSP90 proteins have increased expression in birds contaminated with organochlorine pesticides, favoring ESRI-organochlorines interaction and disturbing the calcium availability related to the eggshell formation. The presence or absence of heat shock proteins, such as HSP90, influences several aspects of reproduction in many species. Therefore, the relationship between the HSP90 protein expression and thin-shell syndrome was identified for the first time in this in silico study.


Resumen En los años 60, los organoclorados fueron responsables del declive de aves de rapiña como Haliaeetus leucocephalus y Falco peregrinus. Pesticidas como el DDT, causan biomagnificación en las aves, afectando las cáscaras de los huevos y dañando su desarrollo. El objetivo de este trabajo fue, a través de herramientas de biología de sistemas, comprender cómo los organoclorados actúan en el organismo de las aves. A través de una revisión bibliográfica se incluyeron dos compuestos, DDT y TCDD. Estos fue ron prospectos en la plataforma STITCH 5.0. Las subredes encontradas fueron aumentadas en 100 interacciones en la plataforma STRING 10.5 y unidas por la herramienta Merge del programa Cytoscape 3.4.0, usando el modelo experimental Gallus gallus. En la red resultante se analizaron la clusterización, la ontología génica y la centralidad. La red resultante presentó 137 nudos y 1.417 interacciones. El análisis de clusterización indicó 4 clusters, siendo que el análisis y ontología génica apuntó procesos biológicos ligados a la señalización y al desarrollo morfológico. El estudio de centralidad apuntó a ESR1 y HSP90AB1 como los hubs-bottle- neck proteínas que estaban involucradas en la vía de recepción de estrógeno y en el transporte de calcio. De acuerdo con los resultados podemos inferir que las proteínas HSP90 tienen su expresión aumentada, en aves contaminadas con pesticidas organoclo rados, favoreciendo la interacción entre ESRI y DDT / TCDD. Con ello, la interacción ESRI y la hormona estrógeno se compromete perjudicando el transporte de calcio y consecuentemente la formación de la cáscara del huevo en aves expuestas. La expresión de proteínas de choque térmico ha sido asociada a varios aspectos de la reproducción en muchas especies, sin embargo, una asociación entre HSP90 y el síndrome de la cáscara fina del huevo fue identificada por primera vez en este experimento in silico.


Subject(s)
Animals , Raptors/abnormalities , Egg Shell/abnormalities , Insecticides, Organochlorine/adverse effects , Computer Simulation , Gene Ontology
17.
Article in English | WPRIM | ID: wpr-811113

ABSTRACT

BACKGROUND: Platelet-rich plasma (PRP) is a plasma component of autologous blood containing a high concentration of platelets. PRP is used to promote healing of damaged tissues. However, there are not many studies on the composition and expression patterns of active proteins in PRP. The purpose of this study was to identify unknown factors that contribute to tissue healing by proteomic analysis of proteins in PRP.METHODS: Three men in their 30s with no basal disease participated in this study. All identified proteins were classified for tissue healing-related functions on the basis of the gene ontology analysis of adhesion molecule with Ig-like domain 2 (AmiGO2). PRP was prepared by using the ACP kit and GPS III kit.RESULTS: We identified a total of 125 proteins related to wound healing, along with three proteins for angiogenesis involved in wound healing, two proteins for fibroblast migration, four proteins for collagen biosynthesis process, two proteins for glycosaminoglycan biosynthesis process, and 13 proteins for glycosaminoglycan binding. So, in addition to the growth factors that have been already known to be involved in tissue healing, 25 new proteins were identified.CONCLUSIONS: We identified the unknown proteins associated with tissue healing in PRP. Our findings may serve as a foundation for the establishment of basic medical evidence for PRP applications.


Subject(s)
Classification , Collagen , Fibroblasts , Gene Ontology , Humans , Intercellular Signaling Peptides and Proteins , Male , Plasma , Platelet-Rich Plasma , Proteome , Wound Healing
18.
Braz. j. med. biol. res ; 53(9): 0-0, 2020. tab, graf
Article in English | LILACS, ColecionaSUS | ID: biblio-1132553

ABSTRACT

Myocardial ischemia/reperfusion (MI/R) injury is a complex phenomenon that causes severe damage to the myocardium. However, the potential molecular mechanisms of MI/R injury have not been fully clarified. We identified potential molecular mechanisms and therapeutic targets in MI/R injury through analysis of Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were found between MI/R injury and normal samples, and overlapping DEGs were found between GSE61592 and GSE67308. Gene Ontology (GO) and pathway analysis were performed for overlapping DEGs by Database for Annotation, Visualization and Integration Discovery (DAVID). Then, a network of protein-protein interaction (PPI) was constructed through the Search Tool for the Retrieval of Interacting Genes (STRING) database. Potential microRNAs (miRNAs) and therapeutic small molecules were screened out using microRNA.org database and the Comparative Toxicogenomics database (CTD), respectively. Finally, we identified 21 overlapping DEGs related to MI/R injury. These DEGs were significantly enriched in IL-17 signaling pathway, cytosolic DNA-sensing pathway, chemokine signaling, and cytokine-cytokine receptor interaction pathway. According to the degree in the PPI network, CCL2, LCN2, HP, CCL7, HMOX1, CCL4, and S100A8 were found to be hub genes. Furthermore, we identified potential miRNAs (miR-24-3p, miR-26b-5p, miR-2861, miR-217, miR-4251, and miR-124-3p) and therapeutic small molecules like ozone, troglitazone, rosiglitazone, and n-3 polyunsaturated fatty acids for MI/R injury. These results identified hub genes and potential small molecule drugs, which could contribute to the understanding of molecular mechanisms and treatment for MI/R injury.


Subject(s)
Myocardial Reperfusion Injury , MicroRNAs , Computational Biology , Gene Expression Profiling , Gene Regulatory Networks , Protein Interaction Maps , Gene Ontology
19.
Article in English | WPRIM | ID: wpr-827442

ABSTRACT

OBJECTIVE@#To seek potential Chinese herbal medicine (CHM) for the treatment of coronavirus disease 2019 (COVID-19) through the molecular docking of the medicine with SARS-CoV-2 3CL hydrolytic enzyme and the angiotensin converting enzyme II(ACE2) as receptors, using computer virtual screening technique, so as to provide a basis for combination forecasting.@*METHODS@#The molecular docking of CHM with the SARS-Cov-2 3CL hydrolase and the ACE2 converting enzyme, which were taken as the targets, was achieved by the Autodock Vina software. The CHM monomers acting on 3CLpro and ACE2 receptors were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, the active ingredients were selected, and the key CHMs and compounds were speculated. Based on the perspective of network pharmacology, the chemical-target network was constructed, and the functional enrichment analysis of gene ontology and the pathway enrichment analysis of Kyoto encyclopedia of genes and genomes were carried out by DAVID to speculate about the mechanism of action of the core drug pairs.@*RESULTS@#There are 6 small molecule compounds that have the optimal binding energy with the two target proteins. Among 238 potential anti-COVID-19 herbs screened in total, 16 kinds of CHM containing the most active ingredients, and 5 candidate anti-COVID-19 herbs that had been used in high frequency, as well as a core drug pair, namely, Forsythiae Fructus-Lonicerae Japonicae Flos were selected.@*CONCLUSION@#The core drug pair of Forsythiae Fructus-Lonicerae Japonicae Flos containing multiple components and targets is easy to combine with 3CLpro and ACE2, and exerts an anti-COVID-19 pneumonia effect through multi-component and multi-target, and plays the role of anti-COVID-19 pneumonia in multi-pathway.


Subject(s)
Betacoronavirus , Metabolism , Computer Simulation , Coronavirus Infections , Drug Therapy , Drugs, Chinese Herbal , Therapeutic Uses , Gene Ontology , Humans , Molecular Docking Simulation , Pandemics , Peptidyl-Dipeptidase A , Metabolism , Pneumonia, Viral , Drug Therapy , Thermodynamics
20.
Chinese Journal of Cardiology ; (12): 587-592, 2020.
Article in Chinese | WPRIM | ID: wpr-941086

ABSTRACT

Objective: Present study investigated the mechanism of heart failure associated with coronavirus infection and predicted potential effective therapeutic drugs against heart failure associated with coronavirus infection. Methods: Coronavirus and heart failure were searched in the Gene Expression Omnibus (GEO) and omics data were selected to meet experimental requirements. Differentially expressed genes were analyzed using the Limma package in R language to screen for differentially expressed genes. The two sets of differential genes were introduced into the R language cluster Profiler package for gene ontology (GO) and Kyoto gene and genome encyclopedia (KEGG) pathway enrichment analysis. Two sets of intersections were taken. A protein interaction network was constructed for all differentially expressed genes using STRING database and core genes were screened. Finally, the apparently accurate treatment prediction platform (EpiMed) independently developed by the team was used to predict the therapeutic drug. Results: The GSE59185 coronavirus data set was searched and screened in the GEO database, and divided into wt group, ΔE group, Δ3 group, Δ5 group according to different subtypes, and compared with control group. After the difference analysis, 191 up-regulated genes and 18 down-regulated genes were defined. The GEO126062 heart failure data set was retrieved and screened from the GEO database. A total of 495 differentially expressed genes were screened, of which 165 were up-regulated and 330 were down-regulated. Correlation analysis of differentially expressed genes between coronavirus and heart failure was performed. After cross processing, there were 20 GO entries, which were mainly enriched in virus response, virus defense response, type Ⅰ interferon response, γ interferon regulation, innate immune response regulation, negative regulation of virus life cycle, replication regulation of viral genome, etc. There were 5 KEGG pathways, mainly interacting with tumor necrosis factor (TNF) signaling pathway, interleukin (IL)-17 signaling pathway, cytokine and receptor interaction, Toll-like receptor signaling pathway, human giant cells viral infection related. All differentially expressed genes were introduced into the STRING online analysis website for protein interaction network analysis, and core genes such as signal transducer and activator of transcription 3, IL-10, IL17, TNF, interferon regulatory factor 9, 2'-5'-oligoadenylate synthetase 1, mitogen-activated protein kinase 3, radical s-adenosyl methionine domain containing 2, c-x-c motif chemokine ligand 10, caspase 3 and other genes were screened. The drugs predicted by EpiMed's apparent precision treatment prediction platform for disease-drug association analysis were mainly TNF-α inhibitors, resveratrol, ritonavir, paeony, retinoic acid, forsythia, and houttuynia cordata. Conclusions: The abnormal activation of multiple inflammatory pathways may be the cause of heart failure in patients after coronavirus infection. Resveratrol, ritonavir, retinoic acid, amaranth, forsythia, houttuynia may have therapeutic effects. Future basic and clinical research is warranted to validate present results and hypothesis.


Subject(s)
Betacoronavirus , COVID-19 , Computational Biology , Coronavirus Infections/complications , Gene Expression Profiling , Gene Ontology , Heart Failure/virology , Humans , Pandemics , Pneumonia, Viral/complications , SARS-CoV-2
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