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Eukaryotic and prokaryotic cell genomes exhibit multiple microsatellites. In this study, we characterized microsatellites in genomes and genes of Nanorana parkeri and Xenopus laevis. This characterization was used for gene ontology (GO) analysis of coding sequences (CDS). Compared to the genome of N. parkeri, the genome of X. laevis is larger and contains more number of microsatellites, but the diversity of both species are similar. Trinucleotide repeats in the genome of N. parkeri and dinucleotide and tetranucleotide repeats in the genome of X. laevis were the most diverse. In both the species, diversity of microsatellites was highest in intergenic regions, followed by intron and exon regions, and lowest in coding regions. Microsatellites in CDS are thus subject to higher selective pressure. Many microsatellites are concentrated upstream and downstream of genes in both species, suggesting suppression of repeats in the middle of protein–CDS. Repeats are enriched in regions near gene termini purely due to the biophysical constraints of protein structure. In GO analysis, two and five unique GO terms, only found in N. parkeri and X. laevis, respectively, indicate advantageous mutations during species evolution. Biological process, cellular component and molecular function ontology reflected in the GO analysis predicted that the microsatellites located in CDS can alter protein function and may provide a molecular basis for species adaptation to new and changing environments
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Objective To investigate the radioresistance factors in non-small cell lung cancer (NSCLC)cell line A549, and provide new targets for radiotherapy sensitization drugs development. Methods Establish the stable model of radioresistant NSCLC cell line A549 under irradiation; investigate the whole-transcriptome alteration of radioresistance cell line and radiosensitive cell line using gene expression microarray; perform bioinformatic approaches gene ontology (GO) analysis and Pathway analysis. Results The expression profile microarray showed that 1410 differentially expressed genes (733 up-regulated and 677 down-regulated) were detected in resistant and sensitive strains; GO analysis showed that it was mainly related to cell cycle and DNA replication; Pathway significant enrichment analysis showed that mitogen-activated protein kiase(MAPK) signaling pathway, phosphatidylinositol 3-kinase/protein kinase B(PI3K/Akt) signaling pathway, were mainly associated with radioresistance. Conclusion Multiple genes and signaling pathways are involved in radioresistance, further studies are needed to investigate the radioresistance factors, which could provide new targets for radiotherapy sensitization drugs development.
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Objective@#To investigate the expression and function of the TNF signaling pathway in the early stage of orthodontic tooth movement with periodontitis and to provide evidence to study the early inflammatory response in patients with periodontitis orthodontic treatment. @*Methods@#Sixteen SD rats were randomly divided into four groups: group A--12 h of orthodontic tooth movement of the bilateral maxillary first molars in rats with periodontitis; group B--periodontitis model of the bilateral maxillary first molars without orthodontic tooth movement; group C--12 h of orthodontic tooth movement of the same teeth in rats with healthy periodontium; group D--control group without operations. The bilateral maxillary first molars and surrounding periodontal tissue of each group were collected for gene chip detection. Pathway enrichment analysis, qRT-PCR and GO (gene ontology) analysis were performed to identify differential genes involved in the TNF signaling pathway. @*Results @#Gene chip results showed that the TNF signaling pathway was significantly upregulated in group A, group B and group C (P <0.01). Among the differential genes involved in the pathway, 28 were upregulated and 5 were downregulated in group A, 12 were upregulated and 4 were downregulated in group B, and 12 were upregulated and 1 was downregulated in group C (P <0.05). The most significant GO items included "response to lipopolysaccharide", "inflammatory response", "positive regulation of NF-κB transcription factor activity", "positive regulation of NF-κB import into nucleus" and "response to hypoxia"(P <0.001). qRT-PCR results showed no significant difference in TNF-α mRNA expression in group C compared with that in group D, TNF-α was upregulated in both groups A and B (P <0.01), and mRNA expression decreased in the following order: group A > group B > group C (P <0.05). Compared with group D, the expression levels of prostaglandin-endoperoxide synthase 2 (PTGS2) and interleukin-6 ( IL-6) in groups A, B and C were significantly upregulated (P <0.05), but the expression levels of PTGS2 and IL-6 in group A were lower than those in group B (P < 0.05). @*Conclusion@#The TNF signaling pathway is activated in the early stage of orthodontic tooth movement in rats with periodontitis. The pathway products participate in many biological processes and play an important role in the inflammatory response and bone absorption.
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@# Objective: To identify the differentially expressed genes (DEGs) between hepatocellular carcinoma (HCC) tissues and normal liver tissues by bioinformatic methods, and to explore the intrinsic mechanism of these candidate genes involving in the occurrence and development of HCC from transcriptome level as well as the clinical significance of their associations with the prognosis of HCC patients. Methods: Gene expression profiles of GSE45267, GSE64041, GSE84402 and TCGA were downloaded from GEO (Gene Expression Omnibus) and TCGA(The Cancer GenomeAtlas), respectively. R software and Bioconductor packages were used to identify the DEGs between HCC tissues and para-cancer tissues, and then Gene Ontology (GO) Enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, Protein-Protein Interaction (PPI) network analysis and survival analysis were performed. Results: Forty-six up-regulated genes and 154 down-regulated genes were screened out,and GO enrichment analysis showed that these DEGs were mainly related to cell division, proliferation, cycle regulation, oxidation-reduction process and certain metabolic pathways. KEGG pathway analysis revealed that DEGs were mainly involved in tryptophan metabolism, retinol metabolism and other metabolic pathways as well as p53 pathway. Over-expression of a panel of up-regulated genes (CCNA2, CDK1, DLGAP5, KIF20A, KPNA2 and MELK) was shown to be significantly negatively correlated with the prognosis of HCC patients in the TCGA dataset (all P<0.01). Conclusion: A set of up-regulated hub genes that are negatively correlated with prognosis will provide potential guiding value for the clinical research on the diagnosis and treatment of HCC.
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Objective To explore the biological function of intercellular adhesion molecule-1 (ICAM-1) gene in coronary heart disease (CHD) and to establish a primary regulatory network mediated by ICAM-1 gene. Methods The databases were searched from January 1st 2006 to December 31st 2018, including Wanfang, CNKI, VIP, Google scholar and PubMed databases for published researches on clinical study of CHD gene ICAM-1. The experimental group was CHD patients, and the control group was healthy people. Meta-analysis was employed to analyze the relationship between ICAM-1 gene and CHD. Gene Ontology (GO) and KEGG Pathway database were employed to conduct function annotation and pathway analysis. Results A total of 8 papers were enrolled into this analysis, Meta-analysis showed that the level of ICAM-1 in the experimental group was significantly higher than that in the control group [mean difference (MD) = 15.29, 95% confidence interval (95%CI) = 10.95-19.62, P < 0.000 01], surface ICAM-1 was significantly related with CHD. The GO analysis results showed that ICAM-1 molecular function mainly involved virus receptor activity, receptor activity, transmembrane signal receptor activity, protein binding, etc.; cell components mainly involve plasma membrane integral components, immune synapses, plasma membrane, etc.; biological processes mainly involve the positive regulation of cell adhesion, leukocyte adhesion, leukocyte migration and leukocyte adhesion, etc. A primary CHD regulatory network mediated by ICAM-1 gene was established based on KEGG Pathway database, and ICAM-1 was mainly expressed in endothelial cells, and further regulated the occurrence and development of CHD by promoting the proliferation of leukocytes. Conclusions ICAM-1 may regulate the occurrence and development of CHD by regulating the related biological processes of leukocytes. The successful establishment of the ICAM-1 mediated CHD regulatory network can lay a theoretical foundation for further exploring the specific regulatory role of ICAM-1 and other related genes in CHD occurrence.
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OBJECTIVE To explore the hypolipidemic mechanisms of the total phenylpropanoid glycosides from Ligustrum robustum (Roxb.)Blume (LRTPG)in hamsters using proteomics technique. METHODS The hamsters were fed with a high fat diet to induce hyperlipidemia.Then LRTPG of high (1.2 g·kg-1),medium(0.6 g·kg-1)and low(0.3 g·kg-1)doses were administrated daily for 4 weeks.Then the concentrations of plasma and hepatic lipids were determined using enzymic methods.The total protein was extracted from livers of the model group and the group treated with the high dose of LRTPG for label-free quantitative proteomics. RESULTS LRTPG significantly reduced the concentrations of plasma and hepatic lipids in hamsters fed a high fat diet. The proteomics data showed that a total of 2231 proteins were identified,and 549 proteins were found to be differentially expressed between the model group and the group treated with LRTPG.Among the 549 proteins,93 proteins were up-regulated and 59 proteins were down-regulated, and 397 proteins were absent or not. And some of these proteins were much related to the lipid metabolism. Further, gene ontology (GO) analysis indicated metabolic process, transport, oxidation-reduction process, phosphorylation, signal transduction, lipid metabolic process were the main biological processes that those differentially expressed proteins participated. KEGG pathway analysis showed that those proteins were involved in several metabolic pathways including oxidative phosphorylation,non-alcoholic fatty liver disease(NAFLD),PI3K-Akt signaling pathway, cAMP signaling pathway, cGMP-PKG signaling pathway. CONCLUSION The proteomics study could provide valuable clues to help us to understand the hypolipidemic mechanisms of LRTPG much better.
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Studies have shown that some plant-specific NAC (NAM, ATAF1/2, CUC2) transcription factors may increase plants resistance to stress. We screened the genes differentially expressed in transgenic SlNAC1 Arabidopsis compared to the wild type by cDNA microarry, to provide scientific basis for studying the genes related to abiotic stress responses in transgenic Arabidopsis. There were 3 046 genes differentially expressed more than twice in the total 43 604 genes of transgenic SlNAC1 Arabidopsis. Gene ontology analysis was used on genes differentially expressed more than five-fold. Genes relevant to cellular components occupied 33.05%, genes correlated with molecular function accounted for 33.95% and genes pertinent to biological process constituted a 33.00% portion. The genes differentially expressed more than twice were processed through kyoto encyclopedia of genes and genomes pathways enrichment (KEGG) analysis. The total 2 431 genes were involved in 88 different signaling pathways. The screened genes related to abiotic stress responses provide direction and theoretical support for the following research on the downstream genes regulated by NAC and construction of the regulatory networks.
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Objective: To identify the changes of gene expression profiles and metastasis ability of rat hepatoma cell line McA-RH7777 after sublethal irradiation, and to explore the underlying molecular mechanism. Methods: Rat hepatoma McA-RH7777 cells were received single exposure of 6 Gy X-ray. Then, the remaining McA-RH7777 cells were continuously passaged and named as McARH7777- 6Gy. The gene expression profiles of McA-RH7777 and McA-RH7777-6Gy cells were detected by gene microarray and compared. Subsequent bioinformatic analysis of the genes with significant changes in expression levels were performed by DAVID software (including GO-analysis and KEGG-analysis). The mRNA expression levels of tissue inhibitor of metalloproteinase 2 (TIMP2), SMAD family member 2 (SMAD2) and MET proto-oncogene in McA-RH7777 and McA-RH7777-6Gy cells were detected by real-time fluorescent quantitative PCR to verify the difference in gene expression profiles of the two cells. The migration and invasion abilities of McA-RH7777 and McA-RH7777-6Gy cells were detected by scratch wound healing assay and Transwell chamber assay, respectively. Results: The gene microarray showed that the expressions of a series of tumor-related genes were changed in McA-RH7777-6Gy cells as compared with wild-type McA-RH7777 cells. Real-time fluorescent quantitative PCR showed that the relative expression levels of TIMP 2, SMAD 2 and MET in McA-RH7777-6Gy cells were raised by 13.000, 14.516 and 6.384 times as compared with McA-RH7777 cells, respectively. GO analysis showed that the remarkably changed genes mainly located in tumor metastasis-associated biological processes, such as Ras protein signal transduction, cell cycle arrest, cell migration, cell adhesion, negative regulation of apoptotic process, positive regulation of cell proliferation, positive regulation of epithelial to mesenchymal transition and positive regulation of MAP kinase activity. KEGG analysis showed these genes mainly involved in proteoglycans signaling pathway, phosphoinositide-3 kinase (PI3K)-protein kinase B (PKB, Akt) signaling pathway, viral carcinogenesis pathway, FoxO signaling pathway, Rap1 signaling pathway, Hippo signaling pathway, Ras signaling pathway, etc. The scratch healing and Transwell chamber tests showed that the migration and invasion abilities of McA-RH7777-6Gy cells were significantly enhanced as compared with McA-RH7777 cells (both P < 0.001). Conclusion: After sublethal radiation, the migration and invasion abilities of hepatoma cells are significantly enhanced, which may be related to the changes of gene expressions in metastasis-associated pathways.
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OBJECTIVE:To study the effect of Shenfu injection(SFI)on the expression profile of myocardial miRNA in rats with chronic congestive heart failure (referring to heart failure). METHODS:40 rats were randomly divided into sham operation group (normal saline,ip),model group (normal saline,ip),valsartan group (positive control,10 mg/kg,ig) and SFI group (0.75 mL/kg,im),10 in each group. Except for sham operation group,another groups were reduced heart failure. After modeling, rats in other groups received related medicines,once a day. Affymetrix miRNA V4.0 chip technology was conducted to analyze the miRNA expression in myocardial tissue of rats with heart failure after administration for 28 d,and screen the miRNA on common differential expression in myocardial tissue of rats in each group. The miRNA associated with heart failure was analyzed by thresh-old of differential gene expression multiple value greater than or equal to 1.1. Gene Ontology (GO) analysis was used to analyze functional classification and biological signaling pathway of differentially expressed genes. RESULTS:There were totally 29 miR-Nas on common differential expression and 7 miRNAs associated with heart failure (rno-miR-30c-1-3p, rno-miR-125b-5p, rno-miR-133a-5p,rno-miR-199a-5p,rno-miR-221-3p,rno-miR-146a-5p and rno-miR-1-3p). SFI can significantly downregulate the expressions of rno-miR-125b-5p,rno-miR-133a-5p,rno-miR-221-3p,rno-miR-1-3p in myocardial tissue of rats (P<0.05 or P<0.01). Results of GO analysis showed,miRNAs on differential expression were mainly related to signal transduction,cytoplasm and nucleotide binding. CONCLUSIONS:SFI plays the role of anti-heart failure by participating in the downregulation of miRNAs associated with heart failure process and then affecting related signal pathways transduction after the combination of cyto-plasm and nucleotide.