Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new op...Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new opportunity for investigating diagnosis,treatment,and prognosis of spinal cord injury.However,differentially expressed genes are not consistent among studies,and many key genes and signaling pathways have not yet been accurately studied.GSE5296 was retrieved from the Gene Expression Omnibus DataSet.Differentially expressed genes were obtained using R/Bioconductor software(expression changed at least two-fold;P < 0.05).Database for Annotation,Visualization and Integrated Discovery was used for functional annotation of differentially expressed genes and Animal Transcription Factor Database for predicting potential transcription factors.The resulting transcription regulatory protein interaction network was mapped to screen representative genes and investigate their diagnostic and therapeutic value for disease.In total,this study identified 109 genes that were upregulated and 30 that were downregulated at 0.5,4,and 24 hours,and 3,7,and 28 days after spinal cord injury.The number of downregulated genes was smaller than the number of upregulated genes at each time point.Database for Annotation,Visualization and Integrated Discovery analysis found that many inflammation-related pathways were upregulated in injured spinal cord.Additionally,expression levels of these inflammation-related genes were maintained for at least 28 days.Moreover,399 regulation modes and 77 nodes were shown in the protein-protein interaction network of upregulated differentially expressed genes.Among the 10 upregulated differentially expressed genes with the highest degrees of distribution,six genes were transcription factors.Among these transcription factors,ATF3 showed the greatest change.ATF3 was upregulated within 30 minutes,and its expression levels remained high at28 days after spinal cord injury.These key genes screened by bioin展开更多
AIM: To investigate the effects of oxymatrine on the gene expression profile of hepatic stellate cell (HSC) and provide novel insights into the mechanism of oxymatrine against hepatic fibrosis. Methods: HSC was isolat...AIM: To investigate the effects of oxymatrine on the gene expression profile of hepatic stellate cell (HSC) and provide novel insights into the mechanism of oxymatrine against hepatic fibrosis. Methods: HSC was isolated from normal SD by in situ perfusion of collagenase and pronase and density Nycodenz gradient centrifugation. MTT colorimetry was used to study the effect of oxymatrine on the proliferation of HSC. Total RNA and mRNA of quiescent HSC, culture-activated HSC and oxymatrine treated HSC were extracted. Effect of oxymatrine on HSC gene expression profile was detected by oligonucleotide microarray analysis with Affymetrix gene chip rat U230A. Differentially expressed genes were annotated with Gene Ontology (GO) and analyzed with Kyoto encyclopedia of genes and genomes (KEGG) pathway using the Database for Annotation, Visualization and Integrated Discovery. Results: Oxymatrine could inhibit the proliferation of HSC in a dose-dependent manner. A total of 4641 differentially expressed genes were identified by cDNA chip between activated and quiescent HSC, among which 2702 genes were upregulated, and 1939 genes were down-regulated in activated HSC. cDNA microarray uncovered downregulation of 56 genes in response to oxymatrine, the representative genes including alpha 2 type I procollagen, alpha-1 type I collagen, tissue inhibitor of metalloproteinase 1, interleukin 1 beta, early growth response 1, chemokine ligand 2, chemokine ligand 1, CTGF, TGFβ1. The most enriched GO terms included response to wounding, inflammatory response, cell migration, cell motility, wound healing, TGFβ receptor signaling pathway. KEGG pathway analysis revealed that oxymatrine affected the ECM-receptor interaction, focal adhesion, cytokine-cytokine recaptor interaction, TGFβ signaling pathway, MAPK signaling pathway. There were 37 genes upregulated significantly following oxymatrine treatment. The most enriched GO terms included oxidation reduction, negative regulation of lipoprotein oxidation, regulation of lipoprotein oxidation展开更多
Acoustic communication is essential for anuran survival and reproduction, and masking background noise can affect the effective acoustic communication. The larger odorous frog(Odorrana graminea) inhabits noise montane...Acoustic communication is essential for anuran survival and reproduction, and masking background noise can affect the effective acoustic communication. The larger odorous frog(Odorrana graminea) inhabits noise montane streams, and it has shown an ultrasound communication adaptation. However, the molecular mechanism underlying their ultrasonic hearing adaptation remains unknown. To characterize and investigate the molecular characteristics and evolution of the high-frequency hearing-sensitive gene(KCNQ4) in O. graminea, termed as OgKCNQ4, the rapid amplification of cDNA ends(RACE) was performed to amplify the cDNA of OgKCNQ4. Different bioinformatics analyses were used to investigate the molecular characteristics. Multiple nucleotide and amino acid sequence alignment were conducted, and phylogenies were reconstructed under the maximum likelihood and Bayesian approaches. The full-length cDNA of OgKCNQ4 was 2065 bp, and the open reading frame(ORF) was 2046 bp encoding for a putative protein with 681 amino acids. The relative molecular weight of OgKCNQ4 was 76.453 kD and the putative PI was 9.69. Secondary structure prediction analyses suggested 42.29% alpha helixes and 43.76% random coils in OgKCNQ4. Gene homology and Phylogenetic analyses revealed the closest relationship between OgKCNQ4 and KCNQ4 of Nanorana parkeri with 96.9% similarity and 95.0% identity. We first determined the full-length cDNA of OgKCNQ4 and the results here could provide foundations for further study on the evolution of KCNQ4 and its relationship to ultrasonic communication in amphibians.展开更多
基金supported by the Natural Science Foundation of Shaanxi Province of China,No.2018JQ8029(to LG)
文摘Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new opportunity for investigating diagnosis,treatment,and prognosis of spinal cord injury.However,differentially expressed genes are not consistent among studies,and many key genes and signaling pathways have not yet been accurately studied.GSE5296 was retrieved from the Gene Expression Omnibus DataSet.Differentially expressed genes were obtained using R/Bioconductor software(expression changed at least two-fold;P < 0.05).Database for Annotation,Visualization and Integrated Discovery was used for functional annotation of differentially expressed genes and Animal Transcription Factor Database for predicting potential transcription factors.The resulting transcription regulatory protein interaction network was mapped to screen representative genes and investigate their diagnostic and therapeutic value for disease.In total,this study identified 109 genes that were upregulated and 30 that were downregulated at 0.5,4,and 24 hours,and 3,7,and 28 days after spinal cord injury.The number of downregulated genes was smaller than the number of upregulated genes at each time point.Database for Annotation,Visualization and Integrated Discovery analysis found that many inflammation-related pathways were upregulated in injured spinal cord.Additionally,expression levels of these inflammation-related genes were maintained for at least 28 days.Moreover,399 regulation modes and 77 nodes were shown in the protein-protein interaction network of upregulated differentially expressed genes.Among the 10 upregulated differentially expressed genes with the highest degrees of distribution,six genes were transcription factors.Among these transcription factors,ATF3 showed the greatest change.ATF3 was upregulated within 30 minutes,and its expression levels remained high at28 days after spinal cord injury.These key genes screened by bioin
文摘AIM: To investigate the effects of oxymatrine on the gene expression profile of hepatic stellate cell (HSC) and provide novel insights into the mechanism of oxymatrine against hepatic fibrosis. Methods: HSC was isolated from normal SD by in situ perfusion of collagenase and pronase and density Nycodenz gradient centrifugation. MTT colorimetry was used to study the effect of oxymatrine on the proliferation of HSC. Total RNA and mRNA of quiescent HSC, culture-activated HSC and oxymatrine treated HSC were extracted. Effect of oxymatrine on HSC gene expression profile was detected by oligonucleotide microarray analysis with Affymetrix gene chip rat U230A. Differentially expressed genes were annotated with Gene Ontology (GO) and analyzed with Kyoto encyclopedia of genes and genomes (KEGG) pathway using the Database for Annotation, Visualization and Integrated Discovery. Results: Oxymatrine could inhibit the proliferation of HSC in a dose-dependent manner. A total of 4641 differentially expressed genes were identified by cDNA chip between activated and quiescent HSC, among which 2702 genes were upregulated, and 1939 genes were down-regulated in activated HSC. cDNA microarray uncovered downregulation of 56 genes in response to oxymatrine, the representative genes including alpha 2 type I procollagen, alpha-1 type I collagen, tissue inhibitor of metalloproteinase 1, interleukin 1 beta, early growth response 1, chemokine ligand 2, chemokine ligand 1, CTGF, TGFβ1. The most enriched GO terms included response to wounding, inflammatory response, cell migration, cell motility, wound healing, TGFβ receptor signaling pathway. KEGG pathway analysis revealed that oxymatrine affected the ECM-receptor interaction, focal adhesion, cytokine-cytokine recaptor interaction, TGFβ signaling pathway, MAPK signaling pathway. There were 37 genes upregulated significantly following oxymatrine treatment. The most enriched GO terms included oxidation reduction, negative regulation of lipoprotein oxidation, regulation of lipoprotein oxidation
基金supported by the National Natural Science Foundation of China to ZC (Grants U1404306 and 31601848), XHC (Grant 31572245, 31372164 and 31872220)the Project funded by China Postdoctoral Science Foundation to ZC (2016M600580)+1 种基金the Excellent Young Scholars Fund of HNNU to ZC (YQ201706)the Young Backbone Teachers Fund of HNNU to ZC
文摘Acoustic communication is essential for anuran survival and reproduction, and masking background noise can affect the effective acoustic communication. The larger odorous frog(Odorrana graminea) inhabits noise montane streams, and it has shown an ultrasound communication adaptation. However, the molecular mechanism underlying their ultrasonic hearing adaptation remains unknown. To characterize and investigate the molecular characteristics and evolution of the high-frequency hearing-sensitive gene(KCNQ4) in O. graminea, termed as OgKCNQ4, the rapid amplification of cDNA ends(RACE) was performed to amplify the cDNA of OgKCNQ4. Different bioinformatics analyses were used to investigate the molecular characteristics. Multiple nucleotide and amino acid sequence alignment were conducted, and phylogenies were reconstructed under the maximum likelihood and Bayesian approaches. The full-length cDNA of OgKCNQ4 was 2065 bp, and the open reading frame(ORF) was 2046 bp encoding for a putative protein with 681 amino acids. The relative molecular weight of OgKCNQ4 was 76.453 kD and the putative PI was 9.69. Secondary structure prediction analyses suggested 42.29% alpha helixes and 43.76% random coils in OgKCNQ4. Gene homology and Phylogenetic analyses revealed the closest relationship between OgKCNQ4 and KCNQ4 of Nanorana parkeri with 96.9% similarity and 95.0% identity. We first determined the full-length cDNA of OgKCNQ4 and the results here could provide foundations for further study on the evolution of KCNQ4 and its relationship to ultrasonic communication in amphibians.
