【目的】本研究旨在通过差异表达基因(differentially expressed gene,DEG)分析以及毒力因子和其他侵染相关因子分析,在转录组水平揭示东方蜜蜂微孢子虫Nosema ceranae侵染意大利蜜蜂Apis mellifera ligustica的分子机制。【方法】基于...【目的】本研究旨在通过差异表达基因(differentially expressed gene,DEG)分析以及毒力因子和其他侵染相关因子分析,在转录组水平揭示东方蜜蜂微孢子虫Nosema ceranae侵染意大利蜜蜂Apis mellifera ligustica的分子机制。【方法】基于前期已获得高质量的东方蜜蜂微孢子虫纯化孢子(NcCK)及侵染意大利蜜蜂工蜂7和10 d的东方蜜蜂微孢子虫(分别为NcT1和NcT2)转录组数据,根据P≤0.05且|log 2(Fold change)|≥1的标准,通过比较分析筛选出NcCK vs NcT1,NcCK vs NcT2和NcT1 vs NcT2比较组的DEG。通过相关生物信息学软件对上述DEG进行Venn分析、GO分类和KEGG代谢通路富集分析。根据Nr和KEGG数据库注释信息和相关文献进行对东方蜜蜂微孢子虫的毒力因子和侵染相关因子的统计和分析。通过RT-qPCR验证转录组数据及DEG表达趋势。【结果】从NcCK vs NcT1,NcCK vs NcT2和NcT1 vs NcT2比较组分别鉴定出1397,1497和52个DEG。Venn分析结果显示各比较组共有的上调和下调基因分别为10和1个。GO分类结果显示,NcCK vs NcT1和NcCK vs NcT2中DEG富集数最多的功能条目为代谢进程、细胞进程、单组织进程、细胞、细胞组件、细胞器、催化活性和结合,而NcT1 vs NcT2中DEG富集数最多的是代谢进程、细胞进程、单组织进程、催化活性和结合。KEGG代谢通路富集分析结果显示,NcCK vs NcT1和NcCK vs NcT2中DEG分别富集到80和79条通路;富集在糖酵解/糖异生和MAPK信号通路的上调基因数量多于下调基因。毒力因子分析结果显示,孢壁蛋白9基因和孢壁蛋白12基因在NcCK vs NcT1和NcCK vs NcT2中均下调表达,孢壁蛋白8基因仅在NcCK vs NcT1中表达量下调;此外孢壁蛋白前体基因、孢壁和锚定盘复合蛋白基因、几丁质合酶基因、极管蛋白基因、蓖麻毒素B凝集素基因的表达水平在NcCK vs NcT1和NcCK vs NcT2中表现为上调。侵染相关因子分析结果表明,糖酵解途径的3个关键酶基�展开更多
Objective: To explore the action mechanisms of Huangqi Decoction Granules(黄芪汤颗粒剂, HQDG) on hepatitis B cirrhosis. Methods: A total of 85 patients with hepatitis B cirrhosis were randomly divided into HQDG group(...Objective: To explore the action mechanisms of Huangqi Decoction Granules(黄芪汤颗粒剂, HQDG) on hepatitis B cirrhosis. Methods: A total of 85 patients with hepatitis B cirrhosis were randomly divided into HQDG group(42 cases) and control group(43 cases) by a random number table and were treated with HQDG or placebo for 48 weeks(6 g per times and orally for 3 times a day), respectively. After RNA-sequencing of serum samples extracted from the patients, the differentially expressed genes(DEGs) in HQDG and control groups before and after treatment were separately screened. The DEGs were then performed pathway enrichment analysis and proteinprotein interaction(PPI) network analysis. The expression levels of key genes were detected by quantitative realtime polymerase chain reaction(qRT-PCR). Results: After the investigation, 4 and 3 cases were respectively excluded from HQD and control groups because of the incomplete data. Additionally, 3 and 5 cases were lost to follow up in HQD and control groups, respectively. Finally, a total of 70 cases with good compliance were included for further DEGs analysis. A total of 1,070 DEGs(including 455 up-regulated genes and 615 down-regulated genes) in HQDG group and 227 DEGs(including 164 up-regulated genes and 63 down-regulated genes) in the control group were identified after treatment. Compared with the control group, 1,043 DEGs were specific in HQDG group. Besides, 1 up-regulated transcription factor(TF, such as GLI family zinc finger 1, GLI1) and 25 down-regulated TFs(such as drosophila mothers against decapentaplegic proteinfamily member 2, SMAD2) were identified. Pathway enrichment analysis showed that down-regulated Ras homolog gene family member A(RHOA) was enriched in pathogenic Escherichia coli infection. In the PPI network, up-regulated epidermal growth factor receptor(EGFR), and down-regulated cell division cycle 42(CDC42) as well as v-akt murine thymoma viral oncogene homolog 1(AKT1) had higher degrees. Moreover, long non-coding RNAs(lncR NA) growth arrest-sp展开更多
文摘【目的】本研究旨在通过差异表达基因(differentially expressed gene,DEG)分析以及毒力因子和其他侵染相关因子分析,在转录组水平揭示东方蜜蜂微孢子虫Nosema ceranae侵染意大利蜜蜂Apis mellifera ligustica的分子机制。【方法】基于前期已获得高质量的东方蜜蜂微孢子虫纯化孢子(NcCK)及侵染意大利蜜蜂工蜂7和10 d的东方蜜蜂微孢子虫(分别为NcT1和NcT2)转录组数据,根据P≤0.05且|log 2(Fold change)|≥1的标准,通过比较分析筛选出NcCK vs NcT1,NcCK vs NcT2和NcT1 vs NcT2比较组的DEG。通过相关生物信息学软件对上述DEG进行Venn分析、GO分类和KEGG代谢通路富集分析。根据Nr和KEGG数据库注释信息和相关文献进行对东方蜜蜂微孢子虫的毒力因子和侵染相关因子的统计和分析。通过RT-qPCR验证转录组数据及DEG表达趋势。【结果】从NcCK vs NcT1,NcCK vs NcT2和NcT1 vs NcT2比较组分别鉴定出1397,1497和52个DEG。Venn分析结果显示各比较组共有的上调和下调基因分别为10和1个。GO分类结果显示,NcCK vs NcT1和NcCK vs NcT2中DEG富集数最多的功能条目为代谢进程、细胞进程、单组织进程、细胞、细胞组件、细胞器、催化活性和结合,而NcT1 vs NcT2中DEG富集数最多的是代谢进程、细胞进程、单组织进程、催化活性和结合。KEGG代谢通路富集分析结果显示,NcCK vs NcT1和NcCK vs NcT2中DEG分别富集到80和79条通路;富集在糖酵解/糖异生和MAPK信号通路的上调基因数量多于下调基因。毒力因子分析结果显示,孢壁蛋白9基因和孢壁蛋白12基因在NcCK vs NcT1和NcCK vs NcT2中均下调表达,孢壁蛋白8基因仅在NcCK vs NcT1中表达量下调;此外孢壁蛋白前体基因、孢壁和锚定盘复合蛋白基因、几丁质合酶基因、极管蛋白基因、蓖麻毒素B凝集素基因的表达水平在NcCK vs NcT1和NcCK vs NcT2中表现为上调。侵染相关因子分析结果表明,糖酵解途径的3个关键酶基�
基金Supported by National Natural Science Foundation of China(No.81774098)Outstanding Leaders Training Program of Pudong Health Bureau of Shanghai(No.PWRL2016-01)
文摘Objective: To explore the action mechanisms of Huangqi Decoction Granules(黄芪汤颗粒剂, HQDG) on hepatitis B cirrhosis. Methods: A total of 85 patients with hepatitis B cirrhosis were randomly divided into HQDG group(42 cases) and control group(43 cases) by a random number table and were treated with HQDG or placebo for 48 weeks(6 g per times and orally for 3 times a day), respectively. After RNA-sequencing of serum samples extracted from the patients, the differentially expressed genes(DEGs) in HQDG and control groups before and after treatment were separately screened. The DEGs were then performed pathway enrichment analysis and proteinprotein interaction(PPI) network analysis. The expression levels of key genes were detected by quantitative realtime polymerase chain reaction(qRT-PCR). Results: After the investigation, 4 and 3 cases were respectively excluded from HQD and control groups because of the incomplete data. Additionally, 3 and 5 cases were lost to follow up in HQD and control groups, respectively. Finally, a total of 70 cases with good compliance were included for further DEGs analysis. A total of 1,070 DEGs(including 455 up-regulated genes and 615 down-regulated genes) in HQDG group and 227 DEGs(including 164 up-regulated genes and 63 down-regulated genes) in the control group were identified after treatment. Compared with the control group, 1,043 DEGs were specific in HQDG group. Besides, 1 up-regulated transcription factor(TF, such as GLI family zinc finger 1, GLI1) and 25 down-regulated TFs(such as drosophila mothers against decapentaplegic proteinfamily member 2, SMAD2) were identified. Pathway enrichment analysis showed that down-regulated Ras homolog gene family member A(RHOA) was enriched in pathogenic Escherichia coli infection. In the PPI network, up-regulated epidermal growth factor receptor(EGFR), and down-regulated cell division cycle 42(CDC42) as well as v-akt murine thymoma viral oncogene homolog 1(AKT1) had higher degrees. Moreover, long non-coding RNAs(lncR NA) growth arrest-sp
