Transcriptional profiling of mouse liver in response to chronic heat stress

Mice were used to study the effects of chronic heat stress on hepatic gene expression. Twenty-five mice were allocated to either chronic heat stress (34 °C) or control (24 °C) conditions for a period of 2 weeks from 47 to 60 d of age. Nineteen genes differentially expressed in liver were identified using DNA microarrays. Genes involved in the anti-oxidant pathway and metabolism were up-regulated. Genes involved in generation of reactive oxygen radicals and mitochondrial expressed genes were down-regulated. Enzyme activity measurements confirmed the array results. Mice exposed to chronic heat stress showed signs of increased oxidative stress in liver cells.     

不同生存条件下东方田鼠肝脏基因表达谱分析

目的比较实验室条件下饲养的东方田鼠和野外捕捉东方田鼠肝脏的基因表达差异,寻找可能参与肝脏病变的关键基因。方法以实验室条件饲养的东方田鼠和野外捕捉东方田鼠为研究对象,分别抽提RNA,逆转录成cDNA,体外转录为cRNA并进行片段化;利用表达谱芯片分别进行杂交,扫描后筛选差异基因,并应用real-time PCR方法对部分基因的表达水平进行进一步测定,验证芯片数据的结果。结果实验室饲养东方田鼠肝组织与野外捕捉东方田鼠相比,共有99个基因和41个EST差异表达。其中参与机体代谢的基因占主导,约占35.4%;其次为参与信号通路的基因,约占24.2%;参与细胞周期和免疫的基因分别占6.1%和3.0%。结论利用基因表达谱芯片初步筛选了可能参与东方田鼠脂肪肝形成过程的基因,发现机体代谢通路的基因占主导,肝脏中细胞色素家族基因表达差异明显。     

Floret-specific differences in gene expression and support for the hypothesis that tapetal degeneration of Zea mays L. Occurs via programmed cell death

The maize (Zea mays) spikelet consists of two florets, each of which contains three developmentally synchronized anthers. Morphologically, the anthers in the upper and lower florets proceed through apparently similar developmental programs. To test for global differences in gene expression and to identify genes that are coordinately regulated during maize anther development, RNA samples isolated from upper and lower floret anthers at six developmental stages were hybridized to eDNA rnicroarrays. Approximately 9% of the tested genes exhibited statistically significant differences in expression between anthers in the upper and lower florets. This finding indicates that several basic biological processes are differentially regulated between upper and lower floret anthers, including metabolism, protein synthesis and signal transduction. Genes that are coordinately regulated across anther development were identified v/a cluster analysis.Analysis of these results identified stage-specific, early in development, late in development and bi-phasic expression profiles. Quantitative RT-PCR analysis revealed that four genes whose homologs in other plant species are involved in programmed cell death are up-regulated just prior to the time the tapetum begins to visibly degenerate (i.e., the mid-microspore stage). This finding supports the hypothesis that developmentally normal tapetal degeneration occurs via programmed cell death.     

Screening and identification of the core immune-related genes and immune cell infiltration in severe burns and sepsis

Severe burns often have a high mortality rate due to sepsis, but the genetic and immune crosstalk between them remains unclear. In the present study, the GSE77791 and GSE95233 datasets were analysed to identify immune-related differentially expressed genes (DEGs) involved in disease progression in both burns and sepsis. Subsequently, weighted gene coexpression network analysis (WGCNA), gene enrichment analysis, protein–protein interaction (PPI) network construction, immune cell infiltration analysis, core gene identification, coexpression network analysis and clinical correlation analysis were performed. A total of 282 common DEGs associated with burns and sepsis were identified. Kyoto Encyclopedia of Genes and Genomes pathway analysis identified the following enriched pathways in burns and sepsis: metabolic pathways; complement and coagulation cascades; legionellosis; starch and sucrose metabolism; and ferroptosis. Finally, six core DEGs were identified, namely, IL10, RETN, THBS1, FGF13, LCN2 and MMP9. Correlation analysis showed that some core DEGs were significantly associated with simultaneous dysregulation of immune cells. Of these, RETN upregulation was associated with a worse prognosis. The immune-related genes and dysregulated immune cells in severe burns and sepsis provide potential research directions for diagnosis and treatment.     

2型糖尿病模型大鼠肝脏脂代谢相关基因的筛选及生物信息学分析

肝的脂肪代谢异常和胰岛素抵抗（insulin resistance,IR）对促进2型糖尿病（type 2 diabetes mellitus,T2DM）的发生与发展具有显著影响。但此过程复杂,参与调控基因目前尚未完全清楚。有研究表明,脂肪酸分解、氨基酸代谢、肝糖原合成等生物过程对糖尿病的形成具有促进作用。为了阐明这一调控机制,本文通过基因芯片技术研究GK（Goto-Kakizaki）大鼠和WKY（Wistar-Kyoto）大鼠肝差异基因对肝的脂肪代谢和胰岛素抵抗的影响,探讨可引起2型糖尿病发病的分子机制。从基因表达数据库（GEO）获取GSE13271基因表达谱,并对原始数据进行标准化处理。通过GO（Gene Ontology）、KEGG（Kyoto Encyclopedia of Genes and Genomes enrichment）、String和Cytoscape软件对差异表达基因进行功能分析。结果从GK和WKY大鼠中分别获得179和278个差异基因,同时从排名前10的路径中筛选出21个差异基因(Aldh1a1, Cyp2c22, bp2,Fabp7,Cyp4a3, Acot1, Acot2,Hsd17b2, Ech1, Hmgcl,Bdh1, Crot, Pex11a, Cpt1a, Hadhb, Gda, Elovl2, Prodh, Agpat3, Sardh, Pigu),将这些基因与前10个的GO term取交集。最终得到10个显著差异基因(Aldh1a1, Fabp2, Acot1, Acot2, Ech1, Hmgcl, Bdh1, Crot, Cpt1a, Hadhb),功能分析结果显示,肝组织相关基因通过一系列生物过程对肝的脂肪代谢和胰岛素抵抗产生调节作用,从而也为临床糖尿病的治疗以及新作用靶点的发现提供更多参考依据。     

Characterization of Differentially Expressed Genes Involved in Pathways Associated with Gastric Cancer

To explore the patterns of gene expression in gastric cancer, a total of 26 paired gastric cancer and noncancerous tissues from patients were enrolled for gene expression microarray analyses. Limma methods were applied to analyze the data, and genes were considered to be significantly differentially expressed if the False Discovery Rate (FDR) value was < 0.01, P-value was <0.01 and the fold change (FC) was >2. Subsequently, Gene Ontology (GO) categories were used to analyze the main functions of the differentially expressed genes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found pathways significantly associated with the differential genes. Gene-Act network and co-expression network were built respectively based on the relationships among the genes, proteins and compounds in the database. 2371 mRNAs and 350 lncRNAs considered as significantly differentially expressed genes were selected for the further analysis. The GO categories, pathway analyses and the Gene-Act network showed a consistent result that up-regulated genes were responsible for tumorigenesis, migration, angiogenesis and microenvironment formation, while down-regulated genes were involved in metabolism. These results of this study provide some novel findings on coding RNAs, lncRNAs, pathways and the co-expression network in gastric cancer which will be useful to guide further investigation and target therapy for this disease.