Mating flight causes genome-wide transcriptional changes in sexually mature honeybee queens

In this study, we analyzed the gene and miRNA expression differences between the courted virgin queen (CVQ) and non-courted virgin queen (NCVQ) of Apis mellifera using a high-throughput sequencing method. Through Digital Gene Expression (DGE) sequencing, 452 genes were differentially expressed, out of which, 90 genes were up-regulated and 362 genes were down-regulated in CVQ compared with NCVQ. Through small RNA sequencing, 27 miRNAs showed significant expression difference between these two samples. Moreover, 9 of the differentially expressed genes are the targets of the 11 differentially expressed miRNAs. Besides, 47 novel miRNA candidates were predicted in these two samples. Our results provided valuable information for understanding the molecular mechanism of the transition to functional queens.     

Gene expression analysis following olfactory learning in Apis mellifera

The honeybee has a strong learning and memory ability, and is recognized as the best model organism for studying the neurobiological basis of learning and memory. In this study, we analyzed the gene expression difference following proboscis extension response-based olfactory learning in the A. mellifera using a tag-based digital gene expression (DGE) method. We obtained about 5.71 and 5.65 million clean tags from the trained group and untrained group, respectively. A total of 259 differentially expressed genes were detected between these two samples, with 30 genes up-regulated and 229 genes down-regulated in trained group compared to the untrained group. These results suggest that bees tend to actively suppress some genes instead of activating previously silent genes after olfactory learning. Our DGE data provide comprehensive gene expression information for olfactory learning, which will facilitate our understanding of the molecular mechanism of honey bee learning and memory.     

婚飞行为影响中华蜜蜂性成熟处女蜂王的基因表达

婚飞是性成熟处女蜂王与雄蜂交配过程中的一个重要前奏, 在该过程中蜂王体内伴随着一系列重要的生理变化。为了探究中华蜜蜂Apis cerana cerana处女蜂王婚飞过程中基因表达变化, 本研究利用数字基因表达谱(digital gene expression, DGE) 技术分析了中华蜜蜂性成熟处女蜂王飞行与未飞行之间的基因表达差异。经DGE测序, 分别从两个样品中获得5.98和6.01 百万条Clean标签。通过分析检测到250个基因有差异表达, 其中133个基因在飞行蜂王中上调表达, 117个基因在飞行蜂王中下调表达。这些差异基因可以归类到348个功能性类别和142个生化途径。结果表明中华蜜蜂性成熟处女蜂王在婚飞过程中大量基因的表达发生了变化。这些结果为进一步研究中华蜜蜂蜂王婚飞过程中生理变化的分子机制提供了重要的基因表达信息。     

脂多糖调控对大鼠心脏微血管内皮细胞的转录组分析

目的探索脂多糖(LPS)对大鼠心脏微血管内皮细胞(rCMECs)转录组的调节作用。方法对照组(正常培养rCMECs),LPS组(100 ng/mL LPS处理6 h的rCMECs),每组进行3个生物学重复转录组测序。得到差异基因后,使用实时定量PCR对部分差异基因mRNA的表达进行验证。分别对上调和下调基因进行GO和KEGG富集,并对差异基因进行共表达网络分析。采用独立t检验进行统计学分析。结果LPS处理后,265个基因表达上调,118个基因的表达下调。前10个最显著上调基因为:Mt2a、Cyp7b1、Sod2、Icam1、Ccl2、AC128848.1、Mt1、Cebpd、Serpinb2和Tnfrsf11b。前10个最显著下调基因为:Cavin2、Ankrd1、Edn1、Prss35、Lmod1、Dhrs3、Ttc22、Sema6a、Map2k3和Sema7a。定量PCR的结果表明Mt2a、Sod、Ccl2、Cxcl1、Icam1和Vcaml基因的表达得到了上调(P均<0.01);而Cavin2、Ankrd1、Edn1和Prss35基因表达下调(P均<0.05)。GO和KEGG富集的结果表明,上调基因与内皮细胞对炎性免疫细胞的趋化作用和黏附作用密切相关;而下调基因则是与钙离子信号和G蛋白相关通路以及内皮通透性增加有关。此外,差异基因进行共表达网络分析发现Sod2处于核心位置,提示其可能与LPS诱导的rCMECs的各种变化密切相关。结论LPS调控了rCMECs中大量与炎性免疫细胞进入心肌组织相关基因的表达。     

低氧对人骨髓间充质干细胞基因表达谱的影响

低氧可以促进人骨髓间充质干细胞（human bone marrow-derived mesenchymal stem cells,hMSCs）增殖。为探讨其可能机制,本实验采用cDNA芯片技术动态检测低氧促进hMSCs增殖过程中基因表达的变化,用RT-PCR验证芯片结果。结果显示,在含21 329条基因探针的芯片上,检测到282个基因差异表达,其中代谢类基因最多;差异表达基因的数目随低氧时间不同而变化,其中24 h时差异表达基因的数目最多。差异表达基因中4个为已知的低氧诱导因子-1（hypoxia- inducible factor 1,HIF-1）靶基因,在低氧处理36 h时都基本上调。此外,差异表达基因中有10个连续变化的基因,这些基因中既有上调基因也有下调基因。4个HIF-1靶基因和连续变化的基因的RT1-PCR结果大部分与cDNA芯片结果一致。结果提示,低氧促进hMSCs增殖是多基因参与的过程,可能与HIF-1及其下游信号通路有关。     

mRNA差异展示研究胃癌差异表达基因

以胃癌细胞株GC7901与胃粘膜细胞株GES-1为对比材料,利用mRNA差异展示技术,研究胃粘膜至胃癌过程的差异表达基因,为建立胃癌预警系统打下基础.获得8个未知的与胃癌相关的cDNA,命名为GCYS-1,2,3,4,5,6,7,20,完成其克隆及序列分析,RNA印迹证实GCYS-1至7片段与GCYS-20基因在GC7901细胞株中呈高表达,在GES-1细胞株中呈低表达.此8个序列在GenBank数据库中登录,接受号为AF054162～AF056168及AF219140.     

应用基因表达谱芯片研究黄药子对小鼠肝脏的毒性机制(简报)

黄药子为薯蓣科植物黄独(Dioscorea bulbifera L．)的块茎,临床常用于治疗甲状腺肿、抗肿瘤、抗炎、抗病毒等。近年来临床上关于黄药子的毒副作用,尤其是对肝、肾的不良反应屡有报道。当黄药子或其代谢物在肝细胞内累积时会直接干扰肝细     

Microarray analysis of differentially expressed genes engaged in fruit development between table and wine grape

Microarray analysis of genes can provide individual gene-expression profiles and new insights for elucidating biological mechanisms responsible for fruit development. To obtain an overall view on expression profiles of metabolism-related genes involved in fruit development of table and wine grapes, a microarray system comprising 15,403 ESTs was used to compare the expressed genes. The expression patterns from the microarray analysis were validated with quantitative real-time polymerase chain reaction analysis of 18 selected genes of interest. During the entire fruit development stage, 2,493 genes exhibited at least 2.0-fold differences in expression levels with 1,244 genes being up-regulated and 1,249 being down-regulated. Following gene ontology analysis, only 929 differentially expressed (including 403 up-regulated and 526 down-regulated) genes were annotated in table and wine grapes. These differentially expressed genes were found to be mainly involved in carbohydrate metabolism, biosynthesis of secondary metabolites as well as energy, lipid and amino acid metabolism via KEGG. Our results provide new insights into the molecular mechanisms and expression profiles of genes in the fruit development stage of table and wine grapes.     

利用生物信息学研究肥胖与2型糖尿病患者肝组织基因表达变化

目的:利用芯片数据分析工具对GEO基因芯片数据进行数据挖掘,系统分析肥胖与2型糖尿病患者肝组织相关基因表达的变化,探讨肥胖与2型糖尿病的联系及糖尿病早期预防和诊断的新靶点。方法:首先在公共芯片数据库中选择肥胖与2型糖尿病相关芯片数据(GSE15653),利用R等芯片数据分析工具分析肥胖与2型糖尿病患者肝组织基因的表达变化,并预测相关差异表达基因在血中蛋白表达。结果:肥胖患者与正常人肝组织比较发现412个差异表达基因,其中上调表达基因212个,下调表达基因200个,2型糖尿病患者中控制良好者与正常人肝组织比较发现486个差异表达基因,其中上调表达基因253个,下调表达基因233个,而2型糖尿病患者中控制不良者与正常人肝组织比较发现1051个差异表达基因,其中上调表达基因560个,下调表达基因491个;2型糖尿病控制良好者与肥胖患者肝组织有263个相同的表达变化基因,而2型糖尿病控制不良者与肥胖患者肝组织有131个相同的表达变化基因;结合蛋白质组学结果分析肥胖与2型糖尿病相关的差异表达基因中有30个蛋白表达产物是分泌型蛋白。结论:肥胖及2型糖尿病患者肝组织与正常肝组织比较基因表达均发生明显变化,其基因表达变化数目随疾病的严重性增加而增多,而且2型糖尿病的控制情况与肝组织基因表达变化有密切关系。肥胖与2型糖尿病相关的差异表达基因中表达分泌型蛋白的可进一步用于研发监测疾病发生发展的候选靶分子。     

基于转录组测序的Cd胁迫下芹菜细胞自噬相关基因的筛选

细胞自噬是植物逆境应答过程中最常见的保护机制之一。动物中,自噬相关基因抵御镉(Cd)毒害的功能研究较清楚,但植物却知之甚少。文中以芹菜品种‘皇后’为试材,采用外源Cd(终浓度为0、2、4、8mg/L)添加营养液水培处理,利用转录组测序(RNA-seq)技术筛选细胞自噬相关差异基因并进行q RT-PCR验证。结果表明Cd胁迫对芹菜植株产生了明显的毒害作用,并与浓度间产生了量效关系。在筛选的8个差异表达的自噬相关基因中,ATG8a、ATG8f、ATG13、AMPK-1、AMPK-2基因随Cd浓度升高表达上调,ATG12、VPS30和VPS34则先上调后下降,说明自噬相关基因可能通过表达上调增加了自噬小体结构以抵御Cd毒性作用;而高浓度Cd(8mg/L)可能超出芹菜的耐受范围,导致多个自噬基因又出现表达下调趋势。以上结果有助于后期自噬相关基因的功能研究,为进一步探讨芹菜对Cd胁迫的耐性机制提供参考依据。