刺芹侧耳不同发育时期的转录组差异分析

为了探讨刺芹侧耳子实体生长发育时期的基因表达变化,本文利用高通量测序技术对刺芹侧耳不同发育时期（菌丝期、原基期、子实体时期）进行RNA-Seq分析,在转录水平上解析差异表达基因在刺芹侧耳生长发育过程中的作用和功能。KEGG功能富集显示,菌丝期差异表达基因主要富集在碳代谢和氨基酸代谢中,其中三羧酸循环中编码柠檬酸合酶、乌头酸水合酶、异柠檬酸脱氢酶、琥珀酰辅酶A合成酶、琥珀酸脱氢酶、苹果酸脱氢酶的基因表达量均上调,说明碳代谢和氨基酸代谢是菌丝时期的主要能量来源;原基期上调的差异表达基因主要富集在脂肪酸代谢,其中RT-PCR定量结果显示原基期编码脂肪酸合酶的基因和编码脂酰辅酶A合成酶的基因下调,编码超氧化物酶的基因和编码过氧化氢酶的基因上调,表明脂肪酸代谢和抗氧化酶对刺芹侧耳原基期维持机体的稳定和生物应激方面起着重要作用。子实体时期上调的差异表达基因主要富集在剪接体、类固醇的生物合成以及AMPK信号通路中,说明环境因子对子实体时期有一定的影响。     

筛选差异表达基因和蛋白质的方法进展

分离和鉴定差异表达基因和蛋白质不仅有助于发现基因和蛋白质的功能,更有助于揭示某些疾病的发生机理.目前筛选差异表达基因的方法主要有差异显示PCR方法(differential display RT-PCR,DDRT-PCR)、消减杂交法(subtractive hybridization,SH)、基因芯片技术(DNA chip technique)和基因表达的系统分析(serial analysis of gene expression,SAGE)等,其中消减杂交法中又先后建立了代表性差异分析技术(representational difference analysis,RDA)、抑制消减杂交法(suppression subtractive hybridization,SSH)和获得全长基因的消减杂交法(full-length-gene-obtainable subtractive hybridization).筛选差异表达蛋白质的方法主要有双向电泳技术(two-dimentional gel electrophoresis)和噬菌体全套抗体库技术(phage display antibody repertoire library technique).这些方法各有特点,各有利弊,研究者可根据自己的需要选择适合于自己的方法.     

转化的大鼠胚胎成纤维细胞系差异表达基因的筛选研究

来源于转化的大鼠胚胎成纤维细胞系的两株细胞,A1－5细胞与B4细胞相比表现出非常强的抗辐射性并伴随不同寻常强的G2延迟效应;用PCR选择性抑制消减杂交方法对这两株细胞进行差减,希望找到对A1－5细胞表现出的不同寻常的表型起关键作用的某一个或某一些基因。结果得到了160个差减转化子,逐个进行序列测定,并进行Dot blot杂交,共得到35个差异表达基因片段（EST）。通过对美国国家生物技术信息中心（NCBI）的非冗余序列库（NT）、鼠EST库及人EST库的BLAST进行同源检索,发现其中21个代表了尚未登录的新基因,另外14个分别与已知基因高度同源。     

Identification of differentially expressed genes and the role of PDK4 in CD14+ monocytes of coronary artery disease

Background. Coronary artery disease (CAD) is a chronic inflammatory disease caused by development of atherosclerosis (AS), which is the leading cause of mortality and disability. Our study aimed to identify the differentially expressed genes (DEGs) in CD14⁺ monocytes from CAD patients compared with those from non-CAD controls, which might pave the way to diagnosis and treatment for CAD. Methods. The RNA-sequencing (RNA-seq) was performed by BGISEQ-500, followed by analyzing with R package to screening DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed by R package. In addition, we validated the results of RNA-seq using real-time quantitative polymerase chain reaction (RT-qPCR). Furthermore, we explored the function of selected ten genes in LDL-treated CD14⁺ monocytes by RT-qPCR. Results. a total of 2897 DEGs were identified, including 753 up- and 2144 down-regulated genes in CD14⁺ monocytes from CAD patients. These DEGs were mainly enriched in plasma membrane and cell periphery of cell component, immune system process of biological process, NF-κB signaling pathway, cell adhesion molecules signaling pathway and cytokine–cytokine receptor interaction signaling pathway. In LDL-treated CD14⁺ monocytes, the mRNA expression of pyruvate dehydrogenase kinase 4 (PDK4) was significantly up-regulated. Conclusion. In the present study, we suggested that PDK4 might play a role in progression of CAD. The study will provide some pieces of evidence to investigate the role and mechanism of key genes in the pathogenesis of CAD.     

Identification of novel therapeutic targets for neuropathic pain based on gene expression patterns

Neuropathic pain (NP) caused by nerve injury or dysfunction is one of the most challenging neurological diseases. In-depth study of disease signatures contributes to the development of novel target treatment for NP. In this study, we analyzed expression profiles of qualified NP datasets (GSE24982 and GSE63442) deposited at Gene Expression Omnibus database by systematic bioinformatics approaches. We analyzed the differentially expressed genes of high and low pain compared with normal control group, and between spinal nerve ligation (SNL) injury model and sham-operation group. A total of 1,243 upregulated and 1,533 downregulated genes were identified in GSE24982, 380 upregulated and 355 downregulated genes were identified in GSE63442. By comparing low-pain samples with the corresponding sham-operation group, we identified 457 upregulated and 409 downregulated genes. Overlapping genes were screened out and signaling pathway and expression regulation model analyses were performed. SCN10A and SST were identified as biomarkers for NP. In conclusion, our study showed the expression pattern of gene about NP. These identified biomarkers could serve as potential therapeutic targets for treating NP.     

鸡胚公母性腺差异表达基因的基因芯片杂交筛选

采用Affymetrix公司鸡基因组芯片对9日龄鸡胚公母性腺总RNA进行了芯片杂交, 并对基因表达谱进行了分析。统计结果显示, 9日龄母鸡性腺表达基因数19 368个, 公鸡性腺表达基因数19 493个; 公母性腺绝对差异表达基因,即公鸡性腺表达而母鸡性腺不表达基因145个, 母鸡性腺表达而公鸡性腺不表达基因189个。绝对差异表达基因功能分类结果显示, 参与细胞组成、细胞加工和分子结合基因占多数, 部分基因参与细胞器组成、代谢加工、生物学调控以及催化反应和细胞信号转导等。值得注意的是, 本研究发现了一些已经报道同性别决定和分化有一定关联的基因, 如ASW、CHD1和SOX9等, 同时也发现了一些未知其同性腺分化和发育有关联的基因和编码假想蛋白的表达序列。进一步分析这些基因和表达序列的生物学功能和表达模式, 将对鸟类性别决定和分化机制的了解提供有益参考。     

Five candidate biomarkers associated with the diagnosis and prognosis of cervical cancer

Purpose: Cervical cancer (CC) is one of the most general gynecological malignancies and is associated with high morbidity and mortality. We aimed to select candidate genes related to the diagnosis and prognosis of CC.Methods: The mRNA expression profile datasets were downloaded. We also downloaded RNA-sequencing gene expression data and related clinical materials from TCGA, which included 307 CC samples and 3 normal samples. Differentially expressed genes (DEGs) were obtained by R software. GO function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed in the DAVID dataset. Using machine learning, the optimal diagnostic mRNA biomarkers for CC were identified. We used qRT-PCR and Human Protein Atlas (HPA) database to exhibit the differences in gene and protein levels of candidate genes.Results: A total of 313 DEGs were screened from the microarray expression profile datasets. DNA methyltransferase 1 (DNMT1), Chromatin Assembly Factor 1, subunit B (CHAF1B), Chromatin Assembly Factor 1, subunit A (CHAF1A), MCM2, CDKN2A were identified as optimal diagnostic mRNA biomarkers for CC. Additionally, the GEPIA database showed that the DNMT1, CHAF1B, CHAF1A, MCM2 and CDKN2A were associated with the poor survival of CC patients. HPA database and qRT-PCR confirmed that these genes were highly expressed in CC tissues.Conclusion: The present study identified five DEmRNAs, including DNMT1, CHAF1B, CHAF1A, MCM2 and Kinetochore-related protein 1 (KNTC1), as potential diagnostic and prognostic biomarkers of CC.     

Comparative mitochondrial genomics and phylogenetic relationships of the Crossoptilon species (Phasianidae,Galliformes)

Background

Phasianidae is a family of Galliformes containing 38 genera and approximately 138 species, which is grouped into two tribes based on their morphological features, the Pheasants and Partridges. Several studies have attempted to reconstruct the phylogenetic relationships of the Phasianidae, but many questions still remain unaddressed, such as the taxonomic status and phylogenetic relationships among Crossoptilon species. The mitochondrial genome (mitogenome) has been extensively used to infer avian genetic diversification with reasonable resolution. Here, we sequenced the entire mitogenomes of three Crossoptilon species (C. harmani, C. mantchuricum and C. crossoptilon) to investigate their evolutionary relationship among Crossoptilon species.

Results

The complete mitogenomes of C. harmani, C. mantchuricum and C. crossoptilon are 16682 bp, 16690 bp and 16680 bp in length, respectively, encoding a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a putative control region. C. auritum and C. mantchuricum are more closely related genetically, whereas C. harmani is more closely related to C. crossoptilon. Crossoptilon has a closer relationship with Lophura, and the following phylogenetic relationship was reconstructed: ((Crossoptilon + Lophura) + (Phasianus + Chrysolophus)). The divergence time between the clades C. harmani-C. crossoptilon and C. mantchuricum-C. auritum is consistent with the uplift of the Tibetan Plateau during the Tertiary Pliocene. The Ka/Ks analysis showed that atp8 gene in the Crossoptilon likely experienced a strong selective pressure in adaptation to the plateau environment.

Conclusions

C. auritum with C. mantchuricum and C. harmani with C. crossoptilon form two pairs of sister groups. The genetic distance between C. harmani and C. crossoptilon is far less than the interspecific distance and is close to the intraspecific distance of Crossoptilon, indicating that C. harmani is much more closely related to C. crossoptilon. Our mito-phylogenomic analysis supports the monophyly of Crossoptilon and its closer relationship with Lophura. The uplift of Tibetan Plateau is suggested to impact the divergence between C. harmani-C. crossoptilon clade and C. mantchuricum-C. auritum clade during the Tertiary Pliocene. Atp8 gene in the Crossoptilon species might have experienced a strong selective pressure for adaptation to the plateau environment.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1234-9) contains supplementary material, which is available to authorized users.     

叉角厉蝽触角转录组及嗅觉相关基因分析

叉角厉蝽Eocanthecona furcellata是一种在生物防治方面有重要作用和潜力的捕食性天敌昆虫,触角是昆虫进行信息交换的重要器官,而嗅觉相关基因则是调控天敌昆虫捕食行为的重要分子基础。为获得叉角厉蝽触角转录组数据库,挖掘叉角厉蝽嗅觉相关基因,本研究利用Illumina高通量测序平台对叉角厉蝽雌雄成虫与5龄若虫触角进行转录组测序。成功构建了叉角厉蝽触角转录组,获得了67 843条unigenes, N50长度为2 300 bp。与七大公共数据库比对注释到27 686条unigenes,其中NR数据库注释最多(33.33%),且与茶翅蝽Halyomorpha halys相似度最高(64.20%)。14 258条注释到GO数据库中,分为生物过程、细胞组分和分子功能3个大类42个亚类;KEGG代谢途径分析表明,7 703条形成282条代谢通路,其中被注释在信号传导通路中的unigenes最多(11.50%)。进一步基因注释分析,鉴定得到134个候选嗅觉相关基因,32个化学感应蛋白基因(Chemosensory protein genes, CSP),10个气味结合蛋白基因(Odor...