在患CyHV-2病的异育银鲫肠道黏膜中胆固醇、胆汁酸代谢通路基因的差异表达

为了探讨CyHV-2疾病条件下异育银鲫胆汁酸肠肝循环代谢途径主要基因表达活性的变化, 以患CyHV-2病的、正常的异育银鲫肠道黏膜为材料, 提取总RNA, 采用RNA-Seq测序、对单一基因进行注释, 并进行KEGG富集分析、单一基因差异表达分析。结果显示, 肠道黏膜组织有7770个基因显著性差异表达, 其中, 差异表达上调基因数为3335个、差异表达下调的基因数为4435个, 表明CyHV-2病的发生对肠道黏膜组织基因表达产生了重大的影响。病鱼胆固醇、胆汁酸生物合成代谢途径的酶、蛋白质的基因显著性差异表达, 显示肠道黏膜胆固醇、胆汁酸合成代谢受到显著性影响。参与胆固醇、胆汁酸合成代谢调节作用, 以及胆固醇、胆汁酸分泌、吸收、转运等生理过程的蛋白质、酶的基因也是差异表达下调, 胆汁酸肠肝循环有出现代谢障碍的趋势。结果表明, CyHV-2病的发生对肠道黏膜组织基因表达产生了严重影响, 对胆固醇、胆汁酸的合成代谢途径、胆汁酸肠肝循环途径的基因表达产生了严重影响, 将导致病鱼体内胆固醇、胆汁酸量的不足。患CyHV-2病病鱼血清胆汁酸含量下降了99%、胆固醇含量下降了10%, 证实了上述基因差异表达的趋势。     

Identification of Differentially Expressed Transcripts and Pathways in Blood One Week and Six Months Following Implant of Left Ventricular Assist Devices

Introduction

Continuous-flow left ventricular assist devices (LVADs) are an established therapy for patients with end-stage heart failure. The short- and long-term impact of these devices on peripheral blood gene expression has not been characterized, and may provide insight into the molecular pathways mediated in response to left ventricular remodeling and an improvement in overall systemic circulation. We performed RNA sequencing to identify genes and pathways influenced by these devices.

Methods

RNA was extracted from blood of 9 heart failure patients (8 male) prior to LVAD implantation, and at 7 and 180 days postoperatively. Libraries were sequenced on an Illumina HiSeq2000 and sequences mapped to the human Ensembl GRCh37.67 genome assembly.

Results

A specific set of genes involved in regulating cellular immune response, antigen presentation, and T cell activation and survival were down-regulated 7 days after LVAD placement. 6 months following LVAD placement, the expression levels of these genes were significantly increased; yet importantly, remained significantly lower than age and sex-matched samples from healthy controls.

Conclusions

In summary, this genomic analysis identified a significant decrease in the expression of genes that promote a healthy immune response in patients with heart failure that was partially restored 6 months following LVAD implant.     

不同海拔饲育的麦洼牦牛肺脏组织转录组学分析

为了探讨牦牛适应高海拔低氧环境的基因表达特征与规律,对在高海拔（3 560 m）和低海拔地区（478 m）饲育4个月的2.5~3岁健康雄性麦洼牦牛肺组织进行转录组测序。转录组测序采用Illumina高通量测序平台(HiSeqTM2500/4000)进行,并以qRT-PCR验证差异表达基因的表达量。结果显示,高海拔组牦牛肺脏转录组平均每个测序样本得到约5.76亿条Clean Reads,低海拔组牦牛中得到约6.10亿条Clean Reads,比对到参考基因组上的Reads数分别占91.74%和91.28%以上,共发现了2 047个新转录本。低海拔组与高海拔组牦牛肺脏组织之间共有199个差异表达基因,其中含89个差异上调表达基因和110个差异下调表达基因。所得差异表达基因富集在297个GO条目和146个KEGG通路中,包含62个低氧适应相关的GO条目和35个低氧适应相关代谢通路。其中低氧适应相关GO条目在生物过程、细胞组成和分子功能三种类别中占比最多的分别为细胞粘附、蛋白复合物和钙离子结合。低氧适应相关KEGG通路中占比最多的为肿瘤坏死因子(TNF)信号通路,其次为低氧诱导因子1(HIF-1)信号通路。qRT-PCR验证结果显示,Ⅱ类人类白细胞抗原α链(HLA-DOA、HLA-DRA)、补体因子 (C2)和甘露糖结合凝集素相关丝氨酸蛋白酶1（MASP1）基因的表达量变化与转录组测序结果相符。本研究为全局和深入理解牦牛肺组织转录本表达对高海拔低氧的响应提供了有价值的切入点。     

Wnt通路中的部分基因在绒山羊胚胎皮肤毛囊中的表达分析

已知绒山羊毛囊的发育受Wnt等信号通路控制,但Wnt通路相关基因在绒山羊胚胎毛囊启动和生长发育过程中的表达及作用机制尚不清楚。本文采用RNA-Seq技术对45 d,55 d和65 d的绒山羊胚胎体侧皮肤进行了转录组测序,鉴定Wnt通路相关基因的表达。 RNA- Seq技术结合blast搜索,将转录组有效测序数据与云南黑山羊参考基因组序列(http://goat. kiz.ac. cn/GGD/download.htm)比对,获得了已知的Wnt通路（pathway hsa04310）中的123个相关基因（86.0%）。进而采用实时荧光定量PCR技术检测,验证了差异表达的Sfrp4、Wnt3、Wnt10a（上调）和Apc2（下调）基因在绒山羊胚胎不同时期皮肤中的表达量,初步探索了绒山羊毛囊在胚胎期启动、发育过程中,Wnt通路部分基因的表达模式,为进一步研究Wnt通路部分基因在绒山羊胚胎毛囊启动、发育过程中的作用机制提供了有意义的线索。     

The effect of short-term hypoxic exposure on metabolic gene expression

The long-term effect of hypoxia is to decrease both the production and use of ATP and thus decrease the reliance on mitochondrial oxidative energy production. Yet, recent studies include more immediate affects of hypoxia on gene expression and these data suggest the maintenance of mitochondrial function. To better understand the short-term physiological response to hypoxia, we quantified metabolic mRNA expression in the heart ventricles and livers of the teleost fish Fundulus grandis exposed to partial oxygen pressure of 2.8?kPa (-13.5% air saturation).Twenty-eight individuals from a single population were exposed to hypoxia for 0, 4, 8, 12, 24, 48, and 96 hr. Liver and cardiac tissues were sampled from the same individuals at 0-48 hr. At 96 hr, only cardiac tissue was assayed. Gene expression was significantly different (ANOVA, P < 0.05) for 17 of 226 metabolic genes (7.5%) in cardiac tissue and for 20 of 256 (7.8%) metabolic genes in hepatic tissue. For the two tissues examined in this study, the maximum response occurred at different times. For cardiac tissue, using Dunnett's post hoc test, most of these significant differences occurred at 96 hr of exposure. For liver, all but one significant difference occurred at 4 hr. Surprisingly, too many (relative to random expectations) of the genes with significant increase in mRNA are involved in the oxidative phosphorylation pathway: 44% of the significant genes at 96 hr in the heart and 33% of the significant genes at 4 hr in the liver are involved in the oxidative phosphorylation pathway. These data indicate that there are tissue-specific differences in the timing of the response to hypoxia, yet both cardiac and hepatic tissues have increases in mRNA that code for enzyme in the oxidative phosphorylation pathway. If these changes in mRNA produce a similar change in protein, then these data suggest that the initial response to hypoxia involves an increase in the oxidative pathway potentially as a mechanism to maintain ATP production.     

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data

Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material.