Effects of Chinese herbs capable of replenishing qi, nourishing yin and activating blood circulation and their compatibility on differentially expressed genes of ischemic myocardium

This study was conducted to investigate the effects of Chinese herbs capable of replenishing qi, nourishing yin and activating blood circulation and their compatibility on differentially expressed genes of ischemic myocardium which were selected from differential expression profile we had established before, and to explore the underlying mechanism. The acute myocardial infarction （AMi） model was established by ligating the left anterior descending （LAD） coronary artery, then the model rats were randomly divided into the model group, the Metoprolol group, the replenishing qi nourishing yin （RN） group, the activating blood circulation （AB） group, and the replenishing qi, nourishing yin and activating blood circulation （RA） group. In addition, the normal group and the sham group were set up. The rats of medication groups were administered by intragastric gavage with corresponding drugs on the second day after operations, and the rats of the normal group and the sham group were given normal saline as the same time.Then the ischemic hearts were harvested on the 8th day after operation. The myocardial pathomorphological changes were observed under a light microscope. The mRNA changes of target genes such as COX5a and ATP5e were detected using Real-time fluorescence quantitative PCR （Q-PCR）, and the activities of related enzymes were detected by colorimetric assay. The main resuits were as follows： the histological changes were observed by HE staining, and cardiocyte swelling, inflammatory cell infiltration and cytolysis were showed in regional ischemic myocardium of the model group, while the pathomorphological changes in all medication groups did not show obvious changes. Two genes related to energy metabolism, COX5a and ATP5e, were selected as the target genes which were down-regulated at the mRNA level in the medication groups. The activities of correlative functional enzymes also decreased in the RA group compared to that in the model group accordingly （P〈0.05）. The results indicated that the abnormal expression of genes involved in energy metabolism pathways could be one of the molecular mechanisms of AMI. The compatibility of Chinese herbs capable of replenishing qi, nourishing yin and activating blood circulation affects the expression of energy-relative gene COX5a, ATP5e, which is probably the mechanism of myocardial preservation, and is more effective than single herb of replenishing qi and nourishing yin or activating blood circulation.     

SO2对大鼠肺基因组表达谱的影响——环境表达不稳定基因组存在的证据

采用A ffym etrix的基因芯片(RAE 230A)研究了SO2短期(56 m g/m3,6 h/day,for 7 days)及长期(14 m g/m3,1 h/day,for 30 days)吸入后对大鼠肺基因表达谱改变的影响.结果表明,与其相应的对照组相比,SO2短期吸入后表达上调的基因有31个,其中包括18个已知基因和13个新基因,而表达下调的基因有30个,其中包括19个已知基因和11个新基因;SO2长期吸入后表达上调的基因有173个,其中包括79个已知基因和94个新基因,而表达下调的基因有85个,其中包括46个已知基因和39个新基因.由此结论:1)高剂量短期吸入与低剂量长期吸入SO2在体内的作用机理不同;2)短期吸入SO2的大鼠肺基因表达谱与其对照组相比,氧化磷酸化相关的一些基因发生了变化,这表明高剂量短期吸入SO2可能导致线粒体功能的恶化;3)长期吸入SO2的大鼠肺基因表达谱与其对照组相比,表达有差异的基因涉及到脂肪酸代谢、免疫、炎症、氧化应激、原癌基因、肿瘤抑制基因和细胞外基质等,表明低剂量长期吸入SO2在体内的机理要更为复杂.本研究证明,在基因组中存在一些基因,它们的表达对环境污染物很敏感,可被称为环境表达不稳定基因组.     

不同运动强度对急性心肌梗死大鼠心功能的影响及循环miRNAs差异表达

研究不同运动强度对急性心肌梗死大鼠心功能的影响, 分析循环微小RNA(microRNAs, miRNAs)的差异表达与靶基因及基因功能. 制作急性心肌梗死大鼠模型40只,分为4组, 每组10只, 分别为假手术组、单纯心肌梗死组、中等强度持续运动(continuous moderate training, CMT)组和间歇高强度运动(high intensity interval training, HIT)组, CMT组和HIT组大鼠接受运动治疗8周, 用超声心动图评估心功能, 用基因芯片技术测定4组大鼠模型循环miRNAs差异表达, 用生物信息学技术分析不同运动强度下循环miRNAs相关靶基因及基因功能. CMT组和HIT组的治疗显著改善了心肌梗死大鼠心功能和运动耐量, HIT组显著优于CMT组. 单纯心肌梗死组与假手术组相比, 明显上调的循环miRNAs有14个, 明显下调的循环miRNAs有4个. 与单纯心肌梗死组相比, CMT组明显上调的循环miRNAs有11个, 明显下调的循环miRNAs有2个; HIT组明显上调的循环miRNAs有53个, 明显下调的关键miRNAs有41个. 与假手术组相比, 单纯心肌梗死组心肌相关循环miRNAs的差异表达有miR-26a-5p, miR-92a-3p和miR-378a-3p; 与单纯心肌梗死组相比, CMT组有miR-92a-3p, HIT组有miR-34c-3p, miR-23a-3p, miR-98-3p, miR-208a-5p和miR-92-3p. 高强度间歇运动对心肌梗死大鼠心功能和运动耐量的改善作用优于中等强度持续运动, 其循环miRNAs及心肌相关循环miRNAs的差异表达数量明显高于中等强度持续运动, 循环miRNAs差异表达有望作为运动强度和运动效果判断的分子生物学标志物.     

基于基因表达谱芯片杂交分析Lamprey-PHB2转染前后Chang liver细胞的基因表达差异

选取了10个物种与本课题组前期克隆得到的东北七鳃鳗抗增殖蛋白2(Lm-PHB2)进行氨基酸序列相似性对比,检测PHB2基因进化水平,结果表明各物种的PHB2氨基酸序列在PHB结构域处高度保守,但在N-端和C-端氨基酸序列保守性较低.将重组质粒pEGFP-N1-Lm-PHB2瞬时转染入张氏肝(CHL)细胞后,利用基因表达谱芯片技术分析基因的表达差异.结果显示CHL细胞中共有270条显著差异表达基因,其中显著上调基因共141条,显著下调基因共129条,涉及细胞信号转导、细胞周期调节、细胞增殖、细胞代谢和细胞凋亡等多个方面.通过实时荧光定量聚合酶链式反应(PCR)对基因表达谱芯片分析结果进行验证,结果显示转染pEGFP-N1-Lm-PHB2质粒后,细胞周期基因CDC25C、氧化应激相关基因(CAT,SOD,GST)和抗细胞凋亡基因HAX1均有显著性差异.     

Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancer

The complex regulatory network between microRNAs and gene expression remains an unclear domain of active research. We proposed to address in part this complex regulation with a novel approach for the genome-wide identification of biomodules derived from paired microRNA and mRNA profiles, which could reveal correlations associated with a complex network of dys-regulation in human cancer. Two published expression datasets for 68 samples with 11 distinct types of epithelial cancers and 21 samples of normal tissues were used, containing microRNA expression and gene expression profiles, respectively. As results, the microRNA expression used jointly with mRNA expression can provide better classifiers of epithelial cancers against normal epithelial tissue than either dataset alone (P=1×10^–10, F test). We identified a combination of 6 microRNA-mRNA biomodules that optimally classified epithelial cancers from normal epithelial tissue (total accuracy = 93.3%; 95% confidence intervals: 86%–97%), using penalized logistic regression (PLR) algorithm and three-fold cross-validation. Three of these biomodules are individually sufficient to cluster epithelial cancers from normal tissue using mutual information distance. The biomodules contain 10 distinct microRNAs and 98 distinct genes, including well known tumor markers such as miR-15a, miR-30e, IRAK1, TGFBR2, DUSP16, CDC25B and PDCD2. In addition, there is a significant enrichment (Fisher’s exact test P=3×10^–10) between putative microRNA-target gene pairs reported in 5 microRNA target databases and the inversely correlated microRNA-mRNA pairs in the biomodules. Further, microRNAs and genes in the biomodules were found in abstracts mentioning epithelial cancers (Fisher’s Exact test, unadjusted P<0.05). Taken together, these results strongly suggest that the discovered microRNA-mRNA biomodules correspond to regulatory mechanisms common to human epithelial cancer samples. In conclusion, we developed and evaluated a novel comprehensive method to systematically identify, on a genome scale, microRNA-mRNA expression biomodules common to distinct cancers of the same tissue. These biomodules also comprise novel microRNA and genes as well as an imputed regulatory network, which may accelerate the work of cancer biologists as large regulatory maps of cancers can be drawn efficiently for hypothesis generation.     

多重PCR技术分析日本对虾Marsupenaeus japonicus精巢和卵巢差异表达基因

通过多重PCR方法,对采用SSH(抑制消减杂交)技术制备日本对虾卵巢特异探针并筛选卵巢cDNA全长文库所获得的8个阳性克隆进行分析,研究这些新克隆的基因在精巢和卵巢的差异表达情况。这8个基因可分为二类,一类为卵巢特异表达的基因,一类为卵巢的表达量高于精巢的差异表达基因。     

Rank sum method for related gene selection and its application to tumor diagnosis

Tumor diagnosis by analyzing gene expression profiles becomes an interesting topic in bioinformatics and the main problem is to identify the genes related to a tumor. This paper proposes a rank sum method to identify the related genes based on the rank sum test theory in statistics. The tumor diagnosis system is constructed by the support vector machine (SVM) trained on the set of the related gene expression profiles. The experiments demonstrate that the constructed tumor diagnosis system with the rank sum method and SVM can reach an accuracy level of 96.2% on the colon data and 100% on the leukemia data.     

抗α毒素单链抗体基因表达载体的构建

将 2种抗A型产气荚膜梭菌α毒素单链抗体 (ScFv)基因ScFv - 2E3和ScFV - 1A8分别克隆至表达质粒pUC119,pET - 2 0b ,pET - 2 8a和pHOG2 1中 ,构建了重组质粒PUC -2E3和pUC - 1A8,pET2 0b - 2E3和pET2 0b - 1A8,pET2 8a - 2E3和pET2 8a - 1A8以及pHOG - 2E3和pHOG - 1A8,然后分别转化至大肠杆菌中 ,提取质粒 ,并进行酶切鉴定和核苷酸序列分析 ,结果表明构建的重组质粒中均含目的ScFv基因片段 ,说明已成功构建了 8个含ScFv基因的表达质粒     

优选Atlas微阵列检测胶质瘤基因表达谱的分析方法

从Atlas微阵列多种分析法中优选获得差异基因信息量大且较准确的方法。使用Atlas微阵列检测2例新鲜胶质母细胞瘤组织、获得相应的基因表达谱,选取不同的标准化基值及内参照共组合成8种不同方法,比较2例肿瘤组织的差异表达基因,并随机抽取部分基因行RT-PCR验证,由不同分析法得到的结果不同,以一种看家基因为标准化基值,且以所有基因表达值的中位数为内参照比较时得到的信息最多,且经RT-PCR证实可靠。证明以看家基因为标准化基值、并以所有差异基因表达值的中位数为内参照,可能是分析Atlas微阵列检测结果的较优方法     

Isolation and expression pattern analysis of novel ESTs from human fetal brain

In order to learn the mechanism of brain development and differentiation, 90 expressed sequence tags (ESTs) were isolated by differential display from the cerebrum and cerebellum of 13-week and 33-week fetal brains. After searching database, 74 of them represented novel genes, some of them were homologous to the brain development related genes. Using total cDNA probes, 79 of the ESTs and their expression differences in fetal brain were further characterized.     

大黄鱼Rnd1基因表达载体构建及表达模式分析

为探究Rnd1基因在大黄鱼免疫应答过程中的作用,采用实时荧光定量PCR技术（qRT-PCR）对该基因的表达模式进行分析,同时构建原核表达载体pET-28a-Rnd1,并转化进大肠杆菌后诱导该蛋白的融合表达。研究结果表明:大黄鱼Rnd1基因ORF为699 bp,编码232个氨基酸;经序列多重比对和进化树构建发现,Rnd1的氨基酸序列高度保守;在健康大黄鱼的8个免疫组织中,Rnd1在肝脏中相对表达量最高,其次为脑,而在肠中表达量最低;变形假单胞菌攻毒后,Rnd1在肝脏中48 h时达到最高值,为对照组的25倍;在脾脏中则持续上调表达,尤其在48 h后升高更为明显。     

基于生物信息学方法分析GABRD基因在结肠癌中的表达及预后情况

采用生物信息学方法探讨GABRD基因在结肠癌样本中的表达及预后情况。通过UCSC XENA下载33种肿瘤类型和正常组织的RNA序列数据和相关临床数据,使用R软件分析GABRD基因在结肠癌样本中的表达,并筛选共表达基因,对其进行富集分析;分析GABRD基因对结肠癌患者生存及预后的影响,并建立预后列线图;构建GABRD基因的蛋白质-蛋白质相互作用(protein-proteininteraction, PPI)网络并筛选关键模块及枢纽基因,验证枢纽基因的生存及临床诊断价值。结果表明：GABRD基因在结肠癌样本中高表达并影响患者生存,筛选得到369个共表达基因,基因本体论(gene ontology, GO)功能富集发现其主要参与G蛋白偶联等生物学过程,京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)通路富集显示其主要参与AMPK等信号通路;构建出由51个节点和523个连接组成的PPI网络,筛选枢纽基因5个,其中2个显著影响生存,5个具有临床诊断价值。综上,GABRD基因在结肠癌样本中高表达,影响结肠癌患者生存及预后,可能...     

基因表达系列分析在肿瘤研究中的应用

基因表达系列分析(serial analysis of gene expression, SAGE)是一种快速分析基因表达信息的技术.它不但能快速、详细地分析成千上万个基因,还能发现新基因,因此是基因表达定性和定量研究的一种新的有效手段.近年来此技术广泛应用于肿瘤的研究,了解肿瘤发病机制,识别诊断和治疗肿瘤的新基因.可以预测SAGE在肿瘤研究和诊断过程中的应用将会对肿瘤的认识和治疗产生深远的影响.     

造血干细胞(CD34+)表达谱数据分析

造血干细胞分化的潜能及自我更新的分子机制是造血干细胞研究中最重要的领域。通过对来自造血干细胞（CD34＾＋）的EST（Expressed　Sequence　Tags）和SAGE（Serial　Analysis　of　Gene　Expression）数据进行系统生物信息学分析,发现了造血干细胞除表达大量下游分化细胞的分子标志外,还表达一些非造血组织的特异基因。在分子调控方面,反义RNA可能是一种非常重要的调控手段。     

基于功能模块的基因表达谱聚类分析

按Gone Ontology基因功能分类体系，将基因模块化地组织成具有显著生物意义的低维功能模块单元，并将其作为新的分析指标用于分类微阵列疾病样本，从而提出了基于功能表达谱的聚类分析新途径、采用NCI60数据集，通过功能表达谱对组织样本进行聚类分析．结果显示，新算法不但得到高准确度的样本分型结果，而且能够直接从功能水平上给出相应的生物学解释．同时，用基于功能表达谱对组织样本进行聚类分析可以显著降低特征维数，有效地处理高检测误差与基因表达变异问题．     

LoG矩阵分解的肿瘤基因特征提取方法

伴随着基因芯片的发展,通过研究海量的基因表达谱数据来识别肿瘤已成为生物信息学研究的热点.提出一种基于LoG(Laplace of Gaussian)矩阵分解的肿瘤基因特征提取方法,该方法首先将样本数据映射为高维空间中的点,然后构建点与点之间的LoG矩阵,在保留样本分类信息的情况下,使得无结构信息的基因表达谱数据变成具有结构信息的图,再对LoG权值矩阵进行非负矩阵分解得到能够表征样本特征的特征分量,最后用KNN对样本进行分类.通过对白血病和结肠癌基因表达谱数据的特征提取,验证该文方法的可行性和有效性.     

Identification of genes associated with cotyledon senescence in upland cotton

Leaf senescence in plants is an essential develop- mental phase, and an understanding of senescence is important not only for pure scientific reasons, but also for practical purposes. During the last decade, a number of senescence-associated genes (SAGs) …