光照和黑暗条件下大豆和玉米基因表达差异的初步研究

光照黑暗条件下，植物幼苗的形态建成差异十分明显，以双子叶植物大豆和单子叶植物玉 材料，利用改进的ｍＲＮＡ差异展示技术分析了黄化苗和苗的基因表达的差异，黄化苗和苗基因表达差异可以归纳为“：黄化苗基因特异表达，绿苗基因特异表达，黄化苗基因表达增强，绿苗基因表达增强，黄化革和绿苗基因表达水平和近五咱类型大豆绿苗中基因特异表达类型比黄化苗要多，玉米中则相反，黄化苗基因特异表达类型多于绿苗，试验中还对差异展     

Cloning and expression of putative ethylene receptor genes in soybean plant

Ethylene plays important roles in plant growth, development, and stress responses, and ethylene receptors have been identified and studied extensively in various plant species. Here we report the cloning of four ethylene receptor genes from soybean, i.e. GmETR1, GmERS1, GmETR2 and GmEIN4. Construction of the phylogenic tree showed that GmETR1 and GmERS1 belong to subfamily I whereas GmETR2 and GmEIN4 belong to subfamily II. The four ethylene receptor genes showed different tissue-specific expression patterns in roots, stems, leaves, cotyledons, flowers, pods and seeds of soybean. These genes were differentially regulated by various abiotic stresses and plant hormones. The possible roles of the four genes in soybean plant were also discussed.     

Cloning and expression of putative ethylene receptor genes in soybean plant

Ethylene plays important roles in plant growth, development, and stress responses, and ethylene receptors have been identified and studied extensively in various plant species. Here we report the cloning of four ethylene receptor genes from soybean, i.e. GmETR1, GmERS1, GmETR2 and GmEIN4. Construction of the phylogenic tree showed that GmETR1 and GmERS1 belong to subfamily I whereas GmETR2 and GmEIN4 belong to subfamily II. The four ethylene receptor genes showed different tissue-specific expression patterns in roots, stems, leaves, cotyledons, flowers, pods and seeds of soybean. These genes were differentially regulated by various abiotic stresses and plant hormones. The possible roles of the four genes in soybean plant were also discussed.     

Sequence identification of 2,375 human brain genes.

We recently described a new approach for the rapid characterization of expressed genes by partial DNA sequencing to generate 'expressed sequence tags'. From a set of 600 human brain complementary DNA clones, 348 were informative nuclear-encoded messenger RNAs. We have now partially sequenced 2,672 new, independent cDNA clones isolated from four human brain cDNA libraries to generate 2,375 expressed sequence tags to nuclear-encoded genes. These sequences, together with 348 brain expressed sequence tags from our previous study, comprise more than 2,500 new human genes and 870,769 base pairs of DNA sequence. These data represent an approximate doubling of the number of human genes identified by DNA sequencing and may represent as many as 5% of the genes in the human genome.     

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.     

甘薯耐旱和耐盐基因的挖掘和表达分析

甘薯是世界第7大粮食作物,具有产量高、营养丰富、耐干旱和盐碱等优点.通过转录组学方法,基于国内3个甘薯品种的综合转录组数据库中进行耐旱和耐盐相关转录本序列的挖掘,共获得238个转录本,随机选取9条具有全长编码序列的转录本进行PCR扩增、克隆和测序后,测定序列与组装序列相似度均高于98%,表明转录本序列是可靠的.分析这些转录本在不同甘薯品种间的表达水平时发现,耐旱基因在京薯6号中表达量普遍较高,而在徐薯18中则普遍偏低,而耐盐相关基因的差异表达模式却与之相反.利用数字基因表达谱数据进一步分析耐旱和耐盐基因在徐薯18的6个组织或生长发育阶段中的差异和特异表达,结果显示:耐旱和耐盐基因在成熟叶和膨大期块根中相对于其他组织具有高表达且差异显著.采用荧光定量PCR方法验证结果表明,耐旱和耐盐基因在徐薯18不同组织器官或发育阶段表达情况与数字基因表达谱分析结果基本一致.     

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。     

Differential gene expression profile in ischemic myocardium of Wistar rats with acute myocardial infarction

To determine the differential genes in ischemic myocardium of Wistar rats with acute myocardial infarction （AMI）, we constructed two differential gene expression profiles. AMI model was generated by Iigation of the left anterior descending coronary artery in Wistar rats. Total RNA was extracted from the normal and the ischemic heart tissues under the IigaUon point at the 8th day after the operation. Differential gene expression profiles of the two samples were constructed by using long serial analysis of gene expression （LongSAGE）. Real time fluorescence quantitative PCR （Q-PCR） was used to confirm the expression changes of partial target genes. The main results were as follows： a total of 15966 tags were screened from the normal and the ischemic LongSAGE maps, and 9646 tags in the normal tissue and 9563 tags in the ischemic tissue were obtained. Among them, 7665 novel tags were identified by NCBI BLAST search. In the ischemic tissue, 142 genes significantly changed compared to those in the normal tissue （P〈0.05）. These differentially expressed genes may play important roles in the pathways of oxidation and phosphorylation, ATP synthesis and glycolysis and so on. Partial genes identified by the LongSAGE were confirmed by Q-PCR. The results show that AMI causes a series of gene expression changes in the regulation of the pathways related to energy metabolism.     

GmGSL7c在大豆抗SMV过程中的作用

为了阐明大豆Glycine max(L.)Merr.胼胝质合酶在大豆抵御大豆花叶病毒(Soybean mosaic virus,SMV)侵染过程中的关键作用,采用生物信息学方法在大豆中鉴定出24个胼胝质合酶,并挑选出受一氧化氮(NO)影响且参与SMV抗性调控的大豆胼胝质合酶Glyma.08G308200(GmGSL7c).使用RT-qPCR验证了清除NO的大豆植株中基因GmGSL7c的表达情况,并借助基于烟草脆裂病毒(TRV)介导的基因沉默(VIGS)技术沉默GmGSL7c基因.结果发现,GmGSL7c的沉默影响了叶片中SMV诱导的胼胝质积累,在沉默植株未被接种的上位叶中可检测到SMV外壳蛋白基因SMV-CP并观察到发病症状,表明GmGSL7c基因的沉默抑制了大豆对SMV的抗性,为进一步研究大豆与SMV间互作的抗病信号通路奠定了基础.     

土壤砷污染对大豆砷含量与分布的影响

通过土壤加砷盆栽大豆实验,利用氢化物发生-分光光度法测定大豆和土壤的砷含量,以研究土壤砷污染对大豆砷含量及其分布的影响.结果表明,大豆根、茎和籽粒砷含量均与土壤加砷水平呈极显著的线性相关,并呈根〉茎〉籽粒的规律.大豆收获后,土壤砷含量与土壤加砷水平呈极显著的线性相关,土壤砷的残留率在82%以上,与土壤加砷水平呈极显著的对数相关.大豆根、茎和籽粒的富砷量均与土壤加砷呈极显著的二次函数相关关系,大豆茎的富砷量是根富砷量的3.4~8.1倍,是籽粒富砷量的2.8~4.6倍.大豆吸收的砷有82%以上存在于地上部分,但大豆对土壤加砷的利用率只在万分之几.大豆富砷量和大豆对土壤砷的利用率均以茎最高,而富集系数则为根〉茎〉籽粒.总之,大豆砷含量受土壤砷水平决定,籽粒含砷量最低有利于砷污染土壤的利用,土壤砷污染具有长效性.     

Identification of genes induced during Medicago sativa nodule development by using the cDNA-AFLP technique

Under limited nitrogen conditions, rhizobia are ableto induce the formation of nitrogen-fixing root nodules on their leguminous plant host. This organogenetic process is triggered by a complex exchange of molecu- lar signals between the host plant and bac…     

Transcritption regulation of soybean ribulose-l,5-bisphos-phate carboxylase small sub-unit gene by external factors

Ribulose-1,5-bisphosphate carboxylase small subunit gene (rbcS) is present with multi-gene family in plant genome. In Glycine max, the rbcS polypeptide (EC4.1.1.39) is encoded by a gene family containing 4—8 members. Three full-length rbcS cDNA clones were isolated and characterized from soybean seedlings, and both of their nucleotide and amino acid sequences showed high similarity. Differential accumulation of the rbcS mRNA was observed among roots, hypocotyls, cotyledons, epicotyls and leaves. The rbcS genes were up-regulated by various external factors such as salicylic acid (SA), salt stress and drought stress. The expression level of rbcS genes after being treated by 2.0 mmol/L SA and 0.4% NaCl, respectively, is 2.5—3.0-fold as high as that of control sample. Moreover, soybean rbcSmRNA was accumulated with diurnal variation but easily influenced by light and low temperature.     

Transcritption regulation of soybean ribulose-1,5-bisphosphate carboxylase small subunit gene by external factors

Ribulose-1,5-bisphosphate carboxylase small subunit gene (rbcS) is present with multi-gene family in plant genome. In Glycine max, the rbcS polypeptide (EC4.1.1.39) is encoded by a gene family containing 4-8 members. Three full-length rbcS cDNA clones were isolated and characterized from soybean seedlings, and both of their nucleotide and amino acid sequences showed high similarity. Differential accumulation of the rbcS mRNA was observed among roots, hypocotyls, cotyledons, epicotyls and leaves. The rbcS genes were up-regulated by various external factors such as salicylic acid (SA), salt stress and drought stress. The expression level of rbcS genes after being treated by 2.0 mmol/L SA and 0.4% NaCl, respectively, is 2.5-3.0-fold as high as that of control sample. Moreover, soybean rbcS mRNA was accumulated with diurnal variation but easily influenced by light and low temperature.     

A comparative analysis of tissue gene expression data from high-throughput studies

High-throughput technologies were employed over the past decade to study the expression profiles of cells and tissues.There are large collections of accumulated data from public databases and numerous research articles were published on these data.In the current study,we performed meta-analysis on the gene expression data from human liver and kidney tissues produced from five different technologies:EST,SAGE,MPSS,microarray,and RNA-Seq.We found RNA-Seq was the most sensitive in the number of genes it detected while SAGE and MPSS were the least sensitive.For the genes detected by all the platforms,there were generally good correlations to the measured expression levels of corresponding genes.We further compared detected genes to liver/kidney proteomics data from the Human Protein Atlas,and found 960 of the 8764 genes only detected by RNA-Seq were validated by proteomics results.In conclusion,RNA-Seq is a more sensitive and consistent technology compared to the other four high-throughput platforms,though their results are in general agreement.Average coverage was determined to be the preferred measurement to represent gene expression levels by RNA-Seq data and will be used in future works.     

Isolation and characterization of soybean NBS analogs

Isolation of plant resistance genes is greatly helpful to crop resistance breeding and the insight of resistance mechanism. The cloned plant resistance genes are classified into four classes according to their putative structural domain, of which the majority possesses nucleotide-binding site (NBS) domain that consists of P-loop, kinase2a and kinase3a. The conservation of this domain affords the potential possibility of cloning the plant resistance genes, which is homology-based cloning technique. In the present study, the degenerate oligonucleotide primers were designed according to the tobaccoN andArabidopsis RPS2, and 358 clones were isolated from the genomic DNA of resistance soybean cultivar Kefengl, resistant to soybean mosaic virus, and 4 open-reading NBS analogs were finally characterized and designated asKNBS1, KNBS2, KNBS3 andKNBS4. Southern hybridization suggested that they were present with multicopy in the soybean genome;KNBS4 was mapped to F linkage group andKNBS2 co-located J linkage group with the SCAR marker ofRsa resistant to soybean mosaic virus by RFLP analysis. Northern analysis suggested thatKNBS2- related sequence was low and constitutively expressed in the root, stem and leaves of soybean. The detailed characterization of NBS analogs is very helpful to ultimately cloning the soybean resistance gene.     

伤寒沙门菌激活TRAIL信号通路促进巨噬细胞凋亡

为探究伤寒沙门菌对巨噬细胞凋亡及肿瘤坏死因子相关凋亡诱导配体(tumor necrosis factor-related apoptosis inducing ligand,TRAIL)信号通路的影响,对伤寒沙门菌感染THP-1细胞早期和后期提取细胞RNA进行转录组测序(RNA-seq).通过定量PCR(qPCR)技术检测凋亡相关基因的转录水平,对RNA-seq结果进行验证,流式细胞术和蛋白质免疫印迹法检测THP-1细胞的凋亡和凋亡相关蛋白;加入TRAIL抗体结合TRAIL蛋白后,流式细胞术和蛋白质免疫印迹法检测感染早期THP-1细胞凋亡的变化.结果显示,伤寒沙门菌感染THP-1细胞后,凋亡相关基因caspase-3、caspase-8、caspase-9在感染后期转录水平显著增加,Tnfsf10、Tnfrsf10b、Tnf、Fas在感染早期和后期转录均增加,细胞凋亡率明显增加,caspase-3、caspase-8、caspase-9蛋白活化增加,TRAIL、DR5蛋白表达增加;与PBS对照组相比,加入TRAIL抗体后caspase-3蛋白活化明显减弱,细胞凋亡率明显下降.综上,伤寒沙门菌通过部分激活TRAIL信号通路来诱导巨噬细胞凋亡.     

大蕉冷诱导差减文库的构建与分析

以低温处理的大蕉幼苗cDNA为检测子,未处理的大蕉幼苗cDNA为驱赶子,利用抑制性差减杂交技术(suppression subtractive hybridization,SSH)构建了大蕉幼苗冷诱导差减cDNA文库,通过点杂交差异筛选cD-NA文库,得到约50个低温下表达增强的候选克隆,对其进行DNA测序和同源性比较,发现获得的ESTs在功能上主要涉及信号传导、表达调控、非生物胁迫防御、蛋白质加工和能量代谢等方面。该SSH文库的构建为克隆大蕉抗寒相关基因奠定了基础。     

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.