中国明对虾和中华绒螯蟹EST的Blast2GO注释及其在免疫基因分布研究中的应用

以dbEST数据库中公布的中国明对虾和中华绒螯蟹的EST序列作为数据源,利用CAP3对其进行聚类拼接,采用Blast2GO软件进行功能注释,并通过查找免疫相关的GO注释和检索免疫关键词的方法寻找免疫相关基因,经与不同物种免疫基因的比较,推测可能的免疫基因序列,并进一步分析免疫基因在不同组织和细胞中的分布.结果表明,通过注释和关键词进行筛选这2种方法具有较好的互补性;预测了位于中国明对虾头胸部的60个可能的免疫基因以及位于中华绒螯蟹血细胞hemocyte、haemocyte、肝胰腺、性腺和精巢中的250个免疫基因,这些基因包括模式识别受体、抗氧化蛋白、抗菌肽、凝集素等,其中部分参与酚氧化酶原激活系统、Toll信号通路等重要免疫过程.中华绒螯蟹血细胞中具有种类丰富的免疫基因,与已有的甲壳动物免疫系统相符合.肝胰腺中发现了模式识别蛋白、蛋白酶以及数量众多的凝集素种类,提示肝胰腺在免疫过程中也发挥了一定作用.     

Identification of true EST alignments and exon regions of gene sequences

Expressed sequence tags (ESTs), which have piled up considerably so far, provide a valuable resource for finding new genes, disease-relevant genes, and for recognizing alternative splicing variants, SNP sites, etc. The prerequisite for carrying out these researches is to correctly ascertain the gene-sequence-related ESTs. Based on analysis of the alignment results between some known gene sequences and ESTs in public database, several measures including Identity Check, Gap Check, Inclusion Check and Length Check have been introduced to judge whether an EST alignment is related to a gene sequence or not. A computational program EDSAcl.0 has been developed to identify true EST alignments and exon regions of query gene sequences. When tested with human gene sequences in the standard dataset HMR195 and evaluated with the standard measures of gene prediction performance, EDSAel.0 can identify proteincoding regions with specificity of 0.997 and sensitivity of 0.88 at the nucleotide level, which outperform that of the counterpart TAP. A web server of EDSAcl.0 is available at http://infosci.hust.edu.cn.     

射干提取物对小鼠免疫功能的影响

摘要：目的研究射干提取物对小鼠免疫功能的影响。方法以环磷酰胺制备小鼠免疫低下模型,测定腹腔注射 印度墨汁后小鼠网状内皮细胞(RES,单核巨噬细胞)炭粒廓清指数,观察其对小鼠非特异性免疫功能的影响;通过 测定正常小鼠血清溶血素水平观察射干提取物对小鼠体液免疫的影响。结果射干提取物可增强小鼠网状内皮 细胞的吞噬功能;促进抗体溶血素的产生。结论射干提取物对非特异性免疫功能和特异性免疫功能都有增强的 作用。     

Microarray-Based Differential Expression Monitoring of 79 Novel Genes in Human Fetal Tissues

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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) …     

Analysis of porcine MHC expression profile

The porcine major histocompatibility complex (MHC, also named swine leukocyte antigen, SLA) is associated not only with immune responsibility and disease susceptibility, but also with some reproductive and productive traits such as growth rate and carcass composition. As yet systematical research on SLA expression profile is not reported. In order to illustrate SLA expression comprehensively and deepen our understanding of its function, we outlined the expression profile of SLA in 51 tissues of Landrace by analyzing a large amount of ESTs produced by ““Sino-Danish Porcine Genome Project““. In addition, we also compared the expression profile of SLA in several tissues from different development stages and from another breed (Erhualian). The result shows: (i) classical SLA genes are highly expressed in immune tissues and middle part of intestine; (ii) although SLA-3 is an SLA la gene, its expression abundance and pattern are quite different from those of the other two SLA la genes. The same phenomenon is seen in HLA-C expression, suggesting that the two genes may function similarly and undergo convergent evolution; (iii) except in jejunum, the antigen presenting genes are more highly expressed in breed Erhualian than in Landrace. The difference might associate with the higher resistance to bad conditions (including pathogens) of Erhualian and higher growth rates of Landrace.     

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.     

Gene expression profiling related to powdery mildew resistance in wheat with the method of suppression subtractive hybridization

“Bainong 3217 × Mardler” BC₅F₄ wheat line at the initial stage of inoculation with powdery mildew pathogen (Erysiphe graminis DC) was used to construct a suppression subtractive hybridization (SSH) cDNA library. Totally 760 ESTs were obtained through sequencing. Similarity analysis of ESTs based on BLASTn and BLASTx with the sequences in GenBank, in combination with macroarray differential screening, revealed that 199 ESTs of 65 kinds were known to be functionally disease resistance related. Based on the gene expression profiling in the present study, it is postulated that salicylic acid (SA) and MAP-related signal transduction pathways were involved in powdery mildew resistance in wheat. System acquired resistance genes were predominant in terms of kinds and quantity. With the initiation of cell defense reaction, the genes conferring anti-oxidation substances were largely expressed and thus cell protection mechanism was activated. Much evidence revealed that phenylpropanes metabolic pathway was involved in phytoalexin synthesis in wheat powdery mildew resistance. Genes conferring some enzymes of structural modification of cell walls and proteinase inhibitors inhibiting pathogen growth were also detected. The genes controlling a few proteinases (mainly cysteine proteinase) had a considerable redundancy of expression.     

黄连治疗新冠肺炎的作用机理——基于网络药理学方法和分子对接技术

基于网络药理学方法和分子对接技术,初步探索了黄连治疗新冠肺炎（COVID-19）的作用机理.使用中草药系统药理学平台筛选黄连的有效活性成分与作用靶点,GeneCards和OMIM数据库筛选COVID-19的疾病靶点,R软件筛选药物与疾病的共同靶点,并利用Cytoscape软件构建“药物—活性成分—靶点—疾病”互作网络,STRING数据库构建共同靶点蛋白互作网络,ClueGo软件对共同靶点进行基因功能分析,R软件对共同靶点进行KEGG通路富集分析,然后将黄连有效成分中的核心成分与其治疗COVID-19的主要靶点进行分子对接.结果表明,黄连的有效活性成分共14种,靶点共235个;COVID-19的相关基因共341个;黄连治疗COVID-19的关键靶点包括VEGFA,IL6,POR,PLAT.分子对接结果显示,黄连中核心化合物榭皮素与PLAT,VEGFA,IL6对接效果良好.     

西藏胡黄连根状茎差异表达基因的筛选及分析

 西藏胡黄连是著名的濒危西藏药材, 其粗壮的根茎部是重要的合成和储存药用萜类物质器官,萜类含量显著高于叶部。为克隆西藏胡黄连根状茎和叶的差异表达基因,利用抑制消减杂交技术,构建了根状茎特定的抑制消减文库。从该SSH文库中随机挑取片段不一的阳性克隆测序,采用Blastx进行同源比对,获得了27个表达序列标签（EST）,并获登录号。序列统计分析结果表明,其中有11个EST在GenBank中无同源性序列,推测可能是新基因片断。蛋白质功能分类结果表明,这些蛋白质与翻译、能量代谢、转运与结合、细胞膜合成、氨基酸生物合成及中间代谢6大类蛋白功能有关。为深入研究与萜类生物合成直接或间接相关基因,选择了长595 bp的差异表达EST序列EX172715进行了同源比对和蛋白系统进化分析。结果表明,EX172715具有细胞色素P450单加氧酶的特征结构,与拟南芥的细胞色素P450单加氧酶蛋白的同源性高于水稻和小麦。提供了一组与西藏胡黄连次生代谢相关的新基因库。     

Cloning and identification of a novel human glioma differentiation related gene GDR1

In order to identify the genes associated with glioblastoma differentiation, some ESTs, expressed differentially in the control cell and the differentiated human glioblastoma cell line BT-325 induced by the all-trans retinoid acid, have been isolated by the method of DDRT-PCR. Of the 46 ESTs sequenced, 19 are from new genes. A full-length 1 535-bp cDNA, termed gene GDR1, has been isolated from the human cDNA library using the probe designed according to one of the novel ESTs, HGBB098. The open reading frame of GDR1 gene encodes a putative protein containing 334 amino acid residues. Blast against the current GenBank DNA and protein sequence database did not reveal significant homology with any known proteins. RT-PCR shows that GDR1 mRNA level increased in the differentiated BT-325 cells after being treated with RA. The different expression patterns of GDR1 mRNA in human tissues have been detected through the multiple tissue Northern blot hybridization.     

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。     

通过差减文库筛选山羊羔肠道淋巴集结特异表达基因

羊羔肠道淋巴集合淋巴结（Peyer's patch，以下简称PP），是B淋巴细胞的主要来源地和发育、成熟场所，兼具中枢淋巴器官和周围淋巴器官的功能.采用抑制性差减杂交（suppression subtractive hybridization，SSH）方法，构建山羊羔肠道淋巴集结与其非PP肠壁组织的差减 cDNA 文库，以期找到在山羊羔肠道淋巴集结中特异表达的与免疫相关的基因. 分别从山羊羔PP与非PP肠壁组织提取总RNA，反转录成cDNA，以PP作为待检组织(tester)，非PP肠壁作为驱动组织(driver)，经过两轮杂交和抑制性PCR扩增，产物与T载体连接，经蓝白斑筛选，提取质粒,经EcoRI酶切鉴定插入片段并测序,由此构建了两种组织间差异表达基因的差减cDNA文库. 对其中160个克隆测序，得到几个可能与免疫相关的基因，为进一步从中挑选和表达活性蛋白基因用于生产免疫增强剂奠定了基础.     

苔藓分子生物学的一些进展

本文简述了近年来苔藓分子生物学的突破性进展。 1995年以前 ,苔藓系统学中尚无DNA序列数据 ,但到 1999年产生了 2 5 0个分类单位的 10 0 0个DNA序列 ,并分析了它们的系统发生信息。在分子遗传学研究中 ,小立碗藓Physcomitrellapatens、葫芦藓Funariahygrometrica、土生墙藓Tortularuralis和角齿藓Cer atodonpurpureus正在发展成有力的工具。表达序列靶 (ESTs)和外源基因的表达已成功地用于这些苔藓植物。同源重组在酵母和小白鼠细胞中已经确定 ,然而至今尚无任何植物模型体系。 1997年Schaefer和Zryd证明 ,小立碗藓具有有效的同源重组能力 ,至今在所有植物中是独特的 ,这在分析植物基因功能中将显示是十分有用的     

苏南丘陵山区森林中冬青幼苗更新影响因子研究

【目的】探究冬青幼苗更新与环境因子的相关关系,为苏南丘陵山区森林抚育和可持续经营提供参考。【方法】对江苏省溧水林场内4块有一定代表性的天然次生林样地进行详细调查,在分析不同群落中冬青幼苗的个体大小-密度分布特征的基础上,运用冗余分析(RDA)的方法对冬青幼苗更新状况与种内、种间、土壤因子的相关关系进行研究。【结果】随着群落中冬青重要值上升,冬青幼苗由“高密度-小株型”的分布特征,逐渐转变为“低密度-大株型”状态。3类环境因子对冬青幼苗更新总体表现为促进作用,但不同林层的林分结构因素间及不同种类的土壤因素间存在一定差异。当冬青重要值较高时,种内因子和种间因子组成的林分结构因素是主要影响因素,土壤因子影响较小,此时种间作用主要体现于上层高大乔木的影响。当冬青重要值较低时,土壤因子的影响超过林分结构因素,此时林分结构的影响主要表现为较强的更新层种间作用。【结论】在苏南丘陵山区森林中,不同类型群落中影响冬青幼苗更新的主导因子不同,林分结构和土壤因子对冬青幼苗更新的作用因群落中冬青重要值高低存在一定差异。     

温度对羊草（Leymuschinensis）生长及无性系分化的影响

根据温室内的人为控制温度试验，观测温度对羊草（Ｌｅｙｍｕｓｃｈｉｎｅｎｓｉｓ）无性系分化和生长的影响，得出如下结论；温度是影响羊草株高的最主要生态因子，适宜的高温显著促进单草的伸展；温度也是促进单草分蘖的主要因子之一，羊草的生物量积累受到温度变化极值的限制，适宜的温度范围显著促进生物量积累．羊草无性系的分化和高温的天数明显正相关，无性系对高温有较强的生态适应性，甚至在高温已经抑制羊草生物量的积累的情况下，仍然对无性系的生长和分化有一定的促进作用，这充分表明了羊草无性系对温度有较强生态适应的特点．