一个鼻咽癌相关EST的鉴定及其全长cDNA序列分析

鼻咽癌是我国南方及东南亚地区常见的恶性肿瘤之一.通过对鼻咽癌染色体高频率杂合性丢失区域3p21的表达序列标签(expressedsequencetag,EST)进行同源性比较分析,运用逆转录聚合酶链式反应的方法,筛选到一个在41.18%(14/34)的鼻咽癌活检组织及20.0%(1/5)的鼻咽癌细胞系中表达下调的ESTBG772301;并用Northern杂交方法,检测了该EST在多种正常成人组织中的表达状况及其所代表基因的转录本大小.在此基础上,对该EST来源的cDNA克隆(IMAGE:4839190)进行直接测序,获得了一个全长为2377bp的新cDNA序列;经生物信息学分析,发现它与已知基因序列无明显同源性,属于一个新基因,定位于染色体3p21.3,被命名为鼻咽癌表达下调基因(NPCEDRG,GenBank登录号:AF538150).其编码的蛋白质含169个氨基酸,与一个已报道的在进化上相对保守、功能未知的人类蛋白Nicolin1(简称NICN1)N端170个氨基酸残基的序列同源性为97%,但缺少NICN1蛋白C端43个氨基酸残基,可能是nicolin1基因不同剪接本的编码产物.     

大黄鱼耐低温性状相关微卫星标记的筛选

鱼类的耐低温性状是一种重要的经济性状。为了初步分析大黄鱼的耐低温性状, 文章采用15对荧光微卫星标记, 以SSR-PCR方法对大黄鱼低温耐受组和正常对照组F₁代共40个个体进行了耐低温性状遗传差异分析。结果显示, 标记LYC0002在两组样品中共扩增出5个等位基因(片段大小分别为112 bp、110 bp、108 bp、106 bp和104 bp), 其中LYC00021_{12 bp}等位基因在低温耐受组的出现频率达60%, 而在正常对照组中的频率为零, 表明该等位基因对大黄鱼的温度敏感特性有较明显的偏好性, 可能与某种耐低温基因存在一定的连锁关系。此外, 对LYC0002_{106 bp、}LYC0002_{108 bp}、LYC0002_{110 bp} 和 LYC0002_{112 bp} 4个等位基因分别进行了回收、克隆及测序。序列比对结果显示, LYC0002_{112 bp}等位基因含有10个(CA)重复单元, 而其他3个等位基因依次缺失1个(CA)重复单元, 说明LYC0002在本研究样本中的突变方式为微卫星逐步突变模型(Stepwise mutation model, SMM)。     

镜鲤繁殖群体的遗传结构及微卫星标记与经济性状的相关性分析

选用35个多态性微卫星分子标记对天津换新良种场镜鲤一个繁殖群体的有效等位基因数(Ae)、观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC) 等进行了检测, 以卡方检验估计群体Hardy-Weinberg平衡。结果表明：在35个基因座共检测到118个等位基因, 平均等位基因数为3.37个, 每个座位检测到的等位基因数2~7个不等, 平均有效等位基因数为2.16, 观测杂合度平均值0.431, 无偏期望杂合度的平均值为0.4736, 平均多态信息含量0.42, 说明这个群体属于中度多态, 遗传多样性水平不高。卡方检验的P值显示多于半数的位点都发生了偏离。并将35个基因座的不同基因型与个体的体重、体长值进行了连锁分析, 得到了4个与体重、体长连锁的基因型, 并将所得结果与鲤鱼体长性状QTL定位结果进行对比, 其中HLJ319标记与QTL定位结果基本一致。分析了几个严重偏离平衡的基因型, 并讨论出现这种现象的可能原因。     

EST的应用现状与前景

综述EST（Expressed sequence tag）的用途,应用现状及其发展前景。     

4龄中华鲟垂体的EST分析

表达序列标签 (Expressed sequence tag, EST) 是鉴定基因表达规律和发现新基因的一种有效的分子生物学手段。为了能在中华鲟(Acipenser sinensis Gray) 中发现与生长和生殖内分泌调控相关的基因,我们构建了中华鲟垂体的SMART cDNA质粒文库。垂体是调节生长和生殖内分泌的重要器官。在本研究中,通过测序筛选得到了944个EST克隆,将所得EST 与 GenBank 数据库中的序列进行比对, 结果表明,802 (84.96%) 个克隆可以找到同源序列,共代表461个基因, 其中含132个已知功能基因;而 142 (15.04%) 个克隆不能找到同源序列。研究发现,在所有基因中,阿黑皮素原基因 (Proopiomelanocortin, POMC) 是出现次数最高的基因,占总EST数的10.17%, 显示出其在垂体中的重要地位。我们还发现了7个未知功能的基因并重点研究了其在心脏、肝脏、脾脏、肾脏、肌肉、精巢、卵巢和垂体等组织中的表达特异性。结果发现,4个基因：EG009334、EG009337、EG009338 和 EG009340为垂体特异性表达或垂体和卵巢特异性表达。对这些基因进一步的功能研究将有利于我们更好地了解中华鲟生长和生殖内分泌调控的分子机制。     

白菜的EST标记及其对油菜的通用性

根据白菜的表达序列标签,设计了28对引物。在对引物、dNTP、MgCl2的浓度及退火温度等参数进行测试后,建立了合适的PCR反应体系。在此反应体系下,以构建EST的白菜自交系A的DNA为模板,对设计的引物进行了筛选,发现有18对引物能对白菜DNA扩增出产物。用筛选出来的引物分别对17个白菜类品种进行PCR扩增,用琼脂糖凝胶电泳分析其产物的多态性,发现10对引物有多态性,这占了筛选引物的55.6%。为检测白菜EST标记的通用性,进一步利用设计的引物对不同油菜品种的DNA进行PCR扩增。在检测的28对引物中,共有24对引物能扩增出产物,占引物总数的85.7%,显示多态性的引物为18对,占引物总数的64.3%.。在对白菜DNA能扩增出产物的18对引物中,对油菜完全可用,且有13对引物产生多态性。而在那些对白菜未扩增出产物的10对引物中,也有6对能扩增出产物,其中5对显示多态性。文章研究结果证明,通过EST建立分子标记是可行的,而且这种标记对近缘物种是可通用的。     

EST分析技术在鸡基因组学研究中的应用

表达序列标签（EST）是由大量随机取出的cDNA库克隆经测序得到的组织或细胞基因组的一段cDNA序列,一个EST代表生物体某种组织某一时期的一个表达基因。综述了EST分析技术在鸡基因组研究中的应用。如用于鉴定、发现和预测鸡的新基因,用于基因图谱的绘制,用于筛选基因的单核苷酸多态性（SNP）位点,用于基因表达分析和基因芯片制作等。EST数据库和生物信息学的联合分析技术在推动家鸡后基因组的研究中发挥着重要的作用。     

柔嫩艾美尔球虫EST序列中SSR的获取及分析

对柔嫩艾美尔球虫EST—SSR进行生物信息学分析,共获取Eimeria tenella EST序列34074条,总长度为16．45Mb,小于12bpSSR的ESTs达7651条,从中获得SSR序列19576条、总长度为0．35Mb,EST—SSRs的频率是48．00％,平均相隔S40bp出现一个长度不小于12bp的SSR。在E．tenella的核苷酸重复基元中,2、3、4、5、6和7bp重复序列在基因组中出现的种类分别有11种472条、49种14710条、31种525条、13种25条、21种43条和15种400条,3碱基重复序列是最丰富的重复单元,占总数的75．14％。各种SSRs中富含G、C碱基的重复单元以GCA出现频率最多（28．63％）,次为AGC（17．59％）,GCT（8．76％）,TGC（7．62％）,CTG（7．15％）。     

EST的研究进展

EST(expressed sequence tags)是指从cDNA文库中随机挑取克隆并对其3′或5′端进行单轮自动测序所获得的短cDNA库列,一般长度为150～500 bp.EST作为一种快捷、高效的揭示基因组信息的方法,为寻找新基因、绘制遗传图谱、研究基因差异表达和比较基因组学及DNA芯片的制备等提供了大量的序列信息.总结了EST标记开发存在的一些问题及解决方法和主要EST标记(EST-SSR、EST-SNP、EST-RFLP、EST-AFLP)的开发策略.     

Analysis of genes expressed in head kidney of common carp Cyprinus carpio L treated with cortisol

We analyzed genes expressed from head kidney of common carp Cyprinus carpio L. treated with cortisol. The results of single-pass sequencing of expressed sequence tags (ESTs) from 188 clones (AU240288–AU240367, AU301120–AU301227) from kidney cDNA are presented. One-hundred-twenty-seven clones (67.6%) were completely unknown and are likely to represent newly described genes, whereas 61 clones (32.4%) were identified based on matches to sequences in the database. The putative genes contain several ribosomal proteins, cytochrome oxidase subunits. Immune related cDNA clones identified from kidney were immunoglobulin light chain (n=4), FK506/rapamycin-binding protein (FKBP), CXC chemokine receptor type 4, complement factor B/C2-A3, peptidylprolyl isomerase (cyclophilin; Cyp)-like1, cyclophilin S1, heat shock-70 kDa protein-4, stress-activated protein kinase-3 (n=2). FKBP and cyclophilin genes expressed in normal tissues (head kidney, spleen, liver, brain and heart). Expression of FKBP and cyclophilin genes were not detected in liver, brain and heart when treated with cortisol for 16 h.     

Microsatellite markers in common carp (Cyprinus carpio L.)

Microsatellite markers of the poly (CA) type in common carp ( Cyprinus carpio L.) are described. Clones containing a (CA) repeat were isolated from a common carp genomic library and sequenced. The number of repeats found was high compared to mammals but comparable with other teleost fishes. Classification of the repeats (perfect, imperfect and compound) are compared with the Atlantic cod ( Gadus morhua L.), rainbow trout ( Oncorhynchus mykiss ), and Atlantic salmon ( Salmo salar L.). A total of 41 primer sets were designed and tested for polymorphism on a test panel of eight animals (derived from outbred lines, inbred lines and gynogenetic clones). Thirty-two markers were found to be polymorphic. The heterozygosity in the outbred animals was 60·4%, 51·1% in the inbred animals and 0% in the gynogenetic clones. The average number of alleles among the eight animals was 4·7 per marker. Six markers (18·8%) gave an additional polymorphic amplification product besides the polymorphic amplification product in the expected size range. The possibility that these loci are tetraploid is discussed. The polymorphic loci described for common carp will be valuable as genetic markers for use in population, breeding, and evolutionary studies.     

鲤鱼微卫星突变速率和模式(英文)

利用150个微卫星分子标记在F1代家系的基因型分析过程中,共有27600个等位基因从亲本向子代传递,其中在5个微卫星座位上检测到6个突变的等位基因。对突变的等位基因数目进行统计分析后得出:鲤鱼平均每个世代每个微卫星座位的突变速率为2.53×10-4。在发现突变的5个位点中,经测序发现,突变序列中插入1个以上的重复单元就导致了突变的发生。这些突变表明,鲤鱼的微卫星突变没有遵循严格的渐变突变模型(stepwise mutation model,SMM)。该文关于鲤鱼微卫星突变速率和模式的研究将会对统计鲤鱼有效群体的统计提供有效参数。     

Genetic evolution and diversity of common carp Cyprinus carpio L.

Knowledge of genetic variation and population structure of existing strains of both farmed and wild common carp Cyprinus carpio L. is absolutely necessary for any efficient fish management and/or conservation program. To assess genetic diversity in common carp populations, a variety of molecular markers were analyzed. Of those, microsatellites and mitochondrial DNA were most frequently used in the analysis of genetic diversity and genome evolution of common carp. Using microsatellites showed that the genome evolution in common carp exhibited two waves of rearrangements: one whole-genome duplication (12–16 million years ago) and a more recent wave of segmental duplications occurring between 2.3 and 6.8 million years ago. The genome duplication event has resulted in tetraploidy since the common carp currently harbors a substantial portion of duplicated loci in its genome and twice the number of chromosomes (n = 100–104) of most other cyprinid fishes. The variation in domesticated carp populations is significantly less than that in wild populations, which probably arises from the loss of variation due to founder effects and genetic drift. Genetic differentiation between the European carp C.c. carpio and Asian carp C.c. haematopterus is clearly evident. In Asia, two carp subspecies, C.c. haematopterus and C.c. varidivlaceus, seem to be also genetically distinct.     

Structure, organization and expression of common carp (Cyprinus carpio L.) SLP-76 gene

SLP-76 is an important member of the SLP-76 family of adapters, and it plays a key role in TCR signaling and T cell function. Partial cDNA sequence of SLP-76 of common carp (Cyprinus carpio L.) was isolated from thymus cDNA library by the method of suppression subtractive hybridization (SSH). Subsequently, the full length cDNA of carp SLP-76 was obtained by means of 3' RACE and 5' RACE, respectively. The full length cDNA of carp SLP-76 was 2007 bp, consisting of a 5'-terminal untranslated region (UTR) of 285 bp, a 3'-terminal UTR of 240 bp, and an open reading frame of 1482 bp. Sequence comparison showed that the deduced amino acid sequence of carp SLP-76 had an overall similarity of 34-73% to that of other species homologues, and it was composed of an NH2-terminal domain, a central proline-rich domain, and a C-terminal SH2 domain. Amino acid sequence analysis indicated the existence of a Gads binding site R-X-X-K, a 10-aa-long sequence which binds to the SH3 domain of LCK in vitro, and three conserved tyrosine-containing sequence in the NH2-terminal domain. Then we used PCR to obtain a genomic DNA which covers the entire coding region of carp SLP-76. In the 9.2k-long genomic sequence, twenty one exons and twenty introns were identified. RT-PCR results showed that carp SLP-76 was expressed predominantly in hematopoietic tissues, and was upregulated in thymus tissue of four-month carp compared to one-year old carp. RT-PCR and virtual northern hybridization results showed that carp SLP-76 was also upregulated in thymus tissue of GH transgenic carp at the age of four-months. These results suggest that the expression level of SLP-76 gene may be related to thymocyte development in teleosts.     

Induced diploid gynogenesis and polyploidy in the ornamental (koi) carp Cyprinus carpio L.

The results of a series of experiments conducted in our laboratory on the ornamental common carp (koi), aimed at optimizing heat-shock chromosome-set manipulation procedures, are described. The timing of heat-shock initiation was expressed in the relative unit of embryological age (₀) in order to standardize this parameter, the absolute time for heat-shock initiation being calculated from duration of one ₀ at two different pre-treatment water temperatures. Heat shocks were applied within the periods of 0.05–0.60 ₀ and 1.20–2.20 ₀ which, respectively, cover the successive phases of the 2nd meiotic division and the 1st cleavage. The highest production of diploid gynogenetic offspring was observed when heat shocks were initiated at 0.15–0.25 ₀ and at 1.5 ₀, after insemination, corresponding to anaphase of meiosis-II, and metaphase of the 1st cleavage, respectively. Similar results were obtained irrespective of the different pre-treatment water temperatures, thus confirming the possibility of standardizing heat-shock timing by ₀.     

Application of PCR-RF-SSCP to study major histocompatibility class II B polymorphism in common carp (Cyprinus carpio L.)

A variety of methods have been applied for the characterization of major histocompatibility (MH) polymorphism in fish. We optimized a technique designated polymerase chain reaction-restriction fragments-single strand conformation polymorphism (PCR-RF-SSCP) for screening a large number of individuals for the Cyca-DAB1 and Cyca-DAB2 genes polymorphism in common carp. The advantages of this technique are simplicity, high sensitivity and low costs. PCR-RF-SSCP analysis revealed different genotypes consisting of unique combinations of the Cyca-DAB1 and Cyca-DAB2 sequences with the number of SSCP bands clearly correlating with the degree of heterozygosity of the Cyca-DAB1 and Cyca-DAB2 genes. We found four alleles for Cyca-DAB1 (*02-*05) gene but only one allele for Cyca-DAB2 (*02) and noted that the Cyca-DAB2 gene was either homozygous or absent. PCR-RF-SSCP analysis of n=79 carp individuals challenged with Aeromonas hydrophila indicated that individuals bearing no Cyca-DAB2 gene showed higher cumulative mortality and lower bacterial agglutination titers during the experiment. We suggest that our PCR-RF-SSCP method can be used to study correlations of different MH class II B genotypes/alleles with resistance of common carp to specific pathogens.     

Kinetics and thiol requirements of iodothyronine 5'-deiodination are tissue-specific in common carp (Cyprinus carpio L.)

Iodothyronine deiodinases determine the biological activity of thyroid hormones. Despite the homology of the catalytic sites of mammalian and teleostean deiodinases, in-vitro requirements for the putative thiol co-substrate dithiothreitol (DTT) vary considerably between vertebrate species. To further our insights in the interactions between the deiodinase protein and its substrates: thyroid hormone and DTT, we measured enzymatic iodothyronine 5′-deiodination, Dio1 and Dio2 mRNA expression, and Dio1 affinity probe binding in liver and kidney preparations from a freshwater teleost, the common carp (Cyprinus carpio L.). Deiodination rates, using reverse T3 (rT3, 3,3′,5′-triiodothyronine) as the substrate, were analysed as a function of the iodothyronine and DTT concentrations. In kidney rT3 5′-deiodinase activity measured at rT3 concentrations up to 10 μM and in the absence of DTT does not saturate appreciably. In the presence of 1 mM DTT, renal rT3 deiodination rates are 20-fold lower. In contrast, rT3 5′-deiodination in liver is potently stimulated by 1 mM DTT. The marked biochemical differences between 5′-deiodination in liver and kidney are not associated with the expression of either Dio1 or Dio2 mRNA since both organs express both deiodinase types. In liver and kidney, DTT stimulates the incorporation of N-bromoacetylated affinity labels in proteins with estimated molecular masses of 57 and 55, and 31 and 28 kDa, respectively. Although primary structures are highly homologous, the biochemistry of carp deiodinases differs markedly from their mammalian counterparts.     

Cadmium-binding to transferrin in the plasma of the common carp Cyprinus carpio

In this study, it was investigated by autoradiography with radioactive cadmium after Western blotting of two-dimensional electrophoresis gels, to which proteins cadmium is mainly bound in plasma of common carp Cyprinus carpio. The obtained results demonstrate that in carp plasma, cadmium is primarily bound to two high molecular weight proteins. Relative small amounts are bound to a protein with M(r) approximately 60000. The other metal-binding protein, with M(r) approximately 70000 and pI approximately 6.7 was identified as transferrin. The conditional equilibrium constants for the binding of cadmium ions to the two metal-binding sites of this protein were calculated as logK(1)=5.40+/-0.12 and logK(2)=4.66+/-0.21, which are comparable to those of human transferrin under the same experimental conditions. Transport of cadmium in plasma of carp was found to be different from that of brown trout Salmo trutta and man, where cadmium is mainly bound to albumin and transferrin. The prominent binding of cadmium to transferrin can be explained by the absence or at least the very low concentrations in which albumin is present in carp plasma.     

Multiple acute temperature stress affects leucocyte populations and antibody responses in common carp, Cyprinus carpio L

Stress is a potential factor causing increased susceptibility of fish to pathogens. In this study, stress-induced immunological changes that may contribute to a decreased immune status were investigated. A 3 h drop in ambient water temperature of 9 degrees C was used as a relative mild and acute stress model for carp. Effects of this stressor on the dynamics of leucocyte populations were determined with specific monoclonal antibodies. The relative number of circulating B-lymphocytes in the total leucocyte population decreased significantly within 4 h after the onset of single or multiple cold shocks. This decrease was reversible, as B-lymphocyte numbers were restored within 24 h. Most probably, a redistribution of B-lymphocytes contributed to this phenomenon. In head kidney, an increase was measured in the relative number of B-lymphocytes. Granulocyte numbers showed opposite reactions: the percentage of granulocytes in the total leucocyte population nearly doubled in circulation and decreased significantly in the head kidney. This demonstrates that in vivo, a mild stressor differentially alters the distribution of leucocytes. In stressed carp, the percentage of apoptotic lymphocytes in blood is significantly higher compared with the unstressed animals. B-lymphocytes as well as Ig- lymphoid cells contributed to this increased apoptosis. Labelling of blood lymphocytes with a polyclonal antiserum against the glucocorticoid receptor also showed, besides B-lymphocytes, part of the Ig- lymphoid cell population to be glucocorticoid receptor positive. As the distribution of B-lymphocytes was substantially affected, the effect of temperature stress on T-lymphocyte-independent (trinitrophenyl-lipopolysaccharide) and T-lymphocyte-dependent (dinitrophenyl-keyhole limpet hemocyanin) humoral antibody responses was determined. Kinetics of the primary antibody response to the T-lymphocyte-independent antigen showed lower antibody titres in stressed carp during the onset of the immune response, implying a slower development of the antibody response against the T-lymphocyte-independent antigen.