胃癌相关cDNA片段的快速克隆和表达分析

利用差异显示PCR技术获得的一条在胃癌和正常组织有差异表达的表达序列标签(EST)-W123(GenBank登录号为AF150631),通过与GenBank的dbest库进行电子杂交,选取了与其同源度高的若干EST,在它们共有的保守序列设计了用于扩增的寡聚核苷酸引物,利用cDNA末端快速扩增PCR（RACE）技术得到了7条带有polyA尾的3′EST,进行序列分析后,发现它们均是代表新基因或不同剪接体的EST,且具有共同的保守序列,已登录GenBank.采用RNA印迹对目的序列进行初步鉴定,并进行了这些基因的组织分布分析.RACE技术和生物信息学相结合,具有快速、高效的特点,有助于疾病相关基因的克隆.     

用表达性差异显示分析技术分离人胎肝组织选择性表达基因

目的：建立4月龄人胎肝组织选择性表达基因EST库,为研究胚胎肝组织特异表达基因提供有力的工具。方法：采用表达性差异显示分析（representational difference analysis,RDA) 技术建立4月龄人胎肝组织选择性表达基因EST库,并测定部分克隆核苷酸序列,以竞争PCR检测代表性基因的差异表达。结果与结论：以珠蛋白家族基因为标志,所建差减cDNA文库中α－珠蛋白家族基因的表达频率较未差减cDNA文库增高7倍,同时该文库也含有多种与肝生长密切相关的基因,表明RDA技术确是研究差异表达基因的有效手段,所建EST库富集胎肝特异表达基因。部分克隆序列分析获得2种未报道序列,其中一株含有丝／苏氨酸激酶结构域,表明可望从此库中分离具有重要未知功能的新基因。     

利用RACE技术和生物信息学资源快速钓取多个侯选同源基因

利用差异显示PCR技术获得的一条在胃癌癌旁和正常组织表达量高的EST－W123,通过与GenBank的dbest库进行电子交,选取了与W123同源度高的若干EST,在它们共有的保守序列设计了用于扩增的寡聚核苷酸引物,利用cDNA末端快速扩增（RACE）技术得到了7条带有polyA尾的3'EST,进行序列分析后,发现它们均是代表新基因或不同剪接体的EST,且具有共同的保守序列,已登录GenBank。     

心脏特异新基因Lrrc10的分子克隆与特性分析

采用表达序列标签(EST)介导的基因克隆和表达谱分析,从小鼠心脏克隆了一个心脏特异新基因Lrrc10（GenBank Acc No. AF527781）.该基因cDNA全长为1 410 bp,定位于小鼠染色体10D2,在基因组中无内含子.Lrrc10的最大开放阅读框编码的假想蛋白由274个氨基酸组成,含有7个亮氨酸重复基序.同源性检索未发现有整体同源性的已知基因.EST数据库中支持该基因cDNA序列的全部18条EST均来自小鼠心脏组织.对小鼠的不同组织cDNA的RT-PCR检测证实该基因主要在心脏中强表达,在肺低表达,而在其他组织中不表达或表达很弱.因此该基因是心脏特异的富亮氨酸重复超家族新成员.     

EST技术及其在哺乳动物早期胚胎研究中的应用

EST(expressed sequence tags ,EST) 是一段长约150～500 bp的基因表达的外源序列片段,是由大规模随机挑取的cDNA克隆测序得到的组织或细胞基因组的表达序列标签。一个EST代表生物某一时期的某种组织或细胞的一个表达基因。本文主要综述了EST技术的原理方法,哺乳动物早期胚胎研究的理论基础以及EST技术在早期胚胎研究方面的应用,并讨论了利用EST进行研究分析的发展趋势。     

静电纺丝的主要参数对PLGA纤维支架形貌和纤维直径的影响

EST(expressed sequence tags,EST)是一段长约150～500bp基因表达的外源序列片段,是由大规模随机挑取的cDNA克隆测序得到的组织或细胞基因组的表达序列标签。一个EST代表生物某一时期的某种组织或细胞的一个表达基因。主要综述了EST技术的原理方法,哺乳动物早期胚胎研究的理论基础以及EST技术在早期胚胎研究方面的应用,并讨论了利用EST进行研究分析的发展趋势。     

新基因人MOB cDNA的克隆与功能分析

人MOB基因被认为是在脑组织中高表达的5次跨膜而功能未知的膜蛋白.从胎儿和成人肾脏消减杂交cDNA文库中获得了一条新的表达序列标签（expressed sequence tag,EST）序列,该序列对应于功能未知的MOB基因.利用生物信息学分析工具和分子生物学技术,从胎儿肝脏中成功地克隆了人MOB基因cDNA序列,同时也获得了含有完整开放读码框的大鼠和鸡MOB的电子全长序列.人MOB基因定位于10q11.1～11.2之间,含有一个1 242 bp的开放阅读框,第415位开始的ATG可能是翻译起始位点.核酸序列相似性搜索发现,其他种属中存在与之高度相似的EST序列,如爪蟾（79%）、羊（87%）、猪（94%）、牛（93%）.蛋白质序列相似性搜索发现,人MOB与大鼠、小鼠和鸡MOB有97%、97%、91％的相似性,与其他一些不同种属来源的假想蛋白有45%～73%的相似性.不同物种之间MOB基因核酸和蛋白质序列的高度相似说明,MOB是进化上高度保守的蛋白质.保守结构域分析发现,人、小鼠、大鼠和鸡MOB结构域组成完全一致,N端均与不育α基序（sterile alpha motif,SAM）结构域显著匹配,随后出现匹配显著性稍差的几个结构域.核酸和蛋白质序列的保守性提示,除N端约70个氨基酸组成SAM结构域外,其余的保守氨基酸可能形成一个新的保守的MOB结构域.表达谱分析表明,人MOB基因在所有被检组织和细胞中都表达.亚细胞定位研究显示,人MOB广泛表达于细胞内,主要在细胞核.DNA含量测定结果表明,人MOB基因过表达并不影响HeLa细胞的细胞周期和凋亡.总之,人MOB蛋白是一个在多种组织和细胞中广泛表达、细胞内广泛分布、进化上十分保守的蛋白质,可能通过特定蛋白质之间的相互作用,参与多种发育过程的调节.其过表达不影响HeLa细胞的周期和凋亡.     

应用cDNA芯片分析79个新基因的人胚组织表达谱

大规模cDNA测序和生物信息学技术相结合,得到来自于商品化的人胚肾cDNA文库79个代表新基因的表达序列标签(EST).随后,采用高速度机械手制备这些cDNA的基因芯片,用于鉴定79个新基因的ESTs在20周、26周两个胚胎时期6种组织中的基因表达状况,以研究这些EST片段代表的新基因功能提供线索.通过芯片杂交及结果分析,得到同一个组织两个不同时相8个差异表达的基因,随后的RNA印迹分析的结果与芯片杂交的结果相一致.     

类固醇5-α还原酶样基因Srd5α2l2的克隆及表达分析

采用表达序列标签（EST）介导的基因克隆和表达谱分析,从小鼠心脏克隆了一个cDNA为2 348 bp,主要在心脏表达的新基因Srd5α2l2（GenBank Acc No.AF548365）.该基因由12个外显子组成,3′非翻译区富含ATTTA序列,最大开放阅读框编码一个由361个氨基酸组成的假定蛋白,该蛋白质C端含有类固醇5-α还原酶的保守结构域（3-oxo-5-alpha-steroid 4-dehydrogenase,STEROID_DH）.生物信息学分析表明,人cDNA 克隆DKFZp313D0829（AL833108）是Srd5α2l2的人同源基因.经同源性检索,支持Srd5α2l2的全部41条EST中25条来自小鼠心脏组织.RT-PCR检测初步证实,该基因主要在心脏中表达,而在其他组织中不表达或弱表达.综合考虑Srd5α2l2的序列特征和表达谱,Srd5α2l2可能在心脏组织中发挥重要作用.     

人鼻咽与鼻咽癌及肺癌基因表达谱差异的研究

研究鼻咽癌、肺癌与正常鼻咽组织基因表达谱差异及筛选鼻咽癌相关基因,采用α- ³²P逆转录标记组织总RNA,将cDNA探针与有5 184个基因或表达序列标签EST(expression sequence tag)的高密度cDNA微阵列GF200杂交,软件分析表达谱差异.结果发现三者均呈低表达为主的表达谱,密度值在200以上的基因及EST在鼻咽癌有110个,肺癌134个而鼻咽组织有158个;5个EST在鼻咽高表达但鼻咽癌低表达,3个EST在鼻咽癌高表达但正常鼻咽低表达.结果表明鼻咽癌与正常鼻咽及肺癌组织存在差异表达基因,可能还有新基因在鼻咽癌发生中起作用;采用高密度cDNA微阵列是一种筛选差异表达基因的快速有效方法.     

Census of orthologous genes and self-organizing maps of biologically relevant transcriptional patterns in chickens (Gallus gallus)

The launch of large-scale chicken expressed sequence tags (EST) projects has placed the chicken in the lead for the number of EST sequences in agriculturally important animals. More than 451,000 chicken ESTs derived from over 158 libraries have been deposited in the NCBI dbEST database as of December 2003. But how many genes these ESTs represent and how they are expressed in different chicken tissues/organs remain undetermined. In the present research, we developed a human gene-based strategy for census of chicken orthologous genes and identification of their expression patterns. Among 34,157 human coding genes used in the study, BLAST analysis revealed that 11,066 genes provisionally matched 248,628 chicken ESTs. Based on the average EST abundance of the orthologous genes, the current public repository of chicken ESTs could represent 20,000 provisional genes. Analysis of gene expression in 14 single tissues/organs showed that approximately 15% of genes were expressed exclusively in single tissue/organ whereas the remaining 85% of genes were co-expressed in two or more tissues/organs. A majority (91.15%) of genes expressed in chicken embryos were also expressed at post-hatch stages, indicating that most genes activated in chicken embryos could serve housekeeping functions. Self-organizing maps (SOM) analysis organized 8807 provisional genes in selected chicken tissues into 98 clusters with each cluster being indicative of common regulatory factors and pathways. A total of 969 provisional orthologous genes were identified as preferentially expressed genes (PEGs) in various chicken tissues/organs (LOD>3.0). No doubt, the present study on gene expression patterns will provide insight into dynamics of metabolic pathways and tissue/organ programming and reprogramming in chickens.     

In Silco Mapping of ESTs from the Turkey (Meleagris Gallopavo)

Sequence similarity was used to predict the position of expressed sequence tags (ESTs) in the genome of the turkey (Meleagris gallopavo). Turkey EST sequences were compared with the draft assembly of the chicken whole-genome sequence and the chicken EST database by BLASTN. Among the 877 ESTs examined, 788 had significant matches in the chicken genome sequence. Position of orthologous sequences in the chicken genome and the predicted position of the EST loci in the turkey genome are presented. Genetic assignments suggest a high level of accuracy for the COMPASS predictions.     

In silco mapping of ESTs from the turkey (Meleagris gallopavo)

Sequence similarity was used to predict the position of expressed sequence tags (ESTs) in the genome of the turkey (Meleagris gallopavo). Turkey EST sequences were compared with the draft assembly of the chicken whole-genome sequence and the chicken EST database by BLASTN. Among the 877 ESTs examined, 788 had significant matches in the chicken genome sequence. Position of orthologous sequences in the chicken genome and the predicted position of the EST loci in the turkey genome are presented Genetic assignments suggest a high level of accuracy for the COMPASS predictions.     

The lamina-associated polypeptide 2 (LAP2) genes of zebrafish and chicken: no LAP2alpha isoform is synthesised by non-mammalian vertebrates

The mammalian lamina-associated polypeptide 2 (LAP2) gene encodes six isoforms (LAP2alpha, beta, delta, epsilon, gamma, zeta) that are synthesised from alternatively spliced mRNAs. The mammalian LAP2alpha is one of the predominant isoforms and localised in the nucleoplasm whereas LAP2beta, delta, epsilon, and gamma are integral membrane proteins of the inner nuclear membrane. We have analysed the LAP2 gene structure of the zebrafish Danio rerio as an attractive lower vertebrate model organism. The zebrafish LAP2 (ZLAP2) gene without regulatory sequences spans approximately 19 kb of genomic DNA. It contains 15 exons that encode the isoforms ZLAP2beta, gamma, and omega which are localised in the inner nuclear membrane. By radiation hybrid mapping, we have located the gene onto linkage group 4 between EST markers fc01g04 (213.97cR) and fb49f01 (215.69cR). The identification of a chicken genomic clone comprising the complete coding region of the avian LAP2 gene enabled us to compare the LAP2 gene structure amongst vertebrates. In contrast to the mammalian LAP2 gene, the zebrafish and the chicken sequences do not encode for an alpha-isoform. In parallel we searched for an alpha-isoform in birds using polyclonal and monoclonal LAP2 antibodies specific for the common evolutionary conserved aminoterminal domain present in all isoforms. We detected LAP2beta as the predominant isoform but no LAP2alpha in tissues of 10-day-old chicken embryos and cultured chicken fibroblasts thus confirming the genomic analysis. The comparison of each zebrafish and chicken LAP2 exon with the corresponding exons of the human LAP2 gene demonstrates that the degree of identity at the amino acid level is much higher between the human and chicken than between the human and zebrafish sequences. By Blast search with the nucleotide and amino acid sequences of the human LAP2alpha, we did not find any significant homologies in databases of the zebrafish and chicken sequences. Our data suggest that LAP2alpha is a novelty of mammals.     

Survey of a cDNA library from the turkey (Meleagris gallopavo).

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon-intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.     

Cloning and Tissue Expression of Chicken Heart Fatty Acid-Binding Protein and Intestine Fatty Acid-Binding Protein Genes

Fatty acid-binding proteins (FABPs) are members of a superfamily of lipid-binding proteins, occurring intracellularly in invertebrates and vertebrates. This study was designed to clone and characterize the genes of heart fatty acid-binding protein and intestine fatty acid-binding protein in the chicken. PCR primers were designed according to the chicken EST sequences to amplify cDNA of H-FABP and I-FABP genes from chicken heart and intestinal tissues. Analysis of sequence showed that the cDNA of the chicken H-FABP gene is 75 to 77% homologues to human, mouse, and pig H-FABP genes, and the chicken I-FABP gene is 71 to 72% homologues to human, mouse, and pig I-FABP genes. In addition, Northern blot analysis indicated that of the two genes, similar to the copartner of the mammal, H-FABP gene was expressed in a wide variety of tissues, and I-FABP gene was expressed only in intestinal tissues. The expression levels of the chicken H-FABP mRNA in heart and I-FABP mRNA in intestine had significant differences between the broilers from fat line and Bai'er layers at six weeks of age. The results of this study provided basic molecular information for studying the role of two FABPs in the regulation of fatty acid metabolism in avian species.     

Interaction between eggshell temperature and carbon dioxide concentration after day 8 of incubation on broiler chicken embryo development

Carbon dioxide (CO₂) is considered to be an important factor during incubation of eggs. Effects attributed to higher CO₂ concentrations during experiment might be due to confounding effects of other environmental conditions, such as incubation temperature. To disentangle effects of eggshell temperature (EST) and CO₂ concentration, an experiment was conducted. A total of 630 Cobb 500 hatching eggs from 37 to 45 wk commercial breeder flocks were collected and incubated according to treatments. The experiment was setup as a complete randomized 2 × 3 factorial design, resulting in 6 treatments. From day 8 of incubation onward, broiler eggs were exposed to one of two EST (37.8 or 38.9 °C) and one of three CO₂ concentrations (0.1, 0.4 or 0.8%). Eggs were incubated in climate-respiration chambers and metabolic heat production was determined continuously. At day 18 of incubation and at 6 h after hatching, embryo and chicken quality were determined by evaluation of organ weights, navel condition, blood metabolites and hepatic glycogen. Hatching time and chicken length at 6 h after hatching showed an interaction between EST and CO₂ concentration (both P = 0.001). Furthermore, no effect of CO₂ concentration was found on embryo development or chicken quality. Metabolic heat production between day 8 and 18 of incubation was not affected by either EST or CO₂. At day 18 of incubation, an EST of 38.9 °C resulted in a higher egg weight loss, longer embryos, higher yolk free body mass (YFBM) and lower heart weight than an EST of 37.8 °C (all P < 0.008). At 6 h after hatching, an EST of 38.9 °C resulted in a higher residual yolk weight and lower YFBM, liver weight and heart weight than an EST of 37.8 °C (all P < 0.003). Lactate, uric acid and hepatic glycogen were not affected by EST at either day 18 of incubation or at hatch. Glucose was not affected by EST at day 18 of incubation, but at hatch, it was higher at an EST of 37.8 °C than at an EST of 38.9 °C (P = 0.02). It can be concluded that effects of CO₂ concentration (at concentrations ≤0.8%) on embryonic development and chicken quality appear to be limited when EST is maintained at a constant level. Moreover, a higher EST from day 8 of incubation onward appears to negatively affect chicken quality at hatch.     

Cloning and tissue expression of chicken heart fatty acid-binding protein and intestine fatty acid-binding protein genes

Fatty acid-binding proteins (FABPs) are members of a superfamily of lipid-binding proteins, occurring intracellularly in invertebrates and vertebrates. This study was designed to clone and characterize the genes of heart fatty acid-binding protein and intestine fatty acid-binding protein in the chicken. PCR primers were designed according to the chicken EST sequences to amplify cDNA of H-FABP and I-FABP genes from chicken heart and intestinal tissues. Analysis of sequence showed that the cDNA of the chicken H-FABP gene is 75 to 77% homologues to human, mouse, and pig H-FABP genes, and the chicken I-FABP gene is 71 to 72% homologues to human, mouse, and pig I-FABP genes. In addition, Northern blot analysis indicated that of the two genes, similar to the copartner of the mammal, H-FABP gene was expressed in a wide variety of tissues, and I-FABP gene was expressed only in intestinal tissues. The expression levels of the chicken H-FABP mRNA in heart and I-FABP mRNA in intestine had significant differences between the broilers from fat line and Bai'er layers at six weeks of age. The results of this study provided basic molecular information for studying the role of two FABPs in the regulation of fatty acid metabolism in avian species.