Abundantly expressed genes in pig adipose tissue: an expressed sequence tag approach

Adipose tissue plays a critical role in metabolism, storage, and release of fatty acids in mammals. Construction of a full-length cDNA library is an effective way to understand the functional expression of genes in adipose tissue, and in addition, novel genes for further research can be found in the library. In this study, adipose tissue RNA was extracted from three 18-mo-old Lee-Sung pigs. The mRNA was isolated, reverse transcribed, and used to construct a cDNA library. After transformation, 2,880 clones were selected and sequenced. Cluster analysis was performed, and the assembled contig of each cluster was subjected to search against DNA sequences in the nucleotide databases (NCBINR/TIGRGI). These sequences were clustered into 1,527 unique sequences; 80% of the sequences were categorized as known genes, and 20% of the sequences were categorized as unknown genes. In this adipose tissue cDNA library, approximately 16% of the genes contained full-length sequences with start and stop codons. Gene ontology analysis was performed to indicate the possible functions of these genes. Genes associated with mitochondrial function were abundant and represented 10% of the total. Several fatty acid transport genes and stearoyl coenzyme A desaturase were among the most abundant genes expressed. Tissue distribution of several abundant genes was analyzed by northern analysis, and many of these genes were transcribed in porcine adipose tissue in high copy number. Our full-length sequence data and tissue distribution data can be used to decipher the functional roles exhibited by the adipocyte under various perturbations via endocrine, environmental, genetic, nutritional, pharmacological, or physiological manipulations.     

柞蚕蛹全长cDNA文库的构建和随机EST测序

采用RNA转录5′末端转换(SMART)技术构建了柞蚕(Antheraea pernyi)蛹的全长cDNA文库。所构建cDNA文库的容量为5×105个独立克隆,插入片段长800~2500 bp,且90%的插入片段大于1 kb。随机挑取288个克隆进行表达序列标签(EST)测序,有效序列为250条,根据EST测序结果计算文库重组率达95%。经序列拼接得到175个unigenes,通过序列比对发现其中97个unigenes与GenBank中的已知基因高度同源,且有88条全长序列,基因的完整性比率达90%。在随机EST测序中获得了具有5′端和3′端非编码区的延伸因子-1α基因(Gen-Bank登录号:FJ788508),该基因cDNA全长1743 bp,有一个1392 bp的开放阅读框,编码含463个氨基酸残基的蛋白,蛋白的理论分子质量为50.4 kD,等电点8.96。EST测序分析表明,柞蚕蛹cDNA文库符合构建基因文库的质量要求,该文库的构建将有助于柞蚕功能基因的克隆和研究。     

桑树幼叶cDNA文库的构建及部分表达序列标签分析

基于为鉴定和克隆桑树功能基因提供基础信息的目的,采用RNA转录5′末端转换(SMART)法构建了桑树幼叶全长cDNA文库。该文库容量为1.02×106pfu/mL,重组率95%,符合构建基因文库的质量要求。从构建的桑树幼叶cDNA文库中随机挑取48个克隆进行表达序列标签(EST)测序,有效序列为32条,经UniGene数据库归并后为32条,UniGene比率为100%;与NCBI核酸数据库进行比对、查询和注释,在32条序列中有29条序列具有同源性,其中16条为全长序列,完整性比率为55.2%;初步发现具有已知功能基因的ESTs 6个,具有推测功能基因的ESTs 5个,未命名或未知功能基因的ESTs 21个。     

羊草叶片cDNA文库的构建及部分表达序列标签的分析

采用SMART技术,以品质优良羊草“吉生一号”叶片为材料,构建了高质量cDNA文库。原始文库滴度达到10⁶cfu/mL,扩增文库滴度接近10¹¹cfu/mL。随机抽样检查结果表明,插入片断大小在0.5~3.0kb,主要集中在1kb左右,其中检测到插入片断大于1kb的占70%,最大达到2.5kb,其重组率达到98%。同时在扩增文库中检测到了羊草维生素E合成途径中的关键酶基因α-生育酚环化酶(TC)及γ-生育酚甲基转移酶(γ-TMT)的特异信号,挑选307个筛选出了285条EST序列,将得到的117条非重复序列与GenBank中已知序列比对,获得了如3-磷酸甘油醛脱氢酶、光系统Ⅱ蛋白D1、翻译起始因子蛋白、翻译延生因子蛋白、RNaseS-likeproteinprecursor蛋白等基因。羊草高质量的cDNA文库的构建为进一步从分子水平研究羊草及开发利用这一基因资源提供了条件。     

Molecular cloning of canine monoamine oxidase subtypes A (MAOA) and B (MAOB) cDNAs and their expression in the brain

The role of monoamine oxidase has been shown to be related to some behavioral changes including aggression and cognitive dysfunction. In order to demonstrate the basic expression patterns of monoamine oxidase in the canine brain, we determined the full-length nucleotide sequences of cDNA for canine monoamine oxidase type A (MAOA) and type B (MAOB) genes that were isolated from the canine brain cDNA library. Oligonucleotide primers for PCR were constructed based on the conserved sequences reported thus far for other mammalian species. The nucleotide sequences had open reading frames of 1584 and 1563 bp for MAOA and MAOB, respectively. Both of these genes showed relatively high homology with other species in both nucleotide (> 81%) and deduced amino acid (> 85%) sequences. In Northern blot analyses MAOA mRNA was expressed broadly in various parts of the canine brain, whereas MAOB mRNA was found only in specific brain regions, such as the hypothalamus, hippocampus, brain stem and olfactory bulb. These results suggest that MAOA and MAOB mRNAs have subtype-specific expression patterns in the canine brain.     

柔嫩艾美耳球虫裂殖子全长cDNA文库的构建及应用

为克隆柔嫩艾美耳球虫裂殖子阶段的功能基因的全长序列,利用SMART技术,采用Clontech公司的Creator TMSMARTTMcDNA Library Construction Kit构建了鸡球虫裂殖子的全长cDNA文库。用试剂盒提取mRNA后,以cDNA合成试剂盒合成cDNA。连接至pDNR-LIB载体,用电转化法将重组质粒转化到E.coli DH10B内得到原始文库,扩增后保存于-80℃冰箱内;最后以文库为模板,分别以研究室已成功克隆序列(EtSAG2、EtMIC-2、EtMCAT)及Sanger的部分EST序列(Contig1218)设计引物,进行PCR扩增并测序检验文库的实用性。经测定,构建的初级cDNA文库约含有8.72×107个重组子,插入的片段多在1kb～3kb之间,平均插入片段长度约1.8kb,扩增后文库保存的滴度为2.4×104 cfu/mL;通过文库的PCR扩增,不仅可以成功扩增出研究室已成功克隆的序列(EtSAG2、EtMIC-2),并成功获得EtMCAT和EST序列(Contig1218)的全长cDNA序列,经比对分析Contig1218所编码的蛋白为组织蛋白酶B样半胱氨酸蛋白酶(Cathepsin B)。结果表明,已成功构建了柔嫩艾美耳球虫裂殖子高质量的全长cDNA文库,从而为筛选鸡球虫的功能基因全长序列奠定了基础。     

西农萨能羊泌乳高峰期和初期乳腺组织差异表达基因研究

利用抑制性削减杂交和实时定量PCR研究西农萨能羊泌乳高峰期差异表达基因,结果表明成功构建泌乳高峰期和泌乳初期乳腺组织差异表达削减eDNA文库,以GAPDH为指标检测文库削减效率为2^5倍,共获得78个阳性克隆,PCR检测插入片段主要分布在150～1000bp,挑选插入片段不等的30个克隆测序,获得25个有效序列,代表18个基因。对文库中所包含的血清淀粉样蛋白A3（SAA3）,ATP结合盒亚家族G成员2（ABCG2）,心脏型脂肪酸结合蛋白（H-FABP）和黄嘌呤脱氢酶（XDH）进行实时定量PCR检测,发现上述4个基因在泌乳高峰期乳腺组织中的表达水平分别是泌乳初期的17．0,7．7,16．3和1．7倍。结论：构建的消减文库可用于筛选泌乳高峰期差异基因,已鉴定的4个基因很可能是调控产奶量和乳成分变化的候选基因。     

犬弓首蛔虫雄虫cDNA文库构建及EST分析

为构建T.canis雄虫cDNA文库,采用Trizol法提取T.canis雄虫的总RNA,合成cDNA,连接到λTripEx2载体上,通过包装蛋白对连接产物的包装,接种到大肠杆菌XL-1-Blue中进行原始文库和扩增文库的滴度测定.经质量鉴定表明:初始文库的滴度为5.25×106 pfu·mL-1,扩增后文库的滴度为6.90×109 pfu ·mL-1.文库的插入片段大小在500～2 000 bp,平均片段大小为1 000 bp,重组率为99.47％.所有指标均显示已成功构建了T.canis雄虫的cDNA文库.利用该文库获得了189条5'有效表达序列标签(EST).对ESTs拼接后代表了101个Unigenes,含有27个Contigs和74个Singletons.其Unigenes在GenBank中的序列号为HO348195～HO348295.同源性分析检索到有56个Unigenes与已知基因同源,其中具有已知或推测功能的基因有40个,未知功能基因有16个,未比对上的基因45个.未比对上的基因与NR数据库中的蛋白序列没有任何意义的匹配,为研究中发现的新基因.这些结果为进一步开展犬弓首蛔虫功能基因及分子机制研究奠定了基础.     

Gene discovery in Eimeria tenella by immunoscreening cDNA expression libraries of sporozoites and schizonts with chicken intestinal antibodies

Specific antibodies were produced ex vivo from intestinal culture of Eimeria tenella infected chickens. The specificity of these intestinal antibodies was tested against different parasite stages. These antibodies were used to immunoscreen first generation schizont and sporozoite cDNA libraries permitting the identification of new E. tenella antigens. We obtained a total of 119 cDNA clones which were subjected to sequence analysis. The sequences coding for the proteins inducing local immune responses were compared with nucleotide or protein databases and with expressed sequence tags (ESTs) databases. We identified new Eimeria genes coding for heat shock proteins, a ribosomal protein, a pyruvate kinase and a pyridoxine kinase. Specific features of other sequences are discussed.     

家蚕第2白卵近等基因系差异表达基因的筛选

为了解与家蚕第2白卵(w-2)性状形成相关的差异表达基因信息,以家蚕正常型黑卵及其第2白卵近等基因系的转色期蚕卵为材料,构建抑制消减杂交(SSH)文库,筛选差异表达基因。对SSH文库中部分克隆的测序分析表明,该文库对差异表达基因的富集性较好。随机挑选SSH文库中的300个克隆制作家蚕cDNA芯片,对家蚕正常型黑卵及第2白卵近等基因系转色期蚕卵进行检测,获得11个差异表达基因。对这11个差异表达基因进行实时荧光定量RT-PCR验证分析,其结果与芯片数据分析结果趋势一致,在正常型黑卵与第2白卵近等基因系之间,这些基因的表达差异为0.1倍至数千倍。     

Isolation and characterization of recombinant cDNA clones corresponding to developmentally regulated genes in pig liver

To identify clones that corresponded to developmentally regulated genes in pig liver, recombinant cDNA libraries were constructed from early fetal (d 40), late fetal (d 110) and adult liver mRNA. Each library was screened by probing with total cDNA prepared from mRNA at different stages of development. Nine clones that gave distinct developmental patterns when hybridized to liver RNA isolated from various stages of development were subsequently isolated and partially sequenced. The cognate proteins for seven of these clones were identified by searching a national DNA sequence resource (Bionet) for similar sequences. Clones hybridizing to mRNA that was most abundant early in development were alpha fetoprotein, alpha 1 antiprotease, alpha globin and an unidentified clone. The mRNA for beta and gamma fibrinogen were most abundant perinatally. The abundance of mRNA for albumin, haptoglobin and a second unidentified clone was low in fetal liver, but increased to adult levels between birth and 3 d of age. These clones provide probes to study the relationship between factors affecting fetal growth and expression of specific genes throughout the development.     

华支睾吸虫成虫cDNA表达文库的构建与筛选

为了获得华支睾吸虫成虫期强反应原性抗原基因,首先利用λZAP栽体构建华支睾吸虫成虫cDNA表达文库:即从我国东北疫区(镇赉县)家犬胆管内分离收集华支睾吸虫成虫,采用Trizol Reagent提取其总RNA,Oligo(dT)纤维素柱纯化mRNA,反转录合成第1链cDNA及第2链cDNA,用CHROMA SPIN-400柱离心层析纯化后,与栽体λZAP Express连接,体外包装后成功获得我国东北疫区华支睾吸虫成虫cDNA表达文库.文库容量为1.5×106pfu,重组率为99%,插入片段长度在0.4～2.0 kb之阀,扩增文库的滴度为1.5×1010pfu/mL.然后利用免疫学方法对该cDNA表达文库进行筛选:以自然感染华支睾吸虫的人血清为抗体探针,从2.0×105个重组噬菌体筛选强反应原性抗原基因,对筛选出的强反应原性克隆进行测序,利用相关分子生物学软件进行序列分析.共获得41个阳性克隆,测序结果分析表明,这些cDNAs根据其编码的蛋白可分为以下几种,即与来自华支睾吸虫的甘氨酸-2、脯氨酸-2及Cs44抗原高同源的基因及分别与来自Nematostella vectensis的未知蛋白、转录延伸因子及果蝇CG3446基因编码蛋白较低同源性的基因.本研究结果为进一步对华支睾吸虫抗原的生物学特性研究及应用奠定了理论基础和实验依据.     

银染mRNA差异显示法克隆柔嫩艾美耳球虫(Eimeria tenella)抗药性相关基因

以柔嫩艾美耳球虫（Eimeria tenella）敏感株、地克珠利抗药株和马杜拉霉素抗药株孢子化卵囊为材料，用银染mRNA差异显示方法筛选和克隆与球虫抗药性相关的基因。首先提取这3个虫株孢子化卵囊的总RNA为模板．用Oligo（dT）12GG为锚定引物和2个10碱基随机引物组合进行RTPCR，产物经变性聚丙烯酰胺凝胶电泳后银染。分别切取5务差异条带，进行2次PCR扩增，产物回收后与PGEM—T—easy Vector连接转化。经PCR鉴定正确后，再进行斑点杂交试验、序列分析和同源性比较。结果发现，地克珠利抗药株和马杜拉霉素抗药株分离的差异片段中都有2个cDNA片段（可能为新的基因片段），这为克隆全长cDNA和探索球虫抗药性产生的分子机理奠定了一定的基础。     

日本血吸虫7d童虫cDNA文库构建及免疫筛选

为了从7 d童虫cDNA文库筛选出童虫发育阶段特异性表达抗原基因。本研究首先构建了日本血吸虫7 d童虫cDNA文库,其次再采用日本吸血虫感染血清进行筛选。结果显示:建立的文库插入片段为0.5~3.0 kb,文库重组率为98%,初始文库滴度为2.4×10~6 pfu/mL,扩增后滴度为1.6×10~9 pfu/mL,利用感染日本血吸虫10 d和42 d的小鼠血清免疫筛选该文库,初筛和复筛后获得17条有效EST序列,其编码7个基因,分别为复制蛋白(2 ESTs)、肝再生增强因子(3 ESTs)、血小板活化因子(6 ESTs)、钙调理蛋白基因(3 EST)、丝束蛋白(1 ESTs)、核糖体RNA(1 EST)和还原型辅酶脱氢酶基因(1 EST)。该研究结果对今后探讨血吸虫的生长发育机制及筛选血吸虫早期诊断抗原具有重要意义。     

Gateway技术构建结缕草低温和干旱诱导cDNA文库及其质量鉴定

为研究结缕草（Zoysia japonica）胁迫响应信号转导途径中的关键基因,揭示结缕草抗逆分子机制,建立结缕草功能基因组学研究基础平台,以经低温、干旱处理的结缕草为材料,采用Gateway技术构建了首个结缕草低温和干旱诱导的标准cDNA文库。文库质量分析表明,未扩增的原始文库滴度1.76×106 pfu·mL-1,库容7.04×106 pfu,插入片段平均大小大于1 kb,重组率90%。文库质量优良,可能包含大量新基因,不仅能为结缕草功能基因组分析提供必要资源,也可为后期进行高通量EST测序、发掘新抗逆相关基因、制作基因芯片等研究奠定基础。     

Initiation of a Sarcocystis neurona expressed sequence tag (EST) sequencing project: a preliminary report

To accelerate genetic and molecular characterization of Sarcocystis neurona, the primary causative agent of equine protozoal myeloencephalitis (EPM), a sequencing project has been initiated that will generate approximately 7000-8000 expressed sequence tags (ESTs) from this apicomplexan parasite. Poly(A)(+) RNA was isolated from culture-derived S. neurona merozoites, and a cDNA library was constructed in a unidirectional lambda phage cloning vector. Sixty phage clones were randomly picked from the library, and the cDNA inserts were amplified from these clones using the T3 and T7 primers that flank the multi-cloning site of the lambda vector. This analysis demonstrated that 100% (60/60) of the clones selected from this library contained recombinant cDNA inserts ranging in size from 0.4 to 4.0 kilobases (kb) with an average size of 1.23kb. Single-pass sequencing from the 5' end of the 60 amplified cDNAs produced high-quality nucleotide sequence from 53 of the clones. Comparison of these ESTs to the current gene databases revealed significant matches for 10 of the ESTs, six of which are similar to sequences from other Apicomplexa (i.e., Toxoplasma gondii). Importantly, none of the ESTs were of obvious mammalian origin, thus indicating that the cDNAs in this library were derived primarily from parasite mRNA and not from mRNA of the bovine turbinate host cells. Collectively, these data indicate that the described cDNA library will provide an excellent substrate for generating a portion of the ESTs that are planned from S. neurona. This sequencing project will greatly hasten gene discovery for this protozoan pathogen thereby enhancing efforts towards the development of improved diagnostics, treatments, and preventatives for EPM. In addition, the S. neurona ESTs will represent a significant contribution to the extensive database of sequences from the Apicomplexa. Comparative analyses of these apicomplexan sequences will likely offer a multitude of important information about the biology and evolutionary history of this phylogenetic grouping of parasites.     

Detection of genomic variability in different populations of the cattle tick Boophilus microplus in southern Brazil

DNA from seven isolates of the cattle tick Boophilus microplus was analyzed by restriction fragment length polymorphism (RFLP). Three different cDNA clones, named P-9, P-25 and CP-12, isolated from a B. microplus cDNA library, were used as DNA probes. DNA sequences of P-9 have high similarity to ribosomal genes, whereas P-25 does not show significant homology with known sequences within databases. CP-12 is a cDNA clone encoding a cysteine endopeptidase gene. A limited degree of polymorphism was detected with P-9 and P-25, while CP-12 showed a different pattern of bands for each tick isolate. These findings suggest the existence of a complex genotypic diversity of the tick B. microplus population in endemic regions.