Isolation of Rice EPSP Synthase cDNA and Its Sequence Analysis and Copy Number Determination

In order to isolate the total cDNA of rice (Oryza sativa L.) epsps gene, RT-PCR was carried out with template of rice first-strand cDNA and primers designed according to rice EPSP synthase genomic sequence obtained in previous study. A 1 585-bp cDNA fragment was amplified and cloned. The 1 585-bp cDNA contains an open reading frame (ORF) comprising of 1 533 nucleotides (nt) which encodes a 511 residue polypepetides, including 67 amino acids chloroplast transit peptide and 444 amino acids EPSP synthase mature peptide. A comparison between the EPSP synthase of different sources indicates that the mature peptide shows more than 51% identity except for the fungi EPSP synthase and the transit peptide shows considerably less sequence conservation. The copy number of rice epsps gene is estimated to be one copy per haploid rice genome using southern blot. RT-PCR indicated that rice epsps gene is expressed in rice leaves, endosperms and roots and has the highest expression level in leaves.

Construction of Midgut Tissue-Specific cDNA Library of Bombyx mandarina M. and Isolation and Sequence Analysis of Serine Protease Gene Fragment

[Objective] The aim of the study is to construct cDNA library of midgut tissue of wild silkworm and isolate the serine protease gene. [Method] The midgut tissue-specific cDNA library of wild silkworm was constructed via cDNA Library Construction Kit (TaKaRa), then the serine protease gene was cloned via sequencing of the yielded cDNA library. [Result] The titer of cDNA library reached 6.2×105 pfu/ml, average insert size was about 1.2 kb. The serine protease gene cDNA fragment was obtained from colony sequencing (Accession No: EU672968). The nucleotide sequence of the cloned 854 bp fragment encodes 284 amino acid residues. Homology analyses showed some homology between putative amino acid sequence of the cloned fragment and amino acid sequences of serine proteases from other ten insects. [Conclusion] The results may avail to reveal the resistance of silkworm and wild silkworm to exotic intrusion.

Molecular Cloning and Sequence Analyses of cDNAs Encoding Seven C-type Lectin-like Protein Subunits from Daboia russellii siamensis

Total mRNA was extracted from a venom gland of snake Daboia russellii siamensis following the manufacturer＇s protocol of the PolyATtract System 1000 kit purchased from Promega Biotech. cDNAs encoding C-type lectins were amplified by RT-PCR and subcloned into a pMD18-T vector. Fourteen positive clones were selected for nucleotide sequencing and seven cDNAs encoding various snake venom C-type lectin-like protein precursors, designated as DRS-L1, DRS-L2, DRS-L3, DRS-L4 DRS-L5, DRS-L6 and DRS-L7, were obtained. Amino acid sequences of these proteins were deduced and each contains a carbohydrate recognition domain. Of all the deduced protein sequences, only DRS-L1 seemed to represent a closer sequence similarity to α subunits of other known snake venom C-type lectin-like proteins using the BLAST program. Homology comparison combined with analysis of cysteine position indicate that DRS-L1 and DRS-L2 are probably the light chain LC2 and LC1 of factor X activator from Daboia russellii siamensis venom, respectively. DRS-L3 and DRS-L4 might be the β subunits of higher molecular weight C-type lectin-like proteins while DRS-L5 and DRS-L6 might be β subunits of lower molecular weight C-type lectin-like proteins. DRS-L7 might be the β subunit of a platelet membrane glycoprotein Ib-binding protein similar to echicetin.

Generation and Analysis of Expressed Sequence Tags(ESTs) from Muscle Full-Length cDNA Library of Wujin Pig

Porcine skeletal muscle genes play a major role in determining muscle growth and meat quality. Construction of a full-length cDNA library is an effective way to understand the expression of functional genes in muscle tissues. In addition, novel genes for further research could be identified in the library. In this study, we constructed a full-length cDNA library from porcine muscle tissue. The estimated average size of the cDNA inserts was 1 076 bp, and the cDNA fullness ratio was 86.2%. A total of 1 058 unique sequences with 342 contigs （32.3%） and 716 singleton （67.7%） expressed sequence tags （EST） were obtained by clustering and assembling. Meanwhile, 826 （78.1%） ESTs were categorized as known genes, and 232 （21.9%） ESTs were categorized as unknown genes. 65 novel porcine genes that exhibit no identity in the TIGR gene index of Sus scrofa and 124 full-length sequences with unknown functions were deposited in the dbEST division of GenBank （accession numbers： EU650784-EU650788, GE843306, GH228978-GH229100）. The abundantly expressed genes in porcine muscle tissue were related to muscle fiber development, energy metabolism and protein synthesis. Gene ontology analysis showed that sequences expressed in porcine muscle tissue contained a high percentage of binding activity, catalytic activity, structural molecule activity and motor activity, which involved mainly in metabolic, cellular and developmental process, distributed mainly in intracellular region. The sequence data generated in this study would provide valuable information for identifying porcine genes expressed in muscle tissue and help to advance the study on the structure and function of genes in pigs.

IDENTIFICATION AND SEQUENCE OF A cDNA CLONE CORRESPONDING TO A GENE INVOLVED IN DEVELOPMENT OF UNDARIA PINNATIFIDA

During the induction of gamete-producing gametangia, induced gametophytes werecollected at 4 days intervals (0,4,8, 12 d) and total RNAs were isolated by CsCl gradient ultracentrifu-gation. Some stage-specific expressed mRNAs were identified by differential display of mRNAs from dif-ferent developing stages of the gametophytes. The cDNA of one specific mRNA was verified, cloned andsequenced. This gene was specifically expressed during 4 days of induction, and had partial homologoussequence with tobacco IAA-binding protein gene. It suggests that this cDNA may represent a gene whichis related to the LAA regulating function during the development of the gametophytes.

cDNA Cloning and Sequence Analysis of Rice Sbe1 and Sbe3 Genes

Two starch-branching enzyme (SBE) in rice, is known to be a key enzyme in amylopectin biosynthesis. The cDNA of two SBE(starch-branching enzyme) genes Sbe1 and Sbc3 encoding SBE Ⅰ and SBE Ⅲ (two major isoforms in rice) were cloned by an improved RT-PCR technique, from a template cDNA library derived from the total mRNAs extracted from the immature seeds of a japonica rice Wuyunjing 7. DNA sequence analysis showed that the size of the cloned Sbe1 and Sbe3 cDNAs were 2490 and 2481 bp long, respectively, including their entire coding sequences. Comparison analysis indicated that the nucleotide sequence of Sbe3 was the same as that of sbc3 (Genbank Accession No. D16201) as reported previously. There were only four base-pairs difference, which resulted in changes of two deduced amino acids between the cloned Sbel cDNA and the reported sbe1 (Genbank Accession No. D11082). The cloned Sbe1 and Sbe3 cDNAs make it possible to improve rice starch quality through genetic engineering

Generation and characterization of expressed sequence tags(ESTs) from coralloid root cDNA library of Cycas debaoensis

A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN （duplex-specific nuclease） normalization method combined with the SMART （Switching Mechanism At 5＇ end of the RNA Transcript） technique. The titer of the original cDNA library was about 1.5 × 10^6 cfu·mL^-1 and the average insertion size was about 1 kb with a high recombination rate （97%）. The 5011 high-quality expressed sequence tags （ESTs） were obtained from 5393 randomly picked cDNA clones. Clustering and assembly of ESTs resulted in 2984 unique sequences, consisting of 618 contigs and 2366 singlets. EST sequence annotation revealed that 2333 and 1901 unigenes were functionally anno- tated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 1495 （50.1%） unigenes were associated with 4082 Gene Ontology （GO） terms. A total of 847 unigenes were grouped into 22 Cluster of Orthologous Groups （COG） functional categories. Based on the EST dataset, 22 ESTs that encoded putative receptor-like protein kinase （RLK） genes were screened. Furthermore, a total of 94 simple sequence repeats （SSRs） were discovered, of which 20 loci were successfully amplified in C debaoensis. This study is the first EST analysis for the coralloid roots of C debaoensis and provides a valuable genomic resource for novel gene discovery, gene expression and comparative genomics, conservation and management studies as well as applications in C debaoensis and related cycad species.

Cloning and Sequence Analysis of Prophenoloxidase from Haemocytes of the Red Swamp Crayfish,Procambarus clarkii

The full-length cDNA sequence of prophenoloxidase was obtained through RACE technology. The complete cDNA sequence is 3 721-bp long, containing an open reading frame （ORF） of 1 881 bp, a 154-bp 5′-untranslated region, and a 1 686- bp 3′-untranslated region with three potential functional poly（A） signals （AATAAA）. The molecular mass of the deduced amino acid sequence （627 aa） was 72.3 kDa with an estimatedpI of 5.88. It contained putative copper-binding sites （copper A： 131, 135, 167 and copper B： 301,305, 341）, and a tentative complement-like motif （GCGWPDHL）. Eight potential N-linked glycosylation sites were predicted to be present in P. clarkii prophenoloxidase. Similar to those in other arthropod prophenoloxidases reported so far, no signal peptide was detected in the crayfish prophenoloxidase. The phylogenetic trees confirmed that P. clarkii prophenoloxidase was most closely related to that of freshwater crayfish P. leniusculus and more closely related to other crustacean prophenoloxidases from shrimp, prawn, and lobster than to the insect prophenoloxidases. Besides, two putative introns were found in this sequence of genomic DNA.

Cloning and Sequence Analysis of Expansin Genes from Litchi chinensis Fruit

Using PCR degenerate primers, designed with reference to the sequences of the conserved amino acids of known expansins, to amplify cDNA fragments in litchi fruit by RT-PCR, two different cDNA fragments , named as Lc-Exp1 and Lc-Exp2 , were cloned. Lc-Exp1 and Lc-Exp2 was respectively composed of 531 bp encoding 177 amino acids and 537 bp encoding 179 amino acids. Eight cysteine residues and three tryp-tophan residues, which is supposed to be the characteristics of expansins, are conserved in both Lc-Exp1 and c-Exp2. In addition, the homology between the two expansins is 71. 6% at nucleotide acid sequences and 76.3% at amino acid sequences. The homology of Lc-Exp1 with Fa-Exp2 or Pp-Exp1 was 92.7% or 92.1%, but that of Lc-Exp2 with Fa-Exp2 or Pp-Exp1 was only 77. 4% or 76.3% at amino acid sequences.

Complementary DNA sequencing (cDNA): an eff ective approach for assessing the diversity and distribution of marine benthic ciliates along hydrographic gradients

The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has never been observed in the microbenthic ciliate communities.Therefore,we hypothesized that benthic ciliates followed a similar distribution pattern as meio-and macrobenthos,but this pattern has not been uncovered by morphological methods.We evaluated the diversity and distribution of benthic ciliates at fi ve stations along hydrographic gradients across the YSCWM and adjacent shallow water by using morphology and DNA and complementary DNA(cDNA)high-throughput sequencing of the V4 region of 18S rRNA gene.Results showed that the diversity of benthic ciliates detected by DNA(303 OTUs),and the cDNA(611 OTUs)sequencing was much higher than that detected by the morphological method(79 species).Morphological method detected roughly diff erent ciliate communities inside and outside of the YSCWM,but without statistical signifi cance.No clear pattern was obtained by DNA sequencing.In contrast,cDNA sequencing revealed a distinct distribution pattern of benthic ciliate communities like meioand macrobenthos,which coincided well with the results of the environmental parameter analysis.More than half of the total sequences detected by DNA sequencing belonged to planktonic ciliates,most(if not all)of which were recovered from historic DNA originating through the sedimentation of pelagic forms because none of them were observed morphologically.The irrelevant historic DNA greatly infl uenced the recovery of rare species and thus limited the understanding of the benthic ciliate diversity and distribution.Our research indicates that the methods used have signifi cant eff ects on the investigation of benthic ciliate communities and highlights that cDNA sequencing has great advantages in estimating the diversity and distribution of benthic ciliates,as well as the potential for benthic environmental assessments.

Analysis of Expressed Sequence Tags from Liver Tissue in Swine

In order to study the expression of function gene and its effect on metabolic control and other physiological function in liver, 438 expressed sequence tags (ESTs) were determined, which were from a cD-NA library of porcine liver tissue. The results showed that the nucleotide sequences of 186 ESTs have already presented in GenBank database, and 37 ESTs could be found the homology with human and other species, while the others were not identified. 45 full length insertion of the clones randomly isolated from cDNA library were also completely sequenced with different size, and the results showed that 19 of them were function-known genes, 11 had no open reading frame ( ORF )at all and 15 had ORF but the function were not elucidated yet.

无蹼壁虎EMC3基因cDNA全长克隆与进化分析

为了探究无蹼壁虎(Gekko swinhonis)EMC3基因(命名为GsEMC3)的序列特征,了解GsEMC3蛋白的结构和功能,探讨GsEMC3蛋白与其他物种EMC3蛋白的进化关系,采用SMART RACE技术克隆获得了GsEMC3的全长cDNA序列,通过信息学分析阐明了GsEMC3基因的序列特征以及GsEMC3蛋白的结构和功能,系统发育和选择压力分析研究了GsEMC3的进化特征.GsEMC3基因的cDNA全长为1023 bp,包含1个786 bp的开放阅读框,基因编码1个含261个氨基酸的多肽.GsEMC3蛋白的相对分子质量约为30.074×10^(3),理论等电点为5.57.生物信息学分析表明,无蹼壁虎GsEMC3为疏水性非分泌型蛋白,有2个跨膜区,可能是一个动态定位的蛋白,无信号肽,直接在细胞内发挥作用.其分子量与已知的其他物种的EMC3蛋白相近.GsEMC3蛋白含有1个DUF106结构域,二级结构包含12个α-螺旋、1个β-折叠、13个无规则卷曲.系统发育分析表明,无蹼壁虎GsEMC3蛋白序列与美国短吻鳄(Alligator mississippiensis)、安乐蜥(Anolis carolinensis)、绿海龟(Chelonia mydas)、科莫多巨蜥(Varanus komodoensis)等爬行动物的EMC3蛋白序列高度同源.选择压力分析表明,无蹼壁虎的GsEMC3蛋白受到纯化选择,其功能可能高度保守.

Cloning and Sequence Analysis of Ribosomal Protein L21 Gene from the Ailuropoda melanoleuca

Ribosonal protein L21 which is a component of the 60s large ribosomal subunit plays an important role in ribosome. To explore the structure characteristic of ribosomal protein L21(rpL21) gene of the Ailuropoda melanoleuca and investigate its homologies with other already reported sequenses' including Rattus norvegicus, Mus musculus, Mus musculus, etc. The cDNA of rpL21 was cloned from the Ailuropoda melanoleuca by RT-PCR. The sequence data were analyzed by Genscan software. Blast 2.1 was used to study the homology of the obtained rpL21 sequence with the gene sequence of other species; Open reading frame (ORF) of the DNA sequence was searched using ORF finder software; Protein structure of the rpL21 sequence cloned was deduced using Predict Protein software. The results indicated that the length of cDNA fragment cloned was 504bp; containing an open reading frame of 483bp. Deduced protein was composed of 160 amino acids with an estimated molecular weight of 18.59kD and pI of 11.10. The length of the genomic sequence is 2254bp, containing 5 exons and 4 introns. Alignment analysis indicates that rpL21 is highly similarity with the reported species both at the level of DNA and protein. Topology prediction shows that 6 different patterns were found in the rpL21 protein of the Ailuropoda melanoleuca. The rpL21 gene of the Ailuropoda melanoleuca was studied in this paper, which will enrich and improve the mammals' rpL21 gene database.

草鱼肠道cDNA文库构建及部分ESTs分析

本项研究以雌性草鱼肠道为实验材料,采用非均一化的Oligo-dT引物定向克隆技术构建了草鱼肠道组织的cDNA文库,对文库质量的分析结果表明:cDNA文库的库容量至少为2.3×105,重组率达95%,平均插入片断长度大于1000bp。挑取cDNA克隆进行5’端测序,总共进行了1571个成功反应,其中1411条ESTs长度大于100bp,初步拼接得到939个单基因簇(Unigene),其中包括188个重叠群(Contigs),751个单拷贝EST(Singletons)。使用BLAST软件将这些序列同GenBank等数据库进行比对、查询和注释,结果显示418条序列有相关同源性,其他的521(55.5%)条序列没有明显的同源性(E-valu 1.00E-10),但是也同时揭示出在这些ESTs中能够发现新功能基因的相当可能性。本研究结果对草鱼以及其他鲤科鱼类的消化系统功能基因的筛选和发现具有指导意义。此外,草鱼肠道cDNA文库的构建和EST测序工作将为草鱼基因组计划的实施奠定基础。

鸡含锰超氧化物歧化酶cDNA克隆及序列分析

为弄清鸡含锰超氧化物歧化酶 (manganese containingsuperoxidedismutase ,MnSOD)的cDNA序列 ,以开展动物锰营养学的深入研究 ,根据已知鸡MnSOD的N端氨基酸序列设计简并引物 ,应用 3′RACE(rapidamplificationofcDNAends)技术 ,扩增克隆了鸡心肌MnSOD 990bp的 3′cDNA片段 .再根据 3′RACE片段测序结果设计引物进行 5′RACE ,结果获取了一个与 3′RACE片段相互重叠的鸡心肌MnSOD 52 1bp的 5′RACE片段 ,并对其进行了克隆测序 .最后根据 3′RACE片段和 5′RACE片段序列信息进行拼接 ,从而获取鸡MnSODcDNA的全序列信息 .研究结果表明 :鸡MnSODcDNA全长为 110 8个核苷酸 ,其中 5′非翻译区 2 5个核苷酸 ,编码区 675个核苷酸 ,3′非翻译区 4 0 8个核苷酸 ,编码一个长 2 2 4个氨基酸残基的蛋白质前体 .其中信号肽长 2 6个氨基酸残基 ,成熟肽长 198个氨基酸残基 ,分子量为 2 2kD .与人、大鼠、线虫、果蝇等真核生物MnSOD氨基酸序列的同源性分别为82 4 %、84 .7%、62 .4 %、59.3% .

7种鲽形目鱼类生长激素基因cDNA序列的克隆及系统分析

从7种重要鲽形目经济鱼类——高眼鲽（Cleisthenes herzensteini）、黄盖鲽（Limanda yokohamae）、木叶鲽（Pleuronichthys Cornutus）、宽体舌鳎（Cynoglossus robustus）、石鲽（Platichthys bicoloratus）和条鳎（Zebrias zebra）、夏鲆（Paralichthys dentatus）的脑垂体中提取mRNA，通过RTPCR方法，克隆了含开放阅读框的生长激素（growth hormone，GH）cDNA序列，与本实验室已克隆的大菱鲆和漠斑牙鲆、已报道的鲆鲽鱼类及外群鱼类共22条生长激素基因cDNA进行了序列比对和同源性分析．测序结果显示，高眼鲽、黄盖鲽、木叶鲽、宽体舌鳎、石鲽、条鳎和夏鲆的GHeDNA长度依次为479，564，519，440，564，440，522bp，编码140～170个氨基酸的成熟GH多肽片段．通过序列比对，这7种蛋白序列与其他已知的鲆鲽鱼类GH序列具有较高的同源性，同科的鱼类之间同源性更高．运用PAUP软件对15种鲽形目鱼类与另外7种不同种属鱼类进行了分子系统进化树分析，结果与根据传统的形态学和生化特征分类进化地位基本一致，大菱鲆和塞内加尔鳎各自单独形成一个分支且与鲆科和鲽科鱼类相距较远，其中寒内加尔鳎等种类的分类地位与根据线粒体DNA序列分析的系统发生模式基本吻合．说明生长激素基因可以有效地用于研究鲽形目等硬骨鱼类的亲缘关系及分类地位．

旋毛虫成虫cDNA文库免疫筛选及序列分析

目的 为获得旋毛虫成虫抗原基因。 方法 应用免疫血清和人工感染血清对旋毛虫成虫cDNA文库进行免疫筛选、克隆测序及核苷酸序列数据库 (GenBank)查寻比较 ,采用DNAstar软件进行基因序列分析。 结果 免疫筛选成虫cDNA文库 ,获得 9个阳性克隆。对其中的Ts87进行测序 ,又采用 5′ RACE ,获取全长为 1172bp的cDNA片段 ,该基因编码 3 47个氨基酸。序列分析表明 ,克隆Ts87是个尚未见报道的旋毛虫基因序列 ,存在预测的抗原表位。 结论 获得具有抗原性的旋毛虫抗原新基因。

东方田鼠感染血清免疫筛选日本血吸虫成虫cDNA文库

东方田鼠 (Microtusfortis ,Mf)对日本血吸虫 (Schistosomajaponicum ,Sj)感染具有抗性 .为探讨Mf感染Sj后是否产生针对虫体某些特异抗原分子的免疫应答 ,用Mf感染血清对Sj成虫cDNA文库进行免疫筛选 .经初筛和复筛 ,共筛选出 12个阳性克隆 .这些阳性克隆经辅助噬菌体自动剪切后PCR扩增显示 ,插入的SjcDNA片段大小在 3 0 0bp至 1 8kb之间 ,其中 1 8kb片段 5个 ,1kb片段 1个 ,3 0 0bp片段6个 .经DNA测序分析 ,鉴定出 3个未曾报道过的Sj新基因 ,分别命名为Sj Mf1、Sj Mf2和Sj胞质氨基肽酶 ,并在GenBank登记注册 .结果说明 ,Mf感染血清可识别Sj的特异性抗原分子 ,这些抗原分子的免疫保护作用值得进一步研究 .

猪带绦虫45W基因家族cDNA克隆和序列分析

根据猪带绦虫45W基因序列设计引物,用反转录-聚合酶链式反应(RT-PCR)对六钩蚴总RNA进行cDNA扩增,扩增产物经琼脂糖凝胶电泳分离、纯化、回收,与载体pGEMT-easyVector连接,转化大肠杆菌JM109,筛选阳性克隆,测序。结果显示,已成功克隆到重要保护性抗原45W基因B型转录本cDNA,完整开放阅读框(ORF)的大小为459bp。序列同源性分析与比较表明,所获得的9个B型转录本cDNA除TSO45W-4B-1和TSO45W-4B-2与已报道的TSO45W-4B同源外,其余均属于首次报道的45W基因家族新成员。各cDNA克隆之间核苷酸序列的差异性为1.5%～19.8%,氨基酸序列之间的差异性为2.6%～29.7%,后者比前者的差异程度更大。

西伯利亚鲟热休克蛋白HSP70cDNA的克隆、序列分析和组织分布

采用普通PCR和RACE技术克隆了西伯利亚鲟Acipenser baerii热休克蛋白HSP70 cDNA的全序列,该序列全长为2 343 bp,其中5'非编码区为140 bp,3'非编码区为256 bp,可读编码框(ORF)为1 947bp,编码为648个氨基酸。该氨基酸序列中含有HSP70家族的3个特征序列——IDLGTTYS、IFDLGGGTFD-VSIL和IVLVGGSTRIPKIQK,细胞质特征性保守序列为EEVD,C端重复序列为GGMP。该cDNA序列与其它生物的HSP70 cDNA序列一样具有很高的相似性。系统发育树显示,西伯利亚鲟与非洲爪蛙蟾Xenopus laevis、密西西比短吻鳄Alligator mississippiensis、美西螈Ambystoma mexicanum的亲缘关系较近。实时定量分析结果表明,水温为17.5℃时,西伯利亚鲟肝脏、鳃、脾脏、心脏、肌肉、中肠、性腺、脑8种组织中均有HSP70表达,其中HSP70在脾脏中的表达量最高,鳃中的次之,肝脏中最低(P<0.05)。