Cloning and Sequence Analysis of Prophenoloxidase from Haemocytes of the Red Swamp Crayfish, Pro
人尿酸氧化酶结构的同源模建和生物信息学分析
心的残基，而且这些残基在序列上和结构上都很保守，说明 人尿酸氧化酶基因发生无义突变之后，基因失去选择压力而 可能发生的错义突变位点却没在酶的活性中心。因此，在其
２００７，２４（１２）
岳俊杰等：人尿酸氧化酶结构的同源模建和生物信息学分析
Ｙｕｅ ＪＪ，Ｒｅｎ ＸＷ，Ｔａｎ ＭＦ，Ｌｉ ＢＰ，Ｗａｎｇ ＹＬ，Ｆａｎｇ ＨＱ ａｎｄ Ｌｉａｎｇ Ｌ．Ｈｏｍｏｌｏｇｙ ｍｏｄｅｌｉｎｇ ａｎｄ ｂｉｏｉｎｆｏｍａｔｉｅｓ ａｎａｌ－ ｙｓｉｓ ｏｆ ｔｈｒｅｅ－ｄｉｍｅｎｓｉｏｎａｌ ｓｔｒｕｃｔｕｒｅ ｏｆ ｈｕｍａｎ ｕｒａｔｅ ｏｘｉｄａｓｅ． Ｃｏｍｐｕｔｅｒｓ ａｎｄ Ａｐｐｌｉｅｄ Ｃｈｅｍｉｓｔｒｙ，２００７，２４（１２）：
１６４３—１６４６．
１ 引言
尿酸氧化酶是生物体内嘌呤降解代谢途径中的一种酶， 能催化尿酸氧化为尿囊素。许多物种体内均发现有尿酸氧 化酶，但在高等哺乳动物（灵长类）体内却缺乏此酶，而以尿 酸作为嘌呤代谢的终产物。尿酸及其盐类在水中溶解度很 低，血液中积累过多会导致高尿酸血症。这样患者体内，尿 酸会在软组织、关节、器官等处形成结晶而沉积，从而出现不 同的临床症状，比如痛风性关节炎、痛风性肾病等。随着社 会的发展和人们生活水平的提高，高尿酸血症和痛风的发病 率一直在上升。另外肿瘤疾病及其治疗过程会引发高尿酸 血症。加强对高尿酸血症的治疗已成为非常迫切的一项任 务。
本研究利用蛋白质结构同源模建技术，预测人尿酸氧化 酶的三维结构，并且在与其他物种的尿酸氧化酶结构比较的 基础上，分析酶的结构与功能的关系，为设计出“复活”突变 基因打下基础。
２ 材料与方法
人尿酸氧化酶序列引自文献［７］，包含３０４个氨基酸残 基。
雨生红球藻植物类型隐花色素基因克隆与序列分析
山西农业科学2020，48（5）：677-682雨生红球藻植物类型隐花色素基因克隆与序列分析杭伟,张宏江,马浩天,王晓丹,许文鑫,赵春超,李润植,崔红利（山西农业大学分子农业与生物能源研究所，山西太谷030801）摘要:为了从雨生红球藻中获得感知蓝光信号的植物类型隐花色素（CRY ）序列，采用同源克隆和RACE 相结合的方法获得了雨生红球藻编码植物类型Hae-P-CRY 的cDNA 全长，并对其序列进行生物信息学分析。
结果表明，Hae-P-CRY 基因的cDNA 全长为3608bp ，包含开放阅读框全长2988bp ，编码995个氨基酸，预测等电点6.19，理论分子质量为107.7ku 。
经Blast P 分析发现，Hae-P-CRY 氨基酸序列与莱茵衣藻来源植物类型CreCRY 氨基酸序列的相似性达到66.6%，与拟南芥CRY 氨基酸序列相似性为46.94%。
系统进化分析表明，Hae-P-CRY 与其他真核绿藻来源的植物型CRY 聚在一支，属于植物类型CRY 。
结构域分析表明，Hae-P-CRY 基因含有光感知PHR 结构域和信号转导CCT 结构域，暗示具有感知和转导光信号功能。
试验从雨生红球藻得到植物类型Hae-P-CRY 基因序列，可为其表达、功能及互作蛋白研究奠定基础，同时为进一步解析雨生红球藻在蓝光响应中的分子机制奠定基础。
关键词:雨生红球藻；隐花色素；基因克隆；生物信息学分析中图分类号:S917.3文献标识码:A文章编号:1002-2481（2020）05-0677-06Cloning and Sequence Analysis of Plant Type CryptochromeGene fromHANG Wei ，ZHANG Hongjiang ，MA Haotian ，WANG Xiaodan ，XU Wenxin ，ZHAO Chunchao ，LI Runzhi ，CUI Hongli（Institute of Molecular Agriculture and Bioenergy ，Shanxi Agricultural University ，Taigu 030801，China ）Abstract ：In this article,a full-length complementary DNA （cDNA ）sequence of plant type CRY （designated Hae-P-CRY ）was cloned from the green alga Haematococcus pluvialis .The homology cloning and rapid-amplification of cDNA ends （RACEs ）methods were applied to get the sequence of Hae-P-CRY .The result showed that the cDNA sequence length of Hae-P-CRY gene was 3608bp,which contained 2988bp open reading frame,294bp 5′-untranslated region （UTR ）,and 198bp 3′-UTR with the characteristic of the poly （A ）tail.The deduced protein （995amino acids ）had a calculated molecular mass of 107.7ku with an estimated isoelectric point （pI ）of 6.19.According to Blast P analysis,the similarity between Hae-P-CRY amino acid sequence and CreCRY amino acid sequence of Chlamydomonas reinhardtii was 66.6%,and that between Hae-P-CRY and CRY amino acid sequence of Arabidopsis was 46.94%.Phylogenetic analysis showed that Hae-P-CRY was a plant type CRY,which was clustered together with other eukaryotic green algae derived CRY.The results of domain analysis showed that Hae-P-CRY gene contained light sensing PHR domain and signal transduction CCT domain,suggesting that Hae-P-CRY gene had the function of sensing and transmitting light signals.The gene sequence of Hae-P-CRY from Haematococcus pluvialis can lay a foundation for the study of its expression,function and interaction protein,as well as for the further analysis of the molecular mechanism of Haematococcus pluvialis in blue-light response.Key words ：Haematococcus pluvialis ;cryptochrome;gene cloning;bioinformatics analysis收稿日期:2020-01-06基金项目:国家自然科学基金项目（31902394）；山西省应用基础研究项目（201801D22125）；辽宁省科学技术计划项目（20170540047）；山西省煤基重大科技专项（FT-2014-01）；山西省重点研发重点项目（201603D312005）；山西农业大学科技创新基金项目（2018YJ16）；山西省研究生教育创新项目（2019SY226）作者简介:杭伟（1991-），男，山西应县人，在读硕士，研究方向：基因工程与分子遗传。
微生物资源及开发利用
nature
Vol 467|2 September 10| doi:10.1038 /nature 09354
Bacterial charity work leads to population-wide resistance Henry H. Lee, Michael N. Molla, Charles R. Cantor & James J. Collins
to understand microbial communities. …individual host properties
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Enterotypes of the human gut microbiome
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分子生物学部分名词解释（Molecularbiology）
分子生物学部分名词解释（Molecular biology）Hypochromic effectBiochemochromic effect, in biochemistry, refers to the reduction of 260nm uv absorption in the form of a double helical structure in the form of denaturation DNA, a phenomenon called hypochromic effect.Hyperchromic effectDefinition 1: nucleic acid (DNA and RNA) molecular degenerative or broken chain, and its uv absorption value (generally measured at 260nm) increases. Applied subjects: biochemistry and molecular biology (first class); Nucleic acid and gene (secondary discipline) definition 2: the effect or property of the uv absorption value increased by the DNA or RNA in the solution in the treatment of heat and alkali. Applied discipline: genetics (first-level discipline); Molecular geneticsHalf-discontinuous replicationDefinition 1: when DNA replicates, a chain (leading chain) is continuously synthesized while the other chain (after chain) is discontinuous. Applied subjects: biochemistry and molecular biology (first class); Nucleic acids and genes (secondary disciplines) 2: double stranded DNA synthesis 5 'to 3' end is continuous synthesis, and 3 'to 5' end is discontinuous synthesis. Applied discipline: genetics (first-level discipline); Molecular genetics (secondary disciplines)Semiconservative replicationA replication model of double chain deoxyribonucleic acid (DNA), in which each single strand is used as a template for the new chain synthesis after the parental double chain separation. Therefore, when the replicates are completed, there will be two subgenerations of DNA molecules, each of which has the same nucleotide sequence as the parental moleculeA leading chainLeading strand: consistent with the direction of the replication fork movement, a new strand of DNA synthesized by successive 5-3 - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -After with chainIn the process of DNA replication, a template chain is 3 'to 5', and the DNA can be synthesized in 5 'to 3' to become the leading chain. Another template strand, is 5 'to 3' direction, on which the synthesis of from 5 'to 3' direction, but is the opposite of the direction of the replication forks mobile, therefore with the moving of the replication forks, to form a number of discrete pieces. The fragments are then linked together into a complete strand of DNA. The chain is called a post-it chainReplication forksIn DNA replication, the y-font structure formed by thecombination of unsoling, dissolving, and SSB proteins in the DNA strand is called a replication fork. In the replication fork, the double stranded DNA of the template is disintegrated and the new strand of DNA is synthesized.Silent mutationsThe same meaning mutation, the mutation replaces the base, but the amino acid sequence has not changed, keeping the function of the wild type.DNA damageDNA damage is a permanent change in the DNA nucleotide sequence that occurs during the replication process and results in changes in the genetic characteristics. To replace (insert) the insertion of (insert) exon (exon)Frameshift mutationsIn the normal DNA molecule, the base deletion or increase of the non-3 diploid number, resulting in a series of coding changes that occurred after this location, the phenomenon called shift code mutationMissense mutationIt is the code that codes for some kind of amino acid that is replaced by the base and becomes the codon of another amino acid, which changes the amino acid variety and sequence of the polypeptide chaintranscriptionThe process of transferring genetic information from genes to RNA.RNA polymerase dynamic complex with a series of component composition, and gene sequence as the genetic information template, catalytic synthesis of sequence complementary RNA, including transcription initiation, elongation, termination, etc. The process of synthesis of complementary single stranded RNA molecules by RNA polymerase is a template for DNA base sequences.The PCRPolymerase Chain Reaction (English full name: Polymerase Chain Reaction), Polymerase Chain ReactionPCR. Polymerase chain reaction (PCR) is a specific DNA fragments in vitro enzymatic synthesis of a kind of method, by the high temperature degeneration (compound) and the optimum temperature, low temperature annealing extension of several steps such as a cycle, cycle, makes the purpose of DNA amplification, rapidly with strong specificity, high sensitivity, convenient operation, time saving, etc. It not only can be used for gene isolation, cloning and sequence analysis of nucleic acids such as basic research, also can be used for the diagnosis of disease or any DNA and RNA. Polymerase Chain Reaction (Polymerase Chain Reaction, PCR), also known as cell free molecular cloning or specific sequences of DNAprimers in vitro directional enzymatic amplification techniques.The promoterDNA molecules can be combined with RNA polymerases to form regions of transcriptional initiation complexes. In many cases, the binding site for the regulating protein that facilitates this process is also included. Determine the DNA sequence of the RNA polymerase initiation site.enhancerThe sequent sequence of the gene promoter's work efficiency can be applied in any direction and in any location (upstream or downstream) of the promoter.operonIt refers to the general term for initiating genes, manipulating genes and a series of tightly linked structural genesexonDNA sequences corresponding to mature mRNA, rRNA or tRNA molecules in eukaryotic genes. Is the encoding sequence.intronsThere is no coding meaning in the eukaryotic gene and thesequence is excised. Introns are sequences that block the linear expression of genesDNA cloningApplication of enzymatic method, the various sources of genetic material in vitro, homology or different source, prokaryotic and eukaryotic, natural or artificial DNA combined with carrier DNA into a DNA molecule with self-replicating ability - replicators, then through the conversion or transfection host cells and extract containing the purpose gene into daughter cells, and then extract amplification, get a lot of the same DNA molecule, namely DNA clones.Gene libraryAn organism's genome DNA with restriction enzymes after part of the enzyme, the enzyme fragment inserted into the carrier DNA molecules, all of these into the genome DNA fragments of an aggregate of carrier molecules, will contain the organism's entire genome, which is constituted the organism's DNA library.A single genome DNA fragment cloned collectionDNA denaturationDNA degeneration refers to the hydrogen bond fracture of nucleic acid double helix base pairs, and the double chain becomes single chain, so that the natural conformation and properties of nucleic acid change.The cloneRestriction enzymes, or PCR, are used to obtain parts of the cloned DNA from the cloned DNA, and then clone the technology in other new carriers.attenuatorWhen RNA synthesis terminates, the DNA sequence that terminates the role of the transcriptional signal is terminated.Recombinant DNAA recombination of genetic information that occurs within or between a DNA molecule. Including homologous recombination, specific site recombination and transposition recombination. Recombinant DNA with artificial DNA is a key step in genetic engineering.Satellite DNAThe DNA of a sequence of highly repetitive nucleotide sequences of eukaryotic cells. The total amount of the DNA is more than 10%, mainly in the centromere region of the chromosome, usually not transcribed. Because of the small amount of GC in its base composition, it has different buoyancy density, and its name is given after centrifugation of cesium density gradient and most of its DNA is different from other "satellites"- 10 sequenceAlso called Pribnow box (prokaryote). Corresponding sequencein eukaryotes is located at - 35 bp, known as the TATA box, also known as the Goldberg - Hognessbox, is the combination of RNA polymerase Ⅱ parts.。
赤点石斑鱼两种芳香化酶cDNA的克隆及其表达的组织特异性(1)
动物学报 50(5):791-799,2004A cta Zoologica S i nica 赤点石斑鱼两种芳香化酶cD NA的克隆及其表达的组织特异性3李广丽1,2 刘晓春1 张 勇1 贝锦新1 林浩然1331.中山大学水生经济动物研究所暨广东省水生经济动物良种繁育重点实验室,广州51027522.湛江海洋大学水产学院,广东 湛江524025摘 要 以赤点石斑鱼(Epinephelus akaara)脑垂体中提取的RNA为模板,根据芳香化酶的保守序列设计引物,利用G eneRacer TM技术,克隆出两种芳香化酶即脑芳香化酶(P450aromB)和性腺芳香化酶(P450aromA)的cDNA,其全长分别为1901bp(编码509aa)和1833bp(编码518aa)。
序列分析结果表明,赤点石斑鱼两种芳香化酶cDNA序列的同源性为5116%,氨基酸序列之间同源性为6215%,与斜带石斑鱼两种芳香化酶氨基酸同源性分别为9417%和9719%。
对8个科的10种鱼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。
以特异性引物扩增雌、雄赤点石斑鱼各种组织(垂体、嗅球、端脑、下丘脑、中脑、后脑、延脑、心脏、肾脏、肝脏、脾脏、性腺、鳃、胃、肠、皮肤、脂肪、肌肉、头肾、胸腺、鳔),以β2actin作内标比较各组织芳香化酶基因表达量的差异,结果表明,赤点石斑鱼脑芳香化酶(P450aromB)有广泛的组织分布,脑和垂体的表达量很高,各组织表达量有明显的雌、雄差异;而性腺芳香化酶(P450aromA)表达主要集中于垂体和性腺,且不论雌雄,其性腺表达量均高于脑垂体,和P450aromB的表达模式明显不同,表现为在脑部,P450aromB表达量高于P450aromA,而在性腺,P450aromA表达量高于P450aromB,两种芳香化酶在脑垂体和性腺出现重叠表达[动物学报50(5):791-799,2004]。
生工引物合成
生工引物合成In the realm of biotechnology, the synthesis of primers is a crucial step in various molecular biology experiments. Primers are short, single-stranded nucleic acid sequences that serve as starting points for DNA replication or amplification processes such as polymerase chain reaction (PCR). The precision and accuracy of these primers are paramount as they directly influence the outcome of experiments, including gene cloning, sequencing, and expression analysis.在生物技术领域，引物的合成是各种分子生物学实验中的关键步骤。
引物是短的、单链的核酸序列，作为DNA复制或扩增过程（如聚合酶链式反应PCR）的起点。
这些引物的精确性和准确性至关重要，因为它们直接影响实验的结果，包括基因克隆、测序和表达分析等。
The process of primer synthesis involves several stages, from design to purification. Initially, the primer sequence is carefully designed based on the target DNA sequence, taking into account factors like melting temperature, GC content, and specificity. This ensures that the primers can effectively bind to the target sequence and initiate the desired reaction.引物合成的过程包括多个阶段，从设计到纯化。
细粒棘球蚴延伸因子-1基因的克隆,测序及特性分析3
文章编号:1001-5949(2005)08-0510-03・论 著・细粒棘球蚴延伸因子-1基因的克隆、测序及特性分析3王 健,赵嘉庆,王娅娜,丁淑琴,赵 巍 [摘要] 目的 对细粒棘球蚴(E.granulosus)翻译延伸因子(translation elongation factor)EF-1基因片段进行分子克隆及序列分析。
方法 从细粒棘球蚴原头蚴中提取RNA,采用RT-PCR技术扩增出细粒棘球蚴EF-1基因片段,与p GE M-T载体重组并转化E.C oli JM109,经筛选扩增获得重组基因克隆,再进行序列测定和分析。
结果 成功构建了EF-1/p GE M-T/JM109克隆体系,测序表明该基因开放阅读框为693bp,与已发表基因核苷酸序列相比,同源性为99%,推导编码氨基酸序列同源性为99%。
结论 扩增获得的基因片段可能为细粒棘球蚴(E.granu2losus)翻译延伸因子EF-1基因片段。
[关键词] 棘球蚴病;基因,结构;克隆,分子;序列分析[中图分类号] R532.32 [文献标识码] ACloning and sequence analyzing of the EF-1gene from echinococcus granulosus of m ankind WANG Jian,ZH AO Jia-qing,WANG Ya-na,et al.(Ningxia Med.C oll.,Y inchuan750004,China)Abstract Objective T o obtain and analyze sequence EF-1gene,and lay bases for screening candidate antigen of echinococcus granulosus.Methods T otal RNA was extracted from protoscoles of cysts from humam.The specific primers were designed according to published nucletid sequence in the genbank database.The EF-1gene of echinococcus granulosus was amplified by RT-PCR and cloned into p GE M-T vector for sequencing and analyzing.R esults A cDNA sequence with an open reading frame of693bp has been amplified success fully by RT-PCR.C omparision of the DNA and amino acid sequence deduced from cDNA with the published EF-1gene sequence of echinococcus granulo2 sus in the genbank revealed99%identity samely.Conclusion Because the EF-1play an importante role in energy metabolism of E.granulo2 sus,EF-1gene gained from protoscoles can be used as candidate antigene gene to develope vaccine and its biological functions studying.K ey w ords Echinococcosis;G enes structural;Cloning molecular;Sequencing 细粒棘球蚴病又称包虫病,是世界上许多国家影响人类健康和经济发展的重要人兽共患病之一。
牦牛谷胱甘肽过氧化酶1基因(GPX1)的克隆及系统发育分析
51卷第1期Vol. 51 ,No. 1青海畜牧兽医杂志Chinese Qinghai Journal of Animal and Veterinary Sciences12/2021试验研究I 牛谷胱甘肽过氧化酶1基因(GPX1)的克隆及系统发育分析李瑞哲，徐惊涛，马志杰，孙永刚,韩银仓，陈生梅(青海大学畜牧兽医科学院，西宁810016)摘 要:本研究克隆了#牛谷胱甘肽过氧化酶1GPX 1基因的CDS 区序列，分析了其核昔酸序列，并进行了系统发育分析。
结果表明,#牛GPX1基因CDS 区全长618 bp,编码205个氨基酸;经与GenBank 中其他物种GPX 1 基因CDS 区比对,#牛GPX 1基因CDS 区与普通牛和瘤牛完全一致，与水牛、绵羊和猪的序列一致性较高，与其他 哺乳动物序列一致性较低。
本研究为深入研究#牛GPX1的生理功能提供了参考资料。
关键词:#牛;谷胱甘肽过氧化酶1;基因克隆;系统发育中图分类号:S823.8 +5 文献标识码:A 文章编号：1003 -7950(2021)01 -0001 -05Cloning and Phylogenetic Analysis ofGlutathione Peroxidases t Gene (GPX1) in YakLI Rui - zhe et al(Academy of Animal Science and Veterinary Medicine of Qinghai University , Xining 810016 )Abstract : Glutathione Peroxidasesl , which is the most abundantly expressed enzymes of glutathione peroxida ses family , plays an important role in inactivating peroxides ( hydrogenperoxides , organic hydroperoxides and lipid peroxides et al. ) and sustaining cellular re 一 dox homeostasis. In this study , we cloned the coding sequence region(CDS ) of GPX1 gene in yak , analyzed its nucleotide sequence and constructed phylogenetic treeusing bioinformatic software. The results showed that the CDS of yak GPX1 gene spans 618 bp , which encodes 205 amino acids. The aligning results showed that the CDS of yak GPX1 gene had an identical sequence with cattle and zebu , a high simi larity with water buffalo , sheep and pig , and a lower similarity with other mammals. This study provided basic ref erence data for further investigating the biological role of GPx1 in yak.Key words ：Yak ； Glutathione peroxidase1; Gene cloning ； Phylogenetic analysis硒是动物机体必需的微量元素之一，在繁殖、免疫、抗氧化、调节机体代谢等生理功能中具有重要作 用⑷o 硒蛋白是指含有硒半胱氨酸(selenocysteine )残基的一类蛋白质，是硒发挥生物学功能的主要载体[2]o 硒蛋白的特殊之处在于编码硒半胱氨酸的 密码子为UGA ,而在其他蛋白质中UGA 一般作为 终止密码子。