马传染性贫血病毒弱毒疫苗株感染性分子克隆的构建

 采用PCR方法分 3段扩增出马传染性贫血病毒驴白细胞弱毒疫苗株 (EIAVDLA)的前病毒DNA ,这 3个片段覆盖马传染性贫血病毒的全部基因组 ,PCR产物经克隆后顺次连接 ,获得 1个含有EIAV全基因 (8.0kb)的重组质粒 ,将其命名为p8.0。将此 8.0kbEIAV全基因再亚克隆到含有一完整EIAVDLA株长末端重复序列的质粒中 ,获得一含有EIAV驴白细胞弱毒前病毒全基因的重组质粒 ,将其命名为p8.2 ,经核苷酸序列分析 ,证明p8.2含有EIAV前病毒的全基因。用p8.2转染驴白细胞 ,将其作为种毒进行传代 ,于感染该克隆毒的细胞培养上清中检测出了反转录酶活性 ,说明在驴白细胞中由p8.2衍生出了EIA病毒。驴白细胞经该克隆毒感染后 ,第 4天出现病变 ,经透射电镜可观察到典型的马传染性贫血病毒粒子 ,进一步证明p8.2具有感染性 ,笔者获得了马传染性贫血病毒驴白细胞弱毒疫苗株的感染性分子克隆 ,为进一步在分子水平上阐明我国EIAV疫苗株的减毒机理和免疫保护机制奠定了基础     

Evolutionary Patterns of the Proviral gp90 V3 to V5 Regions of Equine Infectious Anemia Virus Associated with Immune Selection in Progressors and Nonprogressors

The aim of this study was to determine the genomic evolutionary pattern of virulent equine infectious anemia virus (EIAV)during persistent infection.The evolutionary dynamics of proviral genomes were examined by challenging an EIAV seronegative equine (pony 1) and three EIAV vaccinated equines (ponies 4,7,and 8) with the Chinese virulent strain EIAVL.Ponies I and 7 succumbed to disease and were called progressors,while ponies 4 and 8 lacked clinical symptoms and were considered nonprogressors.Sequences spanning the V3,V4,and V5 hyper-variable regions of the EIAV-L envelope gp90 gene were sequenced from each pony as evolutionary markers of the provirus.The proviral genome of the EIAV-Linoculum evolved during persistent infection and displayed different patterns between EIA progressors and nonprogressors.Inoculum-like variants were isolated from nonprogressors during persistent infection,but only from progressors during acute infection.Variant mutations from nonprogressors were dispersed throughout the sequenced region,while those from progressors were predominantly localized to V3.Humoral immunity and virus variant population selection analyses indicated that immune selection was positive in chronically infected progressors and weak in nonprogressors.In-frame stop codons were frequently localized to a defect "hot spot".The high number of defective variants in nonprogressors may promote disease survival.     

HIV-1 proviral DNA excision using an evolved recombinase

HIV-1 integrates into the host chromosome and persists as a provirus flanked by long terminal repeats (LTRs). To date, treatment regimens primarily target the virus enzymes or virus-cell fusion, but not the integrated provirus. We report here the substrate-linked protein evolution of a tailored recombinase that recognizes an asymmetric sequence within an HIV-1 LTR. This evolved recombinase efficiently excised integrated HIV proviral DNA from the genome of infected cells. Although a long way from use in the clinic, we speculate that this type of technology might be adapted in future antiretroviral therapies, among other possible uses.     

Characterization of envelope and core structural gene products of HTLV-III with sera from AIDS patients

The envelope (env) and structural (gag) gene products of human T-cell leukemia (lymphotropic) virus type III were identified by immunoaffinity chromatography, immunoprecipitation, and two-dimensional oligopeptide mapping methods. The env gene specifies a glycosylated polypeptide with a molecular weight of 160,000 (gp160) that is processed to gp120 and smaller gene products. The gag gene specifies two polypeptides of 70,000 and 55,000 molecular weight (p70 and p55), both of which contain p24, the major structural protein of the mature virion. The techniques in this study can be used to define the extent of variability of the env gene product among different virus isolates and may identify the nature and patterns of the humoral immune response that lead to an immunologically protected state.     

A new class of endogenous human retroviral genomes

Human DNA contains multiple copies of a novel class of endogenous retroviral genomes. Analysis of a human recombinant DNA clone (HLM-2) containing one such proviral genome revealed that it is a mosaic of retroviral-related sequences with the organization and length of known endogenous retroviral genomes. The HLM-2 long terminal repeat hybridized with the long terminal repeat of the squirrel monkey virus, a type D retrovirus. The HLM-2 gag and pol genes share extensive nucleotide sequence homology with those of the M432 retrovirus (a type A-related retrovirus), mouse mammary tumor virus (a type B retrovirus), and the avian Rous sarcoma virus (a type C retrovirus). Nucleotide sequence analysis revealed regions in the HLM-2 pol gene that were as much as 70 percent identical to the mouse mammary tumor virus pol gene. A portion of the putative HLM-2 env gene hybridized with the corresponding region of the M432 viral genome.     

地方品种皖南黄肉种鸡ALV-J与REV的共感染 及其分子变异分析

 【目的】探讨地方品种皖南黄肉种鸡群中禽白血病病毒（ALV）与禽网状内皮增生病病毒（REV）的感染状态,同时对J亚型ALV（ALV-J）分离株的囊膜糖蛋白基因（env）和非编码区3′UTR序列进行分子变异分析,并对近十年的分离株非保守序列区段进行统计比较,探讨ALV-J分子变异趋势。【方法】取7只300日龄皖南黄肿瘤病鸡分别进行病理组织学观察、IFA检测肝脏组织切片后激光共聚焦观察、细胞培养后的IFA以及PCR方法检测。【结果】7只皖南黄肉种鸡有6只同时感染ALV-J与REV,而且ALV-J和REV已经共感染同一个肝细胞。取2个ALV-J分离株进行env基因与非编码区3′UTR扩增与序列分析,两分离株的env全长均为1 704 bp,3′UTR全长均为400 bp,3′UTR区段rTM和E元件同发生双缺失;3′UTR-E元件与近十年国内来自白羽肉鸡的ALV-J分离株比较,基因缺失表现为共性,但3′UTR-rTM基因缺失呈现多样性;5′LTR作为保守序列较之前所有国内外毒株有11 bp缺失。【结论】研究发现,地方品种皖南黄肉种鸡群存在ALV-J与REV的共感染,且呈现普遍性（6/7）,表明地方品种鸡高肿瘤发生率与ALV-J、REV共感染密切相关;ALV-J的基因缺失主要集中于3′UTR-E与3′UTR-rTM, 3′UTR-E元件基因缺失显示,皖南黄肉种鸡群ALV-J分离株与近十年国内来自白羽肉鸡的ALV-J分离株有共同的来源。     

Isolation and characterization of a novel protein (X-ORF product) from SIV and HIV-2

A protein designated p14 was purified from a simian immunodeficiency virus (SIVMne) and was shown by amino acid sequence analysis to be nearly identical to the predicted translational product of a unique open reading frame (X-ORF) in the nucleotide sequences of SIVmac and human immunodeficiency virus type 2 (HIV-2). Thus the X-ORF is proven to be a new retroviral gene. The p14 is present in SIVMne in molar amounts equivalent to those of the gag proteins. This is the first example of a retrovirus that contains a substantial quantity of a viral protein that is not a product of the gag, pro, pol, or env genes. SIV p14 and its homolog in HIV-2 may function as nucleic acid binding proteins since purified p14 binds to single-stranded nucleic acids in vitro. Antisera to the purified protein detected p14 in SIVMne, SIVmac, and a homologous protein (16 kilodaltons) in HIV-2 but did not react with HIV-1. Diagnostic procedures based on this novel protein will distinguish between HIV-1 and HIV-2.     

Nucleotide sequence and expression of an AIDS-associated retrovirus (ARV-2)

The nucleotide sequence of molecular clones of DNA from a retrovirus, ARV-2, associated with the acquired immune deficiency syndrome (AIDS) was determined. Proviral DNA of ARV-2 (9737 base pairs) has long terminal repeat structures (636 base pairs) and long open reading frames encoding gag (506 codons), pol (1003 codons), and env (863 codons) genes. Two additional open reading frames were identified. Significant amino acid homology with several other retroviruses was noted in the predicted product of gag and pol, but ARV-2 was as closely related to murine and avian retroviruses as it was to human T-cell leukemia viruses (HTLV-I and HTLV-II). By means of an SV-40 vector in transfected simian cells, the cloned gag and env genes of ARV-2 were shown to express viral proteins.     

Nucleotide sequence of SRV-1, a type D simian acquired immune deficiency syndrome retrovirus

Simian acquired immune deficiency syndrome (SAIDS) in the macaque genus of monkeys at the California Primate Research Center is apparently caused by infection by a type D retrovirus. The complete nucleotide sequence (8173 base pairs) of a molecular clone of the prototype SAIDS virus isolate, SRV-1, reveals a typical retrovirus structure with long terminal repeats (346 base pairs) and open reading frames for the gag (663 codons), pol (867 codons), and env (605 codons) genes. SRV-1 also has a separate open reading frame of 314 codons between the gag and pol genes that defines the viral protease gene (prt) and a short open reading frame of unknown significance downstream from the env gene. The SRV-1 protease region shows a high degree of homology to its counterpart in the hamster intracisternal A-type particle genome; both these protease genes are about twice as long as the analogous region of other retroviruses. SRV-1 has no notable similarity in either genetic organization or sequence to the human AIDS retroviruses.     

Deleted HTLV-I provirus in blood and cutaneous lesions of patients with mycosis fungoides.

Mycosis fungoides, a rare form of cutaneous T cell leukemia/lymphoma, is suspected of having a viral etiology on the basis of certain similarities to adult T cell leukemia, which is associated with human T cell leukemia/lymphoma virus type I (HTLV-I) infection. Cell lines were established from peripheral blood mononuclear cells (PBMC) of an HTLV-I-seronegative patient with mycosis fungoides. DNA hybridization analysis revealed the presence of HTLV-I-related sequences with unusual restriction endonuclease sites. Sequence analysis of subcloned fragments demonstrated the presence of a monoclonally integrated provirus with a 5.5-kilobase deletion involving large regions of gag and env and all of pol. Additional evidence for the presence of deleted proviruses was found by polymerase chain reaction (PCR) amplification of DNA from cutaneous lesions of five other HTLV-I-seronegative patients. The findings suggest that HTLV-I infection may be involved in the etiology of at least certain cases of mycosis fungoides.     

HTLV x-gene product: requirement for the env methionine initiation codon

The human T-cell leukemia viruses (HTLV) are replication-competent retroviruses whose genomes contain gag, pol, and env genes as well as a fourth gene, termed x, which is believed to be the transforming gene of HTLV. The product of the x gene is now shown to be encoded by a 2.1-kilobase messenger RNA derived by splicing of at least two introns. By means of S1 nuclease mapping of this RNA and nucleic acid sequence analysis of a complementary DNA clone, the complete primary structure of the x-gene product has been determined. It is encoded by sequences containing the env initiation codon and one nucleotide of the next codon spliced to the major open reading frame of the HTLV-I and HTLV-II x gene.     

库尔勒香梨kfpSPL及其启动子克隆分析

【目的】 研究库尔勒香梨萼片脱落、宿存与kfpSPL基因之间存在的关系,并克隆该基因及其启动子。【方法】以库尔勒香梨花器官作为材料,库尔勒香梨kfpSPL基因的cDNA序列以及梨基因组信息为模板设计引物,通过PCR获得该基因及其启动子,进行上游调控序列顺式作用元件的预测分析(PLACE数据库和PlantCare数据库)。【结果】克隆获得kfpSPL基因的基因组DNA序列长度为3 320 bp和2 332 bp的上游启动子调控序列,kfpSPL基因的基因组DNA与Pyrus bretschneideri 数据库中的一段长度相同的序列具有99%的同源性,E值为0,并发现该基因有三段内含子,将克隆得到的启动子序列在梨全基因组序列数据库中进行相似性搜索,发现克隆得到的上游启动子序列的1~796 nt和1 042~2 332 nt分别与scaffold291.0中290 783~289 988 nt和289 990~288 701 nt的同源性为96%和97%,E值均为0。以生物信息学分析为依据,kfpSPL启动子序列中存在一些相关的调控元件,赤霉素响应元件GARE-motif、P-box,光响应中的顺式作用元件ACE、 Box II、CATT-motif、G-box、TCT-motif、Box 4,防御和应激反应中的顺式作用元件TC-rich repeats, 启动子和增强子区的共同顺式作用元件CAAT-box等,转录起始的核心启动子元件TATA-box等。【结论】kfpSPL基因启动子序列中存在与赤霉素、脱落酸、水杨酸等激素相关的顺式作用元件,不同生长调节剂处理脱萼果和宿萼果的花器官可以调控kfpSPL基因的表达水平。     

Complete nucleotide sequence and organization of the Moloney murine sarcoma virus genome

The complete nucleotide sequence of a mammalian transforming retrovirus. Moloney murine sarcoma virus, has been determined. MSV, recombinant virus derived of helper viral and cellular sequences, possesses termini resembling prokaryotic transposable elements. The viral genome has the coding capacity for the Moloney murine leukemia virus gag gene product and contains large deletions in pol and env genes. A large open reading frame encompassing its cell-derived sequences codes for its putative transforming protein. The nature of some of the important domains in the viral genome has been established, and their structure is discussed in relation to their function.     

西农萨能羊乳腺脂肪酸合酶基因exon 9-15的克隆与序列分析

【目的】山羊FAS基因exon 9-15编码的乙酰/丙二酸单酰基转移酶（acetyl-CoA and malonyl-CoA transacylases,AT/MT）区域对山羊乳短、中链脂肪酸的合成起重要调控作用。本研究针对西农萨能羊乳腺FAS基因exon 9-15进行克隆和序列分析。【方法】以处于泌乳期28 d的西农萨能羊乳腺组织mRNA反转录的cDNA为模板,通过RT-PCR方法首次扩增出西农萨能羊乳腺FAS基因exon 9-15的cDNA序列全长及exon 8 的3′端和exon 16 的5′端部分cDNA序列（GenBank收录号为DQ 915966）,并对其进行了同源性分析和功能预测。【结果】克隆片段全长1 449 bp,其中包括exon 9-15共1 388 bp、exon 8的3′端9 bp和exon 16 的5′端52 bp,编码483个氨基酸,包含编码的AT/MT区域951 bp（454～1404 nt）;西农萨能羊乳腺FAS基因exon 9-15与牛（NM_001012669）,人（NM_004104）,大鼠（NM_017332）和鸡（NM_205155）核苷酸序列相似度分别为95%、85.7%、82.7%、73.2%,氨基酸相似度分别为92.9%、77.7%、82.3%、64.7%;exon 10较其它物种缺失1个氨基酸。【结论】克隆获得西农萨能羊FAS基因片段全长1 449 bp,外显子9-15大小分别为463、185、190、95、135、204和116 bp;核苷酸及氨基酸序列与牛相应序列的同源性均高于其它物种;AT/MT区域的活性位点在各物种间均为高度保守的丝氨酸,但西农萨能羊exon 10较其它物种缺失1个氨基酸,这可能对AT/MT区域的空间构象及其生理功能产生重要影响。本研究为西农萨能羊FAS基因cDNA全长克隆以及基因功能研究奠定了重要基础。     

牛ME1基因cDNA编码序列的克隆与分析

在NCBI中GenBank里查询已登录的牛的ME1 mRNA序列(GenBank Accession:XM-613987),发现其1-69 bp序列与已知的人、猪和小鼠的ME1基因mRNA序列没有任何相似性,因此,认为这段序列有误。研究利用人的ME1基因mRNA序列作为电子探针共找到44段牛的相关ESTs序列,然后利用此ESTs重叠群拼接成的序列设计了三对引物。提取牛的肝脏和肌肉总RNA,从中克隆测序得到M1为525 bp、M2为1039 bp和M3为1171bp的三段序列,拼接成长度为2015 bp的序列。此段序列与前述ESTs重叠群一致序列完全相同,并与人、猪和小鼠的ME1基因mRNA序列相似性分别达89%、85%和84%,从而证实了本序列的正确性。本序列已在NCBI登录(GenBank Accession:FJ495084)。研究为进一步研究牛的ME1基因结构提供了真实的序列信息。     

SCAR分子标记方法检测家蚕品种和纯度的研究

 【目的】家蚕（Bombyx mori L.）品种和纯度的鉴别，普遍依靠幼虫斑纹或茧形等形态鉴别方法，该方法易受环境影响，结果时效性和准确性差。【方法】筛选RAPD随机引物，稳定扩增出亲本品种的DNA特异性片段，转换成SCAR标记。 【结果】利用微量DNA抽提法，从家蚕主要品种苏5、苏6及其F1孵化前日卵快速提取单粒卵基因组DNA，筛选出RAPD随机引物S42，稳定扩增出苏5和苏6两个亲本品种的DNA特异性片段R5和R6，克隆和测序确认其大小分别为255bp和343bp。Blastn分析显示，R5的nt7～192与家蚕的一个非长末端逆转录转座子（AB002270.1）的nt183～368片段碱基序列有高达91%的相似性，无缺口序列。R6的nt5～340与家蚕的一个WGS（BAAB01113163.1）的nt675～337有91%的一致性，其中存在13个碱基的缺口序列。将2个亲本的RAPD标记转换成SCAR标记，分别利用合成的S42-255-2（P5-2）和S42-343-2（P6-2）SCAR标记引物，能够准确、快速地鉴别所标记的苏5和苏6及其F1蚕品种。【结论】SCAR分子标记方法能够检测家蚕品种和纯度。     

毛竹Phyllostachys edulis retrotransposon 7（PHRE7）转座子的克隆与鉴定

长末端重复序列（LTR）反转录转座子广泛存在于植物基因组中,本质是一段可移动的脱氧核糖核酸（DNA）序列。大多数LTR反转录转座子在外界环境变化下能够被激活转录,对环境变化做出响应。为研究毛竹基因组中的LTR反转录转座子的转录活性及在非生物环境胁迫下表达量的具体变化,克隆和鉴定了1个毛竹Phyllostachys edulis反转录转座子PHRE7。该转座子全长为6 073 bp,属于Ty1-copia家族中的Tork分支,LTR序列相似性为96.7%,插入时间为126.923万a前。对毛竹实生苗分别进行辐照（30,50,70 Gy）,甲基化抑制剂（50,100,150 μmol·L-1）,高温（42℃）,低温（4℃）,高盐（0.1,0.2,0.3 mol·L-1）等5种不同胁迫处理,通过定量荧光聚合酶链式反应（PCR）检测,PHRE7在INT,RT和RH等3个结构域中的表达量仅在辐照及0.2~0.3 mol·L-1高盐处理下随处理强度的上升而下降,其余所有处理（甲基化抑制剂、高温、低温、高盐0.1~0.2 mol·L-1）的表达量都随处理强度呈上升趋势。这些结果表明:PHRE7转座子是一个具有转录活性的LTR反转录转座子,且外界非生物环境胁迫对其表达模式有较大影响,表明PHRE7转座子能够响应外界环境变化。