大熊猫及其近种活化素基因βA亚基成熟肽序列的克隆分析及其在分类地位上的应用

借鉴互联网中已经克隆到的Activin基因βA亚基成熟肽序列,设计并合成1对兼并引物,利用PCR技术从大熊猫,小熊猫,马来熊的基因组DNA中直接扩增目的基因片段,并分别克隆到大肠杆菌载体pBlueScript^ 当中,然后对培养产物进行行序列测定,DNA序列分析表明,三种物种的Activin基因βA亚基成熟肽序列长度均为359bp,无内含子,基因片段编码一个含有119个氨基酸残基的肽段。大熊猫,小熊猫,马来熊在该成熟肽核苷酸和氨基酸序列上表现出高度的同源性,其中核苷酸同源性为93.9%。氨基酸同源性高达99%以上,此外,3种动物的核酸限制性酶切图谱也高度相似,与GenBank中收录的其他物种Activin基因βA亚基成熟肽序列相比较,显示此片段在处于不同进化程度的物种之间仍具有高度保守性,运用系统发育与进化树软件包PHILIP,并结合克隆序列对大熊猫,小熊猫,马来熊进化与分类地位进行了探讨,采用不同的统计学分析方法,所得到的3个物种系统发育进化树的拓扑结构完全一致,相比较而言,大熊猫与马来熊有着较近的亲缘关系,而小熊猫与上述两个物种的亲缘关系相对疏远,结果支持将大熊猫与马来熊归为熊科,而将小熊猫单列成科的学术观点,这是首次以生殖相关的核基因作为研究对象,为大熊猫及其近种进行系统分类研究所提供的又一分子生物学证据。     

鲤鱼（Cyprinus carpio）生长激素基因的亚克隆及其序列分析

本文对ＰＣＲ扩增的６６８ｂｐ的ＤＮＡ片段进行了亚克隆,然后以Ｓａｎｇｅｒ双脱氧中止法为原理,利用美国ＡＢＩ公司３７０Ａ自动核酸序列分析仪,确定了６６８ｂｐ的核苷酸序列。序列分析表明鲤鱼生长激素基因的开放读框含有６３０ｂｐ,并推测其中包括２２个氨基酸的信号肽和１８８个氨基酸的成熟多肽。鲤鱼生长激素基因的酶切图谱和序列分析的结果都证明我们已获得了全长的鲤鱼生长激素基因。     

应用RAPD技术对大熊猫分类地位的探讨

采用ＰＣＲ和Ｓｏｕｔｈｅｒｎ杂交等方法对大熊猫与小熊猫、马来熊、浣熊等共有的一条１．３ｋｂ的ＲＡＰＤ产物片段进行了初步分析。研究结果显示,来自于大熊猫的此共有片段可能为一重复序列,并且其内部含有多个随机引物ＡＢ１－０８的结合位点。以此来自于大熊猫的１．３ｋｂ片段为探针进行杂交,发现马来熊ＲＡＰＤ产物中的对应片段显示了很高的同源性,而小熊猫和浣熊ＲＡＰＤ产物则无相应的杂交带。这暗示,从分类地位上来看,大熊猫与熊科马来熊的亲缘关系应更近于与小熊猫和浣熊的亲缘关系,应与马来熊一样划分为熊科。本研究为大熊猫分类地位的确定提供了又一分子生物学证据     

人淋巴毒素基因5′端上游NF－KB类因子特异性结合位点的研究

淋巴毒素（Ｌｙｍｐｈｏｔｏｘｉｎ,ＬＴ）是由活化的Ｔ淋巴细胞分泌的一种糖蛋白。ＬＴ基因的表达调控主要是在转录水平上。ＰＨＡ＋ＰＭＡ诱导的Ｊｕｒｋａｔ细胞总ＲＮＡ点渍杂交发现,Ｊｕｒｋａｔ细胞的内源性ＬＴｍＲＮＡ的数量随诱导时间的延长而增加。凝胶迟滞电泳分析发现,ＰＨＡ＋ＰＭＡ诱导４小时的Ｊｕｒｋａｔ细胞核抽提物形成多种复合物,且在诱导不同时间后有明显变化。系列缺失片段的竞争反应表明,这些复合物的形成与ＬＴ基因５＇端上游──１２８ｂｐ──９３ｂｐ左右的序列相关。ＤＮａｓｅｌ足迹法及其竞争实验发现,ＬＴ基因５＇端上游─—１０４ｂｐ──８３ｂｐ（共２２ｂｐ）序列具有明显的蛋白质保护足迹。同源性分析发现此２２ｂｐ的序列中存在一个ＫＢ样结合位点：─１００ｂｐ──９０ｂｐ（５’－ＧＧＧＧＧＣＴＴＣＣＣ－３’）。ＮＰ－ＫＢ类蛋白质因子参与了此序列的ＤＮＡ－蛋白质的特异性结合,可能存在多种类型的ＮＰ－ＫＢ类蛋白因子参与了ＬＴ基因的表达调控。     

酵母转录因子PHO81基因的上游序列功能分析

利用ＰＨＯ８１ｌａｃＺ融合基因,对它的上游进行缺失分析,发现有两个区域对ＰＨＯ８１基因的表达是必需的：－４０１～－２８９ｂｐ和－１０１２～－８０１ｂｐ。比较ＰＨＯ８１和ＰＨＯ５,ＰＨＯ８４基因上游,未发现有较高同源性的序列存在,但在－４０１～－２８９ｂｐ区域有ＰＨＯ４蛋白结合位点的核心序列５′ＣＡＣＧＴＧ／Ｔ３′,以及ＣＡＣＧＴＧ／Ｔ两侧富含Ａ／Ｔ的序列（可能是ＰＨＯ２结合位点）。推测－４０１～－２８９ｂｐ包含了ＰＨＯ８１的上游激活序列（ＵＡＳ）,－１０１２～－８０１ｂｐ可能起增强的作用。用酵母总蛋白质对－１０１２～－８０１ｂｐ进行凝胶阻抑电泳分析,证明有未知的蛋白因子结合在这个区域。     

人端粒酶RNA基因的克隆与鉴定

以人血基因组ＤＮＡ为模板,合成两段２０个寡聚核苷酸为引物,经过ＰＣＲ扩增,得到４８０ｂｐ的片段,克隆到ｐＭＤ１８－Ｔ载体中,经电泳、酶切、ＰＣＲ鉴定后测定序列。序列分析表明氙克隆的人端粒酶ＲＮＡ（ｈｕｍａｎ ｔｅｌｏｍｅａｓｅ ＲＮＡ,ｈＴＲ）基因含有４８０ｂｐ,包括约４５０ｂｐ的编码模板区主序列和约３０ｂｐ的上游调控区序列,其中模板区的１１个核苷酸（５’－ＣＵＡＡＣＣＣＵＡＡＣ－３’）合成端粒亚     

携带p53基因的重组腺病毒的构建及对肿瘤细胞抑制的研究

１　材料与方法１１　质粒ｐＣＭＶｐ５３ＢＡＭ由美国约翰·霍普金斯肿瘤中心ＢｅｒｔＶｏｇｅｌｓｔｅｉｎ教授赠送［５］;ｐＲＳｅｔＡ购于Ｉｎｖｉｔｒｏｇｅｎ公司;ｐＣＡ１３和ｐＢＨＧ１１为ＭｉｃｒｏｂｉｘＢｉｏｓｙｓｔｅｍＩｎｃ．产品。ｐＢＨＧ１１包含腺病毒Ａｄ５基因组３６ｋｂ中的约３４ｋｂ序列,但Ａｄ５Ｅ１区１８８ｂｐ至１３３９ｂｐ缺失,代之以氨苄青霉素抗性基因和复制起始位点。ｐＢＨＧ１１缺少包装信号φ（２２ｂｐ至３４２ｂｐ）和Ａｄ５Ｅ３区（２７８６５ｂｐ至３０９９５ｂｐ序列）。ｐＣＡ１３…     

水稻ADP—葡萄糖焦磷酸化酶的cDNA基因克隆和结构分析

用ＰＣＲ技术从我国水稻品种“中花１０ 号”（Ｏｒｙｚａ ｓａｔｉｖａ ｖａｒ． ｊａｐｏｎｉｃａ ｃｖ． Ｚｈｏｎｇｈｕａ １０）的未成熟种子中克隆到ＡＤＰ－葡萄糖焦磷酸化酶基因,进行了全序列分析,并与国外已报道的同类基因进行了核苷酸及推导氨基酸序列的同源性比较。结果表明,作者克隆的ＡＤＰ－葡萄糖焦磷酸化酶基因全长１４６１ ｂｐ,编码１个由４８３ 个氨基酸组成的多肽,与国外基因的核苷酸和推导氨基酸同源率分别为９９．６％ 和９９．７％ 。此外,还对该基因进行了结构及进化分析。     

番茄抗病基因Cf9的3‘UTR区含有内含子序列

从番茄抗病品种“中杂９号”基因组ＤＮＡ中扩增并克隆了番茄抗叶霉病基因Ｃｆ９。序列分析结果表明,该基因全长２７５１ｂｐ,含有一个编码８６３个氨基酸的开放阅读框架。在该基因的３＇ＵＴＲ区发现了一段未曾报道的内含子序列,长１１５ｂｐ,它所处的位置与番茄另一个抗叶霉病基因Ｃｆ２内含子的位置相似,其５＇和３＇边界序列为一重复序列,ＴＣＣＡＧＧ（Ｔ）ＡＴＴＣ,并与Ｃｆ２基因内含子边界序列高度同源。与已报道的Ｃ     

人分裂细胞核抗原基因片段的筛选、测序及对启动子的分析

经６．６×１０５个克隆筛选,从装在λ噬菌体载体Ｃｈａｒｏｎ３０中的人基因库中筛选到了一个含人分裂细胞核抗原（ＰＣＮＡ）基因的克隆。经Ｓｏｕｔｈｅｒｎ杂交分析插入基因长约１４ｋｂ,有较长的５＇上游区,但３＇端缺少一部分。经亚克隆和测序已确定从５＇上游１２６３ｂｐ到３＇端与λ载体接点共４９６９ｂｐＰＣＮＡ基因片段的核苷酸序列。将ＰＣＮＡ基因启动子核苷酸序列与ＤＮＡ聚合酶α,拓扑异构酶Ⅱα,胸苷酸激酶基因的启动子进行比较有３０％以上同源性,具有“看家基因”特征。在转录起始点的５＇上游几百ｂｐ的范围内都有与ＣＡＴ,ＳＰ１,Ｅ２Ｆ,ＮＦＨＢ,Ｏｃｔ１和ＡＴＦ等转录因子的结合位点相似的核苷酸序列。     

Phylogenetic Relationships of Bears (the Ursidae) Inferred from Mitochondrial DNA Sequences

The phylogenetic relationships among some bear species are still open questions. We present here mitochondrial DNA sequences of D-loop region, cytochrome b, 12S rRNA, tRNA^Pro, and tRNA^Thr genes from all bear species and the giant panda. A series of evolutionary trees with concordant topology has been derived based on the combined data set of all of the mitochondrial DNA sequences, which may have resolved the evolutionary relationships of all bear species: the ancestor of the spectacled bear diverged first, followed by the sloth bear; the brown bear and polar bear are sister taxa relative to the Asiatic black bear; the closest relative of the American black bear is the sun bear. Primers for forensic identification of the giant panda and bears are proposed. Analysis of these data, in combination with data from primates and antelopes, suggests that relative substitutional rates between different mitochondrial DNA regions may vary greatly among different taxa of the vertebrates.     

Mitochondrial DNA sequence variations and systematics of the genus Distoechodon (Teleostei: Cyprinidae)

In the present paper, nucleotide sequences (925–929 bases) of the mitochondrial D-loop region and complete cytochrome b gene (1140 bases) were determined and analysed to investigate the systematic status of the genus Distoechodon . CSB1, CSB2, CSB3, CSB-D and ETAS were successfully identified in the D-loop region. The sequence variations among different samples suggest that Distoechodon compressus is a valid species and has its distribution in Taiwan, and that D. tumirostris multispinnis does not seem to be a valid species.     

Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster

Mitochondrial DNA (mtDNA) regions corresponding to two major tRNA gene clusters were amplified and sequenced for the Japanese pit viper, himehabu. In one of these clusters, which in most vertebrates characterized to date contains three tightly connected genes for tRNA(Ile), and tRNA(Gln), and tRNA(Met), a sequence of approximately 1.3 kb was found to be inserted between the genes for tRNA(Ile) and tRNA(Gln). The insert consists of a control-region-like sequence possessing some conserved sequence blocks, and short flanking sequences which may be folded into tRNA(Pro), tRNA(Phe), and tRNA(Leu) genes. Several other snakes belonging to different families were also found to possess a control-region-like sequence and tRNA(Leu) gene between the tRNA(Ile)and tRNA(Gln) genes. We also sequenced a region surrounded by genes for cytochrome b and 12S rRNA, where the control region and genes for tRNA(Pro) and tRNA(Phe) are normally located in the mtDNAs of most vertebrates. In this region of three examined snakes, a control-region- like sequence exists that is almost completely identical to the one found between the tRNA(Ile) and tRNA(Gln) genes. The mtDNAs of these snakes thus possess two nearly identical control-region-like sequences which are otherwise divergent to a large extent between the species. These results suggest that the duplicate state of the control-region- like sequences has long persisted in snake mtDNAs, possibly since the original insertion of the control-region-like sequence and tRNA(Leu) gene into the tRNA gene cluster, which occurred in the early stage of the divergence of snakes. It is also suggested that the duplicated control-region-like sequences at two distant locations of mtDNA have evolved concertedly by a mechanism such as frequent gene conversion. The secondary structures of the determined tRNA genes point to the operation of simplification pressure on the T psi C arm of snake mitochondrial tRNAs.      

Population structure of the Japanese eel, Anguilla japonica

Mitochondrial DNA (mtDNA) sequences that include (a) a part of the cytochrome b gene, (b) two tRNA genes, and (c) a part of the noncoding D-loop region of 31 Anguilla japonica (Japanese eel) and 1 A. marmorata collected from Taiwan, Japan, and mainland China were determined to evaluate the population structure of Japanese eel. Among 30 genotypes identified from the 31 Japanese eel mtDNAs sequenced, there are 58 variable sites, predominantly clustered at the D-loop region. The phylogenetic tree constructed by the unweighted pair-group method with arithmetic mean shows neither significant genealogical branches nor geographic clusters. Furthermore, the sequence-statistics test reveals little, if any, significant genetic differentiation. These results indicate that the 31 Japanese eels might come from a single population. Analysis of sequence variation in mtDNA by using the relationship between the number of segregating sites and the average number of nucleotide differences under the neutral mutation hypothesis reveals that neutral mutation acts as a major factor influencing the evolutionary divergence of the Japanese eel mitochondrial genome sequenced, especially in the noncoding region.      

Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates

The 16,775 base-pair mitochondrial genome of the white Leghorn chicken has been cloned and sequenced. The avian genome encodes the same set of genes (13 proteins, 2 rRNAs and 22 tRNAs) as do other vertebrate mitochondrial DNAs and is organized in a very similar economical fashion. There are very few intergenic nucleotides and several instances of overlaps between protein or tRNA genes. The protein genes are highly similar to their mammalian and amphibian counterparts and are translated according to the same variant genetic code. Despite these highly conserved features, the chicken mitochondrial genome displays two distinctive characteristics. First, it exhibits a novel gene order, the contiguous tRNA(Glu) and ND6 genes are located immediately adjacent to the displacement loop region of the molecule, just ahead of the contiguous tRNA(Pro), tRNA(Thr) and cytochrome b genes, which border the displacement loop region in other vertebrate mitochondrial genomes. This unusual gene order is conserved among the galliform birds. Second, a light-strand replication origin, equivalent to the conserved sequence found between the tRNA(Cys) and tRNA(Asn) genes in all vertebrate mitochondrial genomes sequenced thus far, is absent in the chicken genome. These observations indicate that galliform mitochondrial genomes departed from their mammalian and amphibian counterparts during the course of evolution of vertebrate species. These unexpected characteristics represent useful markers for investigating phylogenetic relationships at a higher taxonomic level.     

Mitochondrial DNA phylogeography of Acrossocheilus paradoxus (Cyprinidae) in Taiwan

Nucleotide sequences of 3' end of the cytochrome b gene, tRNA genes, D-loop control region, and the 5' end of the 12S rRNA of mitochondrial DNA (mtDNA) were used to assess the genetic and phylogeographic structure of Acrossocheilus paradoxus populations, a Cyprinidae fish of Taiwan. A hierarchical examination of populations in 12 major streams from three geographical regions using an analysis of molecular variance (AMOVA) indicates high genetic differentiation both among populations (PhiST = 0.511, P < 0.001) and among regions (PhiCT = 0.368, P < 0.001). Limited migration largely contributed to the genetic differentiation. High nucleotide diversity (1.13%) and haplotype diversity (0.80%) were detected among populations. The degree of genetic differentiation was correlated with geographical distance between populations, a result consistent with the one-dimensional stepping stone models. A neighbour-joining tree recovered by (DAMBE) supports the pattern of isolation by distance and reveals a closer relationship between populations of the central and southern regions. A minimum spanning network based on nucleotide substitutions reflected migration routes from populations of the central region to the northern and southern regions, respectively. Postglacial colonization and expansion can explain the phylogeographical pattern. Single and ancient migration events may have allowed the northern region to attain the monophyly of mtDNA alleles. In contrast, most populations within geographical regions are either paraphyletic or polyphyletic due to the relatively shorter time period for coalescence. Both low haplotype number and genetic variability suggest a bottleneck event in the Chingmei population of northern Taiwan. Based on coalescence theory, the monophyly of the Tungkang population of the southern region may be associated with a founder event.     

大熊猫气味标记DNA的制备和序列分析

大熊猫气味标记在其个体间的通讯中具有重要意义。用不同方法收集了７只大熊猫个体的９个气味标记样品,运用Ｉｎｓｔａｇｅｎｅ Ｋｉｔ制备出了ＤＮＡ。采用ＰＣＲ扩增线粒体Ｄ－环区和细胞色素ｂ基因、Ｔｈｒ－ｔＲＮＡ基因片段并作序列分析。结果提示,不同收集方式所得气味标记样品均有ＤＮＡ,但用干棉花收集样品的方法最佳。该方法为大熊猫的遗传多样性研究提供了新的简捷有效的ＤＮＡ来源。     

Sequence variation and structural conservation in the D-loop region and flanking genes of mitochondrial DNA from Japanese pond frogs

The nucleotide sequences of the D-loop region and its flanking genes of the mitochondrial DNA (mtDNA) from Japanese pond frogs were determined by the methods of PCR, cloning, and sequencing. The frogs belonged to two species, one subspecies, and one local race. The gene arrangements adjacent to the D-loop region were analyzed. The frogs shared a unique mitochondrial gene order that was found in Rana catesbeiana; i.e., cyt b--D-loop region--tRNA(Leu(CUN))--tRNA(Thr)--tRNA(Pro)--tRNA(Phe)--12S rRNA. The arrangements of the three tRNA genes of these frogs were different from those of X. laevis, a species which has the same overall structure as in mammals. Highly repetitive sequences with repeat units (16-bp or 17-bp sequence specific for each taxon) were found in the D-loop region. The length of repetitive sequences varied from 0.6 kbp to 1.2 kbp, and caused the extensive size variation in mtDNA. Several short sequence elements such as putative TAS, OH, CSB-1, and CSB-2 were found in the D-loop region of these frogs. The sequences of these short regulatory elements were conserved in R. catesbeiana, X. laevis, and also in human. The comparison of sequence divergences of the D-loop region and its adjacent genes among various taxa revealed that the rates of nucleotide substitutions depend on genes. The nucleotide sequences of the 3'-side segment of the D-loop region were the most variable among taxa, whereas those of the tRNA and 12S rRNA genes were the most conservative.     

Sequence length and variation in the mitochondrial control region of two freshwater gobiid fishes belonging to Rhinogobius (Teleostei: Gobioidei)

The control region (D-loop) of mitochondrial DNA (mtDNA) was amplified and sequenced for eight samples of the rhinogobies Rhinogobius maculafasciatus and R. giurinus from Taiwan and southern China. The control regions of both species are of 841–842 bp; the length of these sequences being the most compact among all known sequences in teleost fishes. Three conserved sequence blocks (CSB) were observed. The full D-loop and tRNA Phe gene sequences were determined and compared with other fishes. The interspecific sequence divergence between the two species is 11.3–11.7%; and the intraspecific variation in R. guirinus 0.8–1.8%. Results suggest that the control region of Rhinogobius is informative for phylogenetic reconstruction at both intraspecific and interspecific levels in this gobiid genus.     

湾鳄(Crocodylus porosus)线粒体基因组全序列结构分析与鳄类系统发生

该文测序了湾鳄的线粒体基因组全序列,全长为16,917bp。湾鳄mtDNA结构与其他脊椎动物相似,由22个tRNA,2个rRNA和13个蛋白质编码基因及1个非编码的控制区(D-loop)所组成。除NADH6和tRNAGln、tRNAAla、tRNAAsn、tRNACys、tRNATyr、tRNASer(UCN)、tRNAGlu、tRNAPro在L-链上编码之外,其余基因均在H-链编码。基因排列顺序与已测序的鳄类一致,这显示了鳄类线粒体基因排列顺序上的保守性。但鳄类线粒体基因排列顺序与脊椎动物的典型排列方式相比,有较大的差异,尤其是tRNAPhe基因的重排、tRNASer-tRNAHis-tRNALeu基因族的排列方式等。湾鳄mtDNA和已测序的鳄类一样,缺失轻链复制起始点(OLR)。基于17种鳄mtDNA控制区保守区,采用PAUP4.0最大简约法(Maximumparsimony,MP)构建MP树,邻接法(Neighbor-joiningmethod,NJ)构建NJ树,结果显示:食鱼鳄(Gavialisgangeticus)和假食鱼鳄(Tomistomaschlegelii)聚为一支后再与鳄科(Crocodylidae)的其他物种形成姐妹群,这与基于食鱼鳄和假食鱼鳄的线粒体全序列的分析结果一致,支持将食鱼鳄并入鳄科的观点。结果还支持非洲窄吻鳄(Crocodyluscataphractus)与鳄属(Crocodylus)构成姐妹群,可以单独划分为属的观点。