程序性细胞死亡基因PDCD4的系统发育分析

程序性细胞死亡-4 (programmed cell death 4, PDCD4)基因是抑癌基因,在多种人肿瘤组织细胞中低表达甚至表达缺失,在肿瘤的发生、发展过程中发挥着重要的作用(孙玮等, 2007)。对从NCBI上下载的包括人、黑猩猩、大猩猩等12种哺乳类物种的序列进行分析,引用Blast+、MCScanX (Wang et al., 2012)、Colinearscan等生物信息学工具对核苷酸序列进行同源性共线性分析。用CLUSTALX (Thompson et al., 1997)软件进行多序列比对,基于最大似然法(ML)、最大简约法(MP)和邻接法(NJ)算法,使用系统发育分析软件MEGA7.0软件构建PDCD4基因的系统发育树,3种建树算法得到的拓扑结构基本一致。系统发育树表明:人、黑猩猩、大猩猩、苏门答腊猩猩和白颊长臂猿聚在一支,亲缘关系较近;家鼠、大白鼠、野猪和狗聚为一支;狒狒、猕猴和狨猴聚为一支。PDCD4基因的系统发育树与基于化石证据的物种树的一致,说明该基因的进化是伴随物种分歧一同发生的,是个相对古老的基因,有助于解决动物起源的相关信息和动物物种分化的相关问题。     

SRY基因在人猿超科和旧大陆猴中具有不同的进化规律

通过ＰＣＲ扩增、测序,得到了白臀叶猴和红面猴的ＳＲＹ基因全序列。结合现有的灵长类其他物种序列进行分析,验证了ＨＭＧ盒的保守性。通过构建系统发育树,比较旧大陆猴和人猿超科两个类群内和类群间ＨＭＧ盒侧翼序列Ｋａ／Ｋｓ的比率。有趣的是,人猿超科两物种比较呈现较高的Ｋａ／Ｋｓ比值,但在旧大陆猴中及旧大陆猴与狨猴间的Ｋａ／Ｋｓ比值显著低于人猿超科的,呈现很不同的格局。同时,对于ＨＭＧ盒序列,Ｋａ／Ｋｓ比值在     

人与大猩猩,黑猩猩和猩猩亲缘关系的探讨

有关人锆超科的系统发育仍然存在刍议。争论焦点在与大猩猩和黑猩猩哪 个关系更近一点。酪氨酸酶是黑色素合成中的关键酶,酪氨酶基因的突变将导致白化病。测定了人猿科中大猩猩,黑猩猩、猩猩和长臂锆产基因全部５个外显子的ＤＮＡ序列。     

红毛猩猩会“算计”

红毛猩猩属猿族,与大猩猩、黑猩猩及矮黑猩猩一起被称为“人类最直系的亲属”。目前,红毛猩猩在全世界只剩下不到3万只,主要在印度尼西亚的婆罗洲低地和苏门答腊洲地区生活。     

腊玛古猿和西瓦古猿的形态特征及其系统关系——颅骨的形态与比较

本文通过具体的形态比较指出,禄丰腊玛古猿和西瓦古猿应为同一类型的雌雄个体,它们与现代猩猩比较相似,而与大猩猩和黑猩猩差别较大,因此,它们可看作是猩猩的祖先。猩猩这一支大约是在一千二百万年前开始从人猿超科的进化主干上分化出来的。     

保护动物（灵长类和食肉类）

保护动物（灵长类和食肉类）列入国家保护的灵长类动物有：一级：蜂猴、熊猴、台湾猴、尾猴、菲氏叶猴、灰叶猴、黑叶猴、金丝猴、滇金丝猴、白眉长臂猿、黑长臂猿等十一种。二级：红面猴、猕猴、四川短尾猴等三种。列入国家保护的食肉类动物有：一级：马来熊、大熊猫、紫...     

人天然免疫基因TRIM5α的序列及进化分析

目的：克隆人TRIM5α基因,对其编码序列进行分析,并进行分子进化研究。方法：以HeLa细胞cDNA为模板,用RT-PCR方法克隆人TRIM5α基因,与人基因组序列对比分析其结构;用BioEdit、Genedoc和MEGA4.1软件进行蛋白序列联配和进化分析。结果：扩增了长1482bp的人TRIM5α基因片段,序列分析表明其覆盖了完整编码框,编码由493个氨基酸残基组成的人TRIM5α蛋白;人TRIM5α蛋白与黑猩猩、大猩猩、猩猩、猕猴TRIM5α蛋白的相似度分别为98.2%、96.8%、93.7%和87.6%。结论：克隆了人TRIM5α基因,为进一步研究该基因的功能奠定了基础。     

牦牛Myf-5基因的克隆测序及其系统进化研究

本研究对牦牛(九龙牦牛)的生肌决定因子5(Myf-5)基因进行了T-A克隆测序和分析,并与多个物种的相应基因编码区核苷酸序列、氨基酸序列进行了比对分析,构建了物种间的系统进化树.结果 表明:①牦牛的Myf-5基因大小为3313 bp,由3个外显子和2个内含子组成,与普通牛等9个物种比较,在基因大小上有较大的差异,但外显子和内含子的组成一致.②牦牛、大额牛、瘤牛、水牛、普通牛、人、恒河猴、黑猩猩、狗、家鼠、软体贝壳、鸡、斑马鱼等物种间Myf-5基因编码区的核苷酸序列同源性较高,其中,牦牛、大额牛、瘤牛、水牛、普通牛间的同源性最高,达98.4%以上,说明Myf-5基因编码区核苷酸序列在动物物种间具有较高的保守性.③牦牛、大额牛、瘤牛、水牛、普通牛、黑猩猩、恒河猴、人、狗、家鼠、软体贝壳、鸡、斑马鱼等物种间Myf-5基因编码蛋白的氨基酸序列具有较高的同源性,保守性强,这一结果与编码区核苷酸序列的比对结果基本一致.④根据核苷酸序列,用NJ法构建的牦牛、大额牛、瘤牛、水牛、普通牛、人、恒河猴、黑猩猩、狗、家鼠、软体贝壳、鸡、斑马鱼等13个物种的分子系统进化树显示:牦牛、普通牛、瘤牛、水牛和大额牛在较近的亲缘关系下聚为一大类,人、黑猩猩和恒河猴聚为另一大类,然后这两类再和其他物种相聚.这一分类结果与各物种的动物学分类结果和血液蛋白、mtDNA水平上的聚类结果基本一致,支持牦牛、普通牛和瘤牛3个物种间不应该是属间或亚属间关系,而应是同一属下的不同种,将牦牛、普通牛和瘤牛划分在同一个属--牛属(Bos),而将水牛划分在另一个单独的属的观点.同时也显示该基因序列适合用于动物学分类.     

人类与部分实验动物RETN基因同源性分析

目的分析人类与部分实验动物的RETN基因同源性,为人类RETN基因相关疾病及基因功能研究对理想实验动物的选择提供依据。方法提取猕猴、大鼠、小鼠和树鼩的脂肪组织总RNA,用相应的RETN引物进行RT-PCR,对其产物进行双向测序;同时在GenBank中查询人类、猪、牛的RETN基因序列;再运用ORF Finder软件调取其ORF核苷酸序列和氨基酸序列,用DANMAN软件对所获得的序列进行比对,分析其同源性。结果人类RETN的核苷酸序列与猕猴、小鼠、树鼩、大鼠、猪、牛的同源性分别为95.4%、65.4%、65.4%、66.4%、81.0%、81.0%;氨基酸序列分别为91.7%、55.6%、55.6%、53.7%、75.9%、72.2%。;系统进化树结果表明,就RETN基因而言,人与猕猴的亲缘关系较近。结论基于同源性分析结果,在RETN的进化上猕猴与人类存在较近的亲缘关系,是研究人类RETN生物学功能及其相关疾病的最佳实验动物。     

牦牛与其他物种ZFX/ZFY基因片段间的进化关系

利用PCR扩增、克隆和序列分析法对牦牛ZFX/ZFY基因第11外显子部分片段进行了研究,并同来自于NCBI GenBank中人、猩猩、普通牛等9个物种的ZFX/ZFY基因核苷酸及其氨基酸序列进行了进化分析.结果表明,牦牛ZFX、ZFY基因间核苷酸序列同源性为94.1%,显示同一物种同源基因ZFX/ZFY间存在变异;比较的10个物种间ZFX基因核苷酸序列同源性为87.7%、ZFY基因为81.7%,相应ZFX、ZFY氨基酸同源性分别为96.6%、91.0%,ZFY基因的变异性大于ZFX基因,显示X染色体与Y染色体可能是独立进化.     

Immunoglobulin CH gene family in hominoids and its evolutionary history.

The organization of the human immunoglobulin CH gene suggests that a gene duplication involving the C gamma-C gamma-C epsilon-C alpha region has occurred during evolution. We previously showed that both chimpanzee and gorilla have two 5'-C epsilon-C alpha-3', as in human, and that orangutan, gibbon, and Old World monkeys have one C epsilon gene and one, two, and one C alpha gene(s), respectively. In addition to these clustered CH genes, there is one processed C epsilon pseudogene in each species. The present study revealed that orangutan and crab-eating macaque (an Old World monkey) both have one 5'-C epsilon-C alpha-3' and that gibbon has two 5'-C epsilon-C alpha-3', one C epsilon gene of which is completely deleted. By Southern analysis, the number of C gamma genes in all the nonhuman hominoids was estimated to be four to five, as in human, in comparison with two for crab-eating macaque. The C mu and C delta genes were estimated to be present as single copies in both hominoids and crab-eating macaque. Furthermore, it was proved that there are two copies of the C epsilon 5'-flanking region in both the orangutan and the gibbon genomes. These results show that gene duplication including the C gamma-C gamma-C epsilon-C alpha genes occurred in the common ancestor of hominoids and that subsequent deletion of the C epsilon gene (in orangutan, including one of the C alpha genes) occurred independently in each hominoid species.     

Evolutionary rate of immunoglobulin alpha noncoding region is greater in hominoids than in Old World monkeys.

Recent studies on the molecular evolution of primates show that the evolutionary rate among hominoids is considerably slower than that among nonhominoid primates. However, this observation at the nucleotide-sequence level is restricted to the beta-globin family region. In this study, we sequenced orthologous immunoglobulin alpha (C alpha) genes of chimpanzee, gorilla, orangutan, and crab-eating macaque (an Old World monkey) and compared them with that of the human by using noncoding regions for analysis. Since significant differences in rates among hominoids were not found by using the relative rate test, we evaluated the ratio (R) of the evolutionary distance between Old World monkey and human to the distance between orangutan and human. The R value (1.12) for the C alpha gene was much smaller than the expected value (1.38-2.33), showing that the nucleotide substitution rate (= mutation rate per year under selective neutrality) of the C alpha gene is greater in the human lineage than in the Old World monkey lineage. We also did a similar analysis for the gamma 1-, gamma 2-, psi eta-, and delta-globin genes and found a considerable heterogeneity (1.12-2.37) among the R values, including that for the C alpha gene. This indicates that the hominoid slowdown of the evolutionary rate is not a universal phenomenon in primate evolution.     

Gorilla and orangutan c-myc nucleotide sequences: Inference on hominoid phylogeny

The nucleotide sequences of the gorilla and orangutan myc loci have been determined by the dideoxy nucleotide method. As previously observed in the human and chimpanzee sequences, an open reading frame (ORF) of 188 codons overlapping exon 1 could be deduced from the gorilla sequence. However, no such ORF appeared in the orangutan sequence.The two sequences were aligned with those of human and chimpanzee as hominoids and of gibbon and marmoset as outgroups of hominoids. The branching order in the evolution of primates was inferred from these data by different methods: maximum parsimony and neighborjoining.Our results support the view that the gorilla lineage branched off before the human and chimpanzee diverged and strengthen the hypothesis that chimpanzee and gorilla are more related to human than is orangutan. Correspondence to: F. Galibert     

Comparative immunochemical studies of primate hemoglobins

The antigenic properties of a number of chromatographically purified primate hemoglobins were compared to those of normal human hemoglobin using a sensitive radioimmunochemical procedure. The degree of inhibition of the antigen-antibody reaction with heterologous hemoglobins appeared to be related to the structural similarity of these proteins to the normal human hemoglobin immunogen. With the exception of the baboon hemoglobin, the antigenicity of the hemoglobins paralleled the phylogeny of the primates. The gorilla and chimpanzee hemoglobins were antigenically identical to normal human hemoglobin, whereas the gibbon and orangutan hemoglobins were substantially more variable. Of the Old World monkey hemoglobins examined, the baboon produced lower inhibition values, suggesting a greater degree of structural dissimilarity than other Cercopithecoidea hemoglobins, which is compatible with a greater rate of evolutionary change occurring in this protein. Using the known amino acid sequences of human and other primate hemoglobins, we have attempted to identify antigenic determinant areas of the proteins.     

Examination of hominid evolution by DNA sequence homology

Hominoid phylogeny was investigated in terms of unique DNA sequence homologies. In comparisons from the human standpoint the ΔTe₅₀ DNA values were Man 0, chimpanzee 0·7, gorilla 1·4, gibbon 2·7, orangutan 2·9, and African green monkey 5·7. In comparisons from the orangutan standpoint the ΔTe₅₀ DNA values were orangutan 0, chimpanzee 1·8, Man 1·9, gorilla 2·3, gibbon 2·4 and African green monkey 4·3. These results indicate that chimpanzee and gorilla are cladistically closer to Man than to orangutan and other primates, and that gorilla DNA may have diverged slightly more from the ancestral state than chimpanzee or human DNA. Comparisons from chimpanzee and gorilla DNA standpoints are needed to achieve a more definitive picture of hominoid phylogeny.     

Molecular evolution of IgG subclass among nonhuman primates: implication of differences in antigenic determinants among Apes

The cross-reactivity of five different rabbit polyclonal antibodies to human IgG and IgG subclass (IgG1, IgG2, IgG3, and IgG4) was determined by competitive ELISA with nine nonhuman primate species including five apes, three Old World monkeys, and one New World monkey. As similar to those previously reported, the reactivity of anti-human IgG antibody with plasma from different primate species was closely related with phylogenic distance from human. Every anti-human IgG subclass antibody showed low cross-reactivity with plasma from Old World and New World monkeys. The plasma from all apes except for gibbons (Hylobates spp.) showed 60 to 100% of cross-reactivity with anti-human IgG2 and IgG3 antibodies. On the other hand, chimpanzee (Pan troglodytes andPan paniscus) and orangutan (Pongo pygmaeus) plasma showed 100% cross-reactivity with anti-human IgG1 antibody, but gorilla (Gorilla gorilla) and gibbon plasma showed no cross-reactivity. The chimpanzee and gorilla plasma cross-reacted with anti-human IgG4 antibody at different reactivity, 100% in chimpanzee and 50% in gorilla, but no cross-reactivity was observed in orangutan and gibbon plasma. These results suggest the possibilities that the divergence of “human-type” IgG subclasses might occur at the time of divergence ofHomo sapience fromHylobatidae, and that the molecular evolution of IgG1 as well as IgG4 is different from that of IgG2 and IgG3 in great apes, this is probably caused by different in development of immune function in apes during the course of evolution.     

Analysis of the virogenes related to the rhesus monkey endogenous type C retrovirus in monkeys and apes.

Molecular hybridization studies were carried out by using a [3H]complementary DNA (cDNA) probe to compare the endogenous type C retrovirus of rhesus monkeys (MMC-1) with other known retroviruses and related sequences in various primate DNAs. The genomic RNA of the endogenous type C retrovirus of stumptail monkeys (MAC-1) was found to be highly related to the MMC-1 cDNA probe, whereas the other retroviral RNAs tested showed no homology. Related sequences were found in Old World monkey DNAs and to a lesser extent in gorilla dn chimpanzee DNAs. No homology was detected between MMC-1 cDNA and DNA of gibbon, orangutan, or human origin. Restriction endonuclease analysis of genomic DNA indicated that many of the several hundred sequences related to MMC-1 in rhesus monkey DNA differed from that integrated into DNA of infected canine cells. Gorilla and chimpanzee DNAs contained a specific restriction endonuclease fragment of the MMC-1 genome.     

Molecular evolution of the psi eta-globin gene locus: gibbon phylogeny and the hominoid slowdown

An 8.4-kb genomic region spanning both the psi eta-globin gene locus and flanking DNA was sequenced from the common gibbon (Hylobates lar). In addition, sequencing of the entire orthologous region from galago (Galago crassicaudatus) was completed. The gibbon and galago sequences, along with published orthologous sequences from 10 other species, were aligned. These noncoding nucleotide sequences represented four human alleles, four apes (chimpanzee, gorilla, organgutan, and gibbon), an Old World monkey (rhesus monkey), two New World monkeys (spider and owl monkeys), tarsier, two strepsirhines (galago and lemur), and goat. Divergence and maximum parsimony analyses of the psi eta genomic region first groups humans and chimpanzees and then, at progressively more ancient branch points, successively joins gorillas, orangutans, gibbons, Old World monkeys, New World monkeys, tarsiers, and strepsirhines (the lemuriform-lorisiform branch of primates). This cladistic pattern supports the taxonomic grouping of all extant hominoids into family Hominidae, the division of Hominidae into subfamilies Hylobatinae (gibbons) and Homininae, the division of Homininae into tribes Pongini (orangutans) and Hominini, and the division of Hominini into subtribes Gorillina (gorillas) and Hominina (chimpanzees and humans). The additional gibbon and galago sequence data provide further support for the occurrence of a graded evolutionary-rate slowdown in the descent of simian primates, with the slowing rate being more pronounced in the great-ape and human lineages than in the gibbon or monkey lineages. A comparison of global versus local molecular clocks reveals that local clock predictions, when focused on a specific number of species within a narrow time frame, provide a more accurate estimate of divergence dates than do those of global clocks.     

Serum cholinesterase activities and inhibition profiles of nonhuman primates

Serum cholinesterase activities and inhibition profiles of 169 chimpanzees, 15 gorillas, 26 orangutans, seven gibbons, and 12 rhesus monkeys were determined. Mean values of activities against benzoylcholine (μmols/min/ml) and dibucaine, fluoride, and Ro 2-0683 numbers (percentage inhibition of benzoylcholine hydrolysis) are: chimpanzee, 2.276, 80, 64, and 97; gorilla, 9.403, 82, 71, and 96; orangutan, 0.747, 94, 6, and 98; gibbon, 0.071, 89, 7, and 94; and rhesus monkey, 0.859, 95, 10, and 99, respectively. Sernylan numbers were determined of the last 100 chimpanzee serums collected and of each of the gorilla, orangutan, gibbon, and rhesus monkey serums. Mean values of Sernylan numbers are: chimpanzee, 80; gorilla, 81; orangutan, 95; gibbon, 94; and rhesus monkey, 96. The chimpanzee and the gorilla have dibucaine, fluoride, Ro 2-0683, and Sernylan numbers within the range found in men who are homozygotes for the usual cholinesterase (genotype E₁^uE₁^u). No cholinesterase variant was found in any chimpanzee or gorilla. The orangutan, gibbon, and rhesus monkey have inhibition profiles that resemble one another, with higher dibucaine and Sernylan numbers and much lower fluoride numbers than the chimpanzee or the gorilla. The results of the inhibition tests suggest that the African apes, chimpanzee and gorilla, are related more closely to man than are the Asian apes, orangutan and gibbon.     

Molecular phylogeny and evolution of the human endogenous retrovirus HERV-W LTR family in hominoid primates

Long terminal repeats (LTRs) of human endogenous retrovirus (HERV) have contributed to the structural change or genetic variation of primate genome that are connected to speciation and evolution. Using genomic DNAs that were derived from hominoid primates (chimpanzee, gorilla, orangutan, and gibbon), we performed PCR amplification and identified thirty HERV-W LTR elements. These LTR elements showed a 82-98% sequence similarity with HERV-W LTR (AF072500). Specifically, additional sequences (GCCACCACCACTGTTT in the gorilla and TGCTGCTGACTCCCATCC in the gibbon) were noticed. Clone OR3 from the orangutan and clone GI2 from the gibbon showed a 100% sequence similarity, although they are different species. This indicates that both LTR elements were proliferated during the last 2 to 5 million years from the integration of the original LTR element. A phylogenetic tree that was obtained by the neighbor-joining method revealed a wide overlap of the LTR elements across species, suggesting that the HERV-W LTR family evolved independently during the hominoid evolution.