恒河猴Fas基因的克隆

目的研究猴艾滋病发病机制中细胞凋亡的作用,克隆凋亡相关基因Ｆａｓ的ｃＤＮＡ序列。方法从恒河猴腹股沟淋巴结中提取总ＲＮＡ,根据人的Ｆａｓ ｃＤＮＡ序列设计上、下游引物,通过ＲＴ－ＰＣＲ扩增出目的ｃＤＮＡ片段,将这一片段克隆到ｐＧＦＭ－Ｔ Ｅａｓｙ载体中,筛选阳性克隆并进行序列测定。结果首次克隆了恒河猴Ｆａｓ基因,编码序列为１００５ ｂｐ,将其序列提交ＧｅｎＢａｎｋ,收录号为ＡＹ００７５７２。结论克隆的新序列与ＧｅｎＢａｎｋ已收录的人和食蟹猴的Ｆａｓ基因在编码序列的长度上稍有区别,人的编码序列为１００８ｂｐ,食蟹猴的为９９６ ｂｐ。     

HMR法研究天花粉蛋白TDK肽片段的溶液构象

用１ＨＮＭＲ法测定ＴＤＫ肽在Ｈ２Ｏ（ＨＯＤＫ）,５０％六氟丙醇（ＦＰＤＫ）和２ｍｏｌ／ＬＧｕ·ＨＣｌ（ＧＵＤＫ）中的溶液构象。在ＨＯＤＫ和ＦＰＤＫ中,ＴＤＫ肽的两段序列Ａｓｐ０～Ｉｌｅ４,Ｓｅｒ９～Ｉｌｅ１７分别具有较稳定的α－螺旋含量;而ＧＵＤＫ的ＳＡＬＳ序列仍能检测到有序残存结构。并假设ＳＡＬＳ序列是肽链形成二级结构的原始核心。     

人猿超科和旧大陆猴7种高等灵长类FKN全基因序列的测定及进化分析

测定人猿超科(人、黑猩猩、大猩猩、红毛猩猩和长臂猿)和旧大陆猴(猕猴和叶猴)7种高等灵长类FKN全基因序列, 探讨其系统进化分析。用简并引物PCR(Degenerated PCR)法分别扩增FKN的3个外显子, 其产物经琼脂糖凝胶回收、纯化后测序, 然后用BioEdit软件剪切拼接FKN基因全序列, 用DNAStar比对后比较基因和氨基酸序列同源性, Mega软件重构FKN基因进化树, 应用Datamonkey分析FKN的负选择位点。序列分析发现人猿超科较旧大陆猴FKN基因除了有散在的点突变外, 还有一明显的30 bp的核苷酸缺失突变; 人FKN基因序列与黑猩猩、大猩猩、红毛猩猩、长臂猿、猕猴和叶猴的同源性分别是99.2%、98.4%、98.1%、96.5%、95.9%和93.8%, 由此推导的氨基酸序列同源性分别是98.5%、98.0%、97.7%、94.7%、93.7%和90.5%; FKN基因进化树表明人与黑猩猩关系更近, FKN基因进化和通常认为的物种进化一致; Datamonkey分析结果显示FKN存在3个负选择位点53Q、84D、239N。成功获得人、黑猩猩、大猩猩、红毛猩猩、长臂猿、猕猴和叶猴7种高等灵长类物种FKN全基因序列, 为后续探讨FKN在高等灵长类物种进化过程中免疫学功能演变及其结构与功能的关系奠定基础。     

NMR法研究天花粉蛋白TDK肽片段的溶液构象

用ＨＮＭＲ法测定ＴＤＫ肽在Ｈ２Ｏ（ＨＯＤＫ）,５０％六氟丙醇（ＦＰＤＫ）和２ｍｏｌ／ＬＧｕ．ＨＣｌ（ＧＵＤＫ）溶液构象。在ＨＯＤＫ和ＦＰＤＫ中,ＴＤＫ肽的两段序列Ａｓｐ０－Ｉｌｅ４,Ｓｅｒ９－Ｉｌｉ１７分别具有较稳定的α－螺旋含量;而ＧＵＤＫ的ＳＡＬＳ序列仍能检测到有序残存结构。并假设ＳＡＬＳ序列是肽链形成二级结构的原始核心。     

细胞松驰素B促微丝解聚对DNA合成的作用

利用微丝（ｍｉｃｒｏｆｉｌａｍｅｎｔ,ＭＦ）解聚药物细胞松驰素Ｂ（ｃｙｔｏｃｈａｌａｓｉｎＢ,ＣＢ）处理Ｇ_０期小鼠Ｃ_３Ｈ_（１０）Ｔ_（１／２）成纤维细胞,对Ｇ_０至Ｓ期ＤＮＡ合成,胸腺嘧啶核苷激酶（ｔｈｙｍｉｄｉｎｅｋｉｎａｓｅ,ＴＫ）活性、ＴＫ基因表达、钙调素（ｃａｌｍｏｄｕｌｉｎ,ＣａＭ）水平和一些细胞周期早期基因的表达进行了观察,Ｇ_０期细胞经３ｍｇ／ＬＣＢ处理２ｈ,促ＭＦ解聚增强了血清对Ｓ期细胞ＴＫ活性、ＴＫ基因表达和ＤＮＡ合成的刺激作用,并促进细胞提前进入Ｓ期．血清刺激Ｇ_０期细胞进入晚Ｇ_１期和Ｓ期时,ＣａＭ水平明显升高,而ＣＢ预处理则使ＣａＭ含量进一步增加,特别是ＣＢ处理促使Ｓ期ＣａＭ增加向核内转移．ＣＢ处理明显增强血清对ｃ－ｊｕｎ、ｃ－ｆｏｓ和ｃ－ｍｙｃ基因表达的刺激作用,而ＰＫＣ抑制剂Ｈ_７则抑制ＣＢ处理对这些基因转录的刺激作用,说明ＣＢ使Ｇ_０期细胞ＭＦ解聚刺激ｃ－ｊｕｎ、ｃ－ｆｏｓ和ｃ－ｍｙｃ的转录活性与ＰＫＣ的作用有关．结果表明Ｇ_０至Ｓ期早期ＭＦ的重组可促进细胞进入Ｓ期,增强ＤＮＡ合成．     

中国猕猴类的蛋白多态性及其遗传分化关系

采用蛋白电泳分析技术研究了来源于我国和越南的猕猴属（Ｇｅｎ ｕｓＭａｃａｃａ）５个种（Ｍ．ｍｕｌａｔｔａ、Ｍ．ａｒｃｔｏｉｄｅｓ、Ｍ．ａｓｓａｍｅｎｓｉｓ、Ｍ．ｔｈｉｂｅｔａｎａ、Ｍ．ｆａｓｃｉｃｕｌａｒｉｓ）的蛋白多态性及其遗传分化关系。共分传座位３０个。在分析的１９只恒河猴中,３０个遗传座有位９个座位表现出多态性,多态座位百分比Ｐ＝０．３,平均等位基因数Ａ＝１．４,平均杂合度Ｈ＝０．０１０４５     

离体小鼠胃切片高亲和性GABA摄取及其特性的研究

本文应用同位素示踪法,研究了在３７℃Ｋｒｅｂｓ－ｈｅｎｓｅｌｅｉｔｂｉｃａｒｂｏｎａｔｅｂｕｆｆｅｒ中培育的小鼠胃切片的＾３Ｈ－ＧＡＢＡ摄取及其特性,表明小鼠胃中存在一种高亲和性的（Ｋｒｎ＝４μＭ）,最大摄取速度Ｖｍａｘ为２．７８Ｐｍｏｌ／ｍｇ组织／ｎ的,可饱和的,Ｎａ＾＋依赖的ＧＡＢＡ摄取系统,摄取的最佳条件为ｐＨ７．４,温度３７℃,Ｋ＾＋,Ｃａ＾２＋浓度５ｍｍｏｌ／Ｌ,Ｍｇ＾２＋浓度２．５ｍｍ     

绒山羊转铁蛋白多态性的研究

绒山羊转铁蛋白多态性的研究ＴＲＡＮＳＦＥＲＲＩＮＰＯＬＹＭＯＲＰＨＩＳＭＩＮＣＡＳＨＭＥＲＥＧＯＡＴ关键词绒山羊，转铁蛋白，多态性ＫｅｙｗｏｒｄｓＣａｓｈｍｅｒｅｇｏａｔ，Ｔｒａｎｓｆｅｒｉｎ，Ｐｏｌｙｍｏｒｐｈｉｓｍ转铁蛋白（ｔｒａｎｓｆｅｒｉｎ，...     

在水稻花培后代中RFLP零等位的遗传分析

在构建水稻分子图谱的研究中,有４ 个ＲＦＬＰ探针揭示了一对籼粳稻之间的零等位现象．其中ＲＧ ２２９ 揭示了籼稻“圭６３０”（Ｏｒｙｚａ ｓａｔｉｖａ ｓｓｐ． ｉｎｄｉｃａ）两个零等位位点;ＲＧ ４１９,ＲＧ４２４ 及ＲＧ ３５３ 揭示了粳稻“０２４２８”（Ｏ． ｓａｔｉｖａ ｓｓｐ．ｊａｐｏｎｉｃａ）的零等位． 利用８１ 个圭６３０／０２４２８ 的花培植株（ＤＨ）进行的遗传分析结果表明,这些零等位位点与ＭｃＣｏｕｃｈ 发表的水稻分子图谱中其相邻分子标记间的连锁关系发生了变化．另外,用ＲＧ ６８４ 探针在一些ＤＨ植株中检测出有新的零等位出现,虽然双亲都具有与ＲＧ ６８４ 同源的序列． 零等位的出现可能与转座因子的转位有关     

滇牡丹复合群的GiemsaC—带比较研究

应用ＢＳＧ方法对滇牡丹复合群５个类群的ＧｉｅｍｓａＧ－带进行了比较研究。在５个类群的根尖体细胞有丝分中期观察到１０条染色体,其核型基本一致,均为Ｋ＝２ｎ＝１０＝６ｍ＋２ｓｍ＋２ｓｔ。各类群的１０条染色体都在着丝点附近显示出了ＧｉｅｍｓａＣ－带,所有染色体的长臂上都没有显示出ＧｉｅｍｓａＣ－带,。而短臂上的ＧｉｅｍｓａＣ－带的数量和位置在娄各之间表现了一定的差异。除了滇牡丹第一地同源染色体中只有一条     

Phosphoglucose isomerases of hagfish, zebrafish, gray mullet, toad, and snake, with reference to the evolution of the genes in vertebrates

Phosphoglucose isomerase (PGI) is a protein with multiple functions. To infer its structure changes and evolution in vertebrates, we cloned cDNAs encoding PGI genes from hagfish (Paramyxine yangi), gray mullet (Mugil cephalus), zebrafish (Danio rerio), toad (Bufo melanosticus), and snake (Boiga kraepelini). Only one PGI gene was cloned in each of hagfish, toad, and snake, but two PGI genes were found in zebrafish and gray mullet, respectively. The PGI of hagfish encodes 554 amino acids, in contrast to the PGIs of bonyfishes, toad, and snake which encode 553 amino acids and the PGIs of mammals which encode 558 amino acids. Among 558 aligned amino acid sites, there are 314 sites (56.27%) totally conserved. To see if diversifying selection acts on PGI amino acids of vertebrates, we calculated the pairwise ratio of nonsynonymous versus synonymous substitution per site (Ka/Ks) and the ratio of radical amino acid changes versus conservative amino acid changes per sites (dR/dC) between PGI sequences. The average pairwise ratio between nonsynonymous substitutions per nucleotide (Ka) and synonymous substitutions per nucleotide (Ks) among vertebrate PGI sequences equals 0.047 +/- 0.019. The average pairwise ratio between radical amino acid changes and conservative amino acid changes (dR/dC) among the vertebrate PGIs equal 0.938 +/- 0.158 for charge changes, 0.558 +/- 0.085 for polarity changes, and 0.465 +/- 0.0714 when both polarity and volume are considered. There is no amino acid within the vertebrate PGIs under diversifying selection as analyzed by the method of Yang et al. (2000b). The results suggest that the present vertebrate PGIs are at evolutionary stasis and are being subjected to intense purifying selection. The purifying selection is to maintain polarity and volume of the protein but not the charge groups of amino acids. Phylogenetic analysis reveals that vertebrate PGIs can be classified into three major groups: the mammalian, amphibian-reptilian, and teleostean PGIs. The gene tree suggests that the gene duplication event of PGI in bonyfishes occurred before diversification of Acanthopterygii but after the split of bonyfishes and tetrapods. The evolution of multiple functions of PGI is discussed.     

Evolution of the X-linked Zinc Finger Gene and the Y-linked Zinc Finger Gene in Primates

We have sequenced the partial exon of the zinc finger genes (ZFX and ZFY) in 5 hominoids, 2 Old World monkeys, 1 New World monkey, and 1 prosimian. Among these primate species, the percentage similarities of the nucleotide sequence of the ZFX gene were 96-100% and 91.2-99.7% for the ZFY gene. Of 397 sites in the ZFX and ZFY gene sequences, 20 for ZFX gene and 42 for ZFY gene were found to be variable. Substitution causes 1 amino acid change in ZFX, and 5 in ZFY, among 132 amino acids. The numbers of synonymous substitutions per site (Ks) between human and the chimpanzee, gorilla and orangutan for ZFY gene were 0.026, 0.033, and 0.085, respectively. In contrast, the Ks value between human and hominoid primates for the ZFX gene was 0.008 for each comparison. Comparison of the ZFX and ZFY genes revealed that the synonymous substitution levels were higher in hominoids than in other primates. The rates of synonymous substitution per site per year were higher in the ZFY exon than in the SRY exon, and higher in the ZFY exon than in the ZFY intron, in hominoid primates.     

Evolution of the Sry genes

Existing DNA sequence data on the Sry gene, the mammalian sex- determining locus in the Y chromosome, were analyzed for primates, rodents, and bovids. In all three taxonomic groups, the terminal sequences evolved faster than the HMG (high mobility group) boxes, and this applies both to synonymous (Ks) and nonsynonymous (Ka) nucleotide substitutions. Similar intragenic correlation between synonymous and nonsynonymous substitution rates was not found either in other mammalian genes that contain a conservative box (Sox, Msx) or in the MADS-box genes of plants. The rate of nonsynonymous substitutions exceeds significantly that of synonymous substitutions in the terminal Sry sequences of apes. We did not find good support for the hypothesis that the high evolutionary rate of Sry would be associated with a promiscuous mating system.      

Evolution of Rh Blood Group Genes Have Experienced Gene Conversions and Positive Selection

There are two tightly linked loci (D and CE) for the human Rh blood group. Their gene products are membrane proteins having 12 transmembrane domains and form a complex with Rh50 glycoprotein on erythrocytes. We constructed phylogenetic networks of human and nonhuman primate Rh genes, and the network patterns suggested the occurrences of gene conversions. We therefore used a modified site-by-site reconstruction method by using two assumed gene trees and detected 9 or 11 converted regions. After eliminating the effect of gene conversions, we estimated numbers of nonsynonymous and synonymous substitutions for each branch of both trees. Whichever gene tree we selected the branch connecting hominoids and Old World monkeys showed significantly higher nonsynonymous than synonymous substitutions, an indication of positive selection. Many other branches also showed higher nonsynonymous than synonymous substitutions; this suggests that the Rh genes have experienced some kind of positive selection. Received: 16 March 1999 / Accepted: 17 June 1999     

Positive selection and the molecular evolution of a gene of male reproduction, Acp26Aa of Drosophila

The gene for a male ejaculatory protein, Acp26Aa, in four sibling species of the Drosophila melanogaster subgroup has previously been shown to have a nonsynonymous rate (Ka) of nucleotide substitution that is indistinguishable from the synonymous rate (Ks). By examining this gene in two other species of this subgroup, we found that Ka is generally large and can sometimes be more than twice as large as Ks. This suggests that positive selection may be operating at this locus of male reproduction.      

Synonymous Substitutions in the Xdh Gene of Drosophila: Heterogeneous Distribution along the Coding Region

The Xdh (rosy) region of Drosophila subobscura has been sequenced and compared to the homologous region of D. pseudoobscura and D. melanogaster. Estimates of the numbers of synonymous substitutions per site (Ks) confirm that Xdh has a high synonymous substitution rate. The distributions of both nonsynonymous and synonymous substitutions along the coding region were found to be heterogeneous. Also, no relationship has been detected between Ks estimates and codon usage bias along the gene, in contrast with the generally observed relationship among genes. This heterogeneous distribution of synonymous substitutions along the Xdh gene, which is expression-level independent, could be explained by a differential selection pressure on synonymous sites along the coding region acting on mRNA secondary structure. The synonymous rate in the Xdh coding region is lower in the D. subobscura than in the D. pseudoobscura lineage, whereas the reverse is true for the Adh gene.     

Adaptive evolution of the IgA hinge region in primates

IgA is a major component that prevents the penetration of pathogenic bacteria into mucosal surfaces. The IgA antibody is cleaved at the IgA hinge region with high specificity by IgA-specific proteases produced by several pathogenic bacteria. We conducted a genomic sequence analysis of the IgA genes of a wide spectrum of primates, including the first intron and second exon, which consist of the hinge region and the CH2 domain, to find evidence of positive selection. Because the hinge region is quite small, we combined the largest collection of sequences that could be clearly aligned and evaluated the total numbers of synonymous and nonsynonymous substitutions on the phylogenetic tree. The nonsynonymous to synonymous substitution ratio (d(N)/d(S) test) showed that hominoids, Old World monkeys, and New World monkeys have d(N)/d(S) ratios of 5.4, 6.3, and 4.2, respectively. Fisher's exact probability tests showed statistical significance for the Old World monkey. Because the substitution rates of the flanking sequences are more or less similar to the synonymous rates of the hinge region, these high values of d(N)/d(S) should be the result of positive selection at the hinge region. Combining the high sequence variability in each population and the highly accelerated nonsynonymous substitution rates in the hinge region, we conclude that this unusual IgA evolution is a molecular evidence of adaptive evolution possibly caused by the host-parasite relationship.     

Impact of highly active antiretroviral therapy and immunologic status on hepatitis C virus quasispecies diversity in human immunodeficiency virus/hepatitis C virus-coinfected patients

This study analyzes the effect of highly active antiretroviral therapy (HAART), and thus immunologic status, on hepatitis C virus (HCV) load and quasispecies diversity in patients coinfected with the human immunodeficiency virus (HIV) and HCV. Three cohorts of coinfected patients were analyzed retrospectively over a period of 7 to 10 months: group A was antiretroviral drug na?ve at baseline and then on HAART for the remainder of the study, group B did not receive antiretroviral therapy at any point, and group C was on HAART for the entire study. HCV quasispecies diversity was analyzed by sequencing hypervariable region 1. In a longitudinal analysis, there was no significant change from baseline in any immunologic, virologic, or quasispecies parameter in any of the three groups. However, in comparison to groups A and B, group C had significantly higher CD4+- and CD8+-cell counts, a trend toward a higher HCV load, and significantly increased number of HCV clones, entropy, genetic distance, and ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (Ka/Ks). In addition, CD4+-cell count was positively correlated with HCV load, genetic distance, and Ka. Interestingly, patients infected with HCV genotype 2 or 3 had a significantly higher CD4+-cell count, HCV load, genetic distance, and Ka/Ks than those infected with genotype 1. These results suggest that there is no immediate effect of HAART on HCV but that, with prolonged HAART, immune restoration results in an increase in HCV load and quasispecies diversity.     

Receptor-like genes in the major resistance locus of lettuce are subject to divergent selection.

Disease resistance genes in plants are often found in complex multigene families. The largest known cluster of disease resistance specificities in lettuce contains the RGC2 family of genes. We compared the sequences of nine full-length genomic copies of RGC2 representing the diversity in the cluster to determine the structure of genes within this family and to examine the evolution of its members. The transcribed regions range from at least 7.0 to 13.1 kb, and the cDNAs contain deduced open reading frames of approximately 5. 5 kb. The predicted RGC2 proteins contain a nucleotide binding site and irregular leucine-rich repeats (LRRs) that are characteristic of resistance genes cloned from other species. Unique features of the RGC2 gene products include a bipartite LRR region with >40 repeats. At least eight members of this family are transcribed. The level of sequence diversity between family members varied in different regions of the gene. The ratio of nonsynonymous (Ka) to synonymous (Ks) nucleotide substitutions was lowest in the region encoding the nucleotide binding site, which is the presumed effector domain of the protein. The LRR-encoding region showed an alternating pattern of conservation and hypervariability. This alternating pattern of variation was also found in all comparisons within families of resistance genes cloned from other species. The Ka /Ks ratios indicate that diversifying selection has resulted in increased variation at these codons. The patterns of variation support the predicted structure of LRR regions with solvent-exposed hypervariable residues that are potentially involved in binding pathogen-derived ligands.     

Expansion Mechanisms and Functional Divergence of the Glutathione S-Transferase Family in Sorghum and Other Higher Plants

Glutathione S-transferases (GSTs) exist in various eukaryotes and function in detoxification of xenobiotics and in response to abiotic and biotic stresses. We have carried out a genome-wide survey of this gene family in 10 plant genomes. Our data show that tandem duplication has been regarded as the major expansion mechanism and both monocot and dicot plants may have practiced different expansion and evolutionary history. Non-synonymous substitutions per site (Ka) and synonymous substitutions per site (Ks) analyses showed that N- and C-terminal functional domains of GSTs (GST_N and GST_C) seem to have evolved under a strong purifying selection (Ka/Ks < 1) under different selective pressures. Differential evolutionary rates between GST_N and GST_C and high degree of expression divergence have been regarded as the major drivers for the retention of duplicated genes and the adaptability to various stresses. Expression profiling also indicated that the gene family plays a role not only in stress-related biological processes but also in the sugar-signalling pathway. Our survey provides additional annotation of the plant GST gene family and advance the understanding of plant GSTs in lineage-specific expansion and species diversification.