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%%、95.95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. 作 者： 洪晓武 张亚平 储以微 高海峰 蒋正刚 熊思东 HONG Xiao-Wu ZHANG Ya-Ping CHU Yi-Wei GAO Hai-Feng JIANG Zheng-Gang XIONG Si-Dong 作者单位： 洪晓武,储以微,高海峰,蒋正刚,熊思东,HONG Xiao-Wu,CHU Yi-Wei,GAO Hai-Feng,JIANG Zheng-Gang,XIONG Si-Dong(复旦大学上海医学院免疫学系,免疫生物学研究所,上海,200032) 张亚平,ZHANG Ya-Ping(中国科学院昆明动物研究所细胞与分子进化开放实验室,昆明,650223) 刊 名： 遗传 ISTIC PKU 英文刊名： HEREDITAS 年，卷(期)： 2008 30(5) 分类号： Q94 关键词： 人猿超科 旧大陆猴 FKN 测序 进化分析 机标分类号： R5 S86 机标关键词： 大陆灵长类全基因序列测定系统进化分析phylogenetic analysis基因进化树黑猩猩序列同源性长臂猿物种进化猕猴红毛负选择氨基酸琼脂糖凝胶基因全序列序列分析位点软件重构 基金项目： 国家自然科学基金，复旦大学校科研和教改项目 DOI：

治疗艾滋病的药物及其应用

提供含有治疗艾滋病有效量的式(I)化合物联苯环辛二烯类木脂素及可药用载体和/或赋形剂的治疗艾滋病的药物，以及它们在制备抗艾滋病的药物中的应用。结构式中：R1，R2，R3，R4，R5，R6，R7，R8，R9，R10＝-H，-OCH3，-OH，-OCOR(R为烷基或芳基)；R1R2，R2R3，R4R5，R5R6为右（a）式；R7，R10＝氧桥。

2,4-二取代氨基-6-取代-[1,3,5]三嗪或1,3-嘧啶类化合物、其制备方法、药物组合物及用途

一种新型的2，4-二取代氨基-6-取代-[1，3，5]三嗪或1，3-嘧啶衍生物及其制备方法、药物组合物和其药理用途，其结构通式如式(I)所示，其中R1、R2、R3、R4、R5、R6、A、B、X、Y和Z的定义如说明书中所述。该类化合物与HIV-1整合酶具有很高结合活性，并且在底物竞争测试中能够有效的抑制整合酶对底物的结合。因此该类化合物是较强的HIV-1整合酶抑制剂，有望开发成为新的抗HIV病毒药物。

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

In vitro anti-HIV and -HSV activity and safety of sodium rutin sulfate as a microbicide candidate

Sodium rutin sulfate (SRS) is a sulfated rutin modified from the natural flavonol glycoside rutin. Here, we investigated its in vitro anti-HIV and -HSV activities and its cytotoxic profile. Fifty percent inhibitory concentration (IC50) values of SRS against HIV-1 X4 virus IIIB, HIV-1 R5 isolates Ada-M and Ba-L were 2.3 +/- 0.2, 4.5 +/- 2.0 and 8.5 +/- 3.8 mu M with a selectivity index (SI) of 563, 575 and 329, respectively. Its IC50 against primary R5 HIV-1 isolate from Yunnan province in China was 13.1 +/- 5.5 mu M, with a Sl of 197. In contrast, unsulfated rutin had no activity against any of the HIV-1 isolates tested. Further study indicated that SRS blocked viral entry and virus-cell fusion likely through interacting with the HIV- I envelope glycoprotein. SRS also demonstrated some activity against human herpes simplex virus (HSV) with an IC50 of 88.3 +/- 0.1 mu M and a Sl of 30. The 50% cytotoxicity concentration (CC50) of SRS was >3.0 mM, as determined in human genital ME 180, HeLa and primary human foreskin fibroblast cells. Minimum inhibitory concentration of SRS for vaginal lactobacilli was >3.0 mM. These results collectively indicate that SRS represents a novel candidate for anti-HIV-1/HSV microbicide development. (C) 2007 Elsevier B.V. All rights reserved.

印度人群线粒体 DNA 系统发育基因组学研究

人类线粒体DNA(mtDNA)是一个长度16,569bp 的环状分子，编码13 种蛋白 质、22 种tRNA 和2 种rRNA。由于mtDNA 全基因组信息具有缺乏重组、母系 遗传、高突变速率和相对较高的分辨率等特点，近年来已经成为重建人类历史的 重要工具。这些研究已经证实，mtDNA 最古老的六个单倍型类群，L0-L5，在非 洲特异的出现；而6-7 万年前从L3 衍生出的M 和N 两个超类群最终占领了世界 其他地区。然而，mtDNA 全序列研究在世界上某些特定地区尚是一片空白，其 中之一便是作为人类“走出非洲”的关键区域——印度。 为弥补这一空白，我们从 1200 个印度样品中选择了131 个可以代表所有主 要单倍型类群的个体，进行了全基因组扩增和测序，手工重建并软件验证了系统 发育关系树。我们的结果发现了12 个新的印度特有单倍型类群(N5, R7, R8, R30, R31, M34-M40)，修订了11 个已知特有单倍型类群(N1d, R5, R6, U2a, U2b, U2c, M2, M4, M5, M6, M30)的定义，详细描述了存在于印度的欧洲特有类群(HV, JT, U, N1, W)。 这一工作产生了多个推论。第一个是关于人类“走出非洲”假说长期以来 存在的争论。欧亚大陆和大洋洲mtDNA 在M 和N(包括R)超类群系统发育关系 上星状和不重叠的分布，表明了人类走出非洲是沿着亚洲海岸线(即所谓的“南 方路线”)的一个快速扩散的过程。第二个推论是关于存在于印度的欧洲特有世 系。与典型的欧洲世系相比，这些世系仅仅存在一到两个突变，从而证实了新石 器时代以来来自于近东新月地带或中亚高原的基因流。第三个推论涉及一个早期 的印度全序列研究。仔细分析其数据表明，他们的数据丢失了很多基部的特有突 变并产生了多个幻影突变，从而证实了系统发育思想对检测数据质量的作用。 随着印度人群 mtDNA 全序列研究的完成，人类mtDNA 系统发育的基本框 架得以建立。人类mtDNA 明显地呈现出大洲特异性分布。目前已经有两种假说用来解释这一现象。传统的观点把这一现象归于遗传漂变；而近期的选择假说认 为选择在人类mtDNA 的分化中扮演了极其重要的角色，而气候是主要的选择压 力。为解决这一争论，我们收集了来自南亚、大洋洲和东亚三个具有不同气候的 地区的mtDNA，使用直接计数的办法比较了各个大洲之间同义突变和异义突变 的差异。结果表明，几乎在所有的基因中，异义突变的数量低于同义突变的数量， 从而表明纯净化选择是人类mtDNA 进化中的主要力量。然而，在这三个大洲之 间没有发现显著的差异，表明mtDNA 在这三个区域上所承受的选择压力基本相 同。这一结果表明，气候不大可能是造成人类mtDNA 分化的主要原因。

甘肃临夏盆地龙担剖面晚新生代磁性地层与古环境

Linxia Basin, situated in the northeast belt of the Tibetan Plateau, is a late Cenozoic depression basin bounded by the Tibetan Plateau and the Chinese Loess Plateau. The Cenozoic deposition, spanning over 30Ma, in which very abundant mammal fossils were discovered, is very suitable for study of uplift processes and geo-morphological evolution of the Tibetan Plateau. The Longdan section (35°31′31.6″N，103°29′0.6″E) is famous for the middle Miocene Platybelodon fauna and the late Miocene Hipparion fauna for a long time and is also one of the earliest known places for wooly rhino, which lies on the east slope of Longdan, a small village of township Nalesi in the south of the Dongxiang Autonomous County, Linxia Hui Nationallity Autonomous Prefecture. The Longdan mammal fauna was discovered at the base of the Early Pleistocene loess deposits at Dongxiang, where the lithology is different from the typical Wucheng Loess on the Chinese Loess Plateau. The rich fossils contain many new species and the major two layers of fossils are in the loess beds. Geologically the fossiliferous area is located in the central part of the Linxia Cenozoic sedimentary basin. Tectonically the Linxia Basin is an intermountain fault basin, bordered by the Leijishan major fault in the south and the north Qinling and Qilianshan major faults in the north. The section is 51.6m thick above the gravel layer, including the 1.6m Late Pleistocene Malan Loess on the top and the other loess-paleosol sequences in the middle of the section. The base of the section is the Jishi Formation, consisting of gravel layer of 13 ~ 17m thick. In this study, 972 bulk samples were collected with an interval of 5cm and other 401 orientied samples were taken with a magnetic compass. In the laboratory, the paleomagnetism, medium grain size, susceptibility, color, micromorphology, anisotropy of magnetic susceptibility were analyzed. From the stratigraphic analysis, the Longdan section from the top 0.3m to the bottom 51.6m, containing 5 normal polarities (N1-N5) and 5 reversal polarities (R1-R5). The paleomagnetic results show N3 is the Olduvai subchron in the middle of the Matuyama chron, and then the chronology of the Longdan mammal fauna is constructed along the section. The Matuyama-Gauss boundary is 45m and N5 enters Gauss chron. The Olduvai subchron with the age of 1.77 ~ 1.95Ma is found just in the upper fossiliferous level of Longdan mammal fauna. Taking the deposit rate of the section into account, the geological age of the upper fossiliferous level of Longdan mammal fauna is estimated to be about 1.9Ma. The lower fossiliferous level is just below the Reunion subchron and its age is estimated to be 2.25Ma. In addition, anisotropy of magnetic susceptibility of the loess-paleosol and other climatic indexes were used for discussing the late Cenozoic paleoenvironmental changes at Longdan, from which the Longdan area should have been an area of predominantly steppe the same as the Longdan mammal fauna.