Adaptive evolution of primate TRIM5 alpha, a gene restricting HIV-1 infection

Recent studies showed that nonhuman primate TRIM5 alpha can efficiently block HIV-1 infection in human cell lines. It can also restrict other retroviruses, therefore, suggested as a general defender against retrovirus infection. Here, we present an evolutionary analysis of TRIM5 alpha in primates. Our results demonstrated that TRIM5a has been evolving rapidly in primates, which is likely caused by Darwinian positive selection. The SPRY domain of TRM5 alpha, which may be responsible for recognition of incoming viral capsids showed higher nonsynonymous/synonymous substitution ratios than the non-SPRY domain, indicating that the adaptive evolution of TRIM5a ill primates might be an innate strategy developed in defending retrovirus infection during primate evolution. In addition, the comparative protein sequence analysis suggested that the amino acid substitution pattern at a single site (344R/Q/P) located in the SPRY domain may explain the differences in Susceptibilities of HIV-1 infection in diverse primate species. (c) 2005 Elsevier B.V. All rights reserved.

蟾蜍皮肤活性蛋白与多肽的研究

近年来，我们致力于蟾蛛（Bufo andrewski）皮肤活性组份的研究，构建了缥蛛皮肤cDNA文库，检测了蟾蛛皮肤分泌液中多种生物活性，进一步纯化得到了四个新的生物活性蛋白：溶菌酶、抗爱滋病毒蛋白以及两个丝氨酸蛋粼酶抑制剂，并，简述如下；I、第三章报导了我们从蟾蛛皮肤分泌液中分离得到的一个谊薇酚犷杰女呱BA一娜"zym"）·BA一lvs"Zym"经5DS一PAGE检测为一条带，其分子量约为巧k珍。·它是一个高效的溶菌酶，每毫克蛋白的溶菌活性为2．7xl护俪ts，还能抑制革兰氏阳性菌（金黄色葡萄球菌Slaj，匆褚ococcusaureus）和革兰氏阴性菌（大肠杆菌Esch邵ichiacoli）生长，其最小抑菌浓度（MIC）分别为1．36拼M和84并M。使用PCR筛选法，我们从蟾蛛皮肤c溯A文库中克隆得到编码BA一lyso即me的cDNA序列。BA一lysozymeN末端测序和肤质量图谱确认了蛋白和基因的网一性。它的蛋白全序列与鸡溶菌酶的相似性为5氏5％。系统发育分析显示，与其最相似的是来源于海龟的溶菌酶。11、第四章介绍了我们从蟋蛛皮肤分泌液中分离得到的一个新的抗lllV蛋白，命名为BAS一AH。BAS一AH是一个分子量为63kD。的单链蛋白，每摩尔蛋白质含有0．89摩尔血红素辅基。BAS一AH对人T淋巴细胞系CS166细胞的毒性（CCS。）为9．5尽M。BAs一AH具有较强的抗HIV活性，它对HIV感染和复制具有剂量依赖抑制效应，其选择指数（CCso／Ecs。）分别为14．4和11．4·BAS一麟J也能抑制HIV的逆转录酶，其1C5（）为L32冬以。BAs一AH的N末端氨基酸为NA以KADvIGKIsILLGQDI』slvAAM，与己知的抗Hlv蛋白没有同源性·表明它可能是一个新的抗川v蛋自。BAs一AH没有检测到抗菌活性、蛋自酶水解活性、胰蛋自酶抑制剂活性、L一氨基酸氧化酶活性和过氧化氢酶活性。班、第五伞报导了我们通过离子交换、分子筛和反向层析，从蟾赊皮肤中分离得到的一个新的胰蛋白酶抑制剂，命名为BATI。BATI是一个单链糖蛋自·其分子量为22kD。。它是吵～个热稳定的竞争性的抑制剂，能有效抑制胰蛋自酶·其抑制常数凡为14nM。B灯I对凝血酶、弹性蛋白酶以及糜蛋白酶都没有抑制作用。BATI的N末端序列为El犯ITD，不同于其它物种来源的蛋白酶抑制剂。W、第六章介绍了蟾蛛皮肤分泌液中纯化得到的另外一个蛋白酶抑制剂（命名为baserpin）。与上述BATI不同的是，basel咖n不可逆地抑制多种蛋白酶。它是一个分子量约为60kDa的单链糖蛋白，除了能抑制胰蛋白酶，还能有效抑制糜蛋白酶和弹性蛋白酶。它抑制上述三种酶的二级反应常数（编）分别为4．6x1护M一，s一l、8．9》1护M一15一I以及6．8xl护M一ls一l。BaserPin是第一个来源于两栖类皮肤的不可逆抑制剂，其N末端氨基酸序列为HTQYPDILIAKPxDK，与其它物种来源的蛋白酶抑制剂不同。本论文综述了蟾蛛皮肤中的活性组份，报导了我们近年来研究蟾蛛皮肤活性蛋白与多肤的进展，分四章详细介绍了蟾蛛皮肤中纯化得到的四个活性蛋白。BA一lysozyme是两栖类动物中第一个得到蛋白质全序列的溶菌酶，能有效抑制革兰氏阳性菌和革兰氏阴性菌生长；BA象AH是一个含血红素辅基的抗HIV蛋白，其独特的理化性质和功能证明它是一个新的抗病毒蛋白。根据所鉴定的性质判断，BATI和bos仰in分别属于竞争性抑制剂和不可逆抑制剂。其中，base印in是第一个从两栖类皮肤中分离得到的不可逆抑制剂。

亚洲地形和海陆分布变化对东亚环境格局形成演化的作用：数值模拟与地质记录对比

Earlier studies on the distribution of geological environmental indicators in China revealed drastic changes from a zonal climate pattern (planetary-wave-dominant pattern) in the Paleogene to a monsoon-dominant one in the Neogene, which suggested an inception of the initial East-Asian summer monsoon. However, there are different views about the time and causes of the changes.Here, we attempt to compile a series of paleoenvironmental maps based on newly collected climate indicators from the literatures and chronologically constrained evidence of geological maps in order to re-examine the temporal and spatial evolution of climate belts in China during the Cenozoic with special emphasis on the changes of the arid belt. These indicators include mammalian fauna, coal, carbonate concretions, jarosite, salt, gypsum deposits and pollen assemblages etc, with chronological controls that we believe reliable. Pollen assemblages and mammalian fauna have been classified into three categories (arid, semi-arid/sub-humid, humid) to reflect the intensity of aridity/humidity. Salt, jarosite and gypsum deposits are classified as the arid indicators. Carbonate concretions and coal are classified into the semi-arid/sub-humid and humid one respectively. Paleoenvironmental maps at 8 time slices have been reconstructed. They are the Paleocene, Eocene, Oligocene, Miocene, Early Miocene, Middle Miocene, Late Miocene and Pliocene.And furthermore, we attempt to use IAP^AGCM to simulate the evolution of climate belts in emphasizing on the changes of the rain band, and compare the results with the paleoenvironmental maps in order to examine the causes of the drastic paleoenvironmental changes near the Oligocene/Miocene boundary. 36 sensitive numerical experiments are carried out using the IAP__AGCM to analyze the impacts of the uplift of the Himalayan-Tibetan complex, shrinkage of the Paratethys Sea, expansion of the South China Sea and the development of the polar ice sheets on rain band in China.The main conclusions are as follows:The obtained results essentially confirm the earlier conclusions about a zonal climate pattern in the Paleogene and a different pattern in the Neogene, and illustrate that a monsoon-dominant environmental pattern with inland aridity formed by the Early Miocene, which is temporally consist with the onset of eolian deposits in China.Cenozoic cooling and the formation of polar ice sheets are unlikely the main causes to the changes of environmental patterns mentioned above in China. But northern hemispheric cooling and the ice-sheets can intensify the Siberian High Pressure, and strengthen the winter monsoon circulations and enhance the aridity in the west part of China. These results support the earlier studies.Shrinkage of the Paratethys Sea and uplift of the Himalayan-Tibetan complex played important roles in strengthening the East Asian monsoon and induceing the above changes of environmental pattern, which is consistent with the earlier studies. Furthermore, "the monsoon-dominant pattern" appears when the Himalayan-Tibetan complex reaches to about 1000-2000 meters high and the Paratethys Sea retreats to the Turan Plate.4) Expansion of the South China Sea is another significant factor that drives the evolution of environmental patterns. We believe that the above three factors co-act and drive the change of the environmental patterns from a planetary-wave-dominant one to a monsoon-dominant one. However, the impacts of each factor vary by regions. The uplift mainly increases the humidity in Southwestern China and the aridity in northwestern country. The shrinkage mainly increases the humidity in Northern China and also enhances the aridity in the northwestern country. The expansion greatly increases the humidity in the south part of China.

Comparative studies of AOT and NaDEHP by fluorescence technique and z-potential (ζ) measurements

The aggregation behaviors of two surfactants with the same hydrophobic tail, sodium bis(2-ethylhexyl)sulfosuccinate (AOT) and sodium bis(2-ethylhexyl)phosphate (NaDEHP), have been investigated by the fluorescence technique and z-potential (ζ) measurements. Five fine peaks of the pyrene molecule fluorescence spectroscopy appear in the surfactant solution, and the micropolarity at which pyrene locates is monitored from the intensity ratio of the first (I1) and the third peak (I3). A wide peak around 475 nm, the emission spectra of the excimer of pyrene molecules, is observed in the NaDEHP solution, while this is not found for the AOT system. The value of I1/I3 decreases in a more limited concentration range for the AOT system than for NaDEHP, indicating that small aggregates can be more easily formed by NaDEHP molecules. The z-potential results for the aggregates formed by the two surfactants show that the interaction between AOT and PVP is stronger than that between NaDEHP and PVP.

Shock Tube Studies on the Nonequlibrium Electron Affinity Kinetics of Fluorine Atom at High Temperatures

To study electron affinity kinetics, a shock tube method was applied, in which the test gas was ionized by a reflected shock wave and subsequently quenched by a strong rarefaction wave. As the quenching speed of 106 K/s was reached, a nonequilibrium ionization-recombination process occurred, which was dominated by ion recombination with electrons. A Langmuir electrostatic probe was used to monitor variation in the ion number density at the reflection shock region. The working state of the probe was analyzed...

Experimental Studies on Model Scramjet in a Mach 6 High Enthalpy Free-Jet Wind Tunnel

A side-wall compression scramjet model with different combustor geometries has been tested in a propulsion tunnel that typically provides the testing flow with Mach number of 5.8, total temperature of 1800K, total pressure of 4.5MPa and mass flow rate of 4kg/s. This kerosene-fueled scramjet model consists of a side-wall compression inlet, a combustor and a thrust nozzle. A strut was used to increase the contraction ratio and to inject fuels, as well as a mixing enhancement device. Several wall cavities were also employed for flame-holding. In order to shorten the ignition delay time of the kerosene fuel, a little amount of hydrogen was used as a pilot flame. The pressure along the combustor has an evident raise after ignition occurred. Consequently thrust was observed during the fuel-on period. However, the thrust was still less than the drag of the scramjet model. For this reason, the drag variation produced by different strut and cavities was tested. Typical results showed that the cavities do not influence the drag so much, but the length of the strut does.

Studies of ion energy and yield from argon clusters heated by intense femtosecond laser pulses

Using time-of-flight spectrometry, the interaction of intense femtosecond laser pulses with argon clusters has been studied by measuring the energy and yield of emitted ions. With two different supersonic nozzles, the dependence of average ion energy (E) over bar on cluster size (n) over bar in a large range of (n) over bar approximate to 3 x 10(3) similar to 3 x 10(6) has been measured. The experimental results indicate that when the cluster size (n) over bar <= 3 x 10(5), the average ion energy (E) over bar proportional to (n) over bar (0.5), Coulomb explosion is the dominant expansion mechanism. Beyond this size, the average ion energy gets saturated gradually, the clusters exhibit a mixed Coulomb-hydrodynamic expansion behavior. We also find that with the increasing gas backing pressure, there is a maximum ion yield, the ion yield decreases as the gas backing pressure is further increased.

Property studies of optical waveguide formed by 6.0 MeV carbon ion implantation into Nd : silicate glass

Nd:silicate glass was implanted at room temperature by 6.0 MeV C3+ ions with a dose of 2.0 x 10(15) ions cm(-2). A waveguide with thickness of about 6.3 mu m was formed. The prism-coupling method was used to observe the dark modes of the waveguide at 633 nm and 1539 nm, respectively. There are three dark modes at 633 nm, of which one is the enhanced-index mode. The propagation loss of the enhanced-index mode in the waveguide measured at 633 nm is 0.42 dB cm(-1) after annealing at 217 degrees C for 35 min. The reflectivity calculation method was applied to simulate the refractive index profiles in the waveguide. The mode optical near-field output at 633 nm was presented.

Low “penetrance” of phylogenetic knowledge in mitochondrial disease studies

An up-to-date view of the worldwide mitochondrial DNA (mtDNA) phylogeny together with an evaluation of the conservation of each site is a reliable tool for detecting errors in mtDNA studies and assessing the functional importance of alleged pathogenic mutations. However, most of the published studies on mitochondrial diseases make very little use of the phylogenetic knowledge that is currently available. This drawback has two inadvertent consequences: first, there is no sufficient a posteriori quality assessment of complete mtDNA sequencing efforts; and second, no feedback is provided for the general mtDNA database when apparently new mtDNA lineages are discovered. We demonstrate, by way of example, these issues by reanalysing three mtDNA sequencing attempts, two from Europe and another one from East Asia. To further validate our phylogenetic deductions, we completely sequenced two mtDNAs from healthy subjects that nearly match the mtDNAs of two patients, whose sequences gave problematic results. (c) 2005 Elsevier Inc. All rights reserved.

Phylogenetic studies of pantherine cats (Felidae) based on multiple genes, with novel application of nuclear beta-fibrinogen intron 7 to carnivores

The pantherine lineage of the cat family Felidae (order: Carnivora) includes five big cats of genus Panthera and a great many midsized cats known worldwide. Presumably because of their recent and rapid radiation, the evolutionary relationship among pantherines remains ambiguous. We provide an independent assessment of the evolutionary history of pantherine lineage using two complete mitochondrial (mt) genes (ND2 and ND4) and the nuclear beta-fibrmogen intron 7 gene, whose utility in carnivoran phylogeny was first explored. The available four mt (ND5, cytb, 12S, and 16SrRNA) and two nuclear (IRBP and TTR) sequence loci were also combined to reconstruct phylogeny of 14 closely related cat species. Our analyses of combined mt data (six genes; approximate to 3750 bp) and combined mt and nuclear data (nine genes; approximate to 6500 bp) obtained identical tree topologies, which were well-resolved and strongly supported for almost all nodes. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within this genus revealed a novel branching pattern, with P. tigris diverging first in Panthera genus, followed by P. onca, P. leo, and last two sister species P. pardus and P. uncia. In addition, close association of Neofelis nebulosa to Panthera, the phylogenetic redefinition of Otocolobus manil within the domestic cat group, and the relatedness of Acinonyx jubatus and Puma concolor were all important findings in the resulting phylogenies. The potential utilities of nine different genes for phylogenetic resolution of closely related pantherine species were also evaluated, with special interest in that of the novel nuclear beta-fibrinogen intron 7. (c) 2005 Elsevier Inc. All rights reserved.

In vivo studies on toxin accumulation in liver and ultrastructural changes of hepatocytes of the phytoplanktivorous bighead carp i.p.-injected with extracted microcystins

Phytoplanktivorous bighead carp were injected i.p. with extracted microcystins (mainly MC-RR and -LR) at two doses, 200 and 500 MC-LReq. mu g kg(-1) bw, and the changes in extractable MCs in liver and in the ultrastructure of hepatocytes were studied at 1, 3, 12, 24 and 48 h after injection. Quantitative and qualitative determinations of MCs in the liver were conducted by HPLC and LC-MS, respectively. MC concentration in the liver reached the maxima at 12 It (2.89 mu g MCs g(-1) dry weight at the lower dose) or at 3 h (5.43 mu g MCs g(-1) dry weight at the higher dose) post-injection, followed by sharp declines afterwards, whereas the ultrastructural changes of hepatocytes in both dose groups suggest progressive increases in severity toward the directions of apoptosis and necrosis from I to 24 h, respectively. There were two new findings in fish: widening of intercellular spaces was among the early ultrastructural changes induced by MCs and ultrastructural recovery of hepatocytes was evident at 48 h post-injection in both dose groups. Both the present and previous studies suggest that with in vivo or in vitro exposure to microcystins, hepatocyte damage in fish tends to proceed toward the direction of apoptosis at lower MC concentrations but toward the direction of necrosis at high MC concentrations. The temporal dynamics of MCs in the liver suggest that bighead carp may have a mechanism to degrade or bind MC-LR actively after it enters the blood system. (c) 2005 Elsevier Ltd. All rights reserved.

Phylogenetic studies of Chinese labeonine fishes (Teleostei : Cyprinidae) based on the mitochondrial 16S rRNA gene

The mitochondrial 16S ribosomal RNA gene is sequenced from 24 ingroups taxa, including 18 species from Labeoninae grouped in 13 genera. Phylogenetic analyses are subjected to neighbor joining, maximum parsimony, maximum likelihood and Bayesian analyses. Phylogenetic analysis indicates that Labeoninae is basically a monophyletic assemblage and can be divided into 2 major clades: one comprising the genera Cirrhinus, Crossocheilus and Garra; and the other consisting of the genera Labeo, Sinilabeo, Osteochilus, Pseudoorossocheilus, Parasinilabeo. Ptychidio, Semilabeo, Pseudogyricheilus, Rectori and Discogobio. According to our present analysis, the features such as the presence of the adhesive disc on the chin and the pharyngeal teeth in 2 rows used in the traditional taxonomy of Labeoninae provide scarce information for phylogeny of labeonine fishes.