哺乳动物cd59基因的进化

采用PCR以及BLAST方法从5种哺乳动物中获得了cd59基因的编码区序列, 结合 GenBank中已有的序列, 计算cd59基因在哺乳动物中的核苷酸替换速率. 对非同义替换速率和同义替换速率进行比较的结果显示, cd59在哺乳动物中总体上受到负选择作用; 用PAML软件“位点-特异”模型检测到4个受到正选择作用的位点, 4个位点分布于分子表面, 其中2个位于功能重要的区域; 此外, 用“支-位点-特异”模型在小鼠通过基因复制后形成的cd59a和cd59b上检测正选择引起的加速进化, 并检测到该支系特异的正选择位点1个.     

念珠藻属植物hetR基因的适应性进化分析

以念珠藻属(Nostoc)及其近缘类群hetR基因的51条序列为研究对象,对hetR基因的编码蛋白进行生物信息学分析和系统发育分析,并使用分支模型、位点模型和分支-位点模型进行该基因位点的适应性进化研究。系统发育分析结果显示,51条hetR基因蛋白序列可分为4个大分支。适应性进化分析结果表明,在3种进化模型中,大多数分支及藻株都没有检测到统计学上具有显著性的正选择位点,说明检测的位点大多处于负选择压力下。但在普通念珠藻(Nostoc commune,CHAB2802)中检测到正选择位点(126T),提示念珠藻属植物hetR基因发生了适应性改变。     

趋化因子及其受体家族分子适应性进化分析

Branch-Site模型是检测基因序列中单个密码子位点是否具有选择作用的统计学方法。该模型能有效地检测基因在进化历程中是否受到选择作用, 并预测出那些在进化过程中对功能分化有重要贡献的、受正选择作用的密码子位点。趋化因子是一类控制免疫细胞定向迁移的细胞因子, 其功能行使由趋化因子受体介导。该文用Branch-Site模型分析趋化因子及其受体基因家族的分子适应性, 发现只有少数种类基因受到正选择作用, 如RANTES、CCR5等。并预测出一些可能受到正选择作用的位点, 蛋白3D分析显示, 它们均位于趋化因子和相应受体相互作用的结构区域。     

大足鼠耳蝠短波视蛋白基因的RACE扩增及其进化分析

根据几种哺乳动物的短波视蛋白基因的比对结果,在保守区设计两条基因特异引物扩增大足鼠耳蝠(Myotis ricketti)的短波视蛋白基因,用cDNA末端快速扩增技术(rapid amplincation of cDNA ends,RACE)扩增出其5′和3′末端序列,并结合GenBank中相关哺乳动物短波视蛋白基因编码区进行了进化分析.结果显示,该基因编码区全长为1 050 bp,共编码350个氨基酸.没有发现提前终止密码子,且功能区严格保守,提示是一个有功能的基因;5个关键氨基酸位点分别为52 T、86 F、93 T、114 A和118 S,表明该蝙蝠的短波视蛋白对紫外光最敏感.进化分析表明,兽类的短波视蛋白基因受到正选择压力的影响;相对速率检验结果显示,大足鼠耳蝠与其他兽类的短波视蛋白基因进化速率有明显的差异.提示大足鼠耳蝠的该基因可能发生了功能特化,可能对其夜晚视觉有重要的作用.     

黄麂Mhc-DRB 基因多态性及其维持机制

利用牛DRB3 特异性引物(LA31 和LA32),通过聚合酶链式反应(PCR)、单链构象多态性(SSCP)以及克隆测序技术,从12 只黄麂个体中共获得20 个DRB 第二外显子等位基因,其中6 个个体具有3 ～ 4 个等位基因,提示利用该引物从黄麂中至少可以扩增出2 个DRB 位点。所有序列均无插入、缺失和终止密码子。基于序列比对(与牛DRB3 和鹿科DRB 基因同源性非常高),以及所检测到的氨基酸变异位点主要位于抗原结合区,推测本文所获得的黄麂序列为表达的、且具有重要功能的DRB 位点。抗原结合区氨基酸位点的非同义替换(d_N )显著大于同义替换(d_S )(P < 0.01),说明历史上黄麂DRB 基因经历过正选择作用。CODMEL 程序中的模型M7 和M8 似然比检测(Likelihood ratio test,LRT)结果同样支持上述推论。进一步利用经验贝叶斯法准确地检测出6 个受正选择作用的氨基酸位点(位点11、37、61、67、71、86),其中的5 个位点位于PBR 区。因此,正选择作用可能是维持黄麂DRB 基因多态性的主要机制之一。基于DRB 外显子2 序列利用邻接法(NJ)
构建了部分偶蹄动物系统发生关系,在NJ 树上,黄麂DRB 基因与其它鹿科动物DRB 基因呈镶嵌式分布,提示跨物种进化是维持黄麂DRB 基因多态性的另一重要机制。此外,黄麂两个等位基因(Mure-DRB1 和Mure-DRB11)和马鹿的两个等位基因(Ceel-DRB34 和Ceel-DRB46)与牛科的等位基因构成一个独立的进化枝,说明黄麂和马鹿的某些DRB 基因具有非常古老的谱系。     

蕨类植物叶绿体rps12基因的分子进化研究

以68种蕨类植物和2种石松类植物的rps12基因为对象,在系统发育背景下,结合最大似然法,使用HyPhy和PAML软件对该基因进行进化速率和适应性进化研究。结果显示:位于IR区的外显子2~3,其替换率明显降低,rps12基因编码序列的替换率也随之降低,且rps12基因密码子第3位的GC含量明显升高;在蕨类植物的进化过程中,3′-rps12更倾向定位于IR区,以保持较低的替换率;rps12基因编码的123个氨基酸位点中,共检测到4个正选择位点和116个负选择位点。研究结果表明基因序列进入到IR区后,显示出降低的替换率;强烈的负选择压力表明RPS12蛋白的高度保守性以及rps12基因的功能和结构已经趋于稳定。     

西伯利亚蓼谷氨酰胺合成酶基因的克隆及碱性盐胁迫下的表达

根据西伯利亚蓼(Polygonum sibiricum Laxm.)地下茎抑制消减文库(SSH)中获得的谷氨酰胺合成酶基因(Glutamin synthetase,GS)EST序列,应用RACE技术克隆了具有Poly A的全长cDNA序列,以下简称为PsGS基因。该序列全长1 273 bp,其5'非翻译区178 bp,3'非翻译区24 bp,开放阅读框编码356个氨基酸残基;根据与其他植物谷氨酰胺合成酶的氨基酸序列的比对以及系统进化分析的结果,确定此基因为谷氨酰胺合成酶基因家族成员;经过SignalP3.0预测该蛋白没有信号肽,无切割位点,为非分泌蛋白。经过ProtParam计算该蛋白的理论等电点为5.55,分子量为39.2 kD,不稳定系数为43.82%,为非稳定蛋白。实时定量PCR分析表明,PsGS在西伯利亚蓼叶、茎、地下茎中均有表达。在3%NaHCO3诱导下,该基因在叶和茎中表达升高,在地下茎中表达受到抑制,推测该基因在抵御碱性盐迫时具有重要作用。     

蕨类植物叶绿体rps12基因的分子进化研究

以68种蕨类植物和2种石松类植物的rps12基因为对象,在系统发育背景下,结合最大似然法,使用Hy Phy和PAML软件对该基因进行进化速率和适应性进化研究。结果显示:位于IR区的外显子2～3,其替换率明显降低,rps12基因编码序列的替换率也随之降低,且rps12基因密码子第3位的GC含量明显升高;在蕨类植物的进化过程中,3'-rps12更倾向定位于IR区,以保持较低的替换率; rps12基因编码的123个氨基酸位点中,共检测到4个正选择位点和116个负选择位点。研究结果表明基因序列进入到IR区后,显示出降低的替换率;强烈的负选择压力表明RPS12蛋白的高度保守性以及rps12基因的功能和结构已经趋于稳定。     

蕨类植物psbD基因的适应性进化和共进化分析

D2蛋白是植物光系统Ⅱ复合体（PSⅡ）核心蛋白之一,由叶绿体psbD基因编码。为了深入理解核心薄囊蕨类植物在阴生环境下的“辐射”式演化,我们对12种蕨类植物的psbD基因进行了克隆和测序,然后联合已公布的其他8种蕨类植物的psbD序列,基于ω值（非同义替换率ds和同义替换率ds的比值）探讨了该基因经受的选择压力。发现D2蛋白在大多数分支和位点受到强烈的负选择,但是树蕨类分支的psbD进化速率低且ω值较高。借助多种模型进行的共进化分析显示,树蕨类D2蛋白的168R、245H和272M两两组成具有共进化关系的氨基酸位点对。     

中华蜜蜂囊状幼虫病毒北京分离株VP1蛋白基因序列特征及原核表达

【目的】研究中华蜜蜂囊状幼虫病毒（Chinese sacbrood virus, CSBV）VP1蛋白的分子进化特征及遗传多样性。【方法】利用RT-PCR方法,克隆了8株CSBV北京分离株VP1蛋白的基因编码区。【结果】序列分析表明,VP1蛋白基因编码区开放阅读框长945 bp,编码315个氨基酸,推测编码蛋白的相对分子量和等电点分别为35.42 kDa和9.23,具有亲水性和免疫原性。序列同源性分析表明,不同年份CSBV北京分离株VP1蛋白氨基酸序列间差异较小,仅个别氨基酸存在差异。北京分离株与辽宁分离株及越南分离株VP1核苷酸序列一致性达93%,与印度及韩国分离株VP1核苷酸序列一致性达92%,与英国分离株VP1核苷酸序列一致性最低,为88%。序列分析同时表明,CSBV北京分离株VP1蛋白序列存在特有的序列特征,同其他地区分离株比较,北京分离株VP1蛋白序列中存在着氨基酸的插入突变。序列替换率分析表明,亚洲型分离株间序列替换率低于亚洲分离株与欧洲分离株间的替换率。构建原核表达载体pEASY-E1-VP1,经IPTG诱导,CSBV VP1蛋白在大肠杆菌Escherichia coli BL21（DE3）pLysS菌株中表达。【结论】本研究提示CSBV不同分离株基因序列存在变异,结果为进一步研究CSBV致病性分化的分子机理奠定了基础。     

A Unique Protease Cleavage Site Predicted in the Spike Protein of the Novel Pneumonia Coronavirus (2019-nCoV) Potentially Related to Viral Transmissibility

正Dear Editor,In December 2019, a novel human coronavirus caused an epidemic of severe pneumonia(Coronavirus Disease 2019,COVID-19) in Wuhan, Hubei, China(Wu et al. 2020; Zhu et al. 2020). So far, this virus has spread to all areas of China and even to other countries. The epidemic has caused 67,102 confirmed infections with 1526 fatal cases     

Curcuminoids as inhibitors of thioredoxin reductase: A receptor based pharmacophore study with distance mapping of the active site

Curcumin is the yellow pigment of turmeric that interacts irreversibly forming an adduct with thioredoxin reductase (TrxR), an enzyme responsible for redox control of cell and defence against oxidative stress. Docking at both the active sites of TrxR was performed to compare the potency of three naturally occurring curcuminoids, namely curcumin, demethoxy curcumin and bis-demethoxy curcumin. Results show that active sites of TrxR occur at the junction of E and F chains. Volume and area of both cavities is predicted. It has been concluded by distance mapping of the most active conformations that Se atom of catalytic residue SeCYS498, is at a distance of 3.56 from C13 of demethoxy curcumin at the E chain active site, whereas C13 carbon atom forms adduct with Se atom of SeCys 498. We report that at least one methoxy group in curcuminoids is necessary for interation with catalytic residues of thioredoxin. Pharmacophore of both active sites of the TrxR receptor for curcumin and demethoxy curcumin molecules has been drawn and proposed for design and synthesis of most probable potent antiproliferative synthetic drugs.     

Comparative morphology of the carpel in the Liliaceae: Hewardieae, Petrosavieae, and Tricyrteae

The young pistils in the melanthioid tribes, Hewardieae, Petrosavieae and Tricyrteae, are uniformly tricarpellate and syncarpous. They lack raphide idioblasts. All are multiovulate, with bitegmic ovules. The Petrosavieae are marked by the presence of septal glands and incomplete syncarpy. Tepals and stamens adhere to the ovary in the Hewardieae and the Petrosavieae but not in the Tricyrteae. Two vascular bundles occur in the stamens of the Hewartlieae and Tricyrtis latifolia. Ventral bundles in the upper part of the ovary of the Hewardieae are continuous with compound septal bundles and placental bundles in the lower part. Putative ventral bundles occur in the alternate position in the Tricyrteae and putative placental bundles in the opposite. position in the Petrosavieae. The dichtomously branched stigma in each carpel of the Tricyrteae is supplied by a bifurcated dorsal bundle.     

Selection with two alleles and complete dominance

For a plant selection model with frequency-independent viabilities, fertilities and selfing rates, it is shown that apart from global fixation, for certain parameter combinations a protected polymorphism and facultative fixation (either allele may become fixed according to initial frequencies) may both occur. Facultative fixation requires different selling rates for the dominant and recessive type. Protection of the polymorphism requires resource allocation for male and female function. In this connection the problem of purely genetically caused population extinction is discussed.
For general frequency dependence and regular segregation, the chances for establishment of a completely recessive gene are compared to those of a completely dominant gene. It is proven that the process of establishment of the recessive gene, despite a fitness advantage, may be considerably endangered by drift effects if random mating prevails. The recessive gene may reach the same effectivity in establishment as a dominant gene, only if the recessive homozygote mates exclusively with its own type during the period of establishment.     

Composition and diversity of bird communities in Swedish farmland–forest mosaic landscapes

CapsuleThe amount of forest (at local and landscape scales) and occurrence of residual habitats at the local scale are shown to be the major factors influencing bird community composition in farmland–forest landscapes in central Sweden.

Aims To investigate the importance of local habitat and landscape structure for breeding birds in farmland–forest landscapes in central Sweden.

Methods Breeding birds were censused at 292 points. A detailed habitat mapping was made within 300 m of the points. Within a 300–600 m radius only two major habitats (forests and arable fields) were identified.

Results Cluster analyses of bird communities identified three site types that also differed in habitat composition: (i) partially forested sites in forested landscapes; (ii) heterogeneous sites with residual habitats in mosaic landscapes; and (iii) field-dominated farmland sites in open landscapes. A total of 19 of 25 farmland bird species (restricted to farmland or using both farmland and forest) had the highest abundance in farmland sites with mosaics of forest and farmland, while only six farmland species had the highest abundance in field-dominated sites. The bird community changed from being dominated by farmland species to being dominated by forest species (common in forest landscapes without farmland) at small proportions (10–20%) of forest at the local scale. A major difference in habitat composition between heterogeneous and field-dominated sites was the occurrence of different residual habitats (e.g. shrubby areas and seminatural grasslands). These habitats seemed to influence bird community composition more than land-use, despite covering <10% of the area. Seminatural grasslands were important for bird community composition and species-richness, but grazing seemed to be less important. Among different land-use types, cereal crops were the least preferred fields. Set-asides with tall vegetation and short rotation coppices were positively associated with species-richness of farmland birds.

Conclusion In general, the composition of the landscape was important for bird community composition, although amount and distribution of forests, occurrence of residual habitats and land-use of fields at the local scale had the strongest influence on bird community composition. The possible implications of these patterns for managing farmland–forest landscapes are discussed.     

Chemical constituents from the fruits of Rhus typhina L. and their chemotaxonomic significance

This work describes the isolation and characterization of twenty-nine compounds from the fruits of Rhus typhina L., including eleven flavonoids (1–11), eleven phenols (12–22), two pentacyclic triterpenes (23–24), two organic acids (25–26), one lumichrome (27), one courmarin (28) and one pyrimidine (29) on the basis of their spectroscopic data. Compounds apigenin (1), daidzein (4), orobol (5), 3′, 5, 5′, 7-tetrahydroxyflavanone (6), naringenin (7), butein (8), (-)-catechin (9), quercetin-3-O-α-L-(3″-O-galloyl)-rhamnoside (11), 2-hydroxybenzoic acid (13), 4-hydroxybenzaldehyde (14), vanillin (15), methyl 3,4-dihydroxybenzoate (16), 3,5-dihydroxybenzamide (18), tyrosol (19), caffeic acid (20), 3-(2,4,6-trihydroxyphenyl)-1-(4-hydroxyphenyl)-propan-1-one (21), phlorizin (22), friedelin (23), oleanolic acid (24), 4,4-dimethyl-heptanedioic acid (25), anthranilic acid (26), lumichrome (27), scoparone (28) and uracil (29) have not been recorded before in this plant. This is the first report on the occurrence of compounds 4–7, 9, 11, 13–14, 16, 18–21, 25–29 from the genus Rhus. Moreover, the chemotaxonomic significance of these isolated compounds was also summarized.