蛋白质序列复杂性简化与非比对序列分析

非比对序列分析是最新发展的一种序列分析方法,具有计算效率高并适用于分析低相似性的序列,已成功用于DNA的序列分析中.但是由于蛋白质序列的复杂性,非比对序列分析对于蛋白质序列分析的准确度却不高.用将20种天然氨基酸残基归类的方法,简化了蛋白质序列的复杂性,并运用到对蛋白质的非比对序列分析中,有效地提高了序列分析的准确性.     

用序列周期性指数寻找Alu序列编码方式

将７２０条Ａｌｕ序列组成的序列库分成左臂、右臂和中间序列三个子库。应用Ｚ值算法对三个子库作周期性分析,并与外显子、内含子和随机序列作比较。结果表明,Ａｌｕ序列作为一种潜在的调控资源,可能具有八联体编码。利用本算法作核酸序列周期性分析并研究序列编码方式,有较好的准确性,并且简便易行     

序列的证据

线蕨属Colysis植物主要分布于亚洲热带和亚热带地区, 少数种类分布至非洲、澳大利亚(昆士兰)及新几内亚地区。自1849年成立以来, 线蕨属的分类范畴和系统位置一直有待确定。本文利用叶绿体基因组的rbcL、rps4基因和rps4-trnS基因间隔区序列, 运用最大简约法和贝叶斯方法分析了线蕨属及其近缘类群的系统演化关系。研究结果显示: (1)线蕨属和薄唇蕨属Leptochilus (含似薄唇蕨属Paraleptochilus)组成一个支持率很高的单系分支(C-L Clade), 但是薄唇蕨属的成员位于线蕨属的不同支系内, 支持线蕨属和薄唇蕨属合并为一个属; (2)瘤蕨属Phymatosorus单独形成一个单系分支; (3)星蕨属Microsorum是一个多系类群, 除Microsorium linguiforme、M. varians和M. pustulatum与马来群岛的Lecanopteris聚在一起外, 其他的星蕨属成员均位于不同的支系上。本文的系统发育分析结果为线蕨属和薄唇蕨属的分类处理提供了分子系统学的证据。     

甜瓜抗枯萎病基因同源序列克隆与序列分析

目的:克隆甜瓜抗枯萎病基因同源序列并对其序列分析。方法:根据已发表的甜瓜抗枯萎病基因Fom-2设计引物,从高抗枯萎病甜瓜品种‘日本安农二号’基因组中扩增Fom-2同源序列R-Fom-2。结果:该基因长3307bp,包含一个完整的开放阅读框,编码1073个氨基酸,推测蛋白质分子量123.57kDa,等电点7.06。属于nonTIR-NBS-LRR类抗病基因,在LRR区存在一个可能的CC结构域。但在nonTIR类抗病蛋白中,CC结构域一般位于kin-1a前。氨基酸同源性分析显示,R-Fom-2同Fom-2全长序列具有96%的同源性,对不同甜瓜品种Fom-2的LRR区分析比较,同源性在91%以上。且LRR区的差异主要集中在β-strand/β-turn区域。结论:序列分析揭示Fom-2家族是一个活跃的基因,LRR区可能对Fom-2家族的功能起着重要作用,为进一步研究R-Fom-2基因的结构与生物学功能奠定了基础。     

基因外显子连接序列与相应内含子序列的相互作用

剪接后的内含子与相应mRNA序列的相互作用在基因表达调控过程中起着非常重要的作用。基于27个物种的核糖核蛋白基因序列,采用Smith—Waterman局域比对方法得到外显子连接序列与相应内含子序列的最佳匹配片段,分析了外显子连接序列上的匹配频率分布和匹配片段的序列特征。发现一些低等真核生物EJC结合区域的匹配频率明显低于其它区域,所有物种EJC结合区域的序列构成呈现出相对低的结构序。最佳匹配片段的平均长度和配对率分布与siRNA和miRNA的结合特征相同。推测EJC和内含子在与外显子序列结合的过程中存在相互竞争和相互协作的关系,内含子中部序列在基因表达调控过程中起着重要的作用。     

mRNA序列与相应内含子序列匹配的普适性分析

剪切后的内含子在基因表达和调控过程中发挥重要作用,由此在成熟mRNA与相应的内含子之间也存在相互作用,并且二者协同进化。为了验证这一理论,以13个物种的基因组作为研究样本,凭借Smith-Waterman的局域比对方法,最终得到在成熟mRNA与其内含子序列之间的最佳匹配片段,同时在mRNA序列上显示出最佳匹配强度的分布区。然后对最佳匹配片段的长度、配对率的分布这两项参数进行分析之后,发现最佳匹配片段的这两个参数的特征,与siRNA和miRNA的结合特征是相近的;在mRNA序列上,得出UTR区与内含子相互作用强,GC含量低的片段偏好结合到3’UTR区,相反GC含量高的片段更倾向与5’UTR区发生相互作用。因此,最佳匹配片段的序列特征符合RNA-RNA相互作用规律,可以把内含子看成是一种具有基因表达调控功能的序列。以上研究对于进一步探讨内含子的功能和进化具有重大意义。     

枯草杆菌启动子－信号肽序列的克隆及序列分析

利用含红霉素抗性基因和缺启动子－信号肽序列的氨苄青霉素抗性基因的双功能质粒ｐＧＰＢ１４为探针载体,克隆了枯草杆菌的启动子－信号肽序列并对克隆的片段进行序列分析。枯草杆菌染色体ＤＮＡ经Ｓａｕ３Ａ酶解后与ＢｏｍＨＩ酶切的质粒ｐＧＰＢ１４连接,转化大肠杆菌Ｃ６００,筛选抗氨苄青霉素及抗红霉素的转化子,从双抗性转化子中提取重组质粒并经酶切分析,显示克隆的ＤＮＡ片段在０．２７－１．５ｋｂ之间。用Ｓａｎｇｅｒ的双脱氧链终止法测定了１０个克隆片段的ＤＮＡ顺序,结果表明,克隆的片段都含有启动子、核糖体结合优点及信号肽序列。克隆片段可以在大肠杆菌和枯草杆菌中恢复氨苄青霉素抗性的表型。β－内酰胺酶活力测定结果证明：大肠杆菌的酶活力主要积累在周质空间内而枯草杆菌的酶活力主要分泌到胞外。     

核苷酸序列库

最近,在美国华盛顿建立了核苷酸序列计算机库。这是一种为科研服务的新情报组织,现已有200,000以上核苷酸残基、200以上片段存入库中。九月十五日开始提供信息。目     

基于移动序列模式分析人基因组调控短序列

基因表达过程主要包括转录、剪接和翻译,多种调控元件参与其中,是个高度调控的过程。建模识别分析这些调控元件,对理解基因表达具有重要意义。本研究提出了一个基于移动序列模式的短序列建模模型,并对转录启动子和剪接调控元件进行了建模分析。启动子是基因转录的核心调控元件,剪接调控元件参与调控剪接位点的识别。分类实验结果表明,该模型可有效识别转录启动子序列和剪接调控元件序列。并进一步利用该模型,建模分析已为生物实验验证的、会导致剪接影响的基因组变异,实验结果表明,该模型可有效预测基因组变异的剪接影响,进一步验证了该模型的有效性。     

微卫星序列及其应用

微卫星序列广泛存在于各类真核生物基因组中,一般为散在分布的中等程度重复序列。不同物种中,微卫星序列的含量以及占优势的微卫星序列类型各不相同。复制时,微卫星序列易于发生长度突变,这种突变与微卫星序列的复制滑移有关,同时也受多种因素的影响。微卫星序列可能是原微卫星序列通过复制滑移使序列长度扩增形成的。进化过程中,微卫星序列的长度变化维持在一定的范围内。由于微卫星标记多态性高、重复性好,并且操作简单,因此在基因的定位、人类疾病诊断及预测、亲权分析、品种鉴定、进化研究,以及动植物分子标记辅助选择育种研究等领域中都有着重要的应用价值。 Abstract:Microsatellites,simple sequence repeats (SSR),are abundant and distributed throughout the eukaryote genome.The contents of microsatellites are variant in different creatures.There are also different types of microsatellites,which are dominant in different creatures.One of the most noticeable characters of microsatellites is that they are easy to expand during DNA replication.It is thought to attribute to DNA slippage.This kind of mutation is affected by many factors.It is guessed that microsatellites come from pro-microsatellites,while the pro-microsatellites origin from random point mutations.The length of microsatellites can be maintained under relative conservative ranges during species evolution.As they are abundant,codominatnt,distributed over the euchromatic part of the genome,and have the character of highly polimorphic,microsatellites are useful tools for gene mapping,clinical diagnosis and predicting,paternity or pedigree analysis,evolution study,and marker-assisted breeding.     

编码区和非编码区SSR标记对水稻类群的比较研究

设计14对水稻编码区SSR引物和选取已公布的非编码区SSR引物12对、编码区SSR引物3对,采用SSR技术,对29个标记在60个水稻材料中的多态性进行分析。结果表明,编码区SSR标记平均检测到3.59个多态性位点,多态信息量PIC(polymorphism information conten)在0.032～P0.853之间,平均值为0.447;非编码区SSR标记平均检测到3.92个多态性位点,PIC在0.063～P0.795之间,平均值为0.521。聚类分析显示,非编码区SSR标记能更加精确地区分来自不同地区的水稻类群,编码区SSR标记也具有良好的多态性,同样可以用于分析水稻的亲缘关系。     

The Greater Cape Floristic Region

Aim The Cape Floristic Region (CFR) (Cape Floristic Kingdom) is currently narrowly delimited to include only the relatively mesic Cape fold mountains and adjacent intermontane valleys and coastal plains. We evaluate the floristic support for expanding the delimitation to include the whole winter‐rainfall area (arid and mesic climates) into a Greater CFR. Location Southern Africa, particularly the south‐western tip. Methods The initial divisive hierarchical classification analysis twinspan used the presence/absence of vascular plant genera to obtain major floristic groupings in southern Africa. For the more detailed analyses, we scored the flora as present/absent within a set of centres, among which the floristic relationships were investigated (agglomerative methods, upgma and minimum spanning trees). These analyses were conducted with species, genera and families separately. The centres were grouped into five regions. The species richness and endemism was calculated for the centres, regions and combination of regions. The dominant floristic components of each region were sought by calculating the percentage contribution of each family to the flora. Results The divisive method showed that the winter‐rainfall areas are floristically distinct from the rest of southern Africa. The species‐ and generic‐level analyses revealed five regions: CFR, Karoo Region, Hantam‐Tanqua‐Roggeveld Region, Namaqualand Region and Namib‐Desert Region. The CFR has the highest endemism and richness. However, the combination of the CFR, the Hantam‐Tanqua‐Roggeveld Region and the Namaqualand Region results in a higher total endemism. Combined, these three regions almost match the region delimited by the twinspan analysis, and together constitute the Greater CFR. Main conclusions The CFR constitutes a valid floristic region. This is evident from the endemism and the distinctive composition of the flora. However, the total endemism is higher for the whole winter‐rainfall area, and this supports the recognition of the larger unit. If floristic regions are to be delimited only on endemism, then the Greater CFR is to be preferred. If floristic regions are delimited on the composition of their floras at family level, then the support for such a grouping is weaker.     

Mayr on the Polynesian Region

[Borders and Subdivisions of the Polynesian Region, as based on our Knowledge of the Distribution of Birds, pp. 191–195. The Origin and History of the Bird fauna of Polynesia, pp. 197–216. By Ernst Mayr. Proc. Sixth Pacific Science Congress, held at Berkeley, Wis., in July and August 1939, vol. iv.]     

丙型肝炎病毒Core与NS3基因的不同融合方式及其表达

丙型肝炎病毒(简称ＨＣＶ)是危害人类健康的传染性疾病,预防该病的传播主要借助于ＨＣＶ血清学诊断来筛选献血员和检测临床标本。从国内外已分离到的ＨＣＶ株得知,ＨＣＶ核心蛋白(Ｃｏｒｅ)和非结构蛋白ＮＳ3含有较强的优势抗原表位,其相应的抗体出现早,阳性率高,已成为目前第二、第三代ＨＣＶ免疫诊断试剂的重要成份[1,2]。通常Ｃｏｒｅ蛋白和ＮＳ3蛋白分别用基因工程方法表达,然后作为固定化抗原,检测人体内ＨＣＶ的抗体。我们对Ｃｏｒｅ和ＮＳ3的两种不同组合方式及其表达的研究,对于发展新的ＨＣＶ诊断试剂很有帮助,现将结果报道如下。1…     

River-reef connectivity in the Meso-American Region

The accumulation and seasonal impact of riverine discharge on coral reefs of the Meso-American Region (MAR) were estimated using a numerical simulation of river runoff dispersion. River-reef connectivity, or source-sink dynamics of terrestrial runoff was further assessed from more than 400 watersheds of the region onto discrete coral reef areas. Using land use for 2003 and 2004 in the MAR, this work builds upon a Regional Ocean Modeling System simulation of the MAR validated by ocean color satellite data, and on the monthly river nutrient and sediment load and discharge provided by the World Resources Institute using the N-SPECT model. Analysis of the variability of simulated runoff transport to the reefs showed that reefs of the Mesoamerican Barrier Reef System (MBRS) were mostly impacted from June to September, following the peak time of river discharge. At that time, the coastal and oceanic circulations contribute quickly to expel the runoff from the MBRS. High runoff concentration waters leaving the eastern coast of Honduras during the months of October to December return to the southwestern MAR in March as they are entrained in a cyclonic gyre. Coral reefs of the MAR are thus impacted twice, first from the coastal side with runoff of local origin and later from the oceanic side with runoff from mixed origin. High probability of connectivity between rivers and remote reefs is established as this study revealed that river runoff from the north shore of Honduras has a wide-spread impact on most of the coral reefs of southern Belize, while watersheds on the Gulf of Honduras are mostly connected to coral reefs in the northern shore of Honduras. Although the level of remote influence (or runoff concentration reaching the reef) is lower than the local, the cumulative effect of numerous remote river-reef connections remains significant. Communicated by Biology Editor Michael Lesser     

A Nucleotide State-sensing Region on Actin

The nucleotide state of actin (ATP, ADP-P_i, or ADP) is known to impact its interactions with other actin molecules upon polymerization as well as with multiple actin binding proteins both in the monomeric and filamentous states of actin. Recently, molecular dynamics simulations predicted that a sequence located at the interface of subdomains 1 and 3 (W-loop; residues 165–172) changes from an unstructured loop to a β-turn conformation upon ATP hydrolysis (Zheng, X., Diraviyam, K., and Sept, D. (2007) Biophys. J. 93, 1277–1283). This region participates directly in the binding to other subunits in F-actin as well as to cofilin, profilin, and WH2 domain proteins and, therefore, could contribute to the nucleotide sensitivity of these interactions. The present study demonstrates a reciprocal communication between the W-loop region and the nucleotide binding cleft on actin. Point mutagenesis of residues 167, 169, and 170 and their site-specific labeling significantly affect the nucleotide release from the cleft region, whereas the ATP/ADP switch alters the fluorescence of probes located in the W-loop. In the ADP-P_i state, the W-loop adopts a conformation similar to that in the ATP state but different from the ADP state. Binding of latrunculin A to the nucleotide cleft favors the ATP-like conformation of the W-loop, whereas ADP-ribosylation of Arg-177 forces the W-loop into a conformation distinct from those in the ADP and ATP-states. Overall, our experimental data suggest that the W-loop of actin is a nucleotide sensor, which may contribute to the nucleotide state-dependent changes in F-actin and nucleotide state-modulated interactions of both G- and F-actin with actin-binding proteins.     

丙型肝炎病毒Core与NS3基因的不同融合方式及其表达

丙型肝炎病毒(简称HCV)是危害人类健康的传染性疾病,预防该病的传播主要借助于HCV血清学诊断来筛选献血员和检测临床标本.从国内外已分离到的HCV株得知,HCV核心蛋白(Core)和非结构蛋白NS3含有较强的优势抗原表位,其相应的抗体出现早,阳性率高,已成为目前第二、第三代HCV免疫诊断试剂的重要成份[1,2].通常Core蛋白和NS3蛋白分别用基因工程方法表达,然后作为固定化抗原,检测人体内HCV的抗体.我们对Core和NS3的两种不同组合方式及其表达的研究,对于发展新的HCV诊断试剂很有帮助,现将结果报道如下.