我国草兔的聚类研究

本文用新的聚类方法, 对中国草兔进行系统聚类。     

双绕蛋白质的分类与识别

蛋白质折叠识别是蛋白质结构研究的重要内容。双绕是α/β蛋白质中结构典型的常见折叠类型。选取22个家族中序列一致性小于25%的79个典型双绕蛋白质作为训练集,以RMSD为指标进行系统聚类,并对各类建立基于结构比对的概形隐马尔科夫模型(profile-HMM)。将Astral1.65中序列一致性小于95%的9 505个样本作为检验集,整体识别敏感性为93.9%,特异性为82.1%,MCC值为0.876。结果表明:对于成员较多,无法建立统一模型的折叠类型,分类建模可以实现较高准确率的识别。     

维氏气单胞菌MreB蛋白的结构分析及其系统发育学意义

【目的】认识维氏气单胞菌Mre B蛋白的各级结构,研究Mre B蛋白的保守性与作为分子标记工具的可靠性。【方法】应用Prot Param、Predict Protein和SWISS-MODEL等在线软件分别分析蛋白的一级结构及理化性质,预测蛋白二级、三级结构;利用Clustal X 2.0、ESpript 3.0和MEGA 6等软件对几类细菌中的Mre B蛋白进行氨基酸序列比对分析和系统发育学研究。【结果】维氏气单胞菌Mre B蛋白是由346个氨基酸组成的酸性蛋白,主要定位于细胞膜上;蛋白二级结构主要由α-螺旋、扩展长链和无规则卷曲结构构成,其中无规则卷曲所占比例最高;同源建模的结果显示蛋白的三级结构中含有12个α-螺旋结构、5个β-折叠结构、8个β-发夹结构、22个β-转角和4个γ-转角。【结论】获得了维氏气单胞菌Mre B蛋白详细的理化信息,同源建模构建的模型具有合理的空间结构,PROCHECK评分较高,为实验研究提供了一定的结构基础;Mre B蛋白具有保守位点与结构保守性,属高保守蛋白,且变异度适宜,可作为分子标记工具应用于细菌的分类鉴定。     

蛋白质序列的聚类结构分析

基于模糊邻近关系的粒度空间,对蛋白质序列进行聚类结构分析。利用MEGA软件计算选取的木聚糖酶序列间的比对距离,引入内积将其转化为模糊邻近关系(或矩阵),再应用算法求解其粒度空间,进行序列的聚类结构分析和最佳聚类确定研究。这些研究为蛋白质序列提供了定量分析的工具。     

构建基于折叠核心的全α类蛋白取代矩阵

氨基酸残基取代矩阵是影响多序列比对效果的重要因素,现有的取代矩阵对低相似序列的比对性能较低.在已有的 BLOSUM 取代矩阵算法基础上,定义了基于蛋白质折叠核心结构的序列 结构数据块;提出一种新的基于全α类蛋白质折叠核心结构的氨基酸残基取代矩阵——TOPSSUM25,用于提高低相似度序列的比对效果.将矩阵TOPSSUM25导入多序列比对程序,对相似性小于25%的一组四螺旋束序列 结构数据块的测试结果表明,基于 TOPSSUM25的多序列比对效果明显优于BLOSUM30矩阵;基于一个BAliBASE子集的比对检验也进一步表明, TOPSSUM25在全α类蛋白质的两两序列比对上优于BLOSUM30矩阵.研究结果可为进一步的阐明低同源蛋白质序列 结构 功能关系提供帮助.     

奶杏品种类群的模糊聚类划分

对４２个银杏核用品种的１３个性状特征进行系统聚类分析和主要成份分析,根据系统聚类分析树状图和主成份坐标点图,将银杏品种划分为５个主要类群,并对其进行了简要分析。     

福建省啮齿动物分布的聚类与关联分析

福建省啮齿动物分布的聚类与关联分析王寿昆（福建农业大学动物科学系福州３５０００２）ＣｌｕｓｔｅｒａｎｄＡｓｓｏｃｉａｔｉｏｎＡｎａｌｙｓｅｓｏｎＤｉｓｔｒｉｈｕｔｉｏｎｏｆＲｏｄｅｎｔｓｉｎＦｕｊｉａｎＰｒｏｖｉｎｃｅ．￥ＷａｎｇＳｈｏｕｋｕｎ（Ｄｅ...     

银杏品种类群的模糊聚类划分

对４２个银杏核用品种的１３个性状特征进行系统聚类分析和主成份分析．根据系统聚类分析树状图和主成份坐标点图,将银杏品种划分为５个主要类群,并对其进行了简要分析。     

基于关联规则与熵聚类的安神类中成药组方规律研究

目的：分析常用安神类中成药的处方用药规律。方法：收集《新编国家中成药》中的安神类药品处方,基于中医传承辅助系统建立处方数据库,采用关联规则apriori算法、复杂系统熵聚类等方法开展研究,确定处方中各种药物的使用频次及药物之间的关联规则等。结果：高频次药物包括茯苓、甘草、当归、麦冬、朱砂等;高频次药物组合包括“当归、茯苓”“茯苓、炒酸枣仁”“甘草、茯苓”等;置信度较高的关联规则包括“牛黄、朱砂”“酸枣仁、茯苓”等,新处方包括“茯苓、炒酸枣仁、熟地黄、五味子、丹参、麦冬、生地黄”等。结论：安神类中成药处方药物多具有养血定志,补气滋阴和重镇安神之功效。     

中国葡萄属植物形态学聚类分组研究

对《中国葡萄志》描述的38个中国葡萄属野生种和1个栽培种,按照《葡萄种质资源描述规范和数据标准》的要求,对18个描述符用代码数量化并进行聚类分析,根据形态特征的相似程度,将我国葡萄属野生种和欧亚种划分为8个组和5个亚组。第1组包含毛葡萄、腺枝葡萄、龙泉葡萄、美丽葡萄和庐山葡萄,第2组包含麦黄葡萄和小叶葡萄,第3组包含5个亚组21个种类,其中亚组1包含山葡萄、陕西葡萄、浙江蘡薁、蘡薁和湖北葡萄,亚组2包含绵毛葡萄和勐海葡萄,亚组3包含小果葡萄、云南葡萄和葛藟葡萄,亚组4包含毛脉葡萄、华东葡萄、武汉葡萄和井冈葡萄,亚组5包含刺葡萄、秋葡萄、桦叶葡萄、网脉葡萄、蒙自葡萄、凤庆葡萄和河口葡萄,第4组仅包含欧洲葡萄,第5组包含温州葡萄、红叶葡萄、复叶葡萄、乳源葡萄和狭叶葡萄,第6组包含东南葡萄、罗城葡萄和闽赣葡萄,第7组仅包含菱叶葡萄,第8组仅包含鸡足葡萄一个种。     

Flexible programs for the prediction of average amphipathicity of multiply aligned homologous proteins: application to integral membrane transport proteins

Simple flexible programs (TREEMOMENT and PILEUPMOMENT) are described for depicting the average amphipathicity (hydrophobic moment) along multiply aligned sequences of a family of evolutionarily related proteins. The programs are applicable to any number of aligned sequences and can be set for any desired angle corresponding to a residue repeat unit in a protein secondary structural element such as 100 per residue for an alpha- helix or 180 per residue for a beta-strand. These programs can be used to identify amphipathic regions common to the members of a protein family. The use of these programs is exemplified by showing that some families of integral membrane transport proteins (i.e. permeases of the bacterial phosphotransferase system (PTS) and the anion exchangers of animals) exhibit strikingly amphipathic alpha-helical structures immediately preceding the first hydrophobic transmembrane segment of their membrane-embedded domain(s). Other families, such as the major facilitator superfamily of uniporters, symporters and antiporters, do not exhibit this structural feature. The amphipathic structures in PTS permeases have been implicated in membrane insertion during biogenesis.     

滇西4市县居民区小哺乳动物的群落结构

1983～1996 年对云南瑞丽、陇川、盈江和保山4 市县居民区小哺乳动物的长期调查,经聚类分析,该地区的小哺乳动物可划分为3 种群落: (1) 以黄胸鼠+ 大臭鼠句为主的瑞丽、陇川室内外小哺乳动物群落; (2) 以黄胸鼠+ 大臭鼠句+ 小家鼠为主的盈江、保山室内和盈江室外小哺乳动物群落; (3) 以黄胸鼠+ 大臭鼠句+ 灰麝鼠句为主的保山室外小哺乳动物群落。其群落多样性指数以群落(3) 为最高(1.5897) ,群落(1) 、(2) 较低,分别为1.099 0 ,1.042 5。4 市县在同一坝区小哺乳动物室内、外唯一不能聚为同一群落的保山室外黄胸鼠数量骤减是第3 群落多样性增加的主要原因,亦是鼠疫在该坝区不能长期保存的原因。因此小哺乳动物群落结构与鼠疫的保存和传播机制之间的关系非常密切。     

莫索湾垦区啮齿动物群落结构与物种多样性分析

2004年6～8月对莫索湾垦区啮齿动物调查,按不同生境共抽取18个样地,采用铗日法进行鼠类密度调查,共置10400个铗日,捕获啮齿动物446只,分属3科9属11种。经聚类分析,该垦区鼠类群落可划分为6种群落类型：（1）以大沙鼠（Rhombomys opimus）＋子午沙鼠（Meriones meridianus）为主的荒漠型;（2）以红尾沙鼠（Meriones erythrourus）＋小五趾跳鼠（Allactaga elater）为主的半荒漠灌丛型;（3）以柽柳沙鼠（Meriones tamariscinus）＋小林姬鼠（Apodemus sylvaticus）为主的林地型;（4）以小家鼠（Mus musculus）＋小林姬鼠为主的农田型;（5）以灰仓鼠（Cricetulus migratorius）＋子午沙鼠为主的弃耕地型;（6）以褐家鼠（Rattus norvegicus）为主的城镇型。从原始荒漠到城镇居民区的环境梯度变化中,鼠类群落多样性指数呈上升趋势（1．1053～1．2744）,到农田达到最大,农田到居民区则略有下降;均匀性随各群落生境类型不同,变化无规律性（0．6423≤J≤0．9207）;优势度则呈下降趋势（0．4176～0．3368）。生境差异、植被盖度和人为干扰强度对鼠类群落多样性均有一定影响。     

Omp85 from the Thermophilic Cyanobacterium Thermosynechococcus elongatus Differs from Proteobacterial Omp85 in Structure and Domain Composition

Omp85 proteins are essential proteins located in the bacterial outer membrane. They are involved in outer membrane biogenesis and assist outer membrane protein insertion and folding by an unknown mechanism. Homologous proteins exist in eukaryotes, where they mediate outer membrane assembly in organelles of endosymbiotic origin, the mitochondria and chloroplasts. We set out to explore the homologous relationship between cyanobacteria and chloroplasts, studying the Omp85 protein from the thermophilic cyanobacterium Thermosynechococcus elongatus. Using state-of-the art sequence analysis and clustering methods, we show how this protein is more closely related to its chloroplast homologue Toc75 than to proteobacterial Omp85, a finding supported by single channel conductance measurements. We have solved the structure of the periplasmic part of the protein to 1.97 Å resolution, and we demonstrate that in contrast to Omp85 from Escherichia coli the protein has only three, not five, polypeptide transport-associated (POTRA) domains, which recognize substrates and generally interact with other proteins in bigger complexes. We model how these POTRA domains are attached to the outer membrane, based on the relationship of Omp85 to two-partner secretion system proteins, which we show and analyze. Finally, we discuss how Omp85 proteins with different numbers of POTRA domains evolved, and evolve to this day, to accomplish an increasing number of interactions with substrates and helper proteins.     

On certain homologies between proteins

Summary Using, in part, comparisons between reconstructed ancestral sequences, homologies are suggested between certain proteins. Genetically related groups seem to be: 1. pancreatic and bacterial nucleases, 2. lysozymes and subtilisins, 3. c type cytochromes, ferredoxins and rubredoxins, 4. b type cytochromes, myoglobins and hemoglobins, catalase, and glutamic dehydrogenase. These homologies suggest that a given ancestral sequence can evolve into quite different tertiary structures.     

Phylogenetic Analysis: How Old are the Parts of Your Body?

According to the National Academy of Sciences, biology students in the USA are not being adequately prepared for successful futures. Of paramount concern is a lack of sufficient training in quantitative and computational skills, which are needed to compete effectively for an array of educational and occupational opportunities. In this paper, we introduce a classroom exercise that invites students to solve a simple biological problem and illustrates the need for a computer-assisted strategy to arrive at a solution. The exercise invites students to consider the question “How old are the parts of your body?” Some features of the human body are more ancient than others. For example, our bodies have both hair and backbones, but backbones arose much earlier in evolutionary history. Our exercise relies upon MEGA 4.0, a free, visually appealing, and intuitive computer program that allows students to gather DNA or protein sequences from electronic databases, then use them to infer phylogenetic trees. Student-inferred phylogenies are used to explore the relative order in which diverse aspects of the human form evolved. In the process, students are trained to use powerful features of MEGA and encouraged through group discussion to consider additional applications of the technology they have learned. Our lesson plan includes a brief video, a web site with essential terminology and links for further exploration, a hands-on experience using MEGA, and a follow-up discussion.     

Conserved Properties of Polypeptide Transport-associated (POTRA) Domains Derived from Cyanobacterial Omp85

Proteins of the Omp85 family are conserved in all kingdoms of life. They mediate protein transport across or protein insertion into membranes and reside in the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. Omp85 proteins contain a C-terminal transmembrane β-barrel and a soluble N terminus with a varying number of polypeptide-transport-associated or POTRA domains. Here we investigate Omp85 from the cyanobacterium Anabaena sp. PCC 7120. The crystallographic three-dimensional structure of the N-terminal region shows three POTRA domains, here named P1 to P3 from the N terminus. Molecular dynamics simulations revealed a hinge between P1 and P2 but in contrast show that P2 and P3 are fixed in orientation. The P2-P3 arrangement is identical as seen for the POTRA domains from proteobacterial FhaC, suggesting this orientation is a conserved feature. Furthermore, we define interfaces for protein-protein interaction in P1 and P2. P3 possesses an extended loop unique to cyanobacteria and plantae, which influences pore properties as shown by deletion. It now becomes clear how variations in structure of individual POTRA domains, as well as the different number of POTRA domains with both rigid and flexible connections make the N termini of Omp85 proteins versatile adaptors for a plentitude of functions.     

Insights into the history of the legume‐betaproteobacterial symbiosis

The interaction between legumes and rhizobia has been well studied in the context of a mutualistic, nitrogen‐fixing symbiosis. The fitness of legumes, including important agricultural crops, is enhanced by the plants’ ability to develop symbiotic associations with certain soil bacteria that fix atmospheric nitrogen into a utilizable form, namely, ammonia, via a chemical reaction that only bacteria and archaea can perform. Of the bacteria, members of the alpha subclass of the protebacteria are the best‐known nitrogen‐fixing symbionts of legumes. Recently, members of the beta subclass of the proteobacteria that induce nitrogen‐fixing nodules on legume roots in a species‐specific manner have been identified. In this issue, Bontemps et al. reveal that not only are these newly identified rhizobia novel in shifting the paradigm of our understanding of legume symbiosis, but also, based on symbiotic gene phylogenies, have a history that is both ancient and stable. Expanding our understanding of novel plant growth promoting rhizobia will be a valuable resource for incorporating alternative strategies of nitrogen fixation for enhancing plant growth.