家蚕细胞色素P450基因Bmcyp6u1的克隆、序列分析与表达谱

细胞色素P450第6亚家族基因为昆虫所特有,与抗性相关。为了检测家蚕Bombyx mori cyp6u1基因是否与耐氟性相关,首先克隆了cyp6u1基因。采用生物信息学方法获得与黑腹果蝇Drosophila melanogaster cyp6u1基因同源的家蚕B. mori cyp6u1基因序列, 预测该序列的开放阅读框（ORF）为1 476 bp, 编码491个氨基酸, 推定的蛋白质分子质量为56.15 kD, 等电点为9.23。以家蚕5龄第3天幼虫精巢cDNA为模板, 设计特异引物PCR扩增出一条约1 500 bp的条带, 大小与家蚕cyp6u1序列的ORF预测值接近, 命名为Bmcyp6u1基因（GenBank登录号：HM130560）。同源性分析表明, Bmcyp6u1基因与蜜蜂Apis mellifera的同源基因cyp6AS13的相似性为56%, 与拟南芥Arabidopsis thaliana的cyp72A82的相似性为48%, 与人Homo sapiens的cyp3A7基因的相似性为50%。芯片数据分析表明, Bmcyp6u1基因在家蚕5龄第3天幼虫各组织表达量很低, 只在精巢组织(5龄第3天)稍有表达, 推测该基因具有组织特异性。     

豌豆蚜基因组P450基因家族的分析

细胞色素P450在各种内源和外源物质代谢中起着非常重要的作用。利用豌豆蚜Acyrthosiphon pisum基因组mRNA和氨基酸数据库研究P450基因功能的进化规律。通过生物信息学方法对豌豆蚜全基因组P450进行分析, 结果显示: 在豌豆蚜基因组中发现69个P450基因, 它们分别属于13个P450家族和18个亚家族, 是一个典型的多基因家族。进一步将这些基因与豌豆蚜ESTs数据库进行了比对分析, 其中39个候选基因有EST证据, 证明了这些P450基因在转录水平的真实性。以氨基酸相似度大于60%为标准对豌豆蚜基因组中P450基因进行分组, 69个P450基因中, 除18个基因序列因差异太大, 不能被归入任何一组, 其余51个可归入10个组, 其中8个组(包含47条序列)适合于正选择和基因转换分析。正选择和基因转换分析结果表明: 仅有1个组(含9个基因)显著受到正选择压力作用, 正选择概率大于95%的氨基酸位点分别是20T和27N, 20T位于底物识别位点SRS1, 27N位于D. helix; 有3个组(包含8个基因）显示显著的基因转换事件。 参与基因转换的基因均为CYP4家族成员, 分别是CYP4C, CYP4G和CYP4V亚家族。 参与基因转换的成员之间的蛋白相似度较高（70％~95％）, 且XM_001944991与XM_001951794同存在于SCAFFOLD12542上, XM_001945510与XM_001944057同存在于SCAFFOLD7010上。这可能暗示豌豆蚜P450基因通过基因复制, 然后通过基因转换使P450获得新的功能, 以适应多变的生存环境。此外, 鉴定出20个不同的基序, 其中有5条基序在90％以上的基因中出现。      

中华蜜蜂化学感受蛋白基因Acer-CSP1克隆与表达特征分析

化学感受蛋白(chemosensory proteins, CSPs)是昆虫化学感受系统中重要的组成部分之一。本研究克隆了中华蜜蜂Apis cerana cerana化学感受蛋白基因Acer-CSP1, 其核苷酸全长351 bp （GenBank登录号为FJ157352）, 编码116个氨基酸残基, 预测蛋白分子量为13.85 kD, 等电点为4.89, 且含有4个保守的半胱氨酸残基, 均符合昆虫CSPs的一般特征, 且与意蜂CSP1基因具有99.1%的相似性, 与其他昆虫也有45.3%~68.0%的相似性。利用2^-ΔΔCt法及绝对定量法的real-time PCR技术对Acer-CSP1在中蜂不同器官表达特征进行了研究, 得出的一致结论为Acer-CSP1显著水平地高丰度表达于中华蜜蜂触角, 其次大量表达于头部。由于触角为中华蜜蜂最主要的嗅觉器官, 而头部则具有发达的感觉神经系统和味觉系统, 这也提示Acer-CSP1极有可能参与中华蜜蜂的嗅觉以及其他化学感受功能。     

FAIR: A server for internal sequence repeats

An Internet computing server has been developed to identify all the occurrences of the internal sequence repeats in a protein and DNA sequences. Further, an option is provided for the users to check the occurrence(s) of the resultant sequence repeats in the other sequence and structure (Protein Data Bank) databases. The databases deployed in the proposed computing engine are up-to-date and thus the users will get the latest information available in the respective databases. The server is freely accessible over the World Wide Web (WWW). AVAILABILITY: http://bioserver1.physics.iisc.ernet.in/fair/     

A data-mining approach for multiple structural alignment of proteins

Comparing the 3D structures of proteins is an important but computationally hard problem in bioinformatics. In this paper, we propose studying the problem when much less information or assumptions are available. We model the structural alignment of proteins as a combinatorial problem. In the problem, each protein is simply a set of points in the 3D space, without sequence order information, and the objective is to discover all large enough alignments for any subset of the input. We propose a data-mining approach for this problem. We first perform geometric hashing of the structures such that points with similar locations in the 3D space are hashed into the same bin in the hash table. The novelty is that we consider each bin as a coincidence group and mine for frequent patterns, which is a well-studied technique in data mining. We observe that these frequent patterns are already potentially large alignments. Then a simple heuristic is used to extend the alignments if possible. We implemented the algorithm and tested it using real protein structures. The results were compared with existing tools. They showed that the algorithm is capable of finding conserved substructures that do not preserve sequence order, especially those existing in protein interfaces. The algorithm can also identify conserved substructures of functionally similar structures within a mixture with dissimilar ones. The running time of the program was smaller or comparable to that of the existing tools.     

鹅掌楸配子选择与雄性繁殖适合度

在多父本等量花粉混合授粉的交配实验设计基础上, 利用SSR分子标记对其子代进行父本分析, 研究鹅掌楸的配子选择与雄性繁殖适合度。参试亲本为鹅掌楸2个种的5个单株（鹅掌楸（Liriodendron chinense）2株, 即FY和LS; 北美鹅掌楸（L. tulipifera）3株, 即LYS、MSL和NK）。结果表明： 鹅掌楸的配子选择个体间差异较大。作为母本, NK和LYS倾向于选择异种雄配子, 而MSL和LS则倾向于选择同种雄配子; 在同种雄配子的选择中, NK、LYS和LS倾向于自交, 而MSL则倾向于异交。以北美鹅掌楸为母本时, 北美鹅掌楸与鹅掌楸的雄性繁殖贡献率分别为45.5%和54.5%, 北美鹅掌楸的雄性繁殖适合度为鹅掌楸的0.556倍。以鹅掌楸为母本时, 二者的繁殖贡献率分别为15.6%和84.4%, 北美鹅掌楸的雄性繁殖适合度为鹅掌楸的0.123倍。总体上看, 鹅掌楸的雄性繁殖适合度高于北美鹅掌楸, 鹅掌楸与北美鹅掌楸均表现为自交亲和。     

New syntax to describe local continuous structure-sequence information for recognizing new pre-miRNAs

As an important complement to experimental identification of pre-miRNA, computational prediction methods are attracting more and more attention. Features extracted from pre-miRNA are the key to computational prediction. Among the features, local continuous structure-sequence information is usually employed by existing computational methods. As more and more species-specific miRNAs have been identified, a new syntax is required to describe pre-miRNA local continuous structure-sequence features. Therefore, we proposed here the use of couplet syntax to describe pre-miRNA intrinsic features. When tested on a dataset from miRBase12.0 with the use of features extracted by couplet syntax, the SVM classifier achieves a sensitivity of 81.98% and specificity of 87.16% on a human test set and a sensitivity of 86.71% on all other species. The obtained results indicate that the proposed couplet syntax can describe the intrinsic features of pre-miRNA better than traditional methods. By means of describing pre-miRNA secondary structure more precisely and masking frequently mutated nucleotides, couplet syntax provides a powerful feature-describing method that can be applied to many computational prediction methods.     

Bilateral similarity function: A novel and universal method for similarity analysis of biological sequences

Bilateral similarity function is designed for analyzing the similarities of biological sequences such as DNA, RNA secondary structure or protein in this paper. The defined function can perform comprehensive comparison between sequences remarkably well, both in terms of the Hamming distance of two compared sequences and the corresponding location difference. Compared with the existing methods for similarity analysis, the examination of similarities/dissimilarities illustrates that the proposed method with the computational complexity of O(N) is effective for these three kinds of biological sequences, and bears the universality for them.     

New method for comparing DNA primary sequences based on a discrimination measure

We introduce a new approach to compare DNA primary sequences. The core of our method is a new measure of pairwise distances among sequences. Using the primitive discrimination substrings of sequence S and Q, a discrimination measure DM(S, Q) is defined for the similarity analysis of them. The proposed method does not require multiple alignments and is fully automatic. To illustrate its utility, we construct phylogenetic trees on two independent data sets. The results indicate that the method is efficient and powerful.     

The Efficiency of Selenocysteine Incorporation Is Regulated by Translation Initiation Factors

Selenocysteine (Sec) incorporation is an essential process required for the production of at least 25 human selenoproteins. This unique amino acid is co-translationally incorporated at specific UGA codons that normally serve as termination signals. Recoding from stop to Sec involves a cis-acting Sec insertion sequence element in the 3′ untranslated region of selenoprotein mRNAs as well as Sec insertion sequence binding protein 2, Sec-tRNA^Sec, and the Sec-specific elongation factor, eEFSec. The interplay between recoding and termination at Sec codons has served as a focal point in researching the mechanism of Sec insertion, but the role of translation initiation has not been addressed. In this report, we show that the cricket paralysis virus intergenic internal ribosome entry site is able to support Sec incorporation, thus providing evidence that the canonical functions of translation initiation factors are not required. Additionally, we show that neither a 5′ cap nor a 3′ poly(A) tail enhances Sec incorporation. Interestingly, however, the presence of the internal ribosome entry site significantly decreases Sec incorporation efficiency, suggesting a role for translation initiation in regulating the efficiency of UGA recoding.