从EST出发克隆人基因组Xq13区段一个候选基因的初步研究

人类基因组表达序列筛选是寻找候选基因的重要路线之一，外显子陷阱法，ｃＤＮＡ直接筛筛选法，它们可分别根据表达序列的结构及表达特点进行筛选，ＥＳＴ是表达图的位标，它们是一些位点专一的表达序列位标，根据ＥＳＴ的特征，在国内首次建立了一种从ＥＳＴ出发的筛选候选基因的新方法，用睦方法已在人Ｘ染色体Ｘｑ１３区段筛选得到了一个新的ｃＤＮＡ，总测序徇的１３９８ｂｐ包含了完整的３末端。     

The origin and evolution of repeated sequencesand introns

Because the origin of repeated sequences may date back to the appearance of the first genes and genomes on Earth, they must have been involved in the entire history of genome evolution. Repeated sequences are important components of the primitive genomes that would provide the basis for the origin of split genes. In this sense, introns existed in early genes, and both repeated sequences and introns have always had structural and evolutionary roles. The evolution of the composition of organic genomes may be unified in a general pattern. Nuclear (nucleoid) genomes, mitochondrial genomes, and chloroplast genomes would respectively have evolved according to two scenarios. The small genome scenario would be evolutionary paths in which repeated sequences and introns have been lost, while the large genome scenario would be evolutionary paths in which repeated sequences and introns have been retained and developed.     

人体基因组课题（HGP）计划给分析化学带来的挑战与机会

本文综述了在ＤＮＡ测序方面分析化学的最新进展，包括电泳，毛细管电泳（ＣＥ），质谱（ＭＳ），电喷雾电离－质谱（ＥＳＩ－ＭＳ），荧光光谱、共振离子谱（ＲＩＳ）和单分子测定，同时还叙述了两维技术和多段测序方法的进展。     

Paenibacillus Shenyangensis的DNA序列拼接与组装

在已有测序数据基础上,利用三种常见的序列组装软件对Paenibacillus Shenyangensis全基因组测序结果进行拼接组装,分析比较了不同软件在各自最优参数条件下DNA序列的组装数据,并与NCBI数据库中类芽孢杆菌属其他近缘种进行基因比对与预测.结果表明,SOAPdenovo的组装结果最优,在k-mer为23时,组装基因组总长和N50分别为5 501 467和293 864 bp,预测的4 800个基因中有4 393个与NCBI-Nr数据库比对并注释成功.     

Bioinformatic prediction of selenoprotein genes in the dolphin genome

Selenium (Se), an essential trace element in vivo, is present mainly as selenocystein (Sec) in various selenoproteins. The Sec residue is translated from an in-frame TGA codon, which traditionally functions as a stop codon. Prediction of selenoprotein genes is difficult due to the lack of an effective method for distinguishing the dual function of the TGA codon in the open reading frame of a selenoprotein gene. In this article a eukaryotic bioinformatic prediction system that we have developed was used to predict selenoprotein genes from the genome of the common bottlenose dolphin, Tursiops truncatus. Sixteen selenoprotein genes were predicted, including selenoprotein P and glutathione peroxidase. In particular, a type II iodothyronine deiodinase was found to have two Sec residues, while the type I iodothyronine deiodinase gene has two alternative splice forms. These results provide important information for the investigation of the relationship between a variety of selenoproteins and the evolution of the marine-living dolphin.     

Advances in the study of helminth mitochondrial genomes and their associated applications

Helminths, including flatworms and roundworms, are abundant organisms that have a variety of life histories. Of these, the genera Schistosoma, Echinococcus, Trichinella are notable parasites of veterinary and medical importance, and cause substantial socio- economic losses throughout China and the rest of the world. Genetic markers in the mitochondrial (mt) genome have proven use- ful for systematic, ecological, evolutionary and population studies, and the growth of mt genomic research has increased in the last two decades. Technological improvements, such as the long-polymerase chain reaction method and high-throughput se- quencing have allowed minute amounts of DNA from single worms, biopsy samples or microscopic organisms to be used for whole mt genome characterization. To facilitate the retrieval, annotation and analyses of mitochondrial features, multiple data- bases and specific software have also been designed and established. This review focuses on current progress, applications and perspectives regarding helminth mt genomics. To date, the complete mt genomes for 93 species of helminths have been sequenced and analyzed. Analyses of the mt genes, including gene content, arrangement, composition and variation have revealed unique features among the helminths when compared with other metazoans. This provides important data concerning their functional and comparative mitochondrial genomics, molecular taxonomy and characterization, population genetics and systematics, and evolu- tionary history. Moreover, mt genome data for parasitic helminths are important for diagnosis, epidemiology and ecology of in- fections. Mitochondrial genome data offer a rich source of markers for the systematics and population genetics of socioeconomi- cally important parasitic helminths of humans and other animals.     

Multi-scaling hierarchical structure analysis on the sequence ofE. coli complete genome

We have applied the newly developed hierarchical structure theory for complex systems to analyze the multi-scaling structures of the nucleotide density distribution along a linear DNA sequence from the completeEscherichia coli genome. The hierarchical symmetry in the nucleotide density distribution was demonstrated. In particular, we have shown that the G, C density distribution that represents a strong H-bonding between the two DNA chains is more coherent with smaller similarity parameter compared to that of A, T density distribution, indicating a better organized multi-scaling fluctuation field for G, C density distribution along the genome sequence. The biological significance of these findings is under investigation.     

Perspective on Materials Genome~

The author’s perspective on Materials Genome is presented in this paper through several related projects.Current thermodynamic and kinetic databases of multicomponent materials consist of Gibbs energy functions and atomic mobility of individual phases as functions of temperature,composition,and sometimes pressure,i.e.,with the individual phases based on crystal structures as the genome(building blocks)of materials.It is articulated that if an individual phase has its internal configurations,such as magnetic spin configurations and ferroelectric polarization,change significantly with respect to temperature,stress,and magnetic and electric fields,then those individual configurations instead should be considered as the genome of the individual phase.The‘‘mutation’’of an individual phase is governed by the entropy of mixing among the individual stable and metastable configurations,named as microstate configurational entropy,and responsible to anomalies in individual phases.Our ability to tailor the properties of those individual configurations as a function of compositions is the key for the design of materials.     

扬子鳃蛭线粒体基因组全序列测定及其系统学地位——基于Pacbio和Illumina技术

利用Illumina和Pacbio测序技术对扬子鳃蛭（Ozobranchus jantseanus）线粒体基因组全序列进行测序及注释，并与NCBI数据库中蛭纲（Hirudinea）其他物种的线粒体全序列的排列方式和系统进化关系进行了比较，以确定其系统学地位.结果显示：获得的线粒体基因组序列长度为14 868 bp，蛋白编码基因存在2种起始密码子，分别为ATG和ATT；终止密码子共有4种，分别为TAA，TAG，TA和T；蛭纲10个物种的线粒体基因组全序列基因排序可分为2种类型，其差异表现在tRNAs的互换和长非编码区的长度的不同；扬子鳃蛭所属的吻蛭目（Rhynchobdellida）均为b型，绝大部分无吻蛭目（Arhynchobdellida）的排列方式为a型.基于蛭纲物种的13个蛋白编码基因(PCGs)的Neighbor-Joining（NJ）树进化分析显示，扬子鳃蛭与其他吻蛭目物种聚类.     

21世纪生命科学展望

以近 2 0年来生命科学领域所取得的巨大成就为依据论述了 2 1世纪生命科学在自然科学中的领头地位。同时 ,对 2 1世纪生命科学的几个重要研究领域进行了评述 ,其中包括人类基因组计划、基因组学与发育生物学的关系、基因组学与生物进化及生命起源的关系、生物信息学的作用和地位 ,以及现代生物技术的开发应用对 2 1世纪人类生活的影响。