Phenotypic and genetic characterization of a novel strain of Acidithiobacillus ferrooxidans （AF2）

A comparative study on the phenotypic and genetic characteristics among Acidithiobacillus ferrooxidans (AF2), a typic strain ATCC23270 and a previously isolated strain AF3 was performed. AF2 can use ferrous ion (Fe²⁺) or elemental sulfur (S⁰) as sole energy source, but oxidizes S⁰ more effectively than Fe²⁺, which is different from ATCC23270 and AF3. The G+C content of AF2 is 51.8% (molar fraction), however, ATCC23270 and AF3 strains have G+C content of 63.7% and 64.8% (molar fraction), respectively. The DNA-DNA hybridization results show that AF2 has 41.53% and 52.38% genome similarity to ATCC 23270 and AF3, respectively, but AF3 has a high genome similarity of 89.86% to ATCC 23270 strain. Rusticyanin (rus) and subunit III of aa₃-type cytochrome oxidase (coxC) genes are not detected in AF2, but Fe²⁺ oxidase (iro) gene can be detected. To understand the genomic organization of iro gene, a cosmid library of AF2 genome was constructed and iro gene-containing clone was screened. The sequencing result shows that although the nucleotide sequence of iro gene in AF2 is completely identical to that of ATCC 23270 strain, its genomic organization is different from that of ATCC 23270. In AF2, iro is located at downstream of purA gene, while it is located at downstream of petC-2 gene in ATCC 23270 strain. These results indicate that AF2 is a novel strain of A. ferrooxidans, and that phenotypic differences among the strains of A. ferrooxidans are closely correlated with their genetic polymorphisms.     

枯草芽孢杆菌整合载体的构建及基因组的改造

构建了两种整合载体,分别为单交换整合载体pACC-BdbDC和双交换整合载体pDsbE,pDGC,转化野生型枯草芽孢杆菌Bacillus subtilis168,目的基因整合到基因组上,同时引入氯霉素抗性基因。利用FLP/frt重组系统将氯霉素抗性基因敲除,便于宿主菌的进一步改造。PCR结果表明共重新构建了6种宿主菌。复杂双交换整合载体pDGC成功将3个目的基因整合到基因组上,为多个基因同时整合提供了一种方便可行的方法。     

Analysis on n-gram statistics and linguistic features of whole genome protein sequences

To obtain the statistical sequence analysis on a large number of genomic and proteomic sequences available for different organisms, the n-grams of whole genome protein sequences from 20 organisms were extracted. Their linguistic features were analyzed by two tests ： Zipf power law and Shannon entropy, developed for analysis of natural languages and symbolic sequences. The natural genome proteins and the artificial genome proteins were compared with each other and some statistical features of n-grams were discovered. The results show that： the n-grams of whole genome protein sequences approximately follow the Zipf law when n is larger than 4 ; the Shannon n-gram entropy of natural genome proteins is lower than that of artificial proteins; a simple unigram model can distinguish different organisms ; there exist organism-specific usages of “phrases” in protein sequences. It is suggested that further detailed analysis on n-gram of whole genome protein sequences will result in a powerful model for mapping the relationship of protein sequence, structure and function.     

生物信息学中的MicroRNA预测研究

为microRNA预测的研究提供参考,讨论了生物信息学中有关MicroRNA预测研究的若干问题。根据最新的研究成果,由MicroRNA预测的特征信息和数据源,从结构序列分析方法、比较基因组方法和机器学习方法等方面对MicroRNA预测的生物信息学方法做了回顾和展望,指出了该领域研究的趋势。通过对3类方法的比较结果表明,采用机器学习方法的效果更优越,能较精确地预测出MicroRNA。     

基于PCR技术筛选cDNA和genome文库方法的改进

提出一种改进的基于PCR技术的cDNA和genome文库筛选新方法。该方法利用PCR手段逐步排除文库中的非阳性克隆组分,提高阳性克隆所占比重,最后得到含有一定数量阳性单克隆的最小克隆群体用于直接挑选单个阳性克隆。在筛选cDNA文库时则增加了一个将噬菌体文库转化成质粒文库的步骤。该方法既保留了常规PCR文库筛选方法的灵敏、快捷和经济的特点,又弥补了其筛选周期相对较长、工作量大,以及随着循环数的增加和提取DNA的难度加大,阳性克隆容易丢失等缺陷,尤其在用于筛选cDNA文库时更是免除了繁琐的滴度、侵染和洗脱过程,极大地提高了筛选的成功率。     

令人谈之色变的食品安全名词

<正>[转基因]这个概念的科学解释是这样的:将从特定生物体基因组中需要的目的基因或人工合成指定序列的DNA片段中提取基因片段,转入特定生物中,与其本身的基因组进行重组,再从重组体中进行数代的人工选育,从而获得具有稳定表现的遗传性状的个体。     

人类X染色体Xp21．3－11．3区YAC重叠群的构建

人类Ｘ染色体短臂２１．３—１１．３区是含有视网膜色素变性等数种遗传病基因位点的区域。我们对这个具有重要医学生物学意义的区段进行了ＹＡＣ重叠群构建。用这一区域已知的探针（ＯＴＣ、ＤＸＳ１６６、ＤＭＤｃＤＮＡ）及ＳＴＳ位标，以ＹＡＣ菌落原位杂交法及ＰＣＲ法进行了ＹＡＣ的筛选；也采用了法国ＣＥＰＨ和英国ＩＣＲＦ的部分ＹＡＣ；总共得到了５５个阳性ＹＡＣ。对上述ＹＡＣ进行了长度测定，２６对微卫星ＳＴＳ图谱分析，单拷贝探针的杂交定位，Ａｌｕ－ＰＣＲ指纹图谱分析。综合上述信息，对这些ＹＡＣ进行了排序，在Ｘｐ２１．３－１１．３区得到了６个０ＹＡＣ重叠群，覆盖了约１５Ｍｂ的范围。这些ＹＡＣ重叠群的构建为开展该区域疾病基因的定位克隆（Ｐｏｓｉｔｉｏｎａｌｃｌｏｎｉｎｇ）及ＤＮＡ顺序测定奠定了基础。     

中国材料基因组计划如何跨出第一步？

材料基因组计划（MGI）是用高通量并行迭代替代传统试错法的多次顺序迭代,逐步由“经验指导实验”向“理论预测、实验验证”的材料研究新模式转变,最终实现材料“按需设计”。MGI包括高通量材料计算、高通量材料实验和材料数据库3个要素,是材料创新的基础设施,是MGI的核心。     

不同对虾种间共用微卫星DNA引物的研究

采用已发表的斑节对虾的30对微卫星引物,对部分微卫星引物在中国对虾、凡纳对虾、日本对虾中的通用性进行了研究。通过所建立的降温PCR(Touchdown PCR)方法对3种对虾的DNA进行PCR扩增,筛选出3对引物在3种对虾中均能产生清晰谱带。根据上述结果适当调整PCR反应体系中各试剂的量及反应条件,达到了理想的结果。利用这3对引物对3种对虾进行遗传标记分析,结果显示,PCR扩增产物条带清晰,特异性强,每对引物在3种对虾间扩增出的特异性片段大小几乎一致。研究表明,3种对虾基因组间存在一定程度的相似性,引物W15-16、W21-22和W45-46可直接应用于中国对虾、凡纳对虾、日本对虾、斑节对虾分子标记的基因组比较作图,也为图谱克隆法提供了新的思路。     

猪瘟病毒兔化弱毒(HCLV)疫苗株基因组全长cDNA的克隆与序列分析

根据猪瘟病毒基因组的序列设计合成了覆盖HCLV基因组全部序列的5对引物,通过RT-PCR从感染家兔脾脏中扩增获得了包含HCLV(hog cho1era lapinized virus,HCLV)基因组全序列的5个cDNA片段,并将它们分别克隆至pGEM-T vector中。然后将这5个cDNA片段按它们在HCLV基因组上的位置从5’端至3’端的顺序依次通过酶切连接,一并克隆到pPo1y2载体中得到HCLV基因组全长cDNA的质粒pPOHCLV。序列分析表明,HCLV基因组长度共12310bp,有一个大的ORF,编码-3898个氨基酸的多聚蛋白。其5’—NCR和3’—NCR长度分别是374nt和239nt。与非兔化毒株相比较,HCLV基因组在12133nt处有12个碱基的插入CTTTTTTCTTTT,该序列可能是病毒在适应兔体增殖过程中形成的。基于基因组全序列及其所推导的氨基酸序列的同源性分析表明,毒株的亲缘关系的远近与它们的毒力之间并没有相关性。