一个新的白血病相关基因LRP16全长cDNA的克隆、序列分析及表达特征

 克隆一个与白血病复发相关基因 (LRP1 6)的全长 c DNA序列 ,对其进行染色体定位、组织表达谱分析 ,并对该基因编码蛋白质进行原核表达 .首先用获得的一段 3kb DNA片段在 NCBI提供的 h ESTs数据库中进行电子杂交并对重叠克隆片段组装 ,再设计引物进行 c DNA末端快速扩增(RACE技术 ) .采用 Northern印迹方法进行组织表达分析 .以高通量基因组序列 (HTGS)数据库为基础进行染色体定位 .对构建的克隆菌用 IPTG诱导重组蛋白表达后进行 SDS- PAGE,同时对重组体测序确证 .钓取了该基因全长 c DNA、推导所编码的氨基酸序列 ,并将该基因定位于染色体1 1 q1 2 .2 .原核表达筛选获得了该基因重组子的一个缺失体 .对 LRP1 6基因全长 c DNA的序列分析提示 ,该基因可能编码两种 N端不同的蛋白质 ,且该基因的转录本可能存在一种丰度较低的剪接体 .     

DNA序列的“双符三阶”图形编码

DNA的图形编码是在几何意义下,在不同位置,用不同的标记符号及不同的方向线段,对DNA的序列进行编码．DNA图形编码相对于DNA的字符编码而言,具有直观、简明、形象和便于比较局部DNA序列的相似性等特点。在分析已知各类：DNA的图形表示模式的基础上,提出一种DNA序列的“双符三阶”图形编码,并以此对一些特异DNA编码序列进行分析。DNA图形编码与DNA字符编码呈一一对应关系,具有简便易行、编译方便、形象丰富、便于比较等优点。适用于DNA短序列的相似性检测与分析,在生物信息学上有一定的应用前景。     

DNA序列的多重分形Hurst分析

为了深入研究基因组序列的多重分形性质,首先选取12条较长的DNA序列,并根据此12条DNA序列的编码／非编码片段将DNA序列转换成相应的12条时间序列,其次对这12个时间序列进行多重分形Hurst分析,计算它们的Hurst指数,并且利用Hurst指数分析序列的自相似性,进一步将得到的Hurst指数与DNA一维游走模型相比较,发现12条序列均具有长程相关性,这说明DNA序列中确实存在着长程相关现象。     

侧耳木霉T2-1植酸酶基因的序列分析及蛋白结构预测

利用GenBank发表的植酸酶A编码序列设计的引物,通过PCR的方法对侧耳木霉(Trichoderma pleuroticola)T2-1基因组DNA进行扩增,获得了一条长约1.7 kb的特异性DNA片段.序列测定结果表明,该DNA片段含有植酸酶编码基因的完整序列和3段内舍子序列,其中植酸酶基因全长1 443 bp,编码480个氨基酸,5'端有一段编码23个氨基酸的信号肤序列,其余的457个氨基酸残基为成熟植酸酶的氨基酸序列.对该基因编码的氨基酸序列进行三级结构预测,发现它为磷酸单酯酶.已将侧耳木霉T2-1植酸酶基因序列在GenBank中注册(登录号:GQ325590).这是目前中国在GenBank注册的第一个完整的木霉植酸酶编码基因.     

黑曲霉糖化酶高产和低产菌株糖化酶基因调控区的克隆及其分析比较

以PCR合成的糖化酶高产菌株黑曲霉(Asp. Niger)T21糖化酶基因5’近端非编码区588bp(EcoRI-BamHI)的序列为探针,从T21染色体DNA中克隆到近2.0kb的糖化酶基因5’端非编码区序列,并以此序列为探针从糖化酶低产菌株黑曲霉3.795(T21的诱变出发株)的染色体DNA中克隆到1.5kb的糖化酶基因5’端非编码区序列。该二序列的分析测定结果表明,其结构特征与文献报道的黑曲霉糖化酶基因5’端非编码区的基本一致,被称为“核心启动子”(Core promoter)的TATAAAT框及GCAAT框,分别在翻译起始点的-109bp及-178bp处。此外,在曲霉amdS,amyB基因中已发现有调控功能的CCAAT序列存在于-449bp和-799bp处。高产和低产菌株糖化酶基因5’端非编码区序列的分析比较结果表明,有9个部位的碱基发生了变化。此实验结果为进一步研究黑曲霉糖化酶基因在转录水平上的调控规律打下了基础。     

非编码DNA序列的功能及其鉴定

非编码DNA序列是指基因组中不编码蛋白质的DNA序列。这些序列可以结合调节因子、转录为功能性RNA、单独或协同地调节生理活动和病理过程。文章围绕基因表达调控作用, 总结了近几年非编码DNA序列的研究成果, 对其结构、功能和可能的作用机制进行了初步阐述, 介绍了目前鉴定非编码DNA序列中功能元件的计算方法和实验技术, 并对非编码DNA未来的研究进行了展望。     

蓖麻蚕线粒体基因组细胞色素氧化酶亚基Ⅲ的序列及其分子进化分析

测定了蓖麻蚕Samia cynthia ricini线粒体基因组(mtDNA)含完整的细胞色素氧化酶亚基Ⅲ(COX3)、tRNA-Gly和部分的NADH亚基Ⅲ(ND3)基因的DNA片段序列。COX3基因编码框包含789个核苷酸,编码262个氨基酸的蛋白质。通过同源性比较,发现COX3基因的3′端比5′端要保守,其编码的蛋白在C端有两个保守序列存在。COX3的下游为66 bp的tRNA-Gly基因。蓖麻蚕的COX3与家蚕COX3同源性最高,核苷酸和氨基酸序列同源性分别是80.2%和85.6%。根据COX3氨基酸序列进行了12种无脊椎动物的分子进化树分析,认为在采用线粒体基因序列进行分子进化分析时,应该综合考虑物种的繁殖模式及生态特点。     

大鼠胰岛素样生长因子Ⅰ基因的克隆及表达

以大鼠染色体DNA为模板,PCR分别扩增胰岛素样生长因子Ⅰ（IGF-Ⅰ）基因外显子2编码区和外显子3编码区,并使外显子2编码区的3′端与外显子的3编码区的5′端有相同的40个碱基,采用外显子拼接法,以两种扩增产物为模板再次进行PCR,得到210bp的大鼠IGF-Ⅰ基因编码序列,将此序列克隆入pUC18质粒进一步构建表达型重组粒pGEX-IGF-Ⅰ,并在大肠杆菌DH5α中进行诱导表达。表达产物经SDS－PAGE分析及Western blot检测,并经体外实验证明其具有刺激细胞增殖的生物活性。     

TTV武汉分离株DNA克隆和序列分析

用PCR技术从一武汉病人血清中分离获得TGV DNA片断,把此DNA片断克隆到pMD18-T质粒载体中,进行全序列测定并用计算机软件对核苷酸,氨基酸序列和ORF2多肽特征进行比较和分析。所分离获得的TTV DNA片断全长1333bp,含TTV完整的ORF2及部分ORF1序列,核苷酸和氨基酸序列与其它基因型为1a的TTV分离株具有极高的同源性。ORF2多肽含202个氨基酸,在N端部分和C端部分具有较高的亲水性和较强的抗原性,而中间为一段疏水区域,抗原性较弱。N端结构以α螺旋为主,含有典型的酪氨酸激酶磷酸化价点（RARDWYPGY,38－45aa）和三个潜在的蛋白质激酶C的磷酸化位点,C端富含脯氨酸。结构以β转向为主,含有三个连续的N－十四烷酰化位点,推测ORF2编码的蛋白可能是一种磷酸化蛋白。     

青花菜雄性不育相关基因BoDHAR的克隆与表达分析

以一个与甘蓝显性核不育相关的差异表达片段的序列为信息探针,通过在NCBI与TAIR网站数据库中进行同源EST序列搜索,经人工拼接、RT-PCR、PCR克隆与序列分析,获得了青花菜脱氢抗坏血酸还原酶DHARdehydroascorbatereductase基因的cDNA与DNA全长序列,命名为BoDHAR。并利用双链接头介导PCR的染色体步行技术(genomewalking)克隆了其上游644bp的5′端序列。所获的BoDHAR基因全长1486bp,存在两个内含子,DNA编码区序列633bp,编码210个氨基酸;序列分析表明BoDHAR与同源基因AT1G19570.1cDNA序列有82.3%的一致性,推导的氨基酸序列有79.6%的一致性;编码的水溶性蛋白存在多个磷酸化位点;5′端上游区存在明显的转录调控序列。半定量RT-PCR结果表明BoDHAR在可育系花蕾中的表达量明显高于不育系花蕾,在花药中的表达明显高于其它部位。     

Directed Molecular Evolution

We propose the existence of a relationship of stereochemical complementarity between gene sequences that code for interacting components: nucleic acid-nucleic acid, protein-protein and protein-nucleic acid. Such a relationship would impose evolutionary constraints on the DNA sequences themselves, thus retaining these sequences and governing the direction of the evolutionary process. Therefore, we propose that prebiotic, template-directed autocatalytic synthesis of mutally cognate peptides and polynucleotides resulted in their amplification and evolutionary conservation in contemporary prokaryotic and eukaryotic organisms as a genetic regulatory apparatus. If this proposal is correct, then the relationships between the sequences in DNA coding for these interactions constitute a life code of which the genetic code is only one aspect of the many related interactions encoded in DNA.     

Junk DNA的功能诠释

在庞大的基因组序列中数量占绝对优势的序列因为不编码蛋白质或RNA产物,一直被人们称为junk DNA.事事讲究经济效率的生物在长期的进化中,应该不会让大量无功能的“垃圾”堆积在充满活力的生命细胞中.近年来的研究已揭示junk DNA具有重要的功能,随着研究的深入,一定会发现越来越多的junk DNA决非垃圾,而是基因组的宝贵财富.     

Entropy of the genetic information and evolution

The entropy of the amino acid sequences coded by DNA is considered as a measure of diversity or variety of proteins, and is taken as a measure of evolution. The DNA or m-RNA sequence is corsidered as a stationary second-order Markov chain composed of four kinds of bases. Because of the biased nature of the genetic code table, increase of entropy of amino acid sequences is possible with biased nucleotide sequence. Thus the biased DNA base composition and the extreme rarity of the base doubletC _p G of higher organisms are explained. It is expected that the amino acid composition was highly biased at the days of the origin of the genetic code table, and the more frequent amino acids have tended to get rarer, and the rarer ones more frequent. This tendency is observed in the evolution of hemoglobin, cytochrome C, fibrinopeptide, immunoglobulin and lysozyme, and protein as a whole.     

Structure of mitochondrial DNA control region of Fenneropenaeus chinensis and phylogenetic relationship among different populations

This paper deals with the structure of mitochondrial DNA control region of Fenneropenaeus chinensis. The termination-associated sequence (TAS), cTAS, CSB-D-CSB-F, and CSB-1 are detected in the species. The results indicate that the structures of these parts are similar to those of most marine organisms. Two conserved regions and many stable conserved boxes are found in the extended TAS area, central sequences blocks, and conserved sequences blocks (CSBs). This is the special character of F. chinensis. All the mtDNA control region sequences do not have CSB2 and CSB3 blocks, which is quite different from most vertebrates. In addition, the complete mtDNA control region sequences are used to analyze the phylogenetic relationships of F. chinensis. The phylogenetic trees show a lack of genetic structure among populations, which is similar to many previous studies.     

FACIL: Fast and Accurate Genetic Code Inference and Logo

MOTIVATION: The intensification of DNA sequencing will increasingly unveil uncharacterized species with potential alternative genetic codes. A total of 0.65% of the DNA sequences currently in Genbank encode their proteins with a variant genetic code, and these exceptions occur in many unrelated taxa. RESULTS: We introduce FACIL (Fast and Accurate genetic Code Inference and Logo), a fast and reliable tool to evaluate nucleic acid sequences for their genetic code that detects alternative codes even in species distantly related to known organisms. To illustrate this, we apply FACIL to a set of mitochondrial genomic contigs of Globobulimina pseudospinescens. This foraminifer does not have any sequenced close relative in the databases, yet we infer its alternative genetic code with high confidence values. Results are intuitively visualized in a Genetic Code Logo. Availability and implementation: FACIL is available as a web-based service at http://www.cmbi.ru.nl/FACIL/ and as a stand-alone program.     

Repertoires of the Nucleosome-Positioning Dinucleotides

It is generally accepted that the organization of eukaryotic DNA into chromatin is strongly governed by a code inherent in the genomic DNA sequence. This code, as well as other codes, is superposed on the triplets coding for amino acids. The history of the chromatin code started three decades ago with the discovery of the periodic appearance of certain dinucleotides, with AA/TT and RR/YY giving the strongest signals, all with a period of 10.4 bases. Every base-pair stack in the DNA duplex has specific deformation properties, thus favoring DNA bending in a specific direction. The appearance of the corresponding dinucleotide at the distance 10.4 xn bases will facilitate DNA bending in that direction, which corresponds to the minimum energy of DNA folding in the nucleosome. We have analyzed the periodic appearances of all 16 dinucleotides in the genomes of thirteen different eukaryotic organisms. Our data show that a large variety of dinucleotides (if not all) are, apparently, contributing to the nucleosome positioning code. The choice of the periodical dinucleotides differs considerably from one organism to another. Among other 10.4 base periodicities, a strong and very regular 10.4 base signal was observed for CG dinucleotides in the genome of the honey bee A. mellifera. Also, the dinucleotide CG appears as the only periodical component in the human genome. This observation seems especially relevant since CpG methylation is well known to modulate chromatin packing and regularity. Thus, the selection of the dinucleotides contributing to the chromatin code is species specific, and may differ from region to region, depending on the sequence context.     

Comparative genomics: the key to understanding the Human Genome Project

The sequencing of the human genome is well underway. Technology has advanced, such that the total genomic sequence is possible, along with an extensive catalogue of genes via comprehensive cDNA libraries. With the recent completion of the Saccharomyces cerevisiae sequencing project and the imminent completion of that of Caenorhabditis elegans, the most frequently asked question is how much can sequence data alone tell us? The answer is that that a DNA sequence taken in isolation from a single organism reveals very little. The vast majority of DNA in most organisms is noncoding. Protein coding sequences or genes cannot function as isolated units without interaction with noncoding DNA and neighboring genes. This genomic environment is specific to each organism. In order to understand this we need to look at similar genes in different organisms, to determine how function and position has changed over the course of evolution. By understanding evolutionary processes we can gain a greater insight into what makes a gene and the wider processes of genetics and inheritance. Comparative genomics (with model organisms), once the poor relation of the human genome project, is starting to provide the key to unlock the DNA code.