Specialized DNA polymerases,cellular survival,and the genesis of mutations

Cell death caused by arrested replication of damaged or structurally altered DNA can be avoided in prokaryotic and eukaryotic cells by multiple DNA polymerases that are specialized to bypass DNA damage. Some of these polymerases perform such translesion DNA synthesis of specific types of damage with high genetic fidelity. However, they exhibit greatly reduced fidelity when they operate on undamaged DNA or on DNA with lesions that are (apparently) not cognate substrates. The low fidelity of some of these specialized polymerases when copying undamaged DNA may be physiologically functional, including generating immunoglobulin diversity.     

仿火箭电泳应用于单细胞凝胶电泳技术的优势(摘要)(英文)

[目的]研究仿火箭电泳应用于单细胞凝胶电泳技术,为单细胞凝胶电泳技术寻求另一种可行的电泳方法提供参考。[方法]将仿火箭电泳方法应用于单细胞凝胶电泳技术,检验单细胞水平上的DNA损伤,并与传统的电泳方法比较,分析其优劣势。[结果]在细胞DNA未受损状态下,2种电泳方法所得的结果一致;而在细胞DNA受到损伤时,传统的电泳方法下一些细胞的慧尾发散出现漂移,仿火箭电泳方法得到的慧尾图像集中且未发生偏移。[结论]仿火箭电泳方法较传统的电泳方法存在一定优势。     

仿火箭电泳应用于单细胞凝胶电泳技术的优势

[目的]研究仿火箭电泳应用于单细胞凝胶电泳技术,为单细胞凝胶电泳技术寻求另一种可行的电泳方法提供参考。[方法]将仿火箭电泳方法应用于单细胞凝胶电泳技术,检验单细胞水平上的DNA损伤,并与传统的电泳方法比较,分析其优劣势。[结果]在细胞DNA未受损状态下,2种电泳方法所得的结果一致;而在细胞DNA受到损伤时,传统的电泳方法下一些细胞的慧尾发散出现漂移,仿火箭电泳方法得到的慧尾图像集中且未发生偏移。[结论]仿火箭电泳方法较传统的电泳方法存在一定优势。     

Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes

Interaction of regulatory DNA binding proteins with their target sites is usually preceded by binding to nonspecific DNA. This speeds up the search for the target site by several orders of magnitude. We report the solution structure and dynamics of the complex of a dimeric lac repressor DNA binding domain with nonspecific DNA. The same set of residues can switch roles from a purely electrostatic interaction with the DNA backbone in the nonspecific complex to a highly specific binding mode with the base pairs of the cognate operator sequence. The protein-DNA interface of the nonspecific complex is flexible on biologically relevant time scales that may assist in the rapid and efficient finding of the target site.     

农作物信息垂直搜索引擎的研究

根据中文信息处理的理论分析和当前搜索引擎技术的发展现状,按照软件工程的方法,研究了农作物垂直搜索引擎的总体设计过程,设计过程重点论述了需求分析、功能规划和总结结构,其中详细介绍了信息采集、信息过滤和正文提取等模块的设计与实现流程。通过该搜索引擎不仅能够更加直观地找到需要了解的知识,而且数据的结构化处理、分类整理与知识库的建立,可为今后的专家系统与农作物种植决策支持奠定良好的基础。     

仿火箭电泳应用于单细胞凝胶电泳技术的优势（摘要）

[目的]研究仿火箭电泳应用于单细胞凝胶电泳技术,为单细胞凝胶电泳技术寻求另一种可行的电泳方法提供参考。[方法]将仿火箭电泳方法应用于单细胞凝胶电泳技术,检验单细胞水平上的DNA损伤,并与传统的电泳方法比较,分析其优劣势。[结果]在细胞DNA未受损状态下,2种电泳方法所得的结果一致;而在细胞DNA受到损伤时,传统的电泳方法下一些细胞的慧尾发散出现漂移,仿火箭电泳方法得到的慧尾图像集中且未发生偏移。[结论]仿火箭电泳方法较传统的电泳方法存在一定优势。     

Distinctive termini characterize two families of human endogenous retroviral sequences

Human DNA contains many copies of endogenous retroviral sequences. Characterization of molecular clones of these structures reveals the existence of two related families. One family consists of full-length (8.8 kilobases) proviral structures, with typical long terminal repeates (LTR's). The other family consists of structures, which contain only 4.1 kilobases of gag-pol sequences, bounded by a tandem array of imperfect repeats 72 to 76 base pairs in length. Typical LTR sequences that exist as solitary elements in the genome were cloned and characterized.     

Large-scale and automated DNA sequence determination

DNA sequence analysis is a multistage process that includes the preparation of DNA, its fragmentation and base analysis, and the interpretation of the resulting sequence information. New technological advances have led to the automation of certain steps in this process and have raised the possibility of large-scale DNA sequencing efforts in the near future [for example, 1 million base pairs (Mb) per year]. New sequencing methodologies, fully automated instrumentation, and improvements in sequencing-related computational resources may render genome-size sequencing projects (100 Mb or larger) feasible during the next 5 to 10 years.     

Genomic sequencing of Pleistocene cave bears

Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to the amplification of mitochondrial sequences. Here we describe metagenomic libraries constructed with unamplified DNA extracted from skeletal remains of two 40,000-year-old extinct cave bears. Analysis of approximately 1 megabase of sequence from each library showed that despite significant microbial contamination, 5.8 and 1.1% of clones contained cave bear inserts, yielding 26,861 base pairs of cave bear genome sequence. Comparison of cave bear and modern bear sequences revealed the evolutionary relationship of these lineages. The metagenomic approach used here establishes the feasibility of ancient DNA genome sequencing programs.     

Cystic fibrosis locus defined by a genetically linked polymorphic DNA marker

A polymorphic DNA marker has been found genetically linked, in a set of 39 human families, to an autosomal recessive gene that causes cystic fibrosis (CF), a disease affecting one in 2000 Caucasian children. The DNA marker (called D0CRI-917) is also linked to the PON locus, which by independent evidence is linked to the CF locus. The best estimates of the genetic distances are 5 centimorgans between the DNA marker and PON and 15 centimorgans between the DNA marker and the CF locus, meaning that the location of the disease gene has been narrowed to about 1 percent of the human genome (about 30 million base pairs). Although the data are consistent with the interpretation that a single locus causes cystic fibrosis, the possibility of genetic heterogeneity remains. The discovery of a linked DNA polymorphism is the first step in molecular analysis of the CF gene and its causative role in the disease.     

Synthesis of a site-specific DNA-binding peptide

The Hin recombinase binds to specific sites on DNA and mediates a recombination event that results in DNA inversion. In order to define the DNA-binding domain of the Hin protein two peptides 31 and 52 amino acids long were synthesized. Even though the 31mer encompassed the sequence encoding the putative helix-coil-helix-binding domain, it was not sufficient for binding to the 26-base pair DNA crossover site. However, the 52mer specifically interacted with the site and also effectively inhibited the Hin-mediated recombination reaction. The 52mer bound effectively to both the 26-base pair complete site and to a 14-base pair "half site." Nuclease and chemical protection studies with the 52mer helped to define the DNA base pairs that contributed to the specificity of binding. The synthetic peptide provides opportunities for new approaches to the study of the nature of protein-DNA interaction.     

基于油液监测的柴油机磨损故障诊断系统

运用专家系统的原理和构建万法,建立了知识库模型,编写了搜索推理代码,并在此基础上基于C#和SqlServer采用油液分析技术中的光谱分析、铁谱分析和常规理化分析,建立了柴油机磨损故障诊断系统．该系统可用于诊断磨损的部位、类型和性质．以济南柴油机厂的4190柴油机为研究对象,对该系统进行了检验,实验结果表明该系统能够定位柴油机磨损故障的部位,并诊断其故障性质及原因．     

The molecular basis of the sparse fur mouse mutation

The ornithine transcarbamylase-deficient sparse fur mouse is an excellent model to study the most common human urea cycle disorder. The mutation has been well characterized by both biochemical and enzymological methods, but its exact nature has not been revealed. A single base substitution in the complementary DNA for ornithine transcarbamylase from the sparse fur mouse has been identified by means of a combination of two recently described techniques for rapid mutational analysis. This strategy is simpler than conventional complementary DNA library construction, screening, and sequencing, which has often been used to find a new mutation. The ornithine transcarbamylase gene in the sparse fur mouse contains a C to A transversion that alters a histidine residue to an asparagine residue at amino acid 117.     

Nucleotide sequence and expression of an AIDS-associated retrovirus (ARV-2)

The nucleotide sequence of molecular clones of DNA from a retrovirus, ARV-2, associated with the acquired immune deficiency syndrome (AIDS) was determined. Proviral DNA of ARV-2 (9737 base pairs) has long terminal repeat structures (636 base pairs) and long open reading frames encoding gag (506 codons), pol (1003 codons), and env (863 codons) genes. Two additional open reading frames were identified. Significant amino acid homology with several other retroviruses was noted in the predicted product of gag and pol, but ARV-2 was as closely related to murine and avian retroviruses as it was to human T-cell leukemia viruses (HTLV-I and HTLV-II). By means of an SV-40 vector in transfected simian cells, the cloned gag and env genes of ARV-2 were shown to express viral proteins.     

Detection of single base substitutions by ribonuclease cleavage at mismatches in RNA:DNA duplexes

Single base substitutions can be detected and localized by a simple and rapid method that involves ribonuclease cleavage of single base mismatches in RNA:DNA heteroduplexes. A 32P-labeled RNA probe complementary to wild-type DNA is synthesized in vitro and annealed to a test DNA containing a single base substitution. The resulting single base mismatch is cleaved by ribonuclease A, and the location of the mismatch is then determined by analyzing the sizes of the cleavage products by gel electrophoresis. Analysis of every type of mismatch in many different sequence contexts indicates that more than 50 percent of all single base substitutions can be detected. The feasibility of this method for localizing base substitutions directly in genomic DNA samples is demonstrated by the detection of single base mutations in DNA obtained from individuals with beta-thalassemia, a genetic disorder in beta-globin gene expression.     

DNA序列判别分类模型

[目的]结合生物学知识和数学方法构建DNA序列判别分类模型。[方法]根据氨基酸分子中侧链基的极性性质,从不同序列中氨基酸含量不同提炼出能从碱基含量和碱基排列情况两方面代表序列特征的氨基酸类别信息,用一个四维向量来表征,用马氏距离法和FISHER判别法对给定序列进行分类。[结果]该模型中,2种分类方法所得的样本回代率均达100%,分类一致率为90%。[结论]该模型算法简单,分类结果精度较高,优于仅基于碱基含量的判别分类模型。     

Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe

The farming way of life originated in the Near East some 11,000 years ago and had reached most of the European continent 5000 years later. However, the impact of the agricultural revolution on demography and patterns of genomic variation in Europe remains unknown. We obtained 249 million base pairs of genomic DNA from ~5000-year-old remains of three hunter-gatherers and one farmer excavated in Scandinavia and find that the farmer is genetically most similar to extant southern Europeans, contrasting sharply to the hunter-gatherers, whose distinct genetic signature is most similar to that of extant northern Europeans. Our results suggest that migration from southern Europe catalyzed the spread of agriculture and that admixture in the wake of this expansion eventually shaped the genomic landscape of modern-day Europe.     

稻纵卷叶螟危害孕穗期水稻的光谱诊断

【目的】阐明稻纵卷叶螟（Cnaphalocrocis medinalis）危害孕穗期水稻后,水稻冠层、未受害展开叶和受害已卷叶片的光谱特征,建立基于光谱参数的稻纵卷叶螟危害程度的诊断模型。【方法】利用便携式光谱仪测定不同卷叶率小区水稻的冠层光谱反射率,同时在不同卷叶率小区内采集未受害展开叶和已卷叶带回实验室进行室内单叶的光谱反射率测定,并采用相关分析与回归建模方法组建稻纵卷叶螟危害程度的光谱诊断模型。【结果】水稻冠层光谱反射率在近红外光区域内随卷叶率级别的升高而降低,738-1 000 nm处的反射率可较好地表征出水稻受稻纵卷叶螟危害的程度。不同卷叶率小区内的未受害叶的光谱反射率也可很好地表征水稻的受害级别,在512-606和699-1 000 nm处的反射率与小区卷叶率级别呈极显著的负相关。已受害卷叶的反射率在582-688 nm处与受害级别呈极显著正相关。水稻受稻纵卷叶螟危害后,在冠层、未受害叶及已受害卷叶光谱的红边幅值与红边面积有明显变化。利用水稻冠层光谱的红边幅值、未受害健康叶片550 nm处的反射率建立的稻纵卷叶螟危害程度的一元回归模型的诊断误差较小,而同时利用冠层、受害叶和未受害叶光谱组建的逐步回归模型的诊断误差最小,可用于小区稻纵卷叶螟危害的监测。【结论】受害区域内水稻冠层在738-1 000 nm处和未受害叶片在512-606和699-1 000 nm处的光谱反射率,以及红边幅值和红边面积均可较好地表征水稻受稻纵卷叶螟危害后的卷叶率级别,可利用这两层次的光谱指标分别对小区水稻的受害程度进行诊断。