The genetic code in mitochondria and chloroplasts

The universal genetic code is used without changes in chloroplasts and in mitochondria of green plants. Non-plant mitochondria use codes that include changes from the universal code. Chloroplasts use 31 anticodons in translating the code; a number smaller than that used by bacteria, because chloroplasts have eliminated 10 CNN anticodons that are found in bacteria. Green plant mitochondria (mt) obtain some tRNAs from the cytosol, and genes for some other tRNAs have been acquired from chloroplast DNA. The code in non-plant mt differs from the universal code in the following usages found in various organisms: UGA for Trp, AUA for Met, AGR for Ser and stop, AAA for Asn, CUN for Thr, and possibly UAA for Tyr. CGN codons are not used by Torulopsis yeast mt. Non-plant mt, e.g. in vertebrates, may use a minimum of 22 anticodons for complete translation of mRNA sequences. The following possible causes are regarded as contributing to changes in the non-plant mt: directional mutation pressure, genomic economization, changes in charging specificity of tRNAs, loss of release factor RF2, changes in RF1, changes in anticodons, loss of lysidine-forming enzyme system, and disappearance of codons from coding sequences.     

Prokaryotic genetic code

The prokaryotic genetic code has been influenced by directional mutation pressure (GC/AT pressure) that has been exerted on the entire genome. This pressure affects the synonymous codon choice, the amino acid composition of proteins and tRNA anticodons. Unassigned codons would have been produced in bacteria with extremely high GC or AT genomes by deleting certain codons and the corresponding tRNAs. A high AT pressure together with genomic economization led to a change in assignment of the UGA codon, from stop to tryptophan, in Mycoplasma.     

Selenoprotein W: a review

Purification of selenoprotein W (Se-W) from rat and monkey muscles was shown to exist in multiple forms: with or without reduced glutathione and/or a 41-Da moiety (identity still unknown). TGA is located at coding position 13 in Se-W complementary DNA (cDNA) from all five species studied (rats, mice, sheep, human and monkey). TGA is also the stop codon in the rodents and sheep cDNA, but TAA is the stop codon in primates. There is an 80% homology of the nucleotide sequence in the coding region among the five species of animals, and the predicted amino acid sequences are 83% identical (rodents identical and primates identical). Se-W levels are highest in muscle, heart and brain from sheep and primates, but very low in rodent hearts. Studies with tissue cultures of muscle and brain cells indicated that selenium influenced Se-W levels. Although the metabolic function of Se-W is unknown, preliminary data suggest that it has an antioxidant function.     

Use of the degeneracy of the genetic code by selective pressure to cut up genes of procaryote genomes

The DNA sequences of three bacteriophages are analysed in order to localise those parts coding for a protein. A weak stability on the DNA molecule allows us to characterize the beginning and the end of genes. A survey of the codons used shows that the cause for this weak stability is the systematic use of A-T bases in third position, which is made possible by the degeneracy of the genetic code.     

Nucleotide sequence determination of yeast mitochondrial phenylalanine-tRNA]

The primary structure of mitochondrial tRNAPhe from Saccharomyces cerevisiae, purified by two-dimensional polyacrylamide gel electrophoresis, was determined using, standard procedures on in vivo 32P-labeled tRNA, as well as the new 5'-end postlabeling techniques. We propose a cloverleaf model which allows for tertiary interaction between cytosine in position 46 and guanine in position 15 and maximizes base pairing in the psi C stem, thus excluding the uracile in position 50 from base pairing in the psi C stem. Comparison of the primary structure of this tRNA with all other known procaryotic, chloroplastic or cytoplasmic tRNAsPhe sequences does not lead to any conclusion about the endosymbiotic theory of mitochondria evolution.     

Aminoglycoside antibiotics: old drugs and new therapeutic approaches

Aminoglycoside antibiotics kill bacteria by binding to the ribosomal decoding site and reducing fidelity of protein synthesis. Since the discovery of these natural products over 50 years ago, aminoglycosides have provided a mainstay of antibacterial therapy of serious Gram-negative infections. In recent years, aminoglycosides have become important tools to study molecular recognition of ribonucleic acid (RNA). In an ingenious exploitation of the aminoglycosides’ mechanism of action, it has been speculated that drug-induced readthrough of premature stop codons in mutated messenger RNAs might be used to treat patients suffering from certain heritable genetic disorders. Received 23 January 2007; received after revision 25 February 2007; accepted 29 March 2007     

Structural studies of elongation and release factors

The elongation and termination steps of protein synthesis are controlled by elongation and release factors, respectively. Elongation factors deliver the aminoacyl tRNA to the ribosomal A site, ensuring the elongation of the nascent polypeptide chain by one amino acid at a time, while release factors recognize the stop codons and trigger the release of the polypeptide from the ribosome. Recently, highresolution crystal structures of ribosomes as well as translation factors on and off the ribosome have contributed a great deal to our understanding of the molecular basis of protein synthesis. This review concentrates on recent developments in our understanding of the elongation and termination steps of protein synthesis, particularly the roles of translation factors and their similarities and differences in the eukaryotic cytosol and prokaryotic systems, through a combination of structural and biochemical studies. Received 25 October 2007; received after revision 5 December 2007; accepted 7 December 2007     

Base pairing in messenger RNA's for small peptides

Longest runs of Watson-Crick pairing in hypothetical m-RNA's for a number of natural peptides were no greater than those in the hypothetical m-RNA's for a large number of randomized amino acid sequences from these peptides. This shown that even if base-pairing in m-RNA were a biological requirement, it would little constrain the amino acid sequence.     

Base pairing in messenger RNA's for small peptides

Summary Longest runs of Watson-Crick pairing in hypothetical m-RNA's for a number of natural peptides were no greater than those in the hypothetical m-RNA's for a large number of randomized amino acid sequences from these peptides. This shows that even if base-pairing in m-RNA were a biological requirement, it would little constrain the amino acid sequence.     

基于函数调用路径的软件实现与设计一致性验证

软件系统开发完成后,验证其是否完成了软件设计说明书的所有功能并且与设计算法一致,是软件测试的一项重要工作.通过人工遍历分析源代码来完成实现与设计的一致性验证是复杂费力的,并且需要测试人员具备丰富的编程经验和较强的算法分析能力.论文提出了一种基于函数调用路径的软件实现自动验证方法.从设计文档和源代码两个方面出发,分别分析其函数调用关系,提取函数调用路径,生成功能簇模型.其中文档方面通过人工理解设计文档,确定函数调用关系,然后自动生成标准功能簇模型;源代码方面通过静态分析,自动获取函数调用关系,提取功能点特征,利用这些特征提取功能点的具体实现算法,自动生成软件的实际功能簇模型.对比两个功能簇模型,验证软件实现与设计的一致性.实验结果表明：算法能够准确获得软件系统的功能结构及实现算法特征,对软件实现与设计的一致性做出有效判定,为软件实现与设计的一致性自动化测试提出一种新的思路.     

一类基于B2（mod m）序列的准循环LDPC码

基于B2(modm)序列,提出一种构造二元低密度奇偶校验(LDPC)码的新方法.这类编码的校验矩阵列重为3、行重为任意整数,并且具有准循环(QC)结构.校验矩阵对应的Tanner图围长至少为8,对应的最小距离至少为12.当m为素数时,提出一种减少8环的方法,使得Tanner图中4类可能的8环中两类被完全消除.仿真结果表明,m为素数时新LDPC码的译码性能优于渐进边增长(PEG)算法随机产生的(准)规则LDPC码.此外,提出一种基于邻域扩展搜索的启发式算法,利用该算法可以获得长度接近或达到上界的B2(modm)序列.     

基于主题建模和静态分析技术的软件代码功能性主题获取方法

近年来,基于主题建模技术的代码理解方法成为研究热点之一.该类方法期望利用主题建模技术从软件代码中挖掘功能性主题,进而利用功能性主题帮助开发人员理解软件功能及其代码实现.然而,从代码挖掘出的主题中,功能性主题与其他类型主题(如横切性主题)混杂在一起,需要人工识别功能性主题;由于现有工作大多仅提供主题关联的词等基本信息,导致识别及应用功能性主题的过程费时费力.针对以上问题,本文提出了一种基于主题建模和静态分析技术的软件代码功能性主题获取方法.该方法在利用一组启发式过滤规则对代码进行预处理的基础上,基于主题建模技术从代码中挖掘原始主题;进而,基于代码静态分析获得的代码间结构关系,提出了一种名为主题内聚度的技术从原始主题中自动识别功能性主题;最后,定位主题关联的代码片段,并利用代码及其注释为主题生成自然语言描述文本,进一步帮助开发人员理解主题所体现的软件功能及其代码实现细节.本文基于一组开源软件代码进行了方法评估,评估结果表明本文方法能够有效获取功能性主题及其关联信息,进而帮助开发人员更好地理解软件功能及其代码实现.     

The search for the right partner: Homologous pairing and DNA strand exchange proteins in eukaryotes

Finding the right partner is a central problem in homologous recombination. Common to all models for general recombination is a homologous pairing and DNA strand exchange step. In prokaryotes this process has mainly been studied with the RecA protein ofEscherichia coli. Two approaches have been used to find homologous pairing and DNA strand exchange proteins in eukaryotes. A biochemical approach has resulted in numerous proteins from various organisms. Almost all of these proteins are biochemically fundamentally different from RecA. The in vivo role of these proteins is largely not understood. A molecular-genetical approach has identified structural homologs to theE. coli RecA protein in the yeastSaccharomyces cerevisiae and subsequently in other organisms including other fungi, mammals, birds, and plants. The biochemistry of the eukaryotic RecA homologs is largely unsolved. For the fungal RecA homologs (S. cerevisiae RAD51, RAD55, RAD57, DMC1; Schizosaccharomyces pombe rad51; Neurospora crassa mei3) a role in homologous recombination and recombinational repair is evident. Besides recombination, homologous pairing proteins might be involved in other cellular processes like chromosome pairing or gene inactivation.     

一种基于一阶逻辑的软件代码安全性缺陷静态检测技术

软件代码安全性缺陷是可能引发软件系统高危后果的一类重要缺陷,针对该类缺陷的自动化检测和定位技术在软件维护和演化研究领域具有重要意义.本文提出并实现了一种形式化检测方法——基于一阶逻辑的软件代码安全性缺陷静态检测方法,利用命题逻辑和谓词逻辑定义模式路径公式,引入多个与依赖关系相关的谓词构造逻辑函数表达式,作为模式路径节点产生的制导条件,实现了对多类软件代码安全性缺陷的形式化描述,把安全性缺陷检测问题转化成在中间代码对应的有限状态空间中是否存在相应模式路径公式的判定问题.实验结果表明,该方法能适用于大多数类型的软件代码安全性缺陷检测,在对openssl,wu-ftpd等13个开源程序的测试中,准确重现了10个已公开安全漏洞,发现2个未公开安全漏洞.并且,与现有的模型检验等形式化静态分析方法相比,该方法的测试时间和代码规模成渐近线性关系.     

Retrocyclins and their activity against HIV-1

Primate theta-defensins are physically distinguished as the only known fully-cyclic peptides of animal origin. Humans do not produce theta-defensin peptides due to a premature stop codon present in the signal sequence of all six theta-defensin pseudogenes. Instead, since the putative coding regions of human theta-defensin pseudogenes have remained remarkably intact, their corresponding peptides, called “retrocyclins”, have been recreated using solid-phase synthetic approaches. Retrocyclins exhibit an exceptional therapeutic index both as inhibitors of HIV-1 entry and as bactericidal agents, which makes retrocyclins promising candidates for further development as topical microbicides to prevent sexually transmitted diseases. This review presents the evolution, antiretroviral mechanism of action, and potential clinical applications of retrocyclins to prevent sexual transmission of HIV-1.