Yeast genomic databases and the challenge of the post-genomic era

Since the completion of the yeast genome sequence in 1996, three genomic databases, the Saccharomyces Genome Database, the Yeast Proteome Database, and MIPS (produced by the Munich Information Center for Protein Sequences), have organized published knowledge of yeast genes and proteins onto the framework of the genome. Now, post-genomic technologies are producing large-scale datasets of many types, and these pose new challenges for knowledge integration. This review first examines the structure and content of the three genomic databases, and then draws from them and other resources to examine the ways knowledge from the literature, genome, and post-genomic experiments is stored, integrated, and disseminated. To better understand the impact of post-genomic technologies, 20 collections of post-genomic data were analyzed relative to a set of 243 previously uncharacterized genes. The results indicate that post-genomic technologies are providing rich new information for nearly all yeast genes, but data from these experiments is scattered across many Web sites and the results from these experiments are poorly integrated with other forms of yeast knowledge. Goals for the next generation of databases are set forth which could lead to better access to yeast knowledge for yeast researchers and the entire scientific community. Electronic Publication     

24种香稻品种甜菜碱醛脱氢酶2基因突变位点的分析及分子标记开发

根据香型与非香型水稻甜菜碱醛脱氢酶2基因(badh2)在第2、第4内含子、第7外显子3处序列差异和第2外显子1处序列差异,分别设计了两类检测badh2第7和第2外显子突变的功能性分子标记引物M7和M2;利用两类引物,分别对属于第7外显子突变的香型水稻W香99075和第2外显子突变的香型水稻武香14、非香型水稻以及两种香稻分别与非香稻杂交的F1植株基因组DNA进行PCR检测后发现,M7和M2引物完全能够分别被用于以第7和第2外显子突变的香稻作为亲本,进行分子标记辅助培育香稻新品种的研究.M7引物综合考虑了badh2内含子和外显子两方面突变情况而设计的.以非香稻261S、分别发生第7和第2外显子突变的香稻品种W香99075和武香14为对照,使用M7和M2引物,对本实验室收集的另外22份香稻品种进行badh2突变位点检测,结果可将这些香稻分为badh2第2外显子突变类型、第7外显子突变类型和外显子未发生突变类型,同时明确了大多目前在上海等周边地区种植的香稻品种的badh2所属的突变位点.开展本研究为利用分子标记辅助选育香型水稻新品种研究奠定了重要的基础.     

转基因海带的研究现状

海带是海洋中一种极其重要的经济海藻。转基因技术在海带科研中的应用,将使海带的附加值得到进一步的提高。就海带遗传转化方法,以及转GUS基因、转lacZ基因、转CAT基因、转bar基因等报告基因和转HBsAg基因、转r-PA基因等功能基因海带的研究现状进行了综述。     

Goosecoid基因突变与先天性小耳畸形的关系

目的:对收集的43例先天性小耳畸形患者进行遗传因素分析,对Goosecoid(GSC)基因测序,探讨GSC基因与先天性小耳畸形的关系。方法:采集43例小耳畸形患者的外周血提取基因组DNA,对GSC基因的三个外显子分别设计引物,经PCR扩增纯化后直接测序。结果:6例患者在第二外显子的第197bp处发生了C→T的同义突变,编码氨基酸仍为酪氨酸;2例患者在第三外显子的第125bp处发生了A→G的错义突变,编码氨基酸由谷氨酸变成谷氨酰胺。结论:在先天性小耳畸形的患者中发现了GSC基因的突变。     

Proenkephalin transgenic mice: A short promoter confers high testis expression and reduced fertility

The regulation and possible function of the preproenkephalin gene in testis were studied in vivo in transgenic mice containing: (1) bases ?193 to +210 of the human proenkephalin gene and an additional one kilobase of 3' proenkephalin flanking sequence driving expression of bacterial chloramphenicol acetyltransferase (CAT), and (2) the same promoter and flanking sequences driving expression of a rat proenkephalin cDNA. Five lines of mice, designated HEC1–5, expressed the first construct and 10, HER1–10, the second. Each HEC male and many HER males showed dramatic expression of the transgene in the testis, although much lower expression was observed in the brain and other enkephalin-producing tissues. High levels of expression in testis can thus be achieved with a very short promoter region and do not require intron A sequences previously considered necessary. Altered enkephalin expression may affect testicular function. One founder, HER8, displayed grossly abnormal testicular morphology and was completely infertile. A second founder, HER6, had low sperm motility. Two offspring from other lines also displayed subnormal fertility. These studies support a role for specific promoter sequences in testis expression and may further support a significant role for proenkephalin in testicular function. © 1994 Wiley-Liss, Inc.     

苏云金芽胞杆菌HD-73菌株sigE基因敲除突变株的构建与特点

SigE因子是芽胞杆菌芽胞形成过程中起重要作用的sigma因子,它控制着众多芽胞形成相关基因的表达.在苏云金芽胞杆菌中,Cryl等杀虫晶体蛋白的表达也受SigE因子的控制.本研究利用同源重组技术构建了苏云金芽胞杆菌库斯塔克亚种标准菌株HD-73 sigE缺失突变株.研究表明:突变株衰亡期提前,丧失了形成芽胞和晶体的能力:cryIAa指导的β-半乳糖苷酶活性分析表明sigE基因对crylAa基因的转录有较大影响.利用载体pHT315携带sigE所在操纵子spoIIG及其启动子序列在突变株中表达,使突变株恢复了产生芽胞和形成杀虫晶体的能力,生长基本恢复正常,这些结果表明SigE因子是Bt库斯塔克亚种菌株产生芽胞和形成晶体所必需的.     

Screening for ferrochelatase mutations: molecular heterogeneity of erythropoietic protoporphyria

The DNA of 21 patients from 19 unrelated families with erythropoietic protoporphyria (EPP) were screened for the 6 ferrochelatase point mutations so far described. The mutation previously described by us (A ? t transversion at position ?3 of the donor site of intron 10, causing exon 10 skipping) was detected in two additional unrelated EPP patients: in these patients, cDNA lacking exon 10 was also detected. The mutation described by Nakahashi et al. as responsible for exon 2 skipping (C ? T transition at position ?23 of the acceptor site of intron 1), although also observed in some normal individuals, was invariably observed in all EPP patients tested and may thus play some role in the pathognesis of EPP. Thus, it does not appear that this mutation is the primary mechanism underlying exon 2 skipping. None of the other four previously described mutations were detected. These data demonstrate the heterogeneity of the ferrochelatase locus and of the genetic defect in EPP.     

药用植物功能基因

药用植物功能基因研究是药用植物基因研究中最活跃的领域。以药用植物功能基因在GenBank中注册的统计数据为基础 ,介绍了药用植物功能基因研究的最新进展。注册的功能基因涉及 32属 42种药用植物。统计数据包括 :自 1 992年至 2 0 0 3年 (前 9个月 )每年注册基因总数、基因注册数最多的 1 6种主要的药用植物以及在药用植物功能基因研究方面比较活跃的 1 4个国家。还重点报道了植物功能基因专利注册情况、黄酮类化合物与紫杉醇生物合成基因研究进展以及植物P45 0基因研究现状 ,对药用植物生物合成功能基因研究的发展趋势进行了探讨。     

解脂耶氏酵母tsr1突变体的构建

将解脂耶氏酵母与蛋白质分泌有关的TSR1基因编码区部分缺失的DNA片段转化一株解脂耶氏酵母,通过体内同源重组,部分缺失的外源tsr1片段取代了酵母染色体上的正常的TSR1基因,从而获得tsr1的转化子。Southern杂交结果表明,用该法成功地构建了tsr1突变体,这为进一步研究解脂耶氏酵母TSR1基因的功能奠定了基础。     

On the maintenance of genetic variation: global analysis of Kimura's continuum-of-alleles model

Methods of functional analysis are applied to provide an exact mathematical analysis of Kimura's continuum-of-alleles model. By an approximate analysis, Kimura obtained the result that the equilibrium distribution of allelic effects determining a quantitative character is Gaussian if fitness decreases quadratically from the optimum and if production of new mutants follows a Gaussian density. Lande extended this model considerably and proposed that high levels of genetic variation can be maintained by mutation even when there is strong stabilizing selection. This hypothesis has been questioned recently by Turelli, who published analyses and computer simulations of some multiallele models, approximating the continuum-of-alleles model, and reviewed relevant data. He found that the Kimura and Lande predictions overestimate the amount of equilibrium variance considerably if selection is not extremely weak or mutation rate not extremely high. The present analysis provides the first proof that in Kimura's model an equilibrium in fact exists and, moreover, that it is globally stable. Finally, using methods from quantum mechanics, estimates of the exact equilibrium variance are derived which are in best accordance with Turelli's results. This shows that continuum-of-alleles models may be excellent approximations to multiallele models, if analysed appropriately.     

乙型肝炎病毒（HBV）核心基因的变异及分析

对１８份不同类型的乙型肝炎病毒感染者血清及４份肝癌组织,用套式ＰＣＲ扩增ＰｒｅＣ／Ｃ基因,结果１５份标本可供进行核苷酸序列分析。１２例血清标本在Ｃ区均出现点突变并导致氨基酸改变。１份肝癌患者的血清及癌组织与另１份癌组织中获得的Ｃ基因克隆有２１３－３２４个核苷酸缺失。     

Association of the mutation for the human carboxypeptidase E gene exon 4 with the severity of coronary artery atherosclerosis

Objective: To test the hypothesis that the identification of mutation in the carboxypeptidase E (CPE) gene which leads to marked hyperproinsulinaemia is consistent with a possible role for mutations in CPE in the development of coronary atherosclerosis. Methods: The study subjects consisted of 1084 consecutive patients (812 males and 272 females) who will undergo coronary angiography. The severity of coronary atherosclerosis was defined by the Gensini’s score system. The proinsulin level was measured using highly sensitive two-site sandwich ELISA methods. Screening for mutations of the 4th exon and exon-intron junctional region of the CPE gene was performed by polymerase chain reaction followed by bidirectional sequencing. Results: Sequencing of the CPE gene exon 4 in 1084 consecutive patients revealed 2 genetic variants, the G–to-A substitution at nucleotide 2855 in exon 4 (synonymous mutation) and A-to-G substitution at nucleotide 2925 in intron 4. Although the proinsulin level was not influenced by the presence of the two point mutation, the Gensini score was significantly influenced by the presence of the A2925G mutant (P = 0.023). Furthermore, we found a higher prevalence of subjects with the A2925G heterozygous mutant among higher Gensini score subjects than it among lower Gensini score subjects, and this difference reached statistical significance (P = 0.006, OR 1.465, 95%CI 1.116–1.924). In addition, the frequency distribution of the G2855A mutant was differed in the higher Gensini score subjects than it in the lower Gensini score subjects belonging to high-risk category as smokers, and the statistical significance was reached (P = 0.043, OR 2.075, 95%CI 1.024–4.207). Conclusions: In the present study, the severity of the coronary atherosclerosis estimated by Gensini score was significantly influenced by the presence of the A2925G mutant and G2855A mutant of the CPE gene, and the exactly mechanism underlying the association needs further study.     

香蕉基因组测序及胁迫相关功能基因研究进展

香蕉是重要的热带水果之一,是世界第四大粮食作物。香蕉抗性相关的功能基因组学研究一直是香蕉研究的热点和核心。综述了近年来香蕉基因组测序、胁迫相关功能基因分离和鉴定等方面的最新研究进展,将有助于从源头上对香蕉进行创新性的研究,为香蕉遗传改良和新品种培育提供一定的理论依据。     

Mutations in p53 cDNA sequence introduced by retroviral vector

The high mutation rates of retroviruses are a potential problem with retroviral vectors. We studied the mutation rates and spectra of p53 sequences transduced with a retroviral vector in a cancer gene therapy model. When p53-deficient H358 non-small cell lung cancer cells were treated with a retroviral vector carrying normal p53 cDNA, most of transduced cells were killed by apoptosis. However, a small number of clones escaped p53-mediated apoptosis. We examined the p53 cDNA structure in these resistant clones. PCR-based analysis showed that 88/102 clones had detectable mutations in p53, including gross rearrangements, deletions/insertions, and base substitutions. To study the mutation rate of the p53 sequence in all transduced clones, the retroviral vector containing the non-functional p53 gene and the Neo-resistant marker gene was introduced into H358 cells. Only one of 95 isolated clones showed a base substitution. These results indicate that the mutation rate of p53 is not particularly high, but there is a significant risk that cancer cells will resist p53 gene therapy as a result of retroviral replication errors.     

Protecs,a comprehensive and powerful storage and analysis system for OMICS data,applied for profiling the anaerobiosis response of Staphylococcus aureus COL

Broad functional genomic studies call for comprehensive and powerful data repositories for storage of genome sequences, experimental information, protein identification data, protein properties and expression values. The better such data repositories can integrate and display complex data in a clear and structured way the more biologically meaningful conclusions or novel hypotheses can be derived from extensive omics data sets. This work presents the web accessible database system Protecs and how it was used to support analysis of 50 samples drawn from four Staphylococcus aureus cultivations under anaerobiosis. Protecs incorporates findings from visualization science, e.g. micro charts and heat maps in the user interface. Its integrated tools for expression data analysis in combination with TIGR Multi Experiment Viewer were used to highlight similar gene expression profiles in single or multiple experiments based on the continuously updated S. aureus master gel. Raw data analysis results are available online at www.protecs.uni‐greifswald.de . Our meta‐study revealed that S. aureus responds in different anaerobiotic experimental setups (growth without oxygen; growth without oxygen but with supplemental pyruvate and uracil; growth without oxygen but with NO; growth without oxygen but with NO and without functional nreABC genes) with a general anaerobiosis response. Among others, this response is characterized by an induction of fermentation enzymes (PflB, Ldh1, SACOL0135, SACOL0660) as well as the response regulator SrrA. Interestingly, especially genes with a high codon adaptation index highly overlap with anaerobically induced genes.     

Oxidative stress plays a permissive role in α2-adrenoceptor-mediated events in immortalized SHR proximal tubular epithelial cells

Objective To test the hypothesis that the identification of mutation in the carboxypeptidase E (CPE) gene which leads to marked hyperproinsulinaemia is consistent with a possible role for mutations in CPE in the development of coronary heart disease. Methods The study subjects consisted of 51 consecutive patients (34 males and 17 females) who will undergo coronary angiography for suspected or known coronary atherosclerosis. Coronary heart disease (CHD) was defined as having a luminal diameter stenosis ≥50% in at least one of three major coronary arteries by coronary angiography or based on the Rose Questionnaire. The insulin and proinsulin level were measured using highly sensitive two-site sandwich ELISA methods. Screening for mutations of the eight exons of the CPE gene was performed by polymerase chain reaction followed by bidirectional sequencing. Results We scanned eight exons and exon–intron junctional region. Overall, we found 12 distinct variants in the intron region and three variants in the exon region. Among the 15 variants, 10 mutations were rare. The further explored study reveal that the above five non-rare variants would not affect the level of glucose, insulin, and proinsulin. However, the results suggest that the prevalence of the coronary heart disease was significant difference between the wild type group and mutant type group according to the A4545G (P = 0.020). The results from the logistic regression reveal that the subjects with the CPE mutation of A4545G, the odds ratio for the coronary heart disease was 0.196 (95% CI: 0.046 to 0.830, P = 0.027). Conclusions In the present study, the mutation of CPE gene would not affect the level of glucose, insulin, and proinsulin. The hypothesis of a possible role for mutations in CPE in the development of coronary heart disease needs further study.