猪1型圆环病毒全基因组克隆及其感染性初步鉴定

猪圆环病毒(porcine circovirus,PCV)是由Tis-cher等[1]于1974年在PK-15细胞中发现,当时认为是一种细胞污染物,后被证实为一种新的病毒。病毒粒子为20面体对称,无囊膜,以滚环方式进行复制,可在PK-15细胞上生长但不引起细胞病变。其基因组是一种环状、单股副链DNA,与鸡贫血病毒(chicken anemia virus,CAV)、鹦鹉喙羽病毒(psittacine beak and feather disease circovirus,PBF-DAV)和人的TT病毒(transfusion transmittedvirus,TTV)同属圆环病毒科。猪圆环病毒有两种基因型即:PCV1和PCV2。前者广泛存在于猪源肾细胞中,在猪的组织…     

NMR studies of aurein 1.2 analogs

Aurein 1.2 is an antimicrobial and anticancer peptide isolated from an Australian frog. To improve our understanding of the mechanism of action, two series of peptides were designed. The first series includes the N-terminal membrane anchor of bacterial glucose-specific enzyme IIA, aurein 1.2, and a newly identified aurein 1.2 analog from human LL-37 (LLAA). The order of antibacterial activity is LLAA > aurein 1.2 >> the membrane anchor (inactive). The structure of LLAA in detergent micelles was determined by ¹H NMR spectroscopy, including structural refinement by natural abundance ¹³C^α, ¹³C^β, and ¹⁵N chemical shifts. The hydrophobic surface area of the 3D structure is related to the retention time of the peptide on a reverse-phase HPLC column. The higher activity of LLAA compared to aurein 1.2 was attributed to additional cationic residues that enhance the membrane perturbation potential. The second peptide series was created by changing the C-terminal phenylalanine (F13) of aurein 1.2 to either phenylglycine or tryptophan. A closer or further location of the aromatic rings to the peptide backbone in the mutants relative to F13 is proposed to cause a drop in activity. Phenylglycine with unique chemical shifts may be a useful NMR probe for structure-activity relationship studies of antimicrobial peptides. To facilitate potential future use for NMR studies, random-coil chemical shifts for phenylglycine (X) were measured using the synthetic peptide GGXGG. Aromatic rings of phenylalanines in all the peptides penetrated 2-5 Å below the lipid head group and are essential for membrane targeting as illustrated by intermolecular peptide-lipid NOE patterns.     

Tools for assessing European streams with macroinvertebrates: major results and conclusions from the STAR project

This short paper summarises the information developed in the EU funded research project STAR on autecology databases, metrics, multimetrics and community approaches. For Europe the WFD implementation gave an important stimulus for the development of ecology based assessment techniques. Along with the development of metrics and multimetrics indices taxalists and autecological information were strongly improved. Recommendations are given to further develop ecological assessment in European streams and rivers.     

基于滑动窗口的原核转录起始位点计算定位方法

转录起始位点的计算定位是基因转录调控研究的重要内容,但现有方法的识别性能较低。文章作者在已有原核启动子识别算法的基础上,提出了一种基于滑动窗口的原核转录起始位点计算定位方法,通过在合理限定的定位范围内对序列进行滑动扫描,来预测转录起始位点的位置。首先根据窗口序列的交迭组分特征和启动子其它特征分别建立二次判别分类器,用其计算对应位置的似然得分,再利用转录起始位点与翻译起始位点的间隔经验分布信息对似然得分进行修正,最后依照似然得分的分布情况由阈值定位算法确定预测位置。对大肠杆菌真实序列数据的测试结果表明,该定位算法可实现对真实转录起始位点位置的有效预测,与已有算法相比,当敏感性指标同为0.85左右时,特异性指标可从0.20提高至0.65,从而使得定位准确率提高了约20个百分点。     

Construction of a linkage map of Lentinula edodes (shiitake) with the HEGS (high-efficiency genome scanning) system: use of versatile AFLP and PCR-based gene markers

An improved linkage map of Lentinula edodes (shiitake) was constructed with an HEGS (high-efficiency genome scanning) system. Two hundred twenty-one HEGS-derived amplified fragment length polymorphism (AFLP-H) markers and 21 gene markers were developed and combined with 203 previously developed sequencer-derived AFLP markers (AFLP-S markers) and 3 mating factor loci (A, Bα, and Bβ) to construct a comprehensive linkage analysis. As a result, a novel linkage map with 166 markers including 2 mating factors (A and B), 10 HEGS-derived gene markers, 72 AFLP-H markers, and 82 AFLP-S markers was obtained. Of the total 448 markers, 273 could not be located on a linear map and thus were assigned to linkage groups as accessory markers. The map covers a total length of 1398.4 centimorgans (cM) with an average marker interval distance of 8.4 cM. The map consists of 11 linkage groups (LGs) in agreement with our previous map, and 7 LGs among them were found to contain branched linkages, which may be the result of reciprocal translocations representing dynamic reorganization of the shiitake genome. The previously reported linkage map was improved in terms of number of markers, marker density, linear order of markers, and total map length. Contribution no. 384 of the Tottori Mycological Institute     

Life Cycle Assessment of a Personal Computer and its Effective Recycling Rate (7 pp)

Background, Aims and Scope Telecommunication and information technology, dramatically emerged during the last decade, has generated environmental problems by accelerating mass production, mass consumption, and mass disposal of personal computers (PCs) in Korea. In addition, it has led the Korean new economy. The Korean government has encouraged researchers and industry to study the environmental impact, adequate disposal treatment, and the reasonable recycling rate of an end-of-life personal computer. The main purpose of this research is to investigate the life cycle environmental impact of PCs and to determine the desirable or feasible recycle rate of an end-of-life PC. An LCA on a PC was performed based on different recycling scenario. Target audiences are new product developers, designers, product recovery managers and environmental policy makers who are interested in the environmental impact of PCs and recycling of end-of-life products. Methods A target product is a Pentium IV personal computer made in Korea in 2001, excluding the monitor and peripheral equipment. The procedure of the LCA followed the ISO14040 series. System boundary includes the entire life cycle of the product, including pre-manufacturing (the electrical parts and components manufacturing), manufacturing, transportation, use, and disposal. The LCI and impact assessment database for a PC was constructed using SIMAPRO version 4.0 software and LCI information was compiled by site-specific data and the Korean national database. The LCA was performed on different recycling scenarios: one being that of the current recycling rate of 46%, and the other being the ideal condition of a 100% recycling rate. Results and Discussion Abiotic depletion, global warming, ecotoxicity, human toxicity, acidification, ozone layer depletion, photo-oxidant formation, and eutrophication are adopted as the impact categories. The pre-manufacturing stage was a significant stage for all of the environmental parameters, besides human toxicity potential. PC manufacturing consists of rather simple processes such as assembly and packaging. For improving the environmental performance of PCs, environmental management approaches of design for the environment and green procurement are recommended. The use stage had a significant potential due to the electricity consumption produced by burning fossil fuel. The disposal stage's contribution to environmental impact was largest in human toxicity, and second largest in ozone layer depletion potential. The PC recycling was shown to inhibit all environmental impacts with the exception of the ozone depletion and ecotoxicity potential. The increase of light oil, nitric acid, sulfuric acid, and deoxidating agent consumption during the recycling process contributes to the environmental impact of ozone and ecotoxicity parameters. Current recovery and recycling technologies should be taken into account for enhancing the benefits of recycling. Anyway, the effectiveness of recycling was highlighted by this study. PC recycling reduces the total environmental impact of the product. The PC recycling is recommended to be raised up to at least 63% in order to reduce the environmental burdens of a PC in other life cycle stages. Conclusion and Recommendation This study implies that design for the environment (DfE) in the product design stage and green procurement are recommended for improving the entire environmental performance of electronic equipment such as PCs. The recycling of waste PCs clearly reduces the environmental burden. There are, however, trade-offs among environmental parameters according to the PC recycling rate. Current recycling methods are not effective in reducing ozone depletion and ecotoxicity environmental impact. The product recovery is another key for efficient recycling. Efficient reverse logistics to collect and transport end-of-life PCs should be taken into account to enhance recycling effects. There were several electrical parts not included in this assessment, due to the unavailability of adequate data. Further studies with more detail and reliable inventories for electrical parts and sub-components are recommended. Furthermore, costs of recycling should also be treated in further research.     

应用两种基因组快速扩增方法进行病毒芯片杂交鉴定

为了摸索均衡的病毒基因组扩增方法,建立高通量的病毒检测基因芯片技术平台,本研究以甲病毒属的辛德比斯病毒作为检测模型,分别以随机PCR扩增法和MDA( Multiple Displacement Amplification)扩增法扩增病毒基因组,并以两种扩增产物作为模板,扩增辛德比斯病毒的特异基因片段以验证基因组扩增的均衡性;然后将两种基因组扩增产物标记荧光染料后与基因芯片进行杂交;结果表明从两种基因组扩增产物中正确扩增出了辛德比斯的特定基因片段,作为探针可与基因芯片上的靶标基因特异性结合;基因组扩增产物与基因芯片进行杂交,可成功检测到甲病毒属的特异性信号,充分说明随机PCR扩增法和MDA扩增法用于扩增病毒基因组均具有良好的均衡性,扩增产物可用于病毒性病原体的基因芯片检测。     

细菌人工染色体基因组文库构建方法的改进

目的:建立一种改进的更简便、易操作的细菌人工染色体(BAC)文库构建方法。方法:在构建猪霍乱沙门氏菌基因组大片段DNA的BAC文库时,对改进的基因组BAC文库构建方法和常规的BAC文库构建方法进行比较。结果:利用改进的方法可简便快速地构建猪霍乱沙门氏菌基因组BAC文库。结论:使用2种方法构建BAC文库,其转化效率,以及在BAC克隆中插入的DNA片段的大小和BAC克隆的稳定性等都相同,从而表明改进的方法更简单、更方便,它能使BAC文库的构建更为高效。     

Horizontal gene transfer in eukaryotes: The weak‐link model

The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes.     

Genome reduction as the dominant mode of evolution

A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron‐rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification.