Genome sequence of Yersinia pestis, the causative agent of plague

The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive infectious disease classically referred to as plague, and has been responsible for three human pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to nineteenth centuries) and modern plague (nineteenth century to the present day). The recent identification of strains resistant to multiple drugs and the potential use of Y. pestis as an agent of biological warfare mean that plague still poses a threat to human health. Here we report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is unusually rich in insertion sequences and displays anomalies in GC base-composition bias, indicating frequent intragenomic recombination. Many genes seem to have been acquired from other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins). The genome contains around 150 pseudogenes, many of which are remnants of a redundant enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a unique insight into the ways in which new and highly virulent pathogens evolve.     

Increased virulence of Yersinia pseudotuberculosis by two independent mutations

A chromosomally encoded protein, which mediates invasion into HeLa cells was recently identified in Yersinia pseudotuberculosis. The role of this protein (invasin) in the virulence process was not, however, investigated. We show that mutation of the invasin gene in Y. pseudotuberculosis abolishes the ability of the bacteria to invade HeLa cells. When mice were challenged by intraperitoneal injection both the mutant and the wild-type strain produced infections of similar virulence but mutant showed a slower rate of infection after oral challenge. A double mutant, carrying an additional mutation in the gene coding for the Yop1 protein, was also constructed. The double mutant was significantly more virulent than either the wild-type or the corresponding single mutants. Y. pestis, in contrast to Y. pseudotuberculosis lacks the ability to express either invasin or Yop1, sequence analysis of the yopA gene from both Y. pestis and Y. pseudotuberculosis shows that the yopA gene of Y. pestis contains a point-mutation leading to a reading-frame shift. When the yopA+ gene was introduced into Y. pestis the virulence of this strain was reduced. These results may provide insight into the rise and fall of plague epidemics caused by Y. pestis.     

Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins

Features of the physical environment surrounding an ancestral organism can be inferred by reconstructing sequences of ancient proteins made by those organisms, resurrecting these proteins in the laboratory, and measuring their properties. Here, we resurrect candidate sequences for elongation factors of the Tu family (EF-Tu) found at ancient nodes in the bacterial evolutionary tree, and measure their activities as a function of temperature. The ancient EF-Tu proteins have temperature optima of 55-65 degrees C. This value seems to be robust with respect to uncertainties in the ancestral reconstruction. This suggests that the ancient bacteria that hosted these particular genes were thermophiles, and neither hyperthermophiles nor mesophiles. This conclusion can be compared and contrasted with inferences drawn from an analysis of the lengths of branches in trees joining proteins from contemporary bacteria, the distribution of thermophily in derived bacterial lineages, the inferred G + C content of ancient ribosomal RNA, and the geological record combined with assumptions concerning molecular clocks. The study illustrates the use of experimental palaeobiochemistry and assumptions about deep phylogenetic relationships between bacteria to explore the character of ancient life.     

Evolutionary genetics: Ambiguous role of CCR5 in Y. pestis infection

Mecsas and colleagues suggest that a deficiency in the chemokine receptor CCR5 in humans is unlikely to confer protection against plague, based on their study of Yersinia pestis infection in Ccr5-deficient mice. They were testing the hypothesis that a mutation in the CCR5 gene, frequently found in Caucasians, may have been selected for in the past because it provided protection against (bubonic) plague; the mutation, called CCR5Delta32, is characterized by a 32-base-pair deletion. We have also tested this hypothesis by using Y. pestis infection in mice and, in addition, we have done phagocytosis experiments with macrophages from wild-type and Ccr5-deficient mice. Although, like Mecsas et al., we did not see any difference in the survival of the two groups of mice, we did find that there was a significantly reduced uptake of Y. pestis by Ccr5-deficient macrophages in vitro. Our results indicate that the role of Ccr5 in Y. pestis infection may therefore be more complex than previously thought.     

Community structure and metabolism through reconstruction of microbial genomes from the environment

Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.     

BALB／c小鼠选择与腹水产量和抗体效价间关系的研究

目的观察在鼠疫F1单克隆抗体制备过程中,BALB／c小鼠的选择和饲养与所获腹水量和抗体效价的关系,为大量制备该单克隆抗体提供实验室参考依据。方法根据小鼠周龄、性别和饲养条件对BALB／c小鼠进行分组,并采用动物体内诱生法制备腹水,间接ELISA用来检测腹水中F1单克隆抗体效价。结果12～16周龄组、雄性和加强营养组小鼠所获腹水产量和效价均高于其它周龄组和对照组。结论选择适当周龄的雄性小鼠、饲养过程中加强营养和管理可适当提高腹水产量和抗体的效价。     

Virulent strains of Toxoplasma gondii comprise a single clonal lineage.

The protozoan Toxoplasma gondii is a prevalent parasite in wild and domestic animals worldwide, being transmitted through the food chain by carnivorous feeding and scavenging. Toxoplasma normally divides asexually to yield a haploid form that can infect virtually any vertebrate but it also has a well defined sexual cycle that occurs exclusively in cats. Toxoplasma has become important as an often fatal opportunistic pathogen in patients with AIDS, although the 15-85% of adult human populations that are chronically infected with T. gondii are typically asymptomatic. Infections in immunocompromised hosts have variable outcomes. For example, only 30 to 50% of AIDS patients that are chronically infected with the parasite develop toxoplasmic encephalitis and only about half of acute maternal infections result in congenital disease of the newborn. T. gondii strains differ in their virulence in animals, but the extent to which different strains are related has not been determined. Here we analyse 28 strains from a variety of hosts on five continents and find that the ten virulent strains have an essentially identical genotype, whereas the nonvirulent strains are moderately polymorphic. These data strongly suggest that virulent strains of T. gondii originated from a single lineage which has remained genetically homogeneous despite being globally widespread, and despite the ability of this organism to reproduce sexually.     

如何正视李约瑟博士的中国科技史研究

认为李约瑟博士对中国人民的伟大贡献在于他使中国科学技术史开始获得世界学术界的公认；他的里程碑式的巨著离不开中国政府与海内外华人精神上与金钱上长期的大力支持，同样也离不开众多华裔学者的合作与帮助。     

云南鼠疫菌随机引物扩增DNA多态性指纹图谱分析

目的：分析云南不同地区、不同年代分离鼠疫菌的基因表型。方法：采用随机引物扩增技术（RAPD）对菌株进行分析。结果：共检测了28株鼠疫菌，除一株外，27株均显示有13条带型，并与假结核菌和小肠结肠炎菌有明显的区别。结论：云南家、野两型鼠疫菌株可能具有相同的随机引物扩增基因表征。     

Man-Induced Landscape Evolution in the North Caucasian Piedmont of Russia

Paleosols buried by colluvial deposits and artificial agricultural terraces were investigated to reconstruct natural and man-induced environmental change in the central North Caucasus. The profiles buried under ancient man-made agricultural terraces (1000-1500 years B.P.) are similar to recent surface Chemozems. Minor differences in thickness, humus and carbonate content of Ah horizons are due to anthropogenic disturbance before burial or diagenesis. This indicates that a steppe ecosystem persisted in the central North Caucasian piedmont during late Holocene. The sections of colluvial sediments in downslope positions show alternation of coarse stony slope deposits and well developed though truncated paleosol profiles. This indicates that periods of soil formation and low activity of colluviation alternated with dramatic intensification of mass movement on slopes. The early medieval anthropogenic deforestation may have destabilised slopes and activated development of the upper layer of the coarse colluvium. Pedofeatures related to ancient cultivation were detected in the paleosol below this layer.     

Caenorhabditis elegans: plague bacteria biofilm blocks food intake

Bubonic plague is transmitted to mammals, including humans, by the bites of fleas whose digestive tracts are blocked by a mass of the bacterium Yersinia pestis. In these fleas, the plague-causing bacteria are surrounded by an extracellular matrix of unknown composition, and the blockage depends on a group of bacterial genes known as the hmsHFRS operon. Here we show that Y. pestis creates an hmsHFRS-dependent extracellular biofilm to inhibit feeding by the nematode Caenorhabditis elegans. Our results suggest that feeding obstruction in fleas is a biofilm-mediated process and that biofilms may be a bacterial defence against predation by invertebrates.     

Origin of a gene regulatory mechanism in the evolution of echinoderms

A rich diversity of ancient sea urchin lineages survives to the present. These include several advanced orders as well as the cidaroids, which represent the group ancestral to all other sea urchins. Here we show that all advanced groups of sea urchins examined possess in their eggs a class of maternal messenger RNA (mRNA) encoded by the evolutionarily highly conserved alpha-subtype histone genes. The maternal histone mRNAs are unique in their time of accumulation in oogenesis, their localization in the egg nucleus and their delayed timing of translation after fertilization. Cidaroid sea urchins as well as other echinoderm classes, such as starfish and sea cucumbers, possess the genes but do not have maternal alpha-subtype histone mRNAs in their eggs. Thus, although all the echinoderms examined transcribe alpha-subtype histone genes during embryogenesis, the expression of these genes as maternal mRNAs is confined to advanced sea urchins. The fossil record allows us to pinpoint the evolution of this mode of expression of alpha-histone genes to the time of the splitting of advanced sea urchin lineages from the ancestral cidaroids in a radiation which occurred in a relatively brief interval of time approximately 190-200 Myr ago. The origin of a unique gene regulatory mechanism can thus be correlated with a set of macroevolutionary events.     

客家方言与中古汉语言联系之管窥

汉语方言都具有存古的性质，其中客家方言就保留了不少中古汉语的词汇和语法，博白和北海属于客家人聚居较多的地方，一些仍活跃在博白、北海两地客家人的日常生活中的词汇、语法与古诗文的词汇、语法有惊人的一致性，用北海、博白两地客家人日常生活中还在使用的词汇、语法去解释印证古诗文文献，就可发现现代一些书本对古诗文的一些字词的解释，远不如用客家方言解释得生动形象、贴切。如能从训诂的角度进行深入的发掘研究，将可对客家方言与中古汉语的联系有事深广的冶孤．     

论西方近现代议会政治的中世纪基础

作为近现代西方民主政治核心的议会政治。不是起源于古希腊、罗马的民主政治中，而是起源于中世纪．近现代英国的议会制度就是从中世纪的等级会议一脉相承地发展而来，而在欧洲中世纪中后期普遍存在的市民议会也为各地近现代议会制度的建立创造了条件。     

徽州历史文化资源特色数据库建设研究——以徽州古祠堂为例

徽州古祠堂是徽州历史文化的一个重要组成部分,它反映了明清时期徽州宗法家族制度;为了能够更好地传承和利用徽州古祠堂相关资源和历史文化,同时也是更好地对外宣传徽州文化,对徽州古祠堂相关信息数据化进行了研究,提出建设一个徽州古祠堂特色数据库平台,从特色数据库平台建设资源选择对象和数据库结构设计以及物理实现3个方面展开研究和论述,以期能够为徽州文化历史资源的保护做出应有的贡献,同时也为其他徽州特色资源数据库的建设提供一定的参考价值.     

Low variability in a Y-linked plant gene and its implications for Y-chromosome evolution

Sex chromosomes have evolved independently in several different groups of organisms, but they share common features, including genetic degeneration of the Y chromosome. Suppression of recombination between ancestral proto-X and proto-Y chromosomes is thought to have led to their gradual divergence, and to degeneration of the Y chromosome, but the evolutionary forces responsible are unknown. In non-recombining Y chromosomes, deleterious mutations may be carried to fixation by linked advantageous mutations ("selective sweeps"). Occurrence of deleterious mutations may drive "Muller's ratchet" (stochastic loss of chromosomes with the fewest mutations). Selective elimination of deleterious mutations, causing "background selection" may accelerate stochastic fixation of mildly detrimental mutations. All these processes lower effective population sizes, and therefore reduce variability of genes in evolving Y chromosomes. We have studied DNA diversity and divergence in a recently described X- and Y-linked gene pair (SLX-1 and SLY-1) of the plant Silene latifolia to obtain evidence about the early stages of Y degeneration. Here we show that DNA polymorphism in SLY-1 is 20-fold lower than in SLX-1, but the pattern of polymorphism does not suggest a selective sweep.     

论西方近现代宪法政治的中世纪起源

宪法政治是近现代西方民主政治的重要组成部分。英国近代宪法被认为是世界宪法之母，而英国近代宪法是从中世纪的法律至上原则和制约王权的特殊法规基础之上发展而来的。由此，我们看到西方近现代宪法政治实是从西欧中世纪专制政治的母体中发展而来，而不是来源于古希腊和罗马的民主政治。     

红树林土壤中假单胞菌群的重金属耐受活性

本研究从广西钦州茅尾海红树林保护区土壤中分离出的假单胞菌群着手，对其进行重金属耐受性能筛选，旨在获得可对重金属污染环境进行高效修复的菌株。选用传统稀释涂布法和16S rRNA基因序列的系统发育分析红树林土壤中的可培养假单胞菌；通过肉汤稀释法对菌株展开6种重金属耐受特性研究，对其进行耐受基因检测，并进一步测试重金属耐受活性显著菌株的重金属吸附性能。结果表明，从红树林土壤中共获得23株假单胞菌，18株菌对至少一种重金属表现出耐受活性，总阳性率为78.26%；10株菌的基因组DNA中检测出重金属耐受基因。其中，对铅和/或锌耐受活性显著的11株菌中，Y234、Y123、Y264、Y225和Y346具有显著的吸附性能，铅和/或锌的吸附率均大于50%。广西钦州茅尾海红树林保护区土壤中可培养假单胞菌群丰富，其重金属耐受活性显著，具有较大的挖掘潜力。