Evaluation of the SNP tagging approach in an independent population sample—array-based SNP discovery in Sami

Significant efforts have been made to determine the correlation structure of common SNPs in the human genome. One method has been to identify the sets of tagSNPs that capture most of the genetic variation. Here, we evaluate the transferability of tagSNPs between populations using a population sample of Sami, the indigenous people of Scandinavia. Array-based SNP discovery in a 4.4 Mb region of 28 phased copies of chromosome 21 uncovered 5,132 segregating sites, 3,188 of which had a minimum minor allele frequency (mMAF) of 0.1. Due to the population structure and consequently high LD, the number of tagSNPs needed to capture all SNP variation in Sami is much lower than that for the HapMap populations. TagSNPs identified from the HapMap data perform only slightly better in the Sami than choosing tagSNPs at random from the same set of common SNPs. Surprisingly, tagSNPs defined from the HapMap data did not perform better than selecting the same number of SNPs at random from all SNPs discovered in Sami. Nearly half (46%) of the Sami SNPs with a mMAF of 0.1 are not present in the HapMap dataset. Among sites overlapping between Sami and HapMap populations, 18% are not tagged by the European American (CEU) HapMap tagSNPs, while 43% of the SNPs that are unique to Sami are not tagged by the CEU tagSNPs. These results point to serious limitations in the transferability of common tagSNPs to capture random sequence variation, even between closely related populations, such as CEU and Sami. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

解偶联蛋白2在内皮损伤及血管重构中的作用研究进展

心脑血管疾病是全球最主要的致死性疾病。活性氧(Reactive oxygen species,ROS)产生增多诱发血管内皮细胞损伤、平滑肌细胞迁移、增殖,是导致血管功能障碍、血管重构发生的重要机制。因此,氧化应激被认为是心脑血管疾病发生、发展的关键环节。但通过补充外源性抗氧化剂防治心脑血管疾病一直存在较大争议。机体可通过自身防御体系拮抗氧化应激,维持氧化-还原状态,如通过调控线粒体解偶联蛋白2(Uncoupling protein 2,UCP2)调节ROS生成,改善血管功能障碍及血管重构。本文就UCP2在内皮损伤及血管重构中的作用及机制展开综述,为深入探索这一潜在的防治心脑血管疾病的靶点提供信息。     

Linking Freshwater Flows and Ecosystem Services Appropriated by People: The Case of the Baltic Sea Drainage Basin

Humanity's dependence on ecosystem support is “mentally hidden” to large segments of society; it has no price in the market and is seldom accounted for in decision making. Similarly, the needs of ecosystems for fresh water for generation of nature's services are largely invisible. Freshwater assessments predominantly have focused on human uses of liquid water in rivers, lakes, and reservoirs. We estimated the spatial appropriation of terrestrial and marine ecosystems—the ecological footprint—of the 85 million inhabitants in the Baltic Sea drainage basin with regard to consumption of food and timber and waste assimilation of nutrients and carbon dioxide. We also estimated the amount of fresh water—the water vapor flow—that the inhabitants depend upon for their appropriation of these ecosystem services. The ecological footprint estimate corresponds to an area as large as 8.5–9.5 times the Baltic Sea and its drainage basin with a per capita ecosystem appropriation of 220,000–250,000 m². This large estimate is mainly attributed to carbon sequestering by marine ecosystems and forests. The water vapor flow of the ecological footprint of forests, wetlands, agriculture, and inland water bodies for making the human appropriation of ecosystem services possible is estimated at 1175–2875 km³ y⁻¹. Human dependence on water vapor flows for ecosystem services is as great as 54 times the amount of freshwater runoff that is assessed and managed in society. Decision making on an increasingly human-dominated planet will have to address explicitly the critical interdependencies between freshwater flows and the capacity of ecosystems to generate services. We advocate a dynamic ecohydrological landscape-management approach upstream and downstream in watersheds to reduce unintentional impacts, irreversible change, and further loss of freshwater resources, ecosystem services, and resilience. Received 6 October 1998; accepted 30 March 1999.     

Effects of Plant Growth Characteristics on Biogeochemistry and Community Composition in a Changing Climate

Vegetation growth characteristics influence ecosystem biogeochemistry and must be incorporated in models used to project biogeochemical responses to climate variations. We used a multiple-element limitation model (MEL) to examine how variations in nutrient use efficiency (NUE) and net primary production to biomass ratio (nPBR) affect changes in ecosystem C stocks after an increase in temperature and atmospheric CO₂. nPBR influences the initial rates of response, but the magnitude and direction of long-term responses are determined by NUE. MEL was used to simulate responses to climate change in communities composed of two species differing in nPBR and/or NUE. When only nPBR differed between the species, the high-nPBR species outgrew the low-nPBR species early in the simulations, but the shift in dominance was transitory because of secondary N limitations. High-NUE species were less affected by secondary N limitations and were therefore favored under elevated CO₂. Increased temperature stimulated N release from soil organic matter (SOM) and therefore favored low-NUE species. The combined release from C and N limitation under the combination of increased temperature and elevated CO₂ favored high-NUE species. High C:N litter from high-NUE species limited the N-supply rate from SOM, which favors the dominance of the high-NUE species in the short term. However, in the long term increased litter production resulted in SOM accumulation, which reestablished a N supply rate favorable to the reestablishment and dominance of the low-NUE species. Conditions then reverted to a state favorable to the high-NUE species. Received 8 October 1998; accepted 9 April 1999.     

Oviposition by mutualistic seed-parasitic pollinators and its effects on annual fitness of single- and multi-flowered host plants

The balance of intimate relationships between plants and seed-eating pollinators can depend on pollinator behaviour in relation to floral characters, such as flower size and flower number. Here, we examined how pollinator oviposition in relation to these traits affected annual fitness (seed output) of single- and multi-flowered Trollius europaeus along altitudinal gradients in subarctic Sweden and the French Alps. Small flies (Chiastocheta spp.) pollinate T. europaeus and their larvae feed on developing seeds. Assuming that late flowers in multi-flowered plants attracted flies to the earliest flower on the same plant, we expected more eggs and higher seed predation in early multiple flowers than in single flowers. Relative seed predation would thereby increase with flower number. Both in Sweden and the Alps, more eggs were placed on large flowers. Early multiple flowers were slightly larger than single flowers, and about twice the size of secondary flowers. As a result, and possibly combined with the effects of secondary flowers, early multiple flowers attracted more ovipositing flies and experienced relatively higher seed predation. However, this did not generally result in higher seed predation of multi-flowered hosts. Multiple flowers had greater seed output than single flowers at all altitudes, also in the high alpine and subarctic sites, where single flowers were more abundant. We hypothesise that the distribution of multiple flowers generally is enforced by environmental factors, rather than by fly-host plant interactions, because only very rarely (in triple-flowered alpine plants) was seed predation disproportionate, and the relationship skewed to the disadvantage of the host. The outcome of the mutualistic interaction was often similar in alpine and subarctic populations, but the underlying factors were different. Subarctic flowers had high abortion and low predation rates, while alpine flowers experienced the reversed situation. The higher fly abundance in the Alps suggests a more intense mutualistic interaction than in Sweden. Despite varying ecological and environmental conditions at these sites, the mutualistic relationship was generally in balance. However, when it was unbalanced, this could be explained by fly behaviour in response to floral traits, and by differences in fly abundance. Received: 4 January 1999 / Accepted: 5 May 1999     

花椒潜跳甲生物学特性及防治试验

本文报道了花椒潜跳甲 Podagricomela shirahatai(Chuj)在甘肃舟曲１年发生 ２代,以成虫港入树干基部３～５ｃｍ土层内或砂石缝中越冬,越冬成虫春季出土上树时是防治关键时期,成虫产卵前用５０％增效辛硫磷乳油和４０％氧乐果乳油１２００～１５００倍稀释液在成虫期和幼虫期喷洒叶面,杀虫率在９０％～９８．２％。不发生药害,效果显著。     

利用DREAM设计和同源重组进行一步定点突变

目的：建立基于DREAM设计和同源重组的简便、快速定点突变方法。方法：设计两条包含突变的反向PCR（inverse PCR）引物,使其5'端互补从而产生同源重组,同时使用DREAM设计方案在上述引物中引入限制性内切酶位点以便突变子筛选。用能扩增长片段的高保真耐热 DNA聚合酶扩增全长的质粒DNA,直接转化大肠杆菌。转化到细菌中的全长质粒DNA PCR产物可利用其末端同源序列发生同源重组而环化。利用引入的酶切位点方便地进行突变子的筛选。结果：我们用该方法成功地对长度大于7 kb的质粒进行了定点突变。结论：本定点突变无需任何突变试剂盒和特殊的试剂,只需一步反应即可完成;利用DREAM设计使克隆筛选简便可靠,高保真耐热DNA聚合酶可保证多数突变子克隆不发生意外突变,而该酶扩增长片段的能力使该方法适合于大多数质粒不经亚克隆直接突变。     

东亚飞蝗UBX结构域包含蛋白基因 LmUBX2 的克隆和表达分析

【目的】UBX结构域包含蛋白是p97/CDC48的辅助因子。p97在泛素化相关的多种细胞过程中起着重要的作用,如依赖泛素 蛋白酶体系统的蛋白质降解和同型膜融合等。本研究旨在克隆东亚飞蝗 Locusta migratoria manilensis (Meyen)的UBX结构域包含蛋白基因,分析其组织和发育表达格局,为进一步研究UBX结构域包含蛋白基因的功能奠定基础。【方法】通过分析东亚飞蝗的转录组数据克隆UBX结构域包含蛋白基因,采用实时定量PCR技术分析该基因在不同发育时期和成虫不同组织中的表达水平。【结果】克隆到东亚飞蝗的一个UBX结构域包含蛋白基因,命名为 LmUBX2。 LmUBX2 开放阅读框长1 020 bp,编码399个氨基酸,预测分子量和等电点分别为37.8 kDa和6.03,与其他UBX结构域包含蛋白的氨基酸一致性为37%~64%,N端和C端分别有一个保守的UBA结构域和UBX结构域。序列比较和系统发育分析发现 LmUBX2 属于SAKS1亚家族。定量分析发现,LmUBX2 在整个生命周期中都有表达,但成虫期的表达水平最高;在检测的所有组织中都有表达,但在精巢和卵巢中表达水平最高。【结论】研究结果说明 LmUBX2 可能参与东亚飞蝗多种生理过程,尤其可能与东亚飞蝗的生殖有关,但还需深入研究。