Mapping and sequencing of structural variation from eight human genomes

Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.     

鹅耳枥属树种叶绿体基因组结构及变异分析

[目的]了解鹅耳枥属(Carpinus)树种叶绿体基因组基因组成及结构特征,为鹅耳枥属的系统发育及基因组进化研究提供参考.[方法]获取鹅耳枥属16个树种的叶绿体基因组,对其进行基因注释,利用生物信息学方法比较叶绿体基因组间的结构特征与变异程度,并以麻栎(Quercus acutissima)为外类群分析了鹅耳枥属的系统...     

细菌和酵母基因组中ORF结构特征的统计分析

将第一ATG规则用于细菌Hpyl，Hpyl99，E.coli，Aero，Tmar和Yeast基因组中，并用给出ORF(包含已知基因编码区)进行检验，其结果对以ATG起始的ORF序列正确率皆为89％以上，将五种细菌和酵母基因组中给出ORF分成第一种(已确定的编码序列)和第二种(还未确定为编码序列的)ORF，并计算L—Ter到第一ATG的平均距离，分析了五种细菌和酵母终止密码子在L-Ter位置和Ter位置上的使用频率，发现在Ter位置上终止密码子使用的偏置程度比在L-Ter位置上大．     

Sequence-based characterization of structural variation in the mouse genome

Structural variation is widespread in mammalian genomes and is an important cause of disease, but just how abundant and important structural variants (SVs) are in shaping phenotypic variation remains unclear. Without knowing how many SVs there are, and how they arise, it is difficult to discover what they do. Combining experimental with automated analyses, we identified 711,920 SVs at 281,243 sites in the genomes of thirteen classical and four wild-derived inbred mouse strains. The majority of SVs are less than 1?kilobase in size and 98% are deletions or insertions. The breakpoints of 160,000 SVs were mapped to base pair resolution, allowing us to infer that insertion of retrotransposons causes more than half of SVs. Yet, despite their prevalence, SVs are less likely than other sequence variants to cause gene expression or quantitative phenotypic variation. We identified 24 SVs that disrupt coding exons, acting as rare variants of large effect on gene function. One-third of the genes so affected have immunological functions.     

结构可靠性设计中尺寸变差系数的确定方法

提出了在结构可靠性设计中,根据现有加工条件和设计要求确定几何尺寸变差系数的思想,并给出了当已知精度等级时,直接加工尺寸和组合尺寸变差系数的计算方法和程序。采用该方法使可靠性设计更切合实际。     

河北省棉花生育期连阴雨气候变化特征分析

利用河北省65个气象观测站自1954年(或建站)至2000年的气象资料,分析了河北省棉花四个生育期的连阴雨气候变化特征.结果表明:河北省棉区大部棉花播种出苗期、蕾期、花铃期和吐絮期连阴雨分别为1～2年一遇、1～3年一遇、1～2年一遇和2～6年一遇.不同时期重连阴雨所占比率分别为25%、65%、49%和45%.近50年来,除播种出苗期连阴雨历年出现次数具有增多趋势外,其它各个时期的连阴雨、重连阴雨以及播种出苗期重连阴雨均具有减少趋势,但各时期减少幅度有所不同.     

Dissecting the genomic complexity underlying medulloblastoma

Medulloblastoma is an aggressively growing tumour, arising in the cerebellum or medulla/brain stem. It is the most common malignant brain tumour in children, and shows tremendous biological and clinical heterogeneity. Despite recent treatment advances, approximately 40% of children experience tumour recurrence, and 30% will die from their disease. Those who survive often have a significantly reduced quality of life. Four tumour subgroups with distinct clinical, biological and genetic profiles are currently identified. WNT tumours, showing activated wingless pathway signalling, carry a favourable prognosis under current treatment regimens. SHH tumours show hedgehog pathway activation, and have an intermediate prognosis. Group 3 and 4 tumours are molecularly less well characterized, and also present the greatest clinical challenges. The full repertoire of genetic events driving this distinction, however, remains unclear. Here we describe an integrative deep-sequencing analysis of 125 tumour-normal pairs, conducted as part of the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. Tetraploidy was identified as a frequent early event in Group 3 and 4 tumours, and a positive correlation between patient age and mutation rate was observed. Several recurrent mutations were identified, both in known medulloblastoma-related genes (CTNNB1, PTCH1, MLL2, SMARCA4) and in genes not previously linked to this tumour (DDX3X, CTDNEP1, KDM6A, TBR1), often in subgroup-specific patterns. RNA sequencing confirmed these alterations, and revealed the expression of what are, to our knowledge, the first medulloblastoma fusion genes identified. Chromatin modifiers were frequently altered across all subgroups. These findings enhance our understanding of the genomic complexity and heterogeneity underlying medulloblastoma, and provide several potential targets for new therapeutics, especially for Group 3 and 4 patients.     

The variation in the magnetic fluctuation anisotropy across the front boundaries of magnetic clouds and its geomagnetic response

A statistical study of magnetic fluctuations near the front boundaries of magnetic clouds is approached with the method of Minimum Variance Analysis, based on the data of Imp8 and Wind spacecraft. New discoveries are that (1) fluctuation anisotropy tends to increase across the front boundaries of magnetic clouds; (2) there is a good correlation between the fluctuation anisotropy and the geomagnetic activity indices; and (3) in some cases, although there is southward field component immediately after the front boundary, K_p index descends (or D_st index ascends) with a corresponding decrease of the fluctuation anisotropy; in other cases with no distinct southward field component, K_p index ascends (or D_st index descends) with a corresponding increase of the fluctuation anisotropy. Thus we suggest that the fluctuation anisotropy might be a useful indicator in diagnosing the magnetic activities of magnetic clouds.     

1000例甲状腺机能亢进手术诊治经验

作者等26年来施行甲状腺次全切除术治疗甲亢病人1000例,其中原发性甲亢占90.5％,高功能腺瘤占4％,术后复发甲亢占3.6％,继发性甲亢占1.9％。本文强调用药前甲亢的症状,体征及基础代谢率的测定是诊断甲亢的主要依据。甲状腺次全切除术仍是目前治疗服药未能稳定的壮年人甲亢的积极而有效的一种定型手术,但要求术前准备,麻醉及术中、术后均平稳,手术过程要轻柔、准确、快捷。我们认为甲状腺肿大在80克以下者可不用横断甲状腺前肌群。本文介绍“五钳法”切除甲状腺方法。避免了许多重复切开、缝合、结扎等操作。手术死亡率为零。术后追踪,喉返神经损伤不恢复者0.9％,甲状旁腺功能不足者为0.74％,甲状腺机能低下者0.74％,甲亢复发者5.9％。     

Transposition of structural genes to an expression sequence on a linear plasmid causes antigenic variation in the bacterium Borrelia hermsii

In Borrelia hermsii, a spirochaete that causes relapsing fever, the switch between expression of two frequent variable major protein (VMP) types (7 and 21) is associated with a DNA rearrangement. Both cell types 7 and 21 contain untranscribed 7 and 21 VMP genes on linear plasmids. The serotype 7 cells contain an additional copy of the 7 VMP gene fused to an expression sequence on another linear plasmid. Switching to the 21 serotype involves removal of the transcribed 7 VMP gene and fusion of a copy of the 21 VMP gene to this same expression sequence. Thus recombination between linear plasmids can activate different VMP genes.     

蚜蝇科昆虫比较线粒体基因组分析

通过检索GenBank数据库(截止2018年9月)和查阅文献资料,对已知的6种蚜蝇线粒体基因组全序列进行了分析,其基本结构特点是:1)全序列在碱基组成中表现出很强的AT偏向性; 2)未出现基因重排现象; 3) tRNA基因的二级结构为典型的三叶草结构; 4)大多数线粒体蛋白编码基因的起始密码子都是ATN。同时基于8条线粒体基因组全序列(含3个外群)构建蚜蝇科系统发育关系,结果支持蚜蝇科的单系性。     

Trophic cascades across ecosystems

Predation can be intense, creating strong direct and indirect effects throughout food webs. In addition, ecologists increasingly recognize that fluxes of organisms across ecosystem boundaries can have major consequences for community dynamics. Species with complex life histories often shift habitats during their life cycles and provide potent conduits coupling ecosystems. Thus, local interactions that affect predator abundance in one ecosystem (for example a larval habitat) may have reverberating effects in another (for example an adult habitat). Here we show that fish indirectly facilitate terrestrial plant reproduction through cascading trophic interactions across ecosystem boundaries. Fish reduce larval dragonfly abundances in ponds, leading to fewer adult dragonflies nearby. Adult dragonflies consume insect pollinators and alter their foraging behaviour. As a result, plants near ponds with fish receive more pollinator visits and are less pollen limited than plants near fish-free ponds. Our results confirm that strong species interactions can reverberate across ecosystems, and emphasize the importance of landscape-level processes in driving local species interactions.     

Evolutionary genomics: codon bias and selection on single genomes

The idea that natural selection on genes might be detected using only a single genome has been put forward by Plotkin and colleagues, who present a method that they claim can detect selection without the need for comparative data and which, if correct, would confer greater power of analysis with less information. Here we argue that their method depends on assumptions that confound their conclusions and that, even if these assumptions were valid, the authors' inferences about adaptive natural selection are unjustified.     

Study on young panicle culturein vitro from wild rice of different genomes

Researches have been made on young panicle culturein vitro from wild rice of different genomes. Main results are as follows: 1. The induction frequencies of young panicle culturedin vitro from wild rice varied largely a relation to its genome. The optimal induction period of callus is the stamen and pistil differentiation stage of young panicle development. 2. Plantlets were regenerated through two ways: first, culture method, the induced calli were transferred onto differentiation medium; second, regenerate plantlets directly from young panicles of wild rice that were cultured on the differentiation medium. 3. The regeneration rate of green plantlets that obtained through cryopreservated calli inO. meyeriana was 10 times higher than that of control. Foundation item: Supported by the National Natural Science Foundation of China (39279436) Biography: SHU Li-hui(1937-), Professor, Research in plant tissue culture.     

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.     

Invariant scaling relations across tree-dominated communities

Organizing principles are needed to link organismal, community and ecosystem attributes across spatial and temporal scales. Here we extend allometric theory-how attributes of organisms change with variation in their size-and test its predictions against worldwide data sets for forest communities by quantifying the relationships among tree size-frequency distributions, standing biomass, species number and number of individuals per unit area. As predicted, except for the highest latitudes, the number of individuals scales as the -2 power of basal stem diameter or as the -3/4 power of above-ground biomass. Also as predicted, this scaling relationship varies little with species diversity, total standing biomass, latitude and geographic sampling area. A simulation model in which individuals allocate biomass to leaf, stem and reproduction, and compete for space and light obtains features identical to those of a community. In tandem with allometric theory, our results indicate that many macroecological features of communities may emerge from a few allometric principles operating at the level of the individual.