Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration

We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations.     

Simple nanofabrication of a superhydrophobic and transparent biomimetic surface

This paper describes a simple fabrication method for creating superhydrophobic and transparent glass surfaces that mimic natural surfaces such as lotus leaves, moth eyes or cicada wings. Nanostructured glass surfaces were created by a combination of colloidal lithography and plasma etching. A colloidal mask was formed simply by the spin coating of the polystyrene beads and with modification of the interparticle distance between the beads. The etching of the glasses was conducted by CF4 plasma. Tower-shaped nanostructures at an aspect ratio of 1：4 were treated using fluoroalkylsilane selfassembled monolayers （SAMs） to obtain the hydrophobic surfaces. The treated glass surfaces showed superhydrophobicity with a water contact angle of around 150° and a hexadecane contact angle of around 110° Furthermore, the nanostructured glass was transparent to visible light.     

Constant darkness is a circadian metabolic signal in mammals

Environmental light is the 'zeitgeber' (time-giver) of circadian behaviour. Constant darkness is considered a 'free-running' circadian state. Mammals encounter constant darkness during hibernation. Ablation of the master clock synchronizer, the suprachiasmatic nucleus, abolishes torpor, a hibernation-like state, implicating the circadian clock in this phenomenon. Here we report a mechanism by which constant darkness regulates the gene expression of fat catabolic enzymes in mice. Genes for murine procolipase (mClps) and pancreatic lipase-related protein 2 (mPlrp2) are activated in a circadian manner in peripheral organs during 12 h dark:12 h dark (DD) but not light-dark (LD) cycles. This mechanism is deregulated in circadian-deficient mPer1-/-/mPer2m/m mice. We identified circadian-regulated 5'-AMP, which is elevated in the blood of DD mice, as a key mediator of this response. Synthetic 5'-AMP induced torpor and mClps expression in LD animals. Torpor induced by metabolic stress was associated with elevated 5'-AMP levels in DD mice. Levels of glucose and non-esterified fatty acid in the blood are reversed in DD and LD mice. Induction of mClps expression by 5'-AMP in LD mice was reciprocally linked to blood glucose levels. Our findings uncover a circadian metabolic rhythm in mammals.     

渤海湾盆地东濮凹陷的形成及断裂构造研究

讨论了中、新生代以来．中国东部构造应力场的变化及其对渤海湾地区的影响、作用；提出渤海湾盆地是在中国东部陆壳伸展、拉张作用的构造背景上，叠加右行走滑拉分作用形成的“拉分──伸展型”复合盆地．东濮凹陷作为渤海湾盆地系统的一部分，具有与渤海湾盆地相同的基底构造和相似的构造演化历史．本文通过对东濮凹陷基底断裂构造的特征及沿兰聊断裂两侧众多探井岩芯破裂构造的观察、分析和研究，证实了兰聊断裂在东濮凹陷形成过程中的右行平移作用．     

长白山区次生林恢复过程中天然更新的动态

以长白山区天然次生林为研究对象,采用空间代替时间的方法,分别对不同年度进行择代后形成的天然次生林进行群落学调查,分析择伐后28年恢复期间高度小于3m的幼苗幼树的天然更新过程及特点。结果表明,恢复初期更新幼苗幼树的树种出现比率较低,随着次生林恢复时间的增加,更新幼苗幼树的树种出现比率超过75％,且15年后变化相对较小;次生林内更新幼苗幼树的分布密度随着恢复时间的增加呈增加的趋势,恢复15年时分布密度达7500株／hm^2,此后分布密度的变化相对较小;在次生林内幼苗幼树主要是集中分布在距最近立木1．5～3．5m的范围内,随着次生林恢复时间的增加,幼树的分布范围相对靠近立木,幼苗的分布范围则相对远离立木。     

The medaka draft genome and insights into vertebrate genome evolution

Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination and developmental genetics. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approximately 2,900 new genes, using 5'-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approximately 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.     

Polarity modified triplex DNA by bromide

Conclusion A py-pu-py triplex DNA containing the polarity modification by replacing the atom H5 of cytosine with Br was examined, mainly for the stability of the formation of the triplex DNA. Our computational results show that the conformation of the strand that contained a replaced H5 by cytosine to Br was destabilized, but the Hoogsteen base pairs were stabilized. Although this approach of modifying the polarity of DNA base has not been tried before, it shows the possibility to improve the stability by the polarity modification.     

Modified binary particle swarm optimization

This paper presents a modified binary particle swarm optimization （BPSO） which adopts concepts of the genotype-phenotype representation and the mutation operator of genetic algorithms. Its main feature is that the BPSO can be treated as a continuous PSO. The proposed BPSO algorithm is tested on various benchmark functions, and its performance is compared with that of the original BPSO. Experimental results show that the modified BPSO outperforms the original BPSO algorithm.     

The genome sequence of the rice blast fungus Magnaporthe grisea

Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.