Cyclin-dependent kinases prevent DNA re-replication through multiple mechanisms.

The stable propagation of genetic information requires that the entire genome of an organism be faithfully replicated once and only once each cell cycle. In eukaryotes, this replication is initiated at hundreds to thousands of replication origins distributed over the genome, each of which must be prohibited from re-initiating DNA replication within every cell cycle. How cells prevent re-initiation has been a long-standing question in cell biology. In several eukaryotes, cyclin-dependent kinases (CDKs) have been implicated in promoting the block to re-initiation, but exactly how they perform this function is unclear. Here we show that B-type CDKs in Saccharomyces cerevisiae prevent re-initiation through multiple overlapping mechanisms, including phosphorylation of the origin recognition complex (ORC), downregulation of Cdc6 activity, and nuclear exclusion of the Mcm2-7 complex. Only when all three inhibitory pathways are disrupted do origins re-initiate DNA replication in G2/M cells. These studies show that each of these three independent mechanisms of regulation is functionally important.     

Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli

When present in single-stranded DNA, palindromic or quasi-palindromic sequences have the potential to form complex secondary structures, including hairpins, which may facilitate interstrand misalignment of direct repeats and be responsible for diverse types of replication-based mutations, including deletions, additions, frameshifts and duplications. In regions of palindromic symmetry, specific deletion events may involve the formation of a hairpin or other DNA secondary structures which can stabilize the misalignment of direct repeats. One model suggests that these deletions occur during DNA replication by slippage of the template strand and misalignment with the progeny strand. The concurrent DNA replication model, involving an asymmetric dimeric DNA polymerase III complex which replicates the leading and lagging strands, has significant implications for mutagenesis. The intermittent looping of the lagging strand template, and the fact that the lagging strand template may contain a region of single-stranded DNA the length of an Okazaki fragment, provides an opportunity for DNA secondary-structure formation and misalignment. Here we report our design of a palindromic fragment to create an 'asymmetric palindromic insert' in the chloramphenicol acetyltransferase gene of plasmid pBR325. The frequency with which the insert was deleted in Escherichia coli depends on the orientation of the gene in the plasmid. Our results suggest that replication-dependent deletion between direct repeats may occur preferentially in the lagging strand.     

A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac

With the availability of complete genome sequence for Drosophila melanogaster, one of the next strategic goals for fly researchers is a complete gene knockout collection. The P-element transposon, the workhorse of D. melanogaster molecular genetics, has a pronounced nonrandom insertion spectrum. It has been estimated that 87% saturation of the approximately 13,500-gene complement of D. melanogaster might require generating and analyzing up to 150,000 insertions. We describe specific improvements to the lepidopteran transposon piggyBac and the P element that enabled us to tag and disrupt genes in D. melanogaster more efficiently. We generated over 29,000 inserts resulting in 53% gene saturation and a more diverse collection of phenotypically stronger insertional alleles. We found that piggyBac has distinct global and local gene-tagging behavior from that of P elements. Notably, piggyBac excisions from the germ line are nearly always precise, piggyBac does not share chromosomal hotspots associated with P and piggyBac is more effective at gene disruption because it lacks the P bias for insertion in 5' regulatory sequences.     

A radiation hybrid map of mouse genes

A comprehensive gene-based map of a genome is a powerful tool for genetic studies and is especially useful for the positional cloning and positional candidate approaches. The availability of gene maps for multiple organisms provides the foundation for detailed conserved-orthology maps showing the correspondence between conserved genomic segments. These maps make it possible to use cross-species information in gene hunts and shed light on the evolutionary forces that shape the genome. Here we report a radiation hybrid map of mouse genes, a combined project of the Whitehead Institute/Massachusetts Institute of Technology Center for Genome Research, the Medical Research Council UK Mouse Genome Centre, and the National Center for Biotechnology Information. The map contains 11,109 genes, screened against the T31 RH panel and positioned relative to a reference map containing 2,280 mouse genetic markers. It includes 3,658 genes homologous to the human genome sequence and provides a framework for overlaying the human genome sequence to the mouse and for sequencing the mouse genome.     

Selective Smoothed Finite Element Method

The paper examines three selective schemes for the smoothed finite element method (SFEM) which was formulated by incorporating a cell-wise strain smoothing operation into the standard compatible finite element method (FEM). These selective SFEM schemes were formulated based on three selective integration FEM schemes with similar properties found between the number of smoothing cells in the SFEM and the number of Gaussian integration points in the FEM. Both scheme 1 and scheme 2 are free of nearly incompressible locking, but scheme 2 is more general and gives better results than scheme 1. In addition, scheme 2 can be applied to anisotropic and nonlinear situations, while scheme 1 can only be applied to isotropic and linear situations. Scheme 3 is free of shear locking. This scheme can be applied to plate and shell problems. Results of the numerical study show that the selective SFEM schemes give more accurate results than the FEM schemes.     

有限单元法 并行稀疏静力学和本征值求解

有限单元法（FEM）及其软件是求解大型工程应用的最有效工具之一。在这类应用问题中，有效的方程和本征值求解器扮演着至关重要的角色。稀疏矩阵及其求解技术已经足够成熟并在商用软件中实现。然而，截至目前，关于稀疏系数方程求解、Lanczos域分解或FEM并行计算的详细介绍的书籍尚不多见。     

基于PSO的载荷受限的灾后救援任务分配问题研究

[目的]针对灾后救援问题,研究多直升机多任务含约束灾后救援任务分配问题,给出基于微粒群优化的问题求解方法,以获取各直升机的救援分配方案.考虑救援时间和直升机载荷有限,期望在有限的时间内救援最多的被困人员.[方法]首先,针对问题特性,考虑上述约束和目标,建立问题的数学模型;其次,采用改进的微粒群算法对所建模型进行求解,主要包括微粒的解码方法、微粒的位置和速度更新公式、全局极值更新方法以及局部搜索方法等.[结果]采用所提方法对不同的救援场景进行求解,并与自适应大规模邻域搜索算法进行了比较.[结论]仿真结果验证了所提方法的有效性.     

Radiation hybrid map of the mouse genome.

Radiation hybrid (RH) maps are a useful tool for genome analysis, providing a direct method for localizing genes and anchoring physical maps and genomic sequence along chromosomes. The construction of a comprehensive RH map for the human genome has resulted in gene maps reflecting the location of more than 30,000 human genes. Here we report the first comprehensive RH map of the mouse genome. The map contains 2,486 loci screened against an RH panel of 93 cell lines. Most loci (93%) are simple sequence length polymorphisms (SSLPs) taken from the mouse genetic map, thereby providing direct integration between these two key maps. We performed RH mapping by a new and efficient approach in which we replaced traditional gel- or hybridization-based assays by a homogeneous 5'-nuclease assays involving a single common probe for all genetic markers. The map provides essentially complete connectivity and coverage across the genome, and good resolution for ordering loci, with 1 centiRay (cR) corresponding to an average of approximately 100 kb. The RH map, together with an accompanying World-Wide Web server, makes it possible for any investigator to rapidly localize sequences in the mouse genome. Together with the previously constructed genetic map and a YAC-based physical map reported in a companion paper, the fundamental maps required for mouse genomics are now available.     

去除和添加凋落物对马尾松×红锥混交林土壤呼吸的影响

为探讨凋落物输入量改变对马尾松×红锥混交林碳排放的影响,以马尾松×红锥异龄混交林为研究对象,通过添加和去除凋落物人为地改变碳输入,研究凋落物处理方式对土壤呼吸的影响。结果表明:(1)去除凋落物可降低土壤湿度、提高土壤温度,而添加凋落物则提高土壤湿度、降低土壤温度。去除凋落物使土壤年均呼吸速率显著降低27.88%,而添加凋落物则使土壤年均呼吸速率显著增加34.02%。(2)去除凋落物能降低四季的土壤呼吸累积排放量,而添加凋落物则提高四季的土壤呼吸累积排放量。对照、去除和添加凋落物的土壤呼吸的年累积排放量(以C计)分别为(9.51±0.12) t·hm~(-2)、(6.88±0.21) t·hm~(-2)和(12.70±0.53) t·hm~(-2),可见去除凋落物使土壤呼吸年累积排放量降低27.66%,而添加凋落物使土壤呼吸年累积排放量提高33.54%。(3)不同凋落物处理方式下土壤呼吸速率与土壤温度均呈显著相关,土壤温度解释了土壤呼吸速率变异程度的74.26%～94.28%。去除凋落物增加了土壤呼吸温度敏感性系数Q10值,而添加凋落物则降低Q10值。凋落物处理方式对马尾松×红锥异龄混交林土壤呼吸产生了显著影响,证明凋落物对于改变森林生态系统土壤呼吸和碳循环具有重要作用。