Clustal W—蛋白质与核酸序列分析软件

蛋白质与核酸的序列分析在现代生物学和生物信息学中发挥着重要作用,新的算法和软件层出不穷,本文介绍一个可运行在ＰＣ机上的完全免费的多序列比较软件－ＣｌｕｓｔａｌＷ,它不但可以进行蛋白质与核酸的多序列比较,分析不同序列之间的相似性关系,还可以绘制进化树。由于其灵活的输入输出格式、方便的参数设定和选择、详尽的在线帮助以及良好的可移植性,使得ＣｌｕｓｔａｌＷ在蛋白质与核酸的序列分析中得到了广泛应用。     

一种新的甘露糖结合凝集素--朱顶兰凝集素基因的克隆及序列分析

运用同源克隆的方法设计简并引物,通过3′和5′RACE技术,从石蒜科植物朱顶兰(Amaryllis vittata Ait)总RNA中克隆了编码此凝集素(AVA)的全长cDNA序列.该基因全长686 bp,起始密码子位于第41～43 bp,终止密码子位于515～517 bp处,开放阅读框长474 bp,编码158个氨基酸,包含信号肽序列、成熟蛋白序列和C-末端剪切序列的前体蛋白.成熟蛋白由109个氨基酸残基组成,分子量为11.9kD.成熟蛋白在氨基酸水平上与雪花莲凝集素、水仙凝集素、石蒜凝集素和君子兰凝集素分别有73.4%、85.3%、80.7%和83.5%的同源性;朱顶兰凝集素的分子模式显示其与雪花莲凝集素有极其相似的三维结构;在Blocks数据库中检索AVA蛋白氨基酸序列的结构域,发现有3个凝集素功能结构域,并具有3个典型的甘露糖专一结合位点盒(QDNY).     

微卫星技术分析地方鸡种群体的遗传结构

利用微卫星技术和14对引物MCW150、MCW134、MCW145、MCW104、ADL210、MCW88、ADL237、ADL201、ADL289、MCW5、MCW217、MCW29、ADL176、MCW4对7个地方鸡种和1个引进鸡种的群体遗传结构特征进行了分析。根据池DNA所获得的品种间相似指数计算遗传距离。结果表明:AA鸡与其它品种鸡遗传距离最远,白耳鸡次之,其余品种间较近。这些鸡种的遗传结构特征与其地理分布有关,说明微卫星技术作为畜禽遗传结构分析的辅助手段是可行的,也是高效的 。     

局部环境增温对根田鼠冬季种群的影响

通过建立开顶式增温小室模拟全球变暖的实验, 对海北高寒草甸地区实验增温样地及其对照样地内根田鼠的冬季种群进行调查, 旨在研究局部增温对根田鼠冬季种群的可能影响。结果表明, 在冬季, 实验增温草甸样地和灌丛样地内根田鼠的种群密度均显著高于其对照( P < 0.05) ; 实验增温灌丛样地与对照间性比的差异不显著( P > 0.05) ; 增温样地和对照之间、不同植被类型的增温样地之间、对照样地之间, 根田鼠留存率、平均体重及年龄结构的差异均不显著( P > 0.05) ; 有从对照样地向增温样地单方向迁移的记录。总之, 局部环境增温导致实验样地内根田鼠的冬季种群密度明显上升, 而其性比、存活率、种群平均体重以及年龄结构无明显变化; 在冬季, 根田鼠有从对照样地向增温样地扩散或迁移的趋势。     

Sirt3 controls chromosome alignment by regulating spindle dynamics during mitosis

Sirt3, one of mammalian sirtuins is a prominent mitochondrial deacetylase that controls mitochondrial oxidative pathways and the rate of reactive oxygen species. Sirt3 also regulates energy metabolism by deacetylating enzymes involved in the metabolic pathway related with lifespan. We report here a novel function of Sirt3 which was found to be involved in mitosis. Depletion of the Sirt3 protein generated unaligned chromosomes in metaphase which caused mitotic arrest by activating spindle assembly checkpoint (SAC). Furthermore, the shape and the amount of the spindles in Sirt3 depleted cells were abnormal. Microtubule (MT) polymerization also increased in Sirt3 depleted cells, suggesting that Sirt3 is involved in spindle dynamics. However, the level of acetylated tubulin was not increased significantly in Sirt3 depleted cells. The findings collectively suggest that Sirt3 is not a tubulin deacetylase but regulates the attachment of spindle MTs to the kinetochore and the subsequent chromosome alignment by increasing spindle dynamics.     

Enhanced Enzyme Kinetic Stability by Increasing Rigidity within the Active Site

Enzyme stability is an important issue for protein engineers. Understanding how rigidity in the active site affects protein kinetic stability will provide new insight into enzyme stabilization. In this study, we demonstrated enhanced kinetic stability of Candida antarctica lipase B (CalB) by mutating the structurally flexible residues within the active site. Six residues within 10 Å of the catalytic Ser¹⁰⁵ residue with a high B factor were selected for iterative saturation mutagenesis. After screening 2200 colonies, we obtained the D223G/L278M mutant, which exhibited a 13-fold increase in half-life at 48 °C and a 12 °C higher T₅₀¹⁵, the temperature at which enzyme activity is reduced to 50% after a 15-min heat treatment. Further characterization showed that global unfolding resistance against both thermal and chemical denaturation also improved. Analysis of the crystal structures of wild-type CalB and the D223G/L278M mutant revealed that the latter formed an extra main chain hydrogen bond network with seven structurally coupled residues within the flexible α10 helix that are primarily involved in forming the active site. Further investigation of the relative B factor profile and molecular dynamics simulation confirmed that the enhanced rigidity decreased fluctuation of the active site residues at high temperature. These results indicate that enhancing the rigidity of the flexible segment within the active site may provide an efficient method for improving enzyme kinetic stability.     

On explicit formulas of edge effect correction for Ripley's K-function

Abstract. The analysis of spatial pattern in plant ecology usually implies the solution of some edge effect problems. We present in this paper some explicit formulas of edge effect correction that should enable plant ecologists to analyse a wider range of real field data. We consider the local correcting factor of edge effect for Ripley's K-function, that can also be used for other statistics of spatial analysis based on the counting of neighbours within a given distance. For both circular and rectangular study areas, we provide a review of explicit formulas and an extension of these formulas for long and narrow plots. In the case of irregular-shaped study plots, we propose a generalization of the method that computes edge effect correction by excluding triangular surfaces from a simple (rectangular or circular) initial shape. An example in forest ecology, where the soil characteristics determine a study plot of complex shape, illustrates how this edge effect correction can be effective in avoiding misinterpretations.     

General proof of the validity of a new tensor equation of plant growth

Plant cell/organ growth may be partly described by a local tensor equation. We provide a mathematical proof that the Lockhart (global) equation is the diagonal component of this tensor equation.