Mutagenic inverted repeat assisted genome engineering (MIRAGE)

Here we describe a one-step method to create precise modifications in the genome of Saccharomyces cerevisiae as a tool for synthetic biology, metabolic engineering, systems biology and genetic studies. Through homologous recombination, a mutagenesis cassette containing an inverted repeat of selection marker(s) is integrated into the genome. Due to its inherent instability in genomic DNA, the inverted repeat catalyzes spontaneous self-excision, resulting in precise genome modification. Since this excision occurs at very high frequencies, selection for the integration event can be followed immediately by counterselection, without the need for growth in permissive conditions. This is the first time a truly one-step method has been described for genome modification in any organism.     

Directed evolution of aniline dioxygenase for enhanced bioremediation of aromatic amines

The objective of this study was to enhance the activity of aniline dioxygenase (AtdA), a multi-component Rieske non-heme iron dioxygenase enzyme isolated from Acinetobacter sp. strain YAA, so as to create an enhanced biocatalyst for the bioremediation of aromatic amines. Previously, the mutation V205A was found to widen the substrate specificity of AtdA to accept 2-isopropylaniline (2IPA) for which the wild-type enzyme has no activity (Ang EL, Obbard JP, Zhao HM, FEBS J, 274:928–939, 2007). Using mutant V205A as the parent and applying one round of saturation mutagenesis followed by a round of random mutagenesis, the activity of the final mutant, 3-R21, was increased by 8.9-, 98.0-, and 2.0-fold for aniline, 2,4-dimethylaniline (24DMA), and 2-isopropylaniline (2IPA), respectively, over the mutant V205A. In particular, the activity of the mutant 3-R21 for 24DMA, which is a carcinogenic aromatic amine pollutant, was increased by 3.5-fold over the wild-type AtdA, while the AN activity was restored to the wild-type level, thus yielding a mutant aniline dioxygenase with enhanced activity and capable of hydroxylating a wider range of aromatic amines than the wild type. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

心力衰竭大鼠心肌线粒体蛋白质组学研究

通过差速离心分离大鼠心肌线粒体,利用蛋白质组学技术构建正常大鼠心肌线粒体蛋白质组表达图谱;选用心肌梗死诱导的心力衰竭大鼠模型,分析比较心力衰竭时心肌线粒体蛋白质表达谱的改变.与正常对照组相比,心力衰竭大鼠心肌线粒体共有188个蛋白点的表达量发生了变化,其中有120个蛋白点表达上调2倍以上,有68个蛋白点表达下调1/2以上（P〈0.05）.对差异表达的蛋白点行胶内酶解后质谱鉴定和数据库检索,对蛋白质进行功能注释、亚细胞定位和生物信息学分析,其中有27个蛋白质涉及能量代谢和氧化应激,其中参与糖酵解及三羧酸循环的蛋白质（酶）表达上调,而参与OXPHOS复合体和脂肪酸代谢的蛋白质（酶）表达下调.研究结果表明,心力衰竭时心肌能量代谢模式发生了改变,底物选择从倾向于脂肪酸转为葡萄糖利用增加,糖酵解增强而脂肪酸氧化能力减低;为心肌缺血性损伤时线粒体结构和功能改变提供了分子依据,在蛋白质水平上阐述了线粒体在心力衰竭发展中的可能机制.     

味觉感受细胞离子通道和动作电位的建模与仿真

结合膜片钳测量的味觉感受细胞离子通道实验数据,提出了一个哺乳动物味觉感受细胞动作电位的数学模型.首先,建立了味觉感受细胞的电压门控Na＋通道和外向延迟整流K＋通道的模型,在此基础上建立了味觉感受细胞的单细胞计算模型.其次,仿真研究了味觉感受细胞在电刺激和酸味刺激下产生的动作电位,以及离子通道动力学特性对其的影响.该模型对于研究味觉感受细胞在味觉物质刺激下产生的动作电位及其离子通道的工作机制,以及味觉信息在外周神经的传递和信息编码具有指导意义。     

MicroRNA-21 protects from mesangial cell proliferation induced by diabetic nephropathy in db/db mice

Diabetic nephropathy (DN) is a major diabetic complication. But the initiating molecular events triggering DN are unknown. Recent researches have addressed the role of microRNAs in diabetes and its complications. In this study, we looked for microRNAs expression during early DN, and showed microRNA-21 (miR-21) expression was downregulated in response to early DN in vitro and in vivo. Over-expression of miR-21 inhibited proliferation of mesangial cells and decreased the 24-h urine albumin excretion rate in diabetic db/db mice. Moreover, we identified PTEN as a target of miR-21. We also found PI3 K and p-Akt increased in miR-21 treated mesangial cells and db/db mice. Overall, these studies for the first time provide evidence for the potential role of miR-21 in early DN.     

Industrial biotechnology: Tools and applications

Industrial biotechnology involves the use of enzymes and microorganisms to produce value-added chemicals from renewable sources. Because of its association with reduced energy consumption, greenhouse gas emissions, and waste generation, industrial biotechnology is a rapidly growing field. Here we highlight a variety of important tools for industrial biotechnology, including protein engineering, metabolic engineering, synthetic biology, systems biology, and downstream processing. In addition, we show how these tools have been successfully applied in several case studies, including the production of 1, 3-propanediol, lactic acid, and biofuels. It is expected that industrial biotechnology will be increasingly adopted by chemical, pharmaceutical, food, and agricultural industries.     

In vitro antioxidant activity of acetylated and benzoylated derivatives of polysaccharide extracted from Ulva pertusa (Chlorophyta)

The antioxidant activity of natural ulvan and its derivatives (acetylated and benzoylated ulvans) in vitro was determined, including scavenging activity against superoxide and hydroxyl radicals, reducing power, and chelating ability. Obvious differences in antioxidant activity between natural ulvan and its derivatives were observed, moreover, the antioxidant activity of acetylated and benzoylated ulvans was stronger than that of natural ulvan.     

The solution structure of Escherichia coli Wzb reveals a novel substrate recognition mechanism of prokaryotic low molecular weight protein-tyrosine phosphatases

Low molecular weight protein-tyrosine phosphatases (LMW-PTPs) are small enzymes that ubiquitously exist in various organisms and play important roles in many biological processes. In Escherichia coli, the LMW-PTP Wzb dephosphorylates the autokinase Wzc, and the Wzc/Wzb pair regulates colanic acid production. However, the substrate recognition mechanism of Wzb is still poorly understood thus far. To elucidate the molecular basis of the catalytic mechanism, we have determined the solution structure of Wzb at high resolution by NMR spectroscopy. The Wzb structure highly resembles that of the typical LMW-PTP fold, suggesting that Wzb may adopt a similar catalytic mechanism with other LMW-PTPs. Nevertheless, in comparison with eukaryotic LMW-PTPs, the absence of an aromatic amino acid at the bottom of the active site significantly alters the molecular surface and implicates Wzb may adopt a novel substrate recognition mechanism. Furthermore, a structure-based multiple sequence alignment suggests that a class of the prokaryotic LMW-PTPs may share a similar substrate recognition mechanism with Wzb. The current studies provide the structural basis for rational drug design against the pathogenic bacteria.     

油菜基因流网络的结构特性与小团体分析

为从系统角度掌握转基因油菜(Brassica campestris)基因流规律, 基于常规油菜与十字花科植物杂交的有关文献,构建了油菜基因流网络拓扑图实例并分析其网络结构特性。研究结果表明, 该网络节点度服从幂律分布, 具有无标度特性。从随机攻击和恶性攻击两个方面对标准结构熵和网络效率2个指标的网络稳健性进行分析, 结果显示在随机移除不到10%的顶点时网络表现较好的鲁棒性, 但在受到选择性移除10%的顶点时, 网络具有极弱的抗攻击性。基于软件UCINET对网络进行了小团体和结构同型性分析, 可将网络中298个节点22类十字花科植物划分为2个小团体和5类结构角色, 其中甘蓝型油菜在基因流网络小团体中具有关键性作用。这些研究结果可为揭示转基因油菜基因流规律提供新思路, 同时也可对转基因油菜商业化种植采取合理的农业生产栽培管理措施提供参考。