Homology modeling threedimensional structure of AnxB1 and reducing its immunogenicity by sequence-deleted mutagenesis

AnxB1,a novel annexin previously isolated from Cysticercus cellulose,shows high thrombi affinity and anticoagulant activity in vivo.In order to investigate the relationship between structure and biological function,a predicted three-dimensional(3D)model of AnxB1 was generated by homology modeling.This model contains four homologous internal-domains and the Cα trace of domain Ⅰ,Ⅱ and IV shows high similarity.Based on the structure characterization,four sequence-deleted mutants were constructed and expressed as GST fusion proteins in E.coli.Two of the mutants,GST-M3 and GST-M4 reserved high anticoagulant activity(p＜0.01 vs.GST).Furthermore,compared with the wild type GST-AnxB1,the immunogenicity of GST-M3 and GST-M4 was reduced significantly(p＜0.01)and the molecular weight was lowered to 27 kD and 34 kD,respectively.These observations laid a solid foundation for further study on developing new thrombolytic agents with higher efficiency and lower side effect.     

影响动物模型MBLUP评定准确性的主要因素

标记辅助最佳线性无偏预测（marker-assisted best linear unbiased prediction,MBLUP）是对动物实施标记辅助选择（marker-assisted selection,MAS）的一种重要方法。通过计算机随机模拟研究了所选性状的遗传力、QTL方差和相邻两个标记间图距3个因素对动物模型MBLUP评定准确性的影响。结果表明,性状的遗传力越高、QTL方差和相邻两个标记间图距越小时,动物模型MBLUP评定的准确性越高;相反,当性状的遗传力较低、QTL方差和相邻两个标记间图距较大时,动物模型MBLUP评定的准确性则较低。     

Amino acid sequence and homology modeling of obtustatin,a novel non-RGD-containing short disintegrin isolated from the venom of Vipera lebetina obtusa

Disintegrins represent a group of cysteine-rich peptides occurring in Crotalidae and Viperidae snake venoms, and are potent antagonists of several integrin receptors. A novel disintegrin, obtustatin, was isolated from the venom of the Vipera lebetina obtusa viper, and represents the first potent and selective inhibitor of the binding of integrin alpha(1)beta(1) to collagen IV. The primary structure of obtustatin contains 41 amino acids and is the shortest disintegrin described to date. Obtustatin shares the pattern of cysteines of other short disintegrins. However, in contrast to known short disintegrins, the integrin-binding loop of obtustatin is two residues shorter and does not express the classical RGD sequence. Using synthetic peptides, a KTS motif was identified as the integrin-binding sequence. A three-dimensional model of obtustatin, built by homology-modeling structure calculations using different templates and alignments, strongly indicates that the novel KTS motif may reside at the tip of a flexible loop.     

耐热碱性磷酸酶突变体耐热性变化机理研究

从耐热碱性磷酸酶（TAP）200多个随机突变体的克隆库中选出耐热性明显下降的4株突变体,进行全序列及表达产物的最高耐受温度和最适反应温度测定和酶分子高级结构的模拟,分析突变位点、高级结构和耐热性表现三者的关系,探讨引起耐热性变化的机理。结构模拟显示所有突变位点都仅能引起细微的、局部的结构变化,除T320→I外都未直接触及酶的活性中心;结构上的细微改变虽然对最适反应温度影响不明显,但却使最高耐受温度降低了10℃左右;T320→I靠近酶的活性中心,尽管未能引起结构的较大变化,但却使最高耐受温度和最适反应温度同时显著降低。可见,多数点突变对高级结构的影响都不剧烈,但对耐热性尤其是最高耐受温度的影响却比较明显,一般地,在非活性区的突变通常只能引起最高耐受温度的降低,靠近活性区的突变则能同时引起最适反应温度和最高耐受温度的降低。     

水果中阿斯巴甜的研究

采用高效液相色谱-三重四级杆串联质谱(HPLC-QQQ-MS/MS)对橙等8种水果中的苯丙氨酸、天冬氨酸和阿斯巴甜进行测定,采用气相顶空(HS-GC)对水果中的甲醇进行测定,并进行阿斯巴甜的模拟合成实验,研究在水果中是否存在阿斯巴甜及合成阿斯巴甜所必须的苯丙氨酸、天冬氨酸和甲醇以及它们之间的浓度关系。实验结果表明:8种水果中均含有阿斯巴甜、苯丙氨酸、天冬氨酸和甲醇。其中阿斯巴甜的含量为23.4～117μg/kg,天冬氨酸含量为8.72～186 mg/kg,苯丙氨酸含量为1.84～84.2 mg/kg,甲醇含量为1.81～248mg/kg。不同水果中阿斯巴甜含量差异不大,而苯丙氨酸、天冬氨酸和甲醇的含量差异较大。阿斯巴甜的含量与苯丙氨酸、天冬氨酸和甲醇的含量无明显相关性。     

A dynamic mass balance model for phosphorus fluxes and concentrations in coastal areas

This paper presents a general, process-based mass balance model (CoastMab) for total phosphorus (TP) in defined coastal areas (at the ecosystem scale). The model is based on ordinary differential equations and calculates inflow, outflow and internal fluxes on a monthly basis. It consists of four compartments: surface water, deep water, erosion/transportation areas for fine sediments and accumulation areas for fine sediments. The separation between surface water and deep water is not done based on water temperature, but on sedimentological criteria instead (from the theoretical wave base). There are algorithms for all major internal TP fluxes (sedimentation, resuspension, diffusion, mixing and burial). Validations were performed using data from 21 different Baltic coastal areas. The results show that the model predicts monthly TP in water and chlorophyll a very well (generally within the uncertainty bands of the empirical data). The model has also been put through sensitivity tests, which show that the most important factor regulating the predictions of the model is generally the TP concentration in the sea beyond the coast. The model is simple to apply, since all driving variables may be accessed from maps or monitoring programs. The driving variables include coastal area, section area (between the defined coastal area and the adjacent sea), mean and maximum depths, latitude (used to predict water temperatures, stratification and mixing), salinity and TP concentration in the sea. Many of the model structures are general and could be used for areas other than those included in this study, e.g., for open coasts, estuaries or tidal coasts, as well as for other substances than phosphorus.     

Flux analysis of recombinant Saccharomyces cerevisiae YPB-G utilizing starch for optimal ethanol production

Genetically modified Saccharomyces cerevisiae strain (YPB-G) which secretes a bifunctional fusion protein that contains both Bacillus subtilis -amylase and Aspergillus awamori glucoamylase activities was used for the direct conversion of starch into ethanol. Starch was either supplied initially to different nutrient media or added instantaneously to the reactor at various discrete time instants (pulse feeding). Stoichiometric modeling was used to investigate the effects of initial substrate concentration and growth rate of the recombinant yeast culture on ethanol production. Reaction stoichiometries describing both the anabolism and catabolism of the microorganism were used as an input to flux balance analysis (FBA), the preferred metabolic modeling approach since the constructed stoichiometric network was underdetermined. Experiments for batch and fed-batch systems at different substrate concentrations were analyzed theoretically in terms of flux distributions using ethanol production rate as the maximization criteria. Calculated ethanol rates were in agreement with experimental measurements, suggesting that this recombinant microorganism is sufficiently evolved to optimize its ethanol production. The function of the main pathways of yeast metabolism (PPP, EMP, TCA) are discussed together with the node analyses of glucose-6-P and pyruvate branch points. Theoretical node analysis revealed that if the split ratio in G6P branch point is changed by genetic manipulations, the ethanol yield would be affected considerably.     

站点CERES-Rice模型区域应用效果和误差来源

作物区域模拟是利用有限的空间数据,最大限度地反映出生育期、产量等作物性状的时空变化规律.由于目前的作物模型大多是田间尺度的站点模型,把它运用到区域水平的效果如何研究甚少.文章利用CERES-Rice模型,对作物模型在我国的区域应用效果进行了分析.首先利用田间观测数据在各实验点上对模型进行了详细的站点校准,以验证模型在我国的模拟能力;然后以我国水稻生态区(精确到亚区)为单位,运用均方根差(RMSE)法进行了区域校准和验证;最后利用区域校准后的CERES-Rice模型,模拟了1980～2000年的网格(50km×50km)水稻产量,并与同期农调队调查产量进行统计比较,以验证区域应用的效果,为区域模拟的推广和应用提供参考.结果表明:经过空间校准后的CERES-Rice模型,在水稻的主产区1～4区(占种植面积的95%)模拟的平均产量与调查产量相对均方根差在22%以内,两者的符合度也较好,个别区域(5、6) RMSE%在24%～30%之间;1980～2000年水稻各产区模拟的平均产量与调查产量随时间变化趋势也具有一定的一致性;全国1896个网格中,大部分网格(71.01%)模拟的21年水稻年产量与调查产量的RMSE%在30%之内,且大部分分布在水稻主产区,考虑到水稻种植面积的权重后,认为利用区域校准和验证后的CERES-Rice模型进行水稻区域模拟,可以反映出产量的时空分布特征,能够为宏观决策提供相应的信息.但目前区域模拟中还存在着一定的误差,有待今后进一步研究.     

应用结构方程模型解析影响黄连木果实产量 和种子命运的因素

果实(种子)产量和质量是影响植物种群更新的重要因素。为了探明影响黄连木果实产量和种子命运的因素以及这些影响因素之间的相互作用, 作者于2009年对河南省济源市45株黄连木(Pistacia chinensis)结果样树的植株特征、果实特征、果实产量和种子命运等进行了测定, 并用结构方程模型进行综合分析。结果表明: (1)黄连木果实产量与树高、树冠面积和果序大小等特征成正相关, 但与胸径、果实大小相关性不显著; (2)与捕食者饱和假说的预测不一致, 单株果实产量对黄连木广肩小蜂(Eurytoma plotnikovi)的种子捕食率(即虫蛀率)无显著直接负向效应; (3)树高和果实大小对虫蛀率为显著直接正向效应, 胸径对虫蛀率为显著直接负向效应, 显示黄连木广肩小蜂对植株特征和果实特征有一定的选择能力; (4)空壳率与虫蛀率成显著负相关, 空壳果实越多, 越易逃避黄连木广肩小蜂的寄生, 空壳果实的存在对完好种子起到了一定保护作用, 可能是黄连木防御昆虫寄生的重要机制; (5)空壳率和虫蛀率对种子完好率有显著直接负向效应, 而胸径、果序大小和果实产量对完好率为间接正向效应, 树高和果实大小为间接负向效应。可见, 黄连木植株特征和果实特征均不同程度地影响其果实产量和昆虫寄生, 从而影响黄连木的种子质量和种群更新。     

Function inferences from a molecular structural model of bacterial ParE toxin

Toxin-antitoxin (TA) systems contribute to plasmid stability by a mechanism that relies on the differential stabilities of the toxin and antitoxin proteins and leads to the killing of daughter bacteria that did not receive a plasmid copy at the cell division. ParE is the toxic component of a TA system that constitutes along with RelE an important class of bacterial toxin called RelE/ParE superfamily. For ParE toxin, no crystallographic structure is available so far and rare in vitro studies demonstrated that the target of toxin activity is E. coli DNA gyrase. Here, a 3D Model for E. coli ParE toxin by molecular homology modeling was built using MODELLER, a program for comparative modeling. The Model was energy minimized by CHARMM and validated using PROCHECK and VERIFY3D programs. Resulting Ramachandran plot analysis it was found that the portion residues failing into the most favored and allowed regions was 96.8%. Structural similarity search employing DALI server showed as the best matches RelE and YoeB families. The Model also showed similarities with other microbial ribonucleases but in a small score. A possible homologous deep cleft active site was identified in the Model using CASTp program. Additional studies to investigate the nuclease activity in members of ParE family as well as to confirm the inhibitory replication activity are needed. The predicted Model allows initial inferences about the unexplored 3D structure of the ParE toxin and may be further used in rational design of molecules for structure-function studies.