Using pseudo-amino acid composition and support vector machine to predict protein structural class

As a result of genome and other sequencing projects, the gap between the number of known protein sequences and the number of known protein structural classes is widening rapidly. In order to narrow this gap, it is vitally important to develop a computational prediction method for fast and accurately determining the protein structural class. In this paper, a novel predictor is developed for predicting protein structural class. It is featured by employing a support vector machine learning system and using a different pseudo-amino acid composition (PseAA), which was introduced to, to some extent, take into account the sequence-order effects to represent protein samples. As a demonstration, the jackknife cross-validation test was performed on a working dataset that contains 204 non-homologous proteins. The predicted results are very encouraging, indicating that the current predictor featured with the PseAA may play an important complementary role to the elegant covariant discriminant predictor and other existing algorithms.     

Structure insights into mechanisms of ATP hydrolysis and the activation of human heat-shock protein 90

The activation of molecular chaperone heat-shock protein 90 (Hsp90) is dependent on ATP binding and hydrolysis, which occurs in the N-terminal domains of protein. Here, we have determined three crystal structures of the N-terminal domain of human Hsp90 in native and in complex with ATP and ATP analog, providing a clear view of the catalytic mechanism of ATP hydrolysis by Hsp90. Additionally, the binding of ATP leads the N-terminal domains to be an intermediate state that could be used to partially explain why the isolated N-terminal domain of Hsp90 has very weak ATP hydrolytic activity.     

低压低氧延迟预适应小鼠海马差异表达蛋白的分离及鉴定研究

目的:探索低压低氧延迟预适应(HHDP)小鼠海马差异表达蛋白。方法:建立小鼠海马HHDP动物模型后,用含尿素的细胞裂解液提取海马总蛋白质。经等电聚焦、SDS-PAGE电泳、考马斯亮蓝R250染色,比较对照组及HHDP组双向电泳图谱上蛋白质点的差异。切取HHDP组表达增高的蛋白质点,经脱色、胰蛋白酶酶切、提取肽片段,进行MALDI-TOF-MS检测。结果:在正常对照组和HHDP组海马总蛋白双向电泳图谱上,分别检测到481±38和477±21个点,匹配点为169±6个。其中HHDP组比对照组增高大于2倍的有33±10个点,降低大于2倍的有21±12个点。电泳图谱平均相关系数为0.7748±0.0267。有12个点在HHDP组显著增高(P<0.05,n=4),对其进行了肽质量指纹图谱分析,其中8个蛋白点得到相应的肽质量指纹图谱。数据库检索显示其中一个为果糖二磷酸醛缩酶A。3个在蛋白质数据库中没有检索到与之相匹配的任何蛋白,可能为新蛋白。另外4个可找到与其有部分匹配的氨基酸序列,但分子量和等电点与对应蛋白相差悬殊,它们可能具有同源性。结论:小鼠海马HHDP时,果糖二磷酸醛缩酶A等多种蛋白表达发生改变,可能是产生HHDP的重要机制之一。     

Transport functions and expression analysis of vacuolar membrane aquaporins in response to various stresses in rice

The vacuole, a multifunctional organelle of most plant cells, has very important roles in space filling, osmotic adjustment, storage and digestion. Previous researches suggested that aquaporins in the tonoplast were involved in vacuolar functions. The rice genome contains 33 aquaporin genes, 10 of which encode tonoplast intrinsic proteins (TIPs). However, the function of each individual TIP isoform and the integrated function of TIPs under various physiological conditions remain elusive. Here, five rice TIP members were characterized with water and/or glycerol transport activities using the Xenopus oocyte expression system. OsTIP1;2, OsTIP2;2, OsTIP4;1 and OsTIP5;1 possessed water transport activity. OsTIP1;2, OsTIP3;2 and OsTIP4;1 were demonstrated with glycerol transport activity. Rice TIP expression patterns under various abiotic stress conditions including dehydration, high salinity, abscisic acid (ABA) and during seed germination were investigated by real-time PCR. OsTIP1s (OsTIP1;1 and OsTIP1;2) were highly expressed during seed germination, whereas OsTIP3s (OsTIP3;1 and OsTIP3;2) were specifically expressed in mature seeds with a decrease in expression levels upon germination. The results of this research provided a functional and expression profiles of rice TIPs.     

基于易错PCR技术的短小芽孢杆菌YZ02脂肪酶基因BpL的定向进化

利用易错PCR技术对短小芽胞杆菌(Bacillus pumilus)YZ02脂肪酶基因BpL进行两轮定向进化研究, 分别获得最佳突变株BpL1-7和BpL2-1369, 其脂肪酶活力比出发酶分别提高了2倍和6倍。序列分析表明, 突变体BpL2-1369有4个碱基发生了突变: T61C/C147T/A334G/T371A, 其中有3个碱基突变导致了氨基酸的改变。通过SWISS-MODEL数据库模拟脂肪酶的结构显示, 3个突变氨基酸分别位于第1个a螺旋的第3个氨基酸、第4和第5个b折叠之间的转角以及第5个b折叠的第1个氨基酸位置。将野生型脂肪酶基因BpL和进化后的基因BpL2-1369的高效表达产物经Ni-Agarose柱和Sephadex-G75纯化后, 酶学性质测定表明: 突变脂肪酶的比活力比野生型脂肪酶提高了1.31倍, Km值由8.24 mmol/L降低至7.17 mmol/L; 在pH>8.0时的稳定性较野生型脂肪酶有所提高。     

人结核分枝杆菌特异性核酸探针制备及结核病PCR检测技术的初步临床应用

采用人结核分枝杆菌(Mycobacterium tuberculosis TB)染色体DNA为模板,选择位于插入片段IS6110中884～865和568～588碱基对处的两个片段为引物,扩增出317bp的特异性片段．将其克隆进pUCl9载体。酶切图谱分析和DNA序列测定证实为目的片段。该片段经DIG标记,分别与11种分枝杆菌DNA进行Southern杂交,结果证明只与人型复合分枝杆菌发生杂交反应。利用该对引物建立的PcR检测拄术对74份结核病痰液标本进行检测,并与临床细菌快速培养结果相比较,发现48份临床阳性均为PcR阳性,在26份临床阴性标本中亦发现11份PCR检测阳性。将标本PCR产物与克隆探针进行杂交,显示两者结果完全一致。说明PCR检测体系结果可靠,其灵敏度明显高于目前临床所采用的方法,可作为一种常规技术用于结核病的临床检测。     

植物释放挥发性有机物(VOCs)的研究进展

植物释放的有机物(VOCs)对大气圈臭氧的动态、一氧化碳的产生和甲烷的氧化起重要作用。本文主要综述了异戊二烯、单萜这两种重要的植物释放物,总结了国内外的研究进展,概括了它们的合成、释放以及环境因子的影响。同时简要介绍了其它几种植物释放的有机物,并就有机物的释放对大气化学、温室效应和全球变化的影响也作了简要分析。     

Application of matrix solid-phase dispersion methodology to the extraction of endogenous peptides from porcine hypothalamus samples for MS and LC-MS analysis

In this study, we investigated a novel application of matrix solid-phase dispersion (MSPD) methodology for the extraction of endogenous peptides from porcine hypothalamus tissue samples. Several experimental factors of the MSPD procedure were examined. Finally, silica-based octadecyl was chosen as dispersing material and blended with 0.25 g porcine hypothalamus at a ratio of 5, and 10 mL of 60% acetonitrile with 0.2% formic acid in water was chosen as the extraction and elution solvent. This MSPD extraction method was compared to the classic acid extraction method. More peaks were observed in the MSPD extracts (74±5) by MALDI-TOF MS than in acid extracts (34±5). Moreover, 14 potential endogenous peptides were identified in the MSPD extracts after nanoLC-MS/MS analysis, while only 2 endogenous peptides in the acid extracts. These results indicated that MSPD could be employed as a simple and efficient method for the extraction of endogenous peptides from tissues.     

甘蔗品种资源的表型遗传多样性

为了提高甘蔗品种资源的利用效率, 为甘蔗遗传育种亲本的选择、杂交组合配制及核心种质构建提供理论指导, 我们利用17个质量性状和5个数量性状分析了来自13个国家共20个地区的1,160份甘蔗品种资源的遗传变异、遗传结构和遗传距离等。结果表明: 5个数量性状在不同来源地品种群体之间的变异系数值(CV)变化较大, 说明不同来源地品种群体的数量遗传变异有较大差异, 其中来自海南的品种其群体遗传变异最丰富。质量性状的Shannon-Wiener多样性指数表明, 来自美国的品种群体遗传多样性最高, 其次为中国台湾, 第三为澳大利亚, 说明上述3个地区的甘蔗种质创新比较活跃, 在遗传育种中使用了更多表型性状多样化的亲本。不同来源地品种其群体的遗传分化系数(Gst)和基因流(Nm)显示甘蔗品种群体表型性状的遗传变异主要来自来源地内部, 且不同来源地品种群体之间存在较大的基因交流。遗传距离和UPGMA聚类分析结果表明, 各来源地品种群体之间遗传距离在0.0261–0.2945之间, 其中以福建和广东的品种最为相似, 其次为古巴和美国、广西和云南、澳大利亚和菲律宾、江西和四川、巴西和法国, 说明上述地区在杂交亲本的选择上比较相近。鉴于此, 在遗传育种中应加大利用具有丰富遗传多样性的品种材料并尽量避免选择同一组的品种相互杂交, 同时对于与其他来源地品种群体遗传距离较远的墨西哥品种群体在亲本选配时应给予更多关注。