Predicting Metabolic Pathways of Small Molecules and Enzymes Based on Interaction Information of Chemicals and Proteins

Metabolic pathway analysis, one of the most important fields in biochemistry, is pivotal to understanding the maintenance and modulation of the functions of an organism. Good comprehension of metabolic pathways is critical to understanding the mechanisms of some fundamental biological processes. Given a small molecule or an enzyme, how may one identify the metabolic pathways in which it may participate? Answering such a question is a first important step in understanding a metabolic pathway system. By utilizing the information provided by chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions, a novel method was proposed by which to allocate small molecules and enzymes to 11 major classes of metabolic pathways. A benchmark dataset consisting of 3,348 small molecules and 654 enzymes of yeast was constructed to test the method. It was observed that the first order prediction accuracy evaluated by the jackknife test was 79.56% in identifying the small molecules and enzymes in a benchmark dataset. Our method may become a useful vehicle in predicting the metabolic pathways of small molecules and enzymes, providing a basis for some further analysis of the pathway systems.     

没食子酸对美国白蛾幼虫营养效应及解毒酶活性的影响

美国白蛾是我国重大外来入侵害虫,寄主范围十分广泛。酚类物质是最广泛的植物次生代谢物之一,在植物抵御昆虫取食的化学防御中具有重要作用。本研究通过人工饲料添加没食子酸的方法,探究不同浓度的没食子酸对美国白蛾幼虫的营养效应及解毒酶和乙酰胆碱酯酶活性的影响。结果表明,各浓度(1.0%、1.5%、2.0%、2.5%、3.0%)没食子酸对美国白蛾4龄幼虫的近似消化率、食物利用率、相对取食量和相对生长率均具有显著影响(P<0.05),近似消化率和相对取食量不同程度下降,食物利用率和相对生长率则不同程度上升。不同浓度的没食子酸处理对美国白蛾幼虫的乙酰胆碱酯酶、羧酸酯酶、谷胱甘肽S-转移酶和细胞色素P450的活性均具有显著影响(P<0.05)。1.0%没食子酸作用时间不同,美国白蛾4龄幼虫的乙酰胆碱酯酶、羧酸酯酶、谷胱甘肽S-转移酶和细胞色素P450的活性差异显著(P<0.05)。没食子酸能够始终诱导细胞色素P450的活性,而羧酸酯酶的活性却受到抑制。不同浓度的没食子酸对乙酰胆碱酯酶作用总体上不明显,但较低浓度时(1.0%)对乙酰胆碱酯酶活性却随处理时间延长而抑制作用加强。较低浓度(1.0%~1.5%)的没食子酸对谷胱甘肽S-转移酶的活性有一定诱导作用,但随着没食子酸浓度提高谷胱甘肽S-转移酶的活性却受到一定程度的抑制。没食子酸能抑制美国白蛾幼虫的取食,并且对解毒酶和乙酰胆碱酯酶的活性表现出一定的时间效应和剂量效应,表明美国白蛾幼虫可能通过调节食物利用和解毒代谢等多种途径降低没食子酸的毒害作用,从而对含没食子酸的寄主植物产生适应。     

Prediction and Analysis of Post-Translational Pyruvoyl Residue Modification Sites from Internal Serines in Proteins

Most of pyruvoyl-dependent proteins observed in prokaryotes and eukaryotes are critical regulatory enzymes, which are primary targets of inhibitors for anti-cancer and anti-parasitic therapy. These proteins undergo an autocatalytic, intramolecular self-cleavage reaction in which a covalently bound pyruvoyl group is generated on a conserved serine residue. Traditional detections of the modified serine sites are performed by experimental approaches, which are often labor-intensive and time-consuming. In this study, we initiated in an attempt for the computational predictions of such serine sites with Feature Selection based on a Random Forest. Since only a small number of experimentally verified pyruvoyl-modified proteins are collected in the protein database at its current version, we only used a small dataset in this study. After removing proteins with sequence identities >60%, a non-redundant dataset was generated and was used, which contained only 46 proteins, with one pyruvoyl serine site for each protein. Several types of features were considered in our method including PSSM conservation scores, disorders, secondary structures, solvent accessibilities, amino acid factors and amino acid occurrence frequencies. As a result, a pretty good performance was achieved in our dataset. The best 100.00% accuracy and 1.0000 MCC value were obtained from the training dataset, and 93.75% accuracy and 0.8441 MCC value from the testing dataset. The optimal feature set contained 9 features. Analysis of the optimal feature set indicated the important roles of some specific features in determining the pyruvoyl-group-serine sites, which were consistent with several results of earlier experimental studies. These selected features may shed some light on the in-depth understanding of the mechanism of the post-translational self-maturation process, providing guidelines for experimental validation. Future work should be made as more pyruvoyl-modified proteins are found and the method should be evaluated on larger datasets. At last, the predicting software can be downloaded from http://www.nkbiox.com/sub/pyrupred/index.html.     

金黄色葡萄球菌A型肠毒素双抗体夹心ELISA检测方法的建立及应用

【目的】建立一种快速、灵敏、特异的金黄色葡萄球菌A型肠毒素(Staphylococcal enterotoxin A,SEA)检测方法。【方法】以原核表达的可溶性重组SEA蛋白为免疫原,获得特异性强、亲和力高的单克隆抗体作为捕获抗体,同时制备抗SEA兔多抗血清作为检测抗体建立双抗体夹心ELISA(Double antibody sandwich ELISA,DAS-ELISA)检测方法。【结果】该方法对SEA的线性检测区间为2-128μg/L(y=1.102x-0.07,R2=0.994),检测下限为1.89μg/L,与SEB、SEC2和SED之间无交叉反应;鲜奶SEA人工污染试验测定回收率为94%-114%,变异系数小于10%。应用该方法对46株金黄色葡萄球菌水产品分离株和164株奶牛乳腺炎金黄色葡萄球菌分离株的体外培养上清进行检测,阳性率分别为4.4%和50.6%,表明SEA污染普遍存在。【结论】建立的DAS-ELISA方法特异性、灵敏度和稳定性好,为检测SEA的食源性污染提供了有效手段。     

若干植物分类学术语介绍及中译名商榷

为便于国内外植物分类学同行的交流,本文介绍了48个国内尚未收入的植物分类学术语,提出了建议的中译名,并对10个已有术语的定义和中译名等问题进行了讨论。     

柑橘凤蝶蛹发声器的显微结构及防御作用(英文)

【目的】动物界存在多种用于对抗捕食者的防御机制。一些鳞翅目昆虫的蛹在受到机械刺激时会发出蠕动的声音。【方法】在扫描电镜下对柑橘凤蝶Papilio xuthus蛹的发声器形态特征进行观察,并使用Audacity软件对捕获的声音进行特征分析。【结果】柑橘凤蝶蛹在腹部第4-5节和第5-6节之间的节间膜上存在发声器,有规律地发出嘶嘶声。发声器由多层甲壳素构成的刮器和板组成,刮器和板上有 50~90个突起。当蛹的腹部被寄生蜂触角刺激30 s以上时,刮器和板会迅速相互摩擦,腹部反复摆动发出声音。蛹发出的声音是由一系列每2 000~3 000 ms发生3次的短脉冲组成的。频带很宽,主要分布在5~20kHz范围内。新鲜蛹和越冬蛹的活性不同,声强也不同。【结论】本研究首先描述了柑橘蝴蝶蛹发声器的结构,结果支持了一些蝴蝶蛹对寄生生物进化出一种特殊的防御机制(声学防御)的假说。此外,通过比较两种生境的柑橘凤蝶蛹的声波特征,我们提出了同一物种在不同地理区域可以产生方言的假说。 关键词:     

Hsp90 isoforms: functions, expression and clinical importance

The 90 kDa heat shock protein, Hsp90, is a main functional component of an important cytoplasmic chaperone complex, and it is involved in various cellular processes, such as cell proliferation, differentiation and apoptosis. Identification of Hsp90 as a molecular target of various anticancer drugs highlighted its importance from the clinical point of view. Here we summarize the current knowledge of various Hsp90 isoforms regarding their genomic location, molecular evolution, functional differences, differential induction after various environmental stresses and in pathological conditions as well as the growing importance of discriminating between Hsp90 isoforms in clinical practice.     

Nectar and Pollen Sources for Honeybee （Apis cerana cerana Fabr.） in Qinglan Mangrove Area, Hainan Island, China

In the present study, nectar and pollen sources for honeybee （Apls cerana cerana Fabr.） were studied in Qlnglan mangrove area, Hainan Island, China, based on microscopic analysis of honey and pollen load （corblcular and gut contents） from honeybees collected In October and November 2004. Qualitative and quantitative melittopalynologlcal analysis of the natural honey sample showed that the honey is of unlfloral type with Mimosa pudlca L. （Mlmosaceae） as the predominant （89.14%） source of nectar and pollen for A. cerana cerana In October. Members of Araceae are an Important minor （3%-15%） pollen type, whereas those of Arecaceae are a minor （〈3%） pollen type. Pollen grains of Nypa fruticans Wurmb., Rhlzophora spp., Excoecarla agallocha L., Lumnitzera spp., Brugulera spp., Kandella candel Druce, and Ceriops tagal （Perr.） C. B. Rob. are among the notable mangrove texa growing In Qinglan mangrove area recorded as minor taxa In the honey. The absolute pollen count （I.e. the number of pollen grains/10 g honey sample） suggests that the honey belongs to Group V （〉1 000 000）. Pollen analysis from the corblcular and gut contents of A. cerana cerana revealed the highest representation （95.60%） of members of Sonneratia spp. （Sonneratlaceae）, followed by Bruguiera spp. （Rhizophoraceae）, Euphorblaceae, Poaceae, Fabaceae, Arecaceae, Araceae, Anacardlaceae, and Rublaceae. Of these plants, those belonging to Sonneratla plants are the most Important nectar and pollen sources for A. cerana cerana and are frequently foraged and pollinated by these bees in November.     

拟南芥RopGEFs家族基因在外源脱落酸处理下的表达分析

ABA不同浓度和不同时间处理拟南芥野生型7天龄幼苗,采用实时荧光定量PCR方法,分析小G蛋白ROP10和ROP乌苷酸交换因子RopGEFs基因的表达水平差异。结果表明,RopGEF7-10,12及33没有检测到表达,而RopGEFI-6,11,14ROP10在ABA处理下表现出不同的应答趋势,其中RopGEF5基因的表达变化与ROP10的变化相似。推测RopGEF5有可能在ROP10介导的ABA信号转导途经中起调控作用。