Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry

We describe the application of a peptide retention time reversed phase liquid chromatography (RPLC) prediction model previously reported (Petritis et al. Anal. Chem. 2003, 75, 1039) for improved peptide identification. The model uses peptide sequence information to generate a theoretical (predicted) elution time that can be compared with the observed elution time. Using data from a set of known proteins, the retention time parameter was incorporated into a discriminant function for use with tandem mass spectrometry (MS/MS) data analyzed with the peptide/protein identification program SEQUEST. For singly charged ions, the number of confident identifications increased by 12% when the elution time metric is included compared to when mass spectral data is the sole source of information in the context of a Drosophila melanogaster database. A 3-4% improvement was obtained for doubly and triply charged ions for the same biological system. Application to the larger Rattus norvegicus (rat) and human proteome databases resulted in an 8-9% overall increase in the number of confident identifications, when both the discriminant function and elution time are used. The effect of adding "runner-up" hits (peptide matches that are not the highest scoring for a spectra) from SEQUEST is also explored, and we find that the number of confident identifications is further increased by 1% when these hits are also considered. Finally, application of the discriminant functions derived in this work with approximately 2.2 million spectra from over three hundred LC-MS/MS analyses of peptides from human plasma protein resulted in a 16% increase in confident peptide identifications (9022 vs 7779) using elution time information. Further improvements from the use of elution time information can be expected as both the experimental control of elution time reproducibility and the predictive capability are improved.     

小腹茧蜂亚科的雄外生殖器及族级单元系统发育的研究

对分布在东洋区和古北区的小腹茧蜂亚科 (膜翅目: 茧蜂科)21个属的67个种及外群折脉茧蜂属 (膜翅目: 茧蜂科) 2个种的雄外生殖器的5个性状进行了比较研究。在形态学研究的基础上,通过选用头部、胸部和腹部(包括雌雄外生殖器的性状) 等34个性状,运用支序分析的方法探讨了分布在东洋区和古北区的小腹茧蜂亚科21个属以及它们所属的族间的系统发育关系,并对Mason (1981) 的分类系统进行了重新评价。雄外生殖器和支序分析基本上证实并恢复了由Mason (1981) 确定的2个主要分支,即绒茧蜂族Apantelini+小腹茧蜂族Microgastrini和拱茧蜂族Fornicini+盘绒茧蜂族Cotesiini+侧沟茧蜂族MicroplitinI。绒茧蜂族Apantelini、拱茧蜂族Fornicini和侧沟茧蜂族Microplitini为单系群也被支持,但小腹茧蜂族Microgastrini和盘绒茧蜂族Cotesiini是否为单系群尚难于在树形图中体现,而且族内各属间的分支关系有变动。因此,尽管Mason的族级分类单元有一些欠缺,但仍是可信、实用的,不同意Walker等 (1990) 认为不应再使用Mason分族系统的观点。     

Interclonal differences, plasticity and trade-offs of life history traits of Cyperus esculentus in relation to water availability

Cyperus esculentus is an exotic clonal (or pseudoannual) weed in Japan, and its range is steadily increasing. To investigate its interclonal variation and phenotypic plasticity in response to water availability, five clones of C. esculentus , collected from different sites in Japan, were grown singly in pots placed outdoors under dry and wet conditions. All the traits examined showed considerable variation among the five clones. However, two clones from Tochigi were similar to each other; thus, they might have originated from the same founder population. The clone from Ibaraki was quite different from the others. Therefore, it is suggested that the Japanese populations of C. esculentus might have resulted from multiple introductions of genotypes from geographically separated and, hence, genetically differentiated, source populations. All the clones also showed considerable plasticity in response to water availability. Clones with a larger ramet number had a greater plasticity, whereas tuber size was invariant across water treatments. Highly plastic traits had generally low interclonal variation in plasticity. All the clones had high productivity and produced more ramets and tubers under wet conditions than under dry conditions. Moreover, water availability could partially regulate the mode of its reproduction; wet conditions favored tuber production (vegetative propagation) while dry conditions favored sexual reproduction. A number of trade-offs occurred between the traits of clonal growth, storage and sexual reproduction, indicating that allocation among the competing functions/organs is mutually exclusive in plants. The results obtained here suggest that C. esculentus is more likely to invade wet habitats than dry habitats.     

Flagellar Sensilla of Sphecodes Bees (Hymenoptera, Halictidae)

The antenna of Sphecodes bees were investigated as regards the type and distribution of the sensilla. Eleven species originating from Sweden were used. Totally 325 specimens were studied. The distribution of sensilla placodea and sensilla trichodea on the antennal segments were studied in the light stereomicroscope. One to three antennae per species were also examined by SEM. The following types of sensilla were found: s. placodea; pit organs; s. campaniformia; s. basiconica; s. trichodea A, B and CD; and setae. The distribution of sensilla, especially s. placodea and s. trichodea A, was found to be species-specific in the male sex and their diagnostic value in taxonomy is stressed. In the female sex no specific characteristics were found, although two groups could be distinguished.     

慢性丙型肝炎患者中丙型肝炎病毒准种变异研究进展

丙型肝炎病毒（HCV）具有较高的变异性,通常以准种的形式分布在感染者的体内,病毒容易逃离机体的免疫监控,因而无法被有效地清除,导致机体很难控制其感染的发展,故易转变成慢性肝炎。HCV准种变异在宿主体内的持续存在对病毒感染的控制、抗病毒药物和疫苗的发展都是一个巨大的挑战。,我们重点阐述近年来关于HCV准种变异及其与慢性丙型肝炎患者的机体免疫、疾病进展、治疗效果之间关系的研究进展。     

Kiss-1 及MVD 在非小细胞肺癌中检测的临床意义及其相关性研究

目的:测定NSCLC组织中kiss-1基因表达、MVD分布,探讨其临床意义及其相关性.方法:应用免疫组化SP法检测56例NSCLC组织中Kiss-1表达及MVD分布情况,分析其与NSCLC的临床病理参数的关系及其相关性.结果:Kiss-1在NSCLC表达低于对照组(P＜0.05),MVD在NSCLC分布明显高于对照组(P＜0.05).Kiss-1与NSCLC的临床分期、淋巴结转移、肿瘤大小有关(P＜0.05).MVD与NSCLC分化程度、临床分期及淋巴结转移、肿瘤大小有关(P＜0.05).Kiss-1阳性组MVD分布明显低于Kiss-1阴性表达组,二者呈负相关(P＜0.05,r=-0.363).结论:Kiss-1及MVD在非小细胞肺癌发生、发展中发挥重要作用,二者存在相关性,联合检测可帮助预测NSCLC的侵袭、转移,判断预后.     

化学合成siRNA抑制H5N1亚型禽流感病毒在鸡胚成纤维细胞中的增殖

为研究RNA干涉对H5N1亚型禽流感病毒的增殖抑制作用,针对H5N1亚型禽流感病毒的NP和PA基因,设计4对siRNA干涉序列,并将其转染到鸡胚成纤维细胞,6h后接种H5N1亚型禽流感病毒液,在病毒感染后的16～56h内测定细胞上清中的病毒血凝价及观察细胞病变,并在病毒感染36h后检测NP、PA、HA和β-actin基因的mRNA水平。结果显示4对siRNA均能不同程度地抑制H5N1亚型禽流感病毒在鸡胚成纤维细胞中的增殖,但以PA为靶基因设计的一对干涉序列效果最优;实验还证实随着时间的延长,干涉效应逐渐减弱。本实验为研究RNA干涉技术防控禽流感提供了依据。     

黄芪多糖对大鼠口腔溃疡治疗作用研究

本研究旨在探讨黄芪多糖对患有口腔溃疡大鼠(recurrent aphthous ulcer,RAU)的表皮细胞生长因子(epidermal growth factor,EGF)水平及T淋巴细胞亚群的影响。根据溃疡面的直径计算愈合率及HE染色观察溃疡组织病理学改变,酶联免疫吸附法(ELISA)测定EGF的水平,流式细胞仪检测大鼠外周血CD4+T细胞、CD8+T细胞亚群的百分率。实验结果显示治疗20 d后,黄芪多糖组大鼠溃疡面积减小,愈合率为87.5%～100%。与正常对照组相比,模型对照组大鼠CD4+T细胞数减少、CD8+T细胞数升高,CD4+/CD8+比值降低(P<0.05)。与模型对照组相比,黄芪多糖组大鼠外周血CD4+T细胞数升高、CD8+T细胞数降低,CD4+/CD8+比值回升(P<0.05)。EGF水平在造模后出现明显下降,黄芪多糖灌胃治疗后有升高。提示黄芪多糖能够提高RAU实验性大鼠EGF的水平和改善T细胞亚群的失衡状态,具有明显地促进口腔溃疡愈合的作用。     

Stem tissue mass density is linked to growth and resistance to a stem‐boring insect in Alternanthera philoxeroides

To investigate how stem anatomical structure is linked to growth and resistance to stem‐boring insects in a herbaceous species, six populations of alligatorweed (Alternanthera philoxeroides) were grown in a common garden. Stem growth rate (GR) of A. philoxeroides and pupation rate as an estimate of resistance to a stem‐boring insect (Agasicles hygrophila) were quantified. Stem tissue mass density (TMD) was measured and stem anatomical traits were analysed on cross‐sectional areas (CSA). Stem TMD was positively correlated with resistance (i.e. negatively correlated with pupation rate) and negatively correlated with GR. Stem cortex CSA (%) and vascular bundle (VB) density (no./mm²) were positively related to stem TMD and negatively related to pupation rate. The GR was positively related to VB CSA (%) and negatively related to VB density. These results suggest that stem TMD, which results from a high fraction in cortex CSA and high VB density, is a key determinant of resistance to a stem‐boring specialist in A. philoxeroides. The high resistance of plants with higher stem TMD may partially impose a cost to plant growth.     

不结球白菜种子活力及抗氧化特性在人工老化过程中的变化

以不结球白菜品种‘寒笑’种子为材料,研究高温(42℃)高湿(相对湿度100%)人工老化处理过程中种子活力及抗氧化相关特性的变化。结果显示:不结球白菜种子的发芽率、发芽势、发芽指数和活力指数随老化处理时间的延长而逐渐下降,不正常苗率逐渐增加;种子的超氧阴离子(O2.-)产生速率先增高后降低,过氧化氢(H2O2)含量逐渐增加,脂氧合酶(LOX)活性和丙二醛(MDA)含量下降,种子浸出液相对电导率增加;种子超氧化物歧化酶(SOD)、过氧化氢酶(CAT)和谷胱甘肽还原酶(GR)活性随老化处理时间的延长逐渐下降,抗坏血酸过氧化物酶(APX)和谷胱甘肽过氧化物酶(GPX)活性在老化处理初期(老化3 d前)均增加,APX活性随后降低,GPX活性无显著变化;种子抗坏血酸(AsA)和还原型谷胱甘肽(GSH)含量在老化处理1 d后即显著降低并持续保持较低水平。研究表明,不结球白菜种子在人工加速老化过程中其抗氧化系统代谢紊乱并造成活性氧累积伤害,这可能是引起不结球白菜种子老化的重要原因。