基于添加模体信息和功率谱密度的组合向量预测27类蛋白质折叠子

以序列相似性低于40%的1895条蛋白质序列构建涵盖27个折叠类型的蛋白质折叠子数据库,从蛋白质序列出发,用模体频数值、低频功率谱密度值、氨基酸组分、预测的二级结构信息和自相关函数值构成组合向量表示蛋白质序列信息,采用支持向量机算法,基于整体分类策略,对27类蛋白质折叠子的折叠类型进行预测,独立检验的预测精度达到了66.67%。同时,以同样的特征参数和算法对27类折叠子的4个结构类型进行了预测,独立检验的预测精度达到了89.24%。将同样的方法用于前人使用过的27类折叠子数据库,得到了好于前人的预测结果。     

打分矩阵方法在β-发夹模体识别中的应用

用打分矩阵的五种算法,从蛋白质的氨基酸序列出发,以氨基酸为参数,分别对3088个同源性小于40％的蛋白质和2878个同源性小于33％的蛋白质的β-发夹模体片断进行了识别。利用self—consistency和10—fold cross—validation两种方法对五种算法进行检验,结果表明,Claverie（1996）算法相对较好,对3088个蛋白质的平均识别精度达到了77．7％和76．1％。     

用支持向量机识别 β-发夹模体

基于蛋白质序列,提出了一种新的超二级结构模体β-发夹的预测方法。利用离散增量构成的向量来表示序列信息,并将6个离散增量输入支持向量机,在六维向量空间中寻找最优超平面,将β-发夹和非β-发夹进行分类。计算结果表明,利用所设计的算法预测β-发夹,有较高的预测能力。对于训练集,5-交叉检验的预测总精度为81.24％,相关系数为0．57,β-发夹敏感性为83．06％;对于独立的检验集,预测总精度为78．34％,相关系数0．56,β-发夹敏感性为77．24％。将此预测模型应用于CASP6的63个蛋白质进行检验,得到较好结果。     

2个银叶真藓HSP70序列的生物信息学相关分析

从银叶真藓(Bryum argenteum)转录组数据库出发,使用Pfam数据库提供的HMM模型共得到33条长度大于200aa,注释的热休克蛋白Ba HSP70;其中2条(Ba HSP70-1,Ba HSP70-2)具有完整ORF,NCBI核酸数据库登录号为KP087877和KP087878。使用生物信息学在线分析工具和软件,对真藓HSP70的两条蛋白质序列从氨基酸组成、保守结构域、理化性质、疏水性/亲水性、信号肽、蛋白质结构、模体的识别及同源性分析等方面进行了预测和分析。结果表明:2条Ba HSP70s基因序列ORF全长分别为2 396 bp和2 356 bp,分别编码649aa和650aa。序列模体分析表明Ba HSP70s和其它报道的植物HSP70均含有4个相同的模体,并且各模体在蛋白质序列上顺序一致。通过对2条Ba HSP70s进行氨基酸多序列比对及基因树分析,发现Ba HSP70-1和Ba HSP70-2雪莲相似度最高,分别是91.2%和86.6%。本研究为进一步研究HSP70基因的克隆和功能验证奠定了基础。     

人转化生长因子β1在大肠杆菌中的表达——Ⅰ.胞内直接表达

采用PCR技术 ,扩增了人转化生长因子β1 (hTGFβ1 )成熟肽基因 ,并对其进行了全序列测定 .采用DH5α/ pBV2 2 0表达系统 ,使TGFβ1在大肠杆菌胞内的表达达到 1 6 % .通过N端氨基酸序列测定和免疫印迹分析 ,证实重组蛋白为hTGFβ1单体蛋白 .采用谷胱甘肽法或CHAPS/DMSO法 ,使重组蛋白的复性率达到 30 % .通过纯化获得了银染一条带的重组蛋白 ,MTT法对Mv1Lu细胞的测活表明 ,重组蛋白具有较强的生物活性     

用离散量的方法识别蛋白质的超二级结构

用离散量的方法,对2208个分辨率在2.5I以上的高精度的蛋白质结构中四类超二级结构进行了识别。从蛋白质一级序列出发,以氨基酸(20种氨基酸加一个空位)和其紧邻关联共同为参数,当序列模式固定长取8个氨基酸残基时,对“822”序列模式3交叉检验的平均预测精度达到78.1%,jack-knife检验的平均预测精度达到76.7%;当序列模式固定长取10个氨基酸残基时,对“1041”序列模式3交叉检验的平均预测精度达到83.1%,jack-knife检验的平均预测精度达到79.8%。     

鹅白细胞介素 2基因的克隆与分子模型

对鸡、鸭、火鸡IL-2的核苷酸序列进行比较,在其保守区设计引物,通过RT-PCR方法扩增和克隆了鹅白介素2 (goIL-2) 的核苷酸序列。该序列由768 nt组成,编码一条由141个氨基酸组成的前体蛋白。goIL-2核苷酸序列和氨基酸序列与鸭IL-2(duIL-2)核苷酸序列和氨基酸序列的同源性为90.1%和83.6%,与鸡、火鸡和鹌鹑IL-2的同源性为69.7%-75%和61.0%-63.1%,与哺乳动物IL-2的同源性为25%-30%和14%-17%。氨基酸序列分析表明,N端存在一长21个氨基酸的信号肽,含有形成2个链内二硫键的4个半胱氨酸。goIL-2 mRNA的体外表达动力学分析表明,脾脏T淋巴细胞经Con A诱导2 h至24 h均可检测到goIL-2 mRNA的表达。三维结构预测表明,goIL-2蛋白由A、B、C、D 4个α-螺旋和2个?-折叠构成。遗传进化分析表明,goIL-2和duIL-2的亲缘关系最近。     

不同N端序列长度匍枝根霉△6-脂肪酸脱氢酶重组子的表达

克隆并在酵母中表达两个不同N段序列长度的匍枝根霉△6-脂肪酸脱氢酶重组子,其中长序列的重组子LYRnD6D是从匍枝根霉中克隆的△6-脂肪酸脱氢酶基因,编码459个氨基酸,N端序列为MSTLDRQSIFTIKELESISQRIHDG-DEEAMKFIII;短序列重组子SYRnD6D是预测的匍枝根霉△6-脂肪酸脱氢酶基因的ORF序列,N端序列为MKFIIIDKKVY,编码430个氨基酸;两个重组子均具有△6-脂肪酸脱氢酶保守的组氨酸序列和HPGG序列,长序列的N端比短序列长29个氨基酸残基(MSTLDRQSIFTIKELESISQRIHDGDE-EA)。两个重组子在缺陷型酵母中均得到了的表达,产生了γ-亚麻酸。利用酶的相对活力比较两个重组子在同一温度下的稳定性,长序列重组子的酶在15℃下反应4h后相对活力仍有74%,而短序列酶的相对活力只有43%,所以长序列重组子酶在低温下比短序列酶稳定性高,是因为长序列多出的氨基酸序列增加了酶的稳定性。     

人GM-CSF受体β链胞膜外区域与GM-CSF结合位点的研究

研究了抗人GM-CSF受体β链胞膜外区域4种人工合成多肽D1(9～114),D2(115～225),D3(226～325)和D4(326～422)4个多肽片段多克隆抗血清和McAb对GM-CSF生物学活性的阻断作用,结果首次发现抗D1多克隆抗血清和抗D1McAb 2A_9对 GM-CSF促进的 DMSO诱导的 HL60细胞、正常人胎儿骨髓细胞以及人GM-CSF依赖的TF-1细胞增殖有显著的阻断效应,抗D2McAb 1C₁₂对GM-CSF诱导的 TF-1细胞增殖也有显著的阻断效应,阻断抑制率均可达 90％以上,而其它抗受体 β链 McAb和无关对照 McAb E₇均无阻断活性.此结果表明:抗 D1 McAb2A₉和抗D2 McAb 1C₁₂所识别的表位则可能为受体β链与 GM-CSF的结合位点依据受体β链二级结构预测,受体与细胞因子结合部位的结构理论,设计和合成了受体β链45～75,56～75和 66～75 3个人工合成多肽片段,用间接ELISA结合试验分析表明,McAb 2A₉识别表位位于第 45～55位氨基酸内.应用受体与细胞因子结合部位的结构理论推测 McAb 1C₁₂识别表位可能位于β链内 216～220位氨基酸.此结果对于深入了解受体β链的结构与功能以及细胞因子与受体的相互作用均有十分重要的意义.     

枇杷花茶水提物的镇咳、抗炎与抗氧化作用研究

采用小鼠氨水致咳法研究枇杷花茶水提物镇咳效果,以二甲苯致小鼠耳肿胀法研究其抗炎效果,并从枇杷花茶的还原能力及对超氧阴离子和羟自由基的清除作用分析枇杷花茶水提物的抗氧化效果。结果表明,枇杷花茶的水提物高剂量组(3000 mg·kg-1)、低剂量组(700 mg·kg-1)均有镇咳抗炎效果,水提物的浓度越高,效果越好。各浓度枇杷花茶水提物均表现出一定的还原能力,对于羟基自由基和超氧阴离子都有一定的清除效果。其中,20 mg·mL-1水提物还原效果最好(吸光值0.903),超过0.2 mg·mL-1抗坏血酸(吸光值0.814);10 mg·mL-1的水提物对超氧阴离子的清除率为47.32%;20 mg·mL-1水提物对于羟基自由基的清除效果非常明显,清除率为91.62%。枇杷花茶水提物镇咳、抗炎、抗氧化效果明显。     

基因功能研究方法的新进展

随着生命科学的发展,研究领域的不断开拓,越来越多的未知新基因和基因的新功能被科学家们发现,研究这些未知新基因的功能和已知基因的新功能成为了极其重要的一项内容。本文对基因功能研究的最新方法进行了介绍。     

Nonparametric Tests for Interval‐Censored Failure Time Data

This paper discusses two sample nonparametric comparison of survival functions when only interval‐censored failure time data are available. The problem considered often occurs in, for example, biological and medical studies such as medical follow‐up studies and clinical trials. For the problem, we present and study several nonparametric test procedures that include methods based on both absolute and squared survival differences as well as simple survival differences. The presented tests provide alternatives to existing methods, most of which are rank‐based tests and not sensitive to nonproportional or nonmonotone alternatives. Simulation studies are performed to evaluate and compare the proposed methods with existing methods and suggest that the proposed tests work well for nonmonotone alternatives as well as monotone alternatives. An illustrative example is presented.     

Flavonoids and cognitive function: a review of human randomized controlled trial studies and recommendations for future studies

Evidence in support of the neuroprotective effects of flavonoids has increased significantly in recent years, although to date much of this evidence has emerged from animal rather than human studies. Nonetheless, with a view to making recommendations for future good practice, we review 15 existing human dietary intervention studies that have examined the effects of particular types of flavonoid on cognitive performance. The studies employed a total of 55 different cognitive tests covering a broad range of cognitive domains. Most studies incorporated at least one measure of executive function/working memory, with nine reporting significant improvements in performance as a function of flavonoid supplementation compared to a control group. However, some domains were overlooked completely (e.g. implicit memory, prospective memory), and for the most part there was little consistency in terms of the particular cognitive tests used making across study comparisons difficult. Furthermore, there was some confusion concerning what aspects of cognitive function particular tests were actually measuring. Overall, while initial results are encouraging, future studies need to pay careful attention when selecting cognitive measures, especially in terms of ensuring that tasks are actually sensitive enough to detect treatment effects.     

Haemodynamics using transthoracic echocardiography in healthy pregnant and non-pregnant baboons (Papio hamadryas)

Background To determine systolic and diastolic function using transthoracic echocardiography in the baboon (Papio hamadryas). Methods Transthoracic echocardiography was performed in eight non‐pregnant female and six pregnant baboons according to American Society of Echocardiography recommendations. Results Haemodynamic measurements were obtained from fourteen baboons. Compared to non‐pregnant baboons, pregnant baboons demonstrated: (mean ± SD, pregnant vs. healthy) increased cardiac output (1615 ± 121 ml/minutes vs. 1317 ± 134 ml/minutes P = 0.001) due to an increased heart rate [120 ± 11 beats per minute (BPM) vs. 105 ± 6 BPM P = 0.018]. The inter‐observer and intra‐observer variability (mean difference ± SD) for the left ventricular outflow tract diameter was 0.05 ± 0.07 cm and 0.01 ± 0.03 cm respectively. There was minimal impact to the animal’s daily activities. Conclusions Transthoracic echocardiography was applicable and reproducible for the assessment of haemodynamics in baboons thus enabling translation of animal results to human studies.     

Quantifying protein function specificity in the gene ontology

Quantitative or numerical metrics of protein function specificity made possible by the Gene Ontology are useful in that they enable development of distance or similarity measures between protein functions. Here we describe how to calculate four measures of function specificity for GO terms: 1) number of ancestor terms; 2) number of offspring terms; 3) proportion of terms; and 4) Information Content (IC). We discuss the relationship between the metrics and the strengths and weaknesses of each.     

Enamel microstructure and molar wear in the greater galago,Otolemur crassicaudatus (mammalia,primates)

This study describes the molar enamel microstructure of the greater galago, based on SEM study of four individuals. Galago molar enamel consists primarily of radially oriented Pattern 1 prisms. However, the most superficial enamel is characterized by regions of poorly developed prisms or nonprismatic enamel, and Pattern 3 prisms can be found at depths intermediate and deep to the enamel surface. Orientations of prism long axes relative to wear surfaces differ among functionally distinct regions (cuspal facets, Phase I/II facets, and crushing basins). Consequently, orientations of enamel crystallites relative to these surfaces also differ. Because crystallites are the structural unit involved in enamel abrasion, these differences in orientation may have important effects on molar wear patterns. Crystallite orientations differ most between cuspal facets and Phase I/II facet surfaces. Cuspal facets are characterized by near surface-parallel interprismatic and surface-oblique prismatic crystallites. Previous experimental studies suggest that this arrangement is most resistant to wear when surface-normal (compressive) loads predominate. In contrast, prismatic and interprismatic crystallites intercept Phase I/II facet surfaces obliquely, an arrangement expected to resist abrasion when surface-parallel (shearing) loads predominate. Superficial enamel is preserved at most basin surfaces, indicating that these regions are subject to comparatively little abrasive wear. These results support the hypothesis that galago occlusal enamel is organized so as to resist abrasion of different functional regions, a property that may prove important in maintaining functional efficiency. However, this largely reflects constraints of occlusal topography on a microstructure typical of many mammals and thus does not appear to represent a structural innovation. © 1993 Wiley-Liss, Inc.