应用毒理蛋白质组学技术研究多环芳烃类物质诱导气道上皮细胞毒理作用的机制

为了更好地理解苯并芘(Benzo(a)pyrene, B(a)P)在气道细胞诱导的毒理作用机制. 应用二维凝胶电泳(two-dimensional electrophoresis, 2-DE)分离B(a)P处理组(B(a)P-A549)、对照组(DMSO-A549)的总蛋白质, 图像分析识别差异表达的蛋白质点, 基质辅助激光解吸电离飞行时间质谱(MALDI-TOF-MS)鉴定差异蛋白质点, Western blot验证差异蛋白热激蛋白27 (heat shock protein 27, HSP 27)以及锰超氧化物歧化酶(Mn superoxide dismutase, Mn SOD)的表达, 使用0.1, 1, 10 μmol/L B(a)P处理A549细胞, 应用Western blot及RT-PCR检测各组细胞中Mn SOD的表达, 检测各组细胞中总抗氧化活性(total antioxidant capacity)、总SOD活性(total activity of SOD)、过氧化氢酶活性(catalase activity, CAT)、谷胱甘肽还原酶活性(glutathione reductase, Gr). 本研究首先建立了B(a)P处理组、对照组的2-DE 图谱, 质谱鉴定了23个差异蛋白质, Western blot 证实HSP 27及Mn SOD的表达水平在B(a)P处理组中较对照组明显下调|使用0.1, 1, 10 μmol/L B(a)P处理A549细胞后, 发现随着B(a)P的浓度升高, 虽然Mn SOD的表达及SOD活性出现先诱导后抑制的现象, 但CAT及Gr活性的增高依然提高了机体的总抗氧化活性. 研究结果提示: HSP 27及Mn SOD 与B(a)P在气道细胞诱导的毒理作用相关, CAT及Gr在对抗B(a)P带来的氧化损伤方面可能具有十分重要的作用.     

钝顶螺旋藻Spirulina platenis两种不同形态藻丝体的光合作用和蛋白质差异表达分析

从钝顶螺旋藻Spirulina platenis中分离纯化获得了螺旋形和直线形两种不同形态的藻丝体.通过对二者光合作用的研究发现,螺旋形藻丝体具有较高的光饱和光合作用速率(PChlam)和光饱和点,比直线形藻丝体更能适应较高光强的环境;而直线形藻丝体具有较低的光补偿点,能在更低的光强下进行光合作用.通过双向凝胶电泳对两种不同形态藻丝体的总蛋白进行比较分析,从中找出了9个差异表达的蛋白点.应用基质辅助激光解吸电离质谱对差异表达的蛋白质点进行鉴定和数据库检索,结果表明,3个蛋白与肽聚糖代谢有关,2个蛋白与光合作用有关,1个蛋白与细胞分裂调控相关,1个蛋白为外膜通道蛋白,2个蛋白为功能未知的假想蛋白.     

钝顶螺旋藻Spirulina platensis两种不同形态藻丝体的光合作用和蛋白质差异表达分析

从钝顶螺旋藻Spirulina platensis中分离纯化获得了螺旋形和直线形两种不同形态的藻丝体. 通过对二者光合作用的研究发现, 螺旋形藻丝体具有较高的光饱和光合作用速率(P_m^Chla)和光饱和点, 比直线形藻丝体更能适应较高光强的环境; 而直线形藻丝体具有较低的光补偿点, 能在更低的光强下进行光合作用. 通过双向凝胶电泳对两种不同形态藻丝体的总蛋白进行比较分析, 从中找出了9个差异表达的蛋白点. 应用基质辅助激光解吸电离质谱对差异表达的蛋白质点进行鉴定和数据库检索, 结果表明, 3个蛋白与肽聚糖代谢有关, 2个蛋白与光合作用有关, 1个蛋白与细胞分裂调控相关, 1个蛋白为外膜通道蛋白, 2个蛋白为功能未知的假想蛋白.     

蛋白质组学技术筛选与鉴定癫痫疾病的差异蛋白质

应用蛋白质组学双向凝胶电泳(Two-dimensional gel electrophoresis, 2DE)和质谱技术, 定量分析和鉴定了癫痫组(n=3)和正常组(n=3)脑组织的差异表达蛋白, 以从蛋白质水平上揭示癫痫病的发机制. 结果表明, 凝胶图谱可辨识2500~3000个蛋白点, 对21个显著差异表达蛋白点进行质谱鉴定和SwissProt数据库检索, 得到17个癫痫差异蛋白, 其中2个蛋白在癫痫组织中表达上调, 15个蛋白表达下调. 部分蛋白与癫痫的关系属首次报道. 这些蛋白与癫痫的发生发展相关, 可能成为癫痫的分子标志物和药物治疗的靶向蛋白.     

正常组织和胰腺癌组织中差异表达蛋白的鉴定

采用双向凝胶电泳和生物质谱技术, 对12对胰腺癌组织和癌旁组织样品、3个胰腺良性疾病样品、3个正常胰腺组织样品的蛋白质进行了分离和鉴定, 获得了重复性较好的双向凝胶电泳图谱; 鉴定了胰腺癌和癌旁组织的差异表达蛋白质, 发现了30个差异表达蛋白质; 应用MALDI-TOF-MS/MS技术对差异表达蛋白质进行鉴定, 共有24个蛋白质得到鉴定, 其中15个蛋白质在胰腺癌组织中表达上调, 9个蛋白质表达下调. 这些蛋白质与胰腺癌的发生相关, 可能成为胰腺癌的分子标志物和药物治疗的靶蛋白.     

Characterization of Unique and Differentially Expressed Proteins in Anthracnose-Tolerant Florida Hybrid Bunch Grapes

Anthracnose is a major disease in Florida hybrid bunch grapes, caused by a fungus viz. Elsinoe ampelina. Florida hybrid bunch grapes are grown in southeastern USA for their superior wine characteristics. However, the effect of anthracnose on grape productivity and wine quality is a major concern to grape growers. Our research is aimed at determining biochemical basis of anthracnose tolerance in Florida hybrid bunch grape. Leaf samples were collected from the plants infected with E. ampelina at different periods and analyzed for differential protein expression using high throughput two-dimensional gel electrophoresis. Among the 32 differentially expressed leaf proteins, two were uniquely expressed in tolerant genotypes in response to E. ampelina infection. These proteins were identified as mitochondrial adenosine triphosphate synthase and glutamine synthetase, which are known to play a major role in carbohydrate metabolism and defense. Several proteins including ribulose 1-5 bisphosphate-carboxylase involved in photosynthesis were found to be suppressed in susceptible genotypes compared to tolerant genotypes following E. ampelina infection. The results indicate that the anthracnose-tolerant genotypes have the ability to up-regulate and induce new proteins upon infection to defend the invasion of the pathogen as well as maintain the normal regulatory processes.     

High Performance Liquid Chromatography of Proteins on a Hydroxyapatite Column

Abstract

High performance liquid chromatography on a spherical ceramic type hydroxyapatite has been applied successfully for the separation of various kinds of proteins. Twenty-one proteins of various origin, having an isoelectric point of 3.3–11.0 and a molecular weight of 11,000–190,000 daltons, were loaded on the column and eluted by linear gradient of sodium phosphate at pH 6.8. The chromatography showed good resolution and high recovery for the proteins. The analysis of the retention behavior, relation between capacity ratio and physicochemical properties of proteins, showed a tendency that the capacity ratio of protein increased with the pI value of the protein.     

非小细胞肺癌患者尿中Exosomes蛋白质组的差异表达分析

除血浆之外,尿液是另一种寻找潜在生物标志物的重要生物材料。本研究以200000×g超速离心法分离正常人和非小细胞肺癌(NSCLC)患者尿液中的Exosomes,运用1DSDS-PAGE对Exosomes蛋白质组进行分组,从电泳胶上切取正常组和疾病组的20～31kDa条带,胰蛋白酶酶解后,进行HPLC-CHIP-MS/MS分析,并通过UniProtKB/SWISS-PORT数据库搜索鉴定了24种蛋白质,其中在NSCLC患者尿液Exosomes蛋白质组中发现了8种差异表达蛋白,包括免疫球蛋白κ的3个片段、2种Ras相关蛋白、谷胱甘肽S转移酶A2、血清淀粉样P成分前体和磷脂酰乙醇胺结合蛋白1。     

Proteomic Analysis of Differentially Expressed Proteins of Arabidopsis thaliana Response to Specialist Herbivore Plutella xylostella

The changes of the proteome in Arabidopsis thaliana leaves were examined by specialist Plutella xylostella.Analysis of about 1100 protein spots on each 2DE gel revealed 38 differentially expressed protein spots in abun-dance of which 34 proteins were identified by MALDI-TOF/TOF MS.Among the insect feeding responsive proteins,a few proteins involved in carbon metabolism were identified including proteins associated with the Calvin cycle in the chloroplast and TCA cycle in the mitochondria,indicating carbon metabolism related proteins may play crucial roles in induced defense response in plants under insect infestation.The analysis elucidates the subcellular location of proteins demonstrates that about 50% of proteins are in the chloroplast,which shows the chloroplast has a key role in the insect feeding response for plant.Gene expression analysis of 10 different proteins by quantitative real-time PCR shows that four proteins of the mRNA level were correlated well with the protein level.This study further dissected the nature of insect infestation as a stress signal and some novel insect feeding responsive proteins identified may play an important role in induced defence machanism for plant.     

不相交主成分分析(PCA)和遗传算法(GA)用于差异表达基因的识别

建立了一种基于不相交主成分分析(Disjoint PCA)和遗传算法(GA)的特征变量选择方法, 并用于从基因表达谱(Gene expression profiles)数据中识别差异表达的基因. 在该方法中, 用不相交主成分分析评估基因组在区分两类不同样品时的区分能力; 用GA寻找区分能力最强的基因组; 所识别基因的偶然相关性用统计方法评估. 由于该方法考虑了基因间的协同作用更接近于基因的生物过程, 从而使所识别的基因具有更好的差异表达能力. 将该方法应用于肝细胞癌(HCC)样品的基因芯片数据分析, 结果表明, 所识别的基因具有较强的区分能力, 优于常用的基因芯片显著性分析(Significance analysis of microarrays, SAM)方法.     

2D-DIGE-HPLC-nESIMS/MS对2,4-二硝基苯磺酸损伤HaCaT细胞差异蛋白质的鉴定

采用Cy2、Cy3和Cy5荧光染料标记蛋白,建立了人角质形成细胞HaCaT受2,4-二硝基苯磺酸(DNBS)刺激前后的双向胶内差异凝胶电泳(2D-DIGE)图谱,每组平行样本数为3。凝胶采用蛋白荧光染料Deep Purple进行后染色(Post-stain)。DeCyder定量分析软件在每块凝胶上平均检测到1 200个以上蛋白斑点,每块胶上都匹配得到的相同蛋白质斑点有846个。其中有7个斑点丰度变化在50%以上,统计学意义显著(P值小于0.05)。利用高效液相色谱-电喷雾串联质谱(HPLC-nESI MS/MS)成功鉴定5个表达上调的斑点分别为X染色体开放阅读框26(Cxorf26)、人辅分子伴侣23(PTGES3)、钙调蛋白(CALM3)、肌球蛋白轻链6(MYL6)和断裂点丛集区蛋白1(BANF1);2个表达下调蛋白斑点被鉴定为转录延伸因子B肽链2(TCEB2)和核糖体蛋白L23(RPL23)。除MYL6被报道与皮肤疾病相关外,其它蛋白与皮肤病变的关系有待研究。该研究得到的7个差异表达蛋白为DNBS类化学致癌物职业接触者皮肤病变研究提供了有价值的线索。     

Identification of Colorectal Cancer Using Near-Infrared Spectroscopy and Adaboost with Decision Stump

Rapid and objective detection of cancer is crucial for successful treatment. Near-infrared (NIR) spectroscopy is a vibrational technique capable of optically probing molecular changes associated with disease. The purpose of this study was to explore NIR spectroscopy for discriminating cancer from normal colorectal tissues. A total of 110 tissue samples from patients who underwent operations were characterized in this study. The popular ensemble technique AdaBoost was used to construct the diagnostic model. A decision stump was used as the weak learning algorithm. Adaboost with decision stump, an ensemble of weak classifiers, was compared with the most suitable single model, a strong classifier. Only the 20 most significant variables were selected as inputs for the model based on measured defined variable importance. Using an independent test set, the single strong classifier provided diagnostic accuracy of 89.1%, sensitivity of 100%, and specificity of 78.6%, whereas the ensemble of weak stumps provided accuracy of 96.3%, sensitivity of 96.3%, and specificity of 96.3% for distinguishing cancer from normal colorectal tissues. Therefore, NIR spectroscopy in combination with AdaBoost with decision stumps has demonstrated potential for rapid and objective diagnosis of colorectal cancer.     

SDS-PAGE研究丝素蛋白的组成

ＳＤＳ－ＰＡＧＥ研究丝素蛋白的组成于同隐,蔡再生,黄伟达（复旦大学高分子科学研究所,生物化学系,上海,２００４３３）关键词丝素蛋白,亚基组成,聚丙烯酰胺凝胶,电泳由于丝素蛋白结构的复杂性及其易变性、水解等原因,致使研究结果往往互不相同。Ｔａｓｈｉｒｏ...     

Proteomics Analysis of Up-regulated NPM1 Protein in Colorectal Cancer

In order to identify potential protein targets involved in colorectal cancer(CRC), we used a liquid chromatography coupled with mass spectrometry(LC-MS)/MS-based proteomics approach to characterize global protein expression patterns in malignant tissues and their adjacent healthy tissues from Dukes C stage CRC patients. A total number of 34 differentially expressed proteins were detected and identified by LC-MS/MS and database searching, which are supposed to be relevant to progression of colorectal tumor. Among these proteins, nucleophosmin 1(NPM1) was found to be remarkably up-regulated in colorectal carcinoma tissues, as compared with that in their normal counterparts. The results presented here could provide clues to elucidate the pathological significance of NPM1 in regulation of carcinogenesis of Dukes C stage colorectal tumors.     

核酸适配子探针对转移性大肠癌细胞的多靶点成像及其靶标的定量分析

利用核酸适配子对肿瘤细胞的高亲和力靶向识别功能以及量子点的高荧光发射强度和光稳定性等特性,制备了识别不同靶点的核酸适配子探针,将其联合使用实现了对肿瘤细胞的多靶点成像及其靶标的定量分析.使用通过Cell-SELEX技术筛选得到的可特异性识别转移性大肠癌细胞系Lo Vo的7个核酸适配子,分别与量子点QD605偶联制备分子探针.基于流式细胞术的竞争实验结果表明,7个探针可特异性识别靶细胞的不同靶点,相互之间无识别干扰.对靶细胞的荧光成像表明,与单一探针相比,多个探针联合使用可明显提高细胞表面的荧光信号强度,且阳性细胞检出率明显增多,显示出更高的检测灵敏度.使用流式细胞术及荧光成像定量方法分析了7个探针对不同转移特性大肠癌细胞系的识别能力,结果表明,多个探针联合使用可有效评价大肠癌细胞的转移潜能.本研究证实通过多个核酸适配子探针的联合使用可有效提高对靶细胞识别的灵敏度和准确性,为核酸适配子的广泛应用及大肠癌的靶向诊断提供了新的思路和手段.     

双龙方组分诱导大鼠BMSCs分化的差异基因筛选及聚类分析

利用基因芯片筛选双龙方有效组分(总人参皂苷及总丹酚酸)诱导大鼠骨髓间充质干细胞(BMSCs)类心肌细胞分化过程中的差异表达基因, 并对其进行聚类分析, 在基因水平研究了双龙方组分对大鼠BMSCs分化的影响. 对大鼠BMSCs进行分组培养, 分别收集10, 20, 30及40 d的细胞样本, 提取tRNA, 经基因芯片检测, 筛选出BMSCs变化过程中的差异表达基因并进行生物信息学分析, 同时通过差异表达基因对样本进行Hierarchical聚类分析. 在BMSCs的分化过程中, 筛选出179条差异表达基因, 经分析发现它们与能量代谢和信号传导等多类基因密切相关. 对样本进行聚类分析发现其聚为两大类: 10和20 d的样本聚为一类, 30和40 d的样本聚为一类. 说明BMSCs在20~30 d之间可能发生了显著的改变.     

谷胱甘肽键合柱对蛋白的选择性研究

通过将谷胱甘肽键合到硅胶表面合成了同时具有弱阳离子交换(WCX)、疏水(HIC)和氢键作用的多功能色谱填料, 该固定相在HIC和WCX模式下对蛋白都有很好的分离效果. 实验通过计量置换保留模型对蛋白在谷胱甘肽键合柱上的色谱保留行为及机理进行了研究, 结果发现, 在流动相盐浓度较低时蛋白根据自身等电点高低通过静电作用力得以分离, 而在高盐浓度下疏水和氢键作用力共同决定蛋白的保留. 这种多作用力保留模式可有效提高色谱柱的选择性, 尤其为蛋白质、多肽及氨基酸的高效分离提供新的解决思路.     

Preparation of a Polymer Monolithic Column Using Ionic Liquid as Porogen and Its Application in Separations of Proteins and Small Molecules

A polymer-based monolithic column was prepared for high-performance liquid chromatography (HPLC), using ionic liquids as porogen within the confines of a stainless steel column (50 × 4.6 mm i.d.). In the process, 1-butyl-3-methylimidazolium chloride and dodecyl alcohol were used as bi-porogens, vinyl ester resin as the monomer, ethyleneglycol dimethacrylate as the crosslinker, CCl₄ as the initiator, and FeCl₂ as the catalytic agent to prepare the polymer-based monolithic column. Scanning electron microscopy, nitrogen adsorption–desorption instrument, and mercury intrusion porosimetry were used to assay the characteristics of the monolith, respectively. The optimized monolith showed uniform structure and good permeability. Then, the column was used as the stationary phase of HPLC to separate standard proteins and human plasma with gradient elution. Besides, the monolith was used to separate aromatic compounds from the mixture. The results showed that the addition of IL could effectively improve the structure of monoliths prepared by atom transfer radical polymerization technique. The results also suggested that this kind of monolith could be used as a simple, cheap and effective stationary phase for HPLC.     

A New Spherical Hydroxyapatite for High Performance Liquid Chromatography of Proteins

Abstract

Basic properties of a newly developed hydroxyapatite column and results of its application to the separation of proteins are described. The hydroxyapatite was completely spherical and porous beads in appearance by scanning electron microscopy, and showed superior properties to other types of hydroxyapatite column. The column was mechanically strong enough to show the pressure limit of 140–150 kg/cm². The hydroxyapatite column showed excellent mechanical and chemical stability, and was applicable to high speed and high resolution separation of proteins. Proteins are recovered in high yield after the chromatography.