Global gene expression analysis for evaluation and design of biomaterials

Abstract

Comprehensive gene expression analysis using DNA microarrays has become a widespread technique in molecular biological research. In the biomaterials field, it is used to evaluate the biocompatibility or cellular toxicity of metals, polymers and ceramics. Studies in this field have extracted differentially expressed genes in the context of differences in cellular responses among multiple materials. Based on these genes, the effects of materials on cells at the molecular level have been examined. Expression data ranging from several to tens of thousands of genes can be obtained from DNA microarrays. For this reason, several tens or hundreds of differentially expressed genes are often present in different materials. In this review, we outline the principles of DNA microarrays, and provide an introduction to methods of extracting information which is useful for evaluating and designing biomaterials from comprehensive gene expression data.     

低剂量γ射线辐照对人淋巴母细胞基因表达转录谱的影响

为探讨低剂量电离辐射生物效应作用机制,本文研究了不同剂量单次辐照后,人淋巴母细胞基因表达转录谱的变化。采用0．1Gy、0．5Gy和1．0Gy剂量的γ射线照射人淋巴母细胞,未照射细胞为对照组。照射后4h提取细胞总RNA,用含有45033个基因的人类全基因组表达谱芯片检测分析。对差异表达基因进行层次聚类分析、基因本体论分析和通路分析,并用实时荧光定量PCR验证。结果表明,3个剂量组均上调表达的基因1330个,下调表达的基因1002个。基因表达量与吸收剂量相关的基因共18个,其中与剂量正相关的基因16个,负相关的基因2个。层次聚类分析结果表明,4个实验组中,0．1Gy和1．0Gy照射组差异表达基因相似程度最高。这些差异表达的基因涉及到多条通路,如细胞周期、p53信号通路、碱基切除修复、RNA转运和内质网蛋白加工等。实时荧光定量PCR检测结果表明,CASP9（caspase9）mRNA在照射后4h随吸收剂量表达变化与基因芯片检测结果一致。基因芯片筛选出的差异表达基因有助于阐明低剂量辐射生物效应作用机理,与辐射剂量相关的差异表达基因有可能成为低剂量辐射暴露的生物剂量计。     

142例新生儿溶血病血清学检测结果分析

目的对本地区142名新生儿溶血病患者进行血清学检测,评价直接抗人球蛋白试验、游离抗体试验和抗体释放试验在该病诊断中的价值。方法对2005年1月~2007年6月各医院送检的高胆红素血症新生儿血液标本进行"三项试验"。结果142名新生儿溶血病患者中,血型分布规律为:B>A>AB>O,54.22%为B型,43.66%为A型,二者差异有显著意义。直抗试验阳性率为76.76%,释放试验阳性率为100%,游离试验阳性率为50.70%。释放试验阳性的A型患者中,抗-AB检出率为47.17%,B型患者中的检出率为53.03%,二者差异无显著意义。结论释放试验敏感度最高,是判定新生儿溶血病最有力的证据,在本地区,B型新生儿可能更易患新生儿溶血病。     

电纺法制备Pd基修饰ITO电极及其电化学传感NO2-

应用静电纺丝法制备纳米纤维修饰电极,之后分别在空气和N2环境下煅烧制备Pd纳米粒子微阵列修饰的ITO电极,应用SEM对电极表面形貌进行了表征。应用循环伏安法对修饰电极的电化学行为进行研究,并与直径是25μm的Pt微电极进行了比对,结果证明,它们都具有微米电极的电化学行为,但修饰电极的信号值远高于单根Pt微电极,具有较高的信噪比和极低的检出限。     

基于遗传算法的基因微阵列数据聚类

微阵列基因数据用以挖掘特定的生物信息,聚类分析对于研究基因功能和基因调控机制有重要意义.结合改进的遗传算法对基因微阵列数据进行聚类分析,并且通过实验与K均值聚类进行比较.仿真实验表明,该算法可以有效改进基因微阵列数据的聚类准确率.     

Large-scale genome reorganization in Saccharomyces cerevisiae through combinatorial loss of mini-chromosomes

A highly efficient technique, termed PCR-mediated chromosome splitting (PCS), was used to create cells containing a variety of genomic constitutions in a haploid strain of Saccharomyces cerevisiae. Using PCS, we constructed two haploid strains, ZN92 and SH6484, that carry multiple mini-chromosomes. In strain ZN92, chromosomes IV and XI were split into 16 derivative chromosomes, seven of which had no known essential genes. Strain SH6484 was constructed to have 14 mini-chromosomes carrying only non-essential genes by splitting chromosomes I, II, III, VIII, XI, XIII, XIV, XV, and XVI. Both strains were cultured under defined nutrient conditions and analyzed for combinatorial loss of mini-chromosomes. During culture, cells with various combinations of mini-chromosomes arose, indicating that genomic reorganization could be achieved by splitting chromosomes to generate mini-chromosomes followed by their combinatorial loss. We found that although non-essential mini-chromosomes were lost in various combinations in ZN92, one mini-chromosome (18kb) that harbored 12 genes was not lost. This finding suggests that the loss of some combination of these 12 non-essential genes might result in synthetic lethality. We also found examples of genome-wide amplifications induced by mini-chromosome loss. In SH6484, the mitochondrial genome, as well as the copy number of genomic regions not contained in the mini-chromosomes, was specifically amplified. We conclude that PCS allows for genomic reorganization, in terms of both combinations of mini-chromosomes and gene dosage, and we suggest that PCS could be useful for the efficient production of desired compounds by generating yeast strains with optimized genomic constitutions.     

相似性度量在基因表达聚类分析中的应用研究

聚类分析是基因表达数据分析研究的主要技术之一,其算法的基本出发点在于根据对象间相似度将对象划分为不同的类,选择适当的相似性度量准则是获得有效聚类结果的关键。采用预处理过的基因数据集在不同相似性度量准则下进行的不同聚类算法的聚类分析,并得到聚类结果评价。其中算法本身的缺陷及距离相似性度量的局限性都是影响结果评价的因素,为了获得更有效的聚类结果,改进相关聚类算法并提出了一种比例相似性度量准则。     

食品过敏原及其检测分析技术

本文综述了食品过敏原、检测分析技术等方面的研究现状及发展趋势,涉及过敏性食物种类、主要的食品过敏原、过敏原的生物活性及形成机制,并对食品过敏原现有的检测分析技术及其发展方向做了相关的介绍。