Gene association study with SVM, MLP and cross validation for diagnosis of diseases

Gene association study is one of the major challenges of biochip technology both for gene diagnosis where only a gene subset is responsible to some diseases, and for treatment of curse of dimensionality which occurs especially in DNA microarray datasets where there are more than thousands of genes and only a few number of experiments (samples). This paper presents a gene selection method by training linear support vector machine (SVM)/nonlinear MLP (multi-layer perceptron) classifiers and testing them with cross validation for finding a gene subset which is optimal/suboptimal for diagnosis of binary/multiple disease types. Genes are selected with linear SVM classifier for the diagnosis of each binary disease types pair and tested by leave-one-out cross validation; then, genes in the gene subset initialized by the union of them are deleted one by one by removing the gene which brings the greatest decrease of the generalization power, for samples, on the gene subset after removal, where generalization is measured by training MLPs with leave-one-out and leave-4-out cross validations. The proposed method was tested with experiments on real DNA microarray MIT data and NCI data. The result shows that it outperforms conventional SNR method in separability of the data with expression levels on selected genes. For real DNA microarray MIT/NCI data, which is composed of 7129/2308 effective genes with only 72/64 labeled samples belonging to 2/4 disease classes, only 11/6 genes are selected to be diagnostic genes. The selected genes are tested by classification of samples on these genes with SVM/MLP with leave-one-out/both leave-one-out and leave-4-out cross validations. The result of no misclassification indicates that the selected genes can be really considered as diagnostic genes for the diagnosis of the corresponding diseases.     

马铃薯低温启动子CIP的克隆及其功能鉴定

合适的启动子有利于基因的高效表达．本研究从鄂马铃薯-3中克隆了低温诱导的启动子（CIP）,并调控转化酶抑制子基因转化马铃薯植株,以抑制马铃薯块茎发生的“低温糖化”．实验结果表明,克隆的CIP与报道的低温诱导的启动子序列同源性达98．9％,含有启动子的典型结构．构建CIP与转化酶抑制子（St-VIF）基因的载体成功转化马铃薯并获得转基因株系．转基因株系收获块茎在4℃和20℃贮藏lm,Nothern杂交显示St-VIF基因在4℃大量表达,检测转化酶活性表明,与对照比较液泡转化酶活性大大降低,说明通过低温诱导CIP调控St-VIF基因的表达能够抑制转化酶的活性,从而降低还原糖的积累．     

新型Ⅰ型普鲁兰酶基因的克隆表达及酶学性质

【目的】筛选并克隆表达高酶活且具有一定热稳定性的新型普鲁兰酶。【方法】克隆Tumebacillus flagellatus GST4的普鲁兰酶基因pulB,构建重组质粒后转化宿主菌大肠杆菌进行诱导表达,再运用亲和层析进行纯化并分析其酶学性质和结构。【结果】pulB在大肠杆菌中实现可溶性表达,发酵液上清酶活力达到78U/mL,粗酶液经纯化后比活力为258U/mg。重组酶PulB最适反应温度和pH值分别为55℃和5.0,在较窄的酸性范围内(pH值4.5~5.5)酶活力比较稳定;对普鲁兰糖的Km=(16.28±0.03)mg/mL,Vmax=(22.05±0.02)μmol·min-1·mg-1。PulB的DNA序列与GenBank数据库里的任何序列都没有同源性,在蛋白质序列上,由基因pulB编码的氨基酸序列与T.aegyptius的环麦芽糖糊精酶相似性最高,BlastX比对的Identities为54%,Positives为69%,SMART结构预测分析发现,pulB具有淀粉酶的结构域。底物特异性分析表明,它可水解普鲁兰糖和支链淀粉生成线性的低聚糖或麦芽三糖。【结论】重组酶PulB是尚未报道的新型普鲁兰酶,它可水解普鲁兰糖和支链淀粉,属Ⅰ型普鲁兰酶。     

Experimental philosophy of biology: notes from the field

I use a recent ‘experimental philosophy’ study of the concept of the gene conducted by myself and collaborators to discuss the broader epistemological framework within which that research was conducted, and to reflect on the relationship between science, history and philosophy of science, and society.     

未知二粒子纠缠态的辅助克隆

提出一个以三粒子GHZ态为量子信道的未知二粒子纠缠态及其正交态的概率克隆方案.此方案中,发送方Alice和接收方Bob对未知态的信息一无所知.首先Alice对他的粒子实施贝尔测量,在得知Alice的测量结果后,通过引入辅助粒子并执行控制非门操作后,Bob可成功地接收未知态.随后在态的制备方Victor的帮助下,Alice以一定的概率获得未知二粒子纠缠态及其正交态的复制.该方案同样适合量子信道是非最大纠缠态的情况.此外,量子纠缠资源和经典信息损耗在该方案中均得到了节省.     

细胞凋亡与肿瘤治疗

细胞凋亡是机体维持自身稳定的一种生理机制,是由基因编码的控制细胞主动参与“自杀”的过程.细胞凋亡与肿瘤密切相关,已成为肿瘤治疗研究的新思路.本文主要阐述细胞凋亡及生理生化特征和肿瘤的形成与肿瘤的治疗.     

青岛文昌鱼hedgehog及两个hedgehog-like片段的克隆

采用RT-PCR方法获得了青岛文昌鱼2497bp长的hedgehog基因片段,其所编码的氨基酸序列与多种生物hh基因家族成员的相应片段显示了较高的同源性.同时获得2个含有部分hedgehog基因片段的序列hedgehog-like-1和hedgehog-like-2,提示文昌鱼中发生hedgehog基因倍增过程和有多拷贝hh基因存在的可能性.为研究hh基因的分子进化提供了线索.     

致绵羊脑炎型粪肠球菌tuf和esp基因的克隆及序列分析

根据GenBank公开序列分别自行设计粪肠球菌保守基因tuf及表面蛋白基因esp二对引物,采用RT-PCR扩增出致绵羊脑炎型肠球菌tuf及esp基因,并将其克隆于pMD18-T Vector,对PCR产物进行测序及分析。该tuf序列及esp序列在GenBank上注册（注册登录号分别为EU239535,EU239534）。应用DNAStar软件对扩增esp基因与GenBank上已发表的粪肠球菌esp基因序列比较,同源性都达99．0％以上。     

大引物PCR定点突变方法的改进

对大引物PCR定点突变方法进行改进,主要包括：避免在一个PCR反应中同时使用扩增全长基因的常规引物,选择不同载体克隆原始基因和突变基因,通过抗性选择筛选突变子,从而完全避免原始基因的干扰．实验结果证明利用改进后的方法进行基因点突变,可以减少操作步骤,提高突变频率．     

蚯蚓纤溶酶在大肠杆菌中的克隆与表达

根据蚯蚓纤溶酶最佳组分的N-末端氨基酸序列设计简并引物,以蚯蚓cDNA为模板,获得该组分蛋白质的部分编码序列(AF432224,GenBank 登陆号).BLAST相似性分析表明,该序列与U25643和U25648的部分序列相似性达91%, 根据5' 和3' 末端保守序列设计引物,经PCR获得全长cDNA编码序列.将该序列插入pTBY-11质粒,转化大肠杆菌,表达蛋白以包含体形式存在.