Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data

MOTIVATION: Because co-expressed genes are likely to share the same biological function, cluster analysis of gene expression profiles has been applied for gene function discovery. Most existing clustering methods ignore known gene functions in the process of clustering. RESULTS: To take advantage of accumulating gene functional annotations, we propose incorporating known gene functions into a new distance metric, which shrinks a gene expression-based distance towards 0 if and only if the two genes share a common gene function. A two-step procedure is used. First, the shrinkage distance metric is used in any distance-based clustering method, e.g. K-medoids or hierarchical clustering, to cluster the genes with known functions. Second, while keeping the clustering results from the first step for the genes with known functions, the expression-based distance metric is used to cluster the remaining genes of unknown function, assigning each of them to either one of the clusters obtained in the first step or some new clusters. A simulation study and an application to gene function prediction for the yeast demonstrate the advantage of our proposal over the standard method.     

脱氧核酶的研究进展

具有RNA裂解活性的DNA分子称为脱氧核酶。它是经过体外选择技术经多次筛选获得的。脱氧核酶在切割与其互补的RNA底物分子时具有极高的特异性和切割效率,有望成为新的RNA灭活工具。     

5-酮基-D-葡萄糖酸发酵生产的工艺条件优化

葡萄糖酸氧化杆菌可将葡萄糖转化为5-酮基-D-葡萄糖酸(5-KGA),而5-KGA是重要食品添加剂L(+)-酒石酸的合成前体。为提高5-KGA产量及其对葡萄糖的转化率,对5-KGA发酵生产的工艺条件进行优化。在摇瓶水平最适的培养基和培养条件下,5-KGA最高产量为19.7 g/L,较优化前提高43.8%。在5 L发酵罐上控制恒定pH值5.5、溶氧浓度15%条件下,5-KGA产量达到46.0 g/L,较摇瓶最高产量提高1.3倍,应用葡萄糖流加工艺,5-KGA最高产量达到75.5 g/L,转化率超过70%,与已见报道的最高水平相比提高了32.0%,为实现微生物发酵生产5-KGA、进而合成L(+)-酒石酸的工业化提供了切实有效的途径。     

核糖核酸酶抑制因子对H_2O_2损伤的大鼠神经胶质瘤细胞系C6的影响

核糖核酸酶抑制因子 (ribonucleaseinhibitor,RI)是广泛存在于哺乳动物细胞浆中的一种酸性糖蛋白 .为了进一步了解RI的功能 ,根据RI分子结构富含巯基的特点 ,研究了RI对过氧化氢(H2 O2 )损伤的大鼠神经胶质瘤细胞 (C6 )的影响 .用不同浓度的H2 O2 分别作用于转染有RIcDNA并且RI过表达的C6细胞和正常C6细胞 ,对比损伤前后 2者的细胞存活率、LDH漏出量、细胞内GSH和MDA含量差别 ,以及细胞内抗氧化酶类GPX、CAT和GST活性的差别 .结果表明 ,与正常C6细胞相比 ,RI过表达的C6细胞在H2 O2 作用下存活率高 ,LDH漏出量、MDA含量明显减少 ,而细胞内GSH较多 ;RI过表达的C6细胞在损伤前后均表现出更强的CAT和GST活性 .提示RI具有抗氧化功能 ,能够减轻H2 O2 所致的细胞过氧化损伤 .     

Preparation and characterization of radioactive castanospermine

A procedure for the preparation of tritiated castanospermine is described. The tritiated alkaloid was shown to be chromatographically identical to the native material and exhibited the same inhibitory properties. Radiolabeled castanospermine tightly bound to purified intestinal sucrase. Following gel chromatography, each mole of enzyme was shown to have bound 1 mol of the radioactive alkaloid. Cultured MDCK cells were also shown to take up the labeled castanospermine. This compound should be a useful tool in the investigation of enzymes that are responsible for the processing of glycoprotein oligosaccharides.     

Selection of trkB-binding peptides from a phage-displayed random peptide library

Brain-derived neurotrophic factor (BDNF) shows potential in the treatment of neurodegenerative diseases, but the therapeutic application of BDNF has been greatly limited because it is too large in molecular size to permeate blood-brain barrier. To develop low-molecular-weight BDNF-like peptides, we selected a phage-displayed random peptide library using trkB expressed on NIH 3T3 cells as target in the study. With the strategy of peptide library incubation with NIH 3T3 cells and competitive elution with 1 μg/mL of BDNF in the last round of selection, the specific phages able to bind to the natural conformation of trkB and antagonize BDNF binding to trkB were enriched effectively. Five trkB-binding peptides were obtained, in which a core sequence of CRA/TXΦXXΦXXC (X represents the random amino acids, Φ represents T, L or I) was identified. The BDNF-like activity of these five peptides displayed on phages was not observed, though all of them antagonized the activity of BDNF in a dose-dependent manner. Similar results were obtained with the synthetic peptide of C1 clone, indicating that the 5 phage-derived peptides were trkB antagonists. These low-molecular-weight antagonists of trkB may be of potential application in the treatment of neuroblastoma and chronic pain. Meanwhile, the obtained core sequence also could be used as the base to construct the secondary phage-displayed peptide library for further development of small peptides mimicking BDNF activity.