水稻条纹病毒胁迫下的水稻全基因组表达谱

水稻条纹叶枯病由水稻条纹病毒(Rice stripe virus, RSV)引起,对我国水稻生产危害严重.为了明确RSV侵染对水稻基因表达谱的影响,采用Affymetrix水稻全基因组芯片对RSV接种后出现条纹症状第7天的武育粳3号水稻病叶和相应的健康叶片进行了全基因组表达谱分析,得到3 517个差异基因,其中2 002个表达上调,1 515个表达下调.根据TIGR数据库注释(http://www.tigr.org/tdb/e2k1/osa1/)和MIPS基因功能分类标准(http://mips.gsf.de/projects/funcat)将差异基因归类为15个功能类别,多数差异基因与植物防御、信号传导及蛋白质、碳水化合物的代谢相关,一些转录因子的表达也发生了明显的变化.代谢途径分析表明,RSV侵染后磷酸戊糖途径、类黄酮合成途径和芸苔素合成途径的相关基因表达明显增强,赤霉素合成途径相关基因的表达受到了抑制.     

A network-based gene-weighting approach for pathway analysis

Classical algorithms aiming at identifying biological pathways significantly related to studying conditions frequently reduced pathways to gene sets, with an obvious ignorance of the constitutive non-equivalence of various genes within a defined pathway. We here designed a network-based method to determine such non-equivalence in terms of gene weights. The gene weights determined are biologically consistent and robust to network perturbations. By integrating the gene weights into the classical gene set analysis, with a subsequent correction for the "over-counting" bias associated with multi-subunit proteins, we have developed a novel gene-weighed pathway analysis approach, as implemented in an R package called "Gene Associaqtion Network-based Pathway Analysis" (GANPA). Through analysis of several microarray datasets, including the p53 dataset, asthma dataset and three breast cancer datasets, we demonstrated that our approach is biologically reliable and reproducible, and therefore helpful for microarray data interpretation and hypothesis generation.     

特征代谢通路上的基因表达相关性及共调控表达模式

利用随机森林-通路分析法,通过袋外样本OOB的分类错误率筛选特征代谢通路,在特征通路上作基因表达相关性研究并对通路上的基因采用MAP(Mining attribute profile)算法挖掘不同实验条件下基因的共调控表达模式,对共调控表达模式进行聚类.分析结果显示同一特征代谢通路上的基因表达倾向相似,有2条特征代谢通路存在共表达模式.其中一条通路含108个表达模式,对这些模式进行聚类,其最低聚类的相似系数仍高达0.623.说明同一特征代谢通路上的基因共表达模式在不同实验条件下仍具有高度的相似性.对以通路作为基因模块进行复杂疾病的研究具有借鉴意义.     

人睾丸与脑基因表达谱的相似性

人类的物种形成与进化问题一直是研究的一个焦点。近年来,对于人和灵长类以及果蝇等其他一些动物多种组织基因表达谱的研究表明,在人的进化过程中脑基因表达的改变最为显著,并且脑中许多基因的表达呈显著上调。信息学分析显示,在多种组织当中,人的脑与睾丸可能存在最为相似的基因表达谱。这些结果提示睾丸可能与脑类似,也在人的物种形成和进化历程中起着重要作用。本文对人睾丸和脑基因表达谱的研究进行了回顾,并提出了该研究方向今后的一些研究设想。     

Synthesis and transport of storage proteins by testes in Heliothis virescens.

The synthesis of two storage protein subunits, 76,000-Mr and 82,000-Mr polypeptides, by the testes sheath has been studied in Heliothis virescens. Like fat body, which is the primary site of synthesis for the large extratesticular pool, cells of the testes sheath secrete glycosylated storage proteins assembled into hexamers. The testis sheath differed from fat body in several important respects, including the failure to synthesize an abundant (in the hemolymph) 74,000-Mr storage protein, its relatively reduced expression of the 76,000-Mr polypeptide, and the absence of resorption of storage proteins from the lumen of the testis during pupal development. Cyst cells were also shown to import actively the 82,000-Mr storage protein by pinocytosis of testicular fluid and transfer it to the developing spermatids. Unlike other cell types that sequester storage proteins in the form of cytoplasmic granules, their localization within spermatids was exclusively mitochondrial. These observations suggest that expression of the storage protein genes is regulated tissue specifically and reveal novel pathways for their transport and, perhaps, utilization and function during development.