Systematic analysis of expression and function of developmental genes of model organisms towards computer simulation

1)我们获得了13万条线虫EST，从中我们鉴定了14,000条独特的cDNA的基因结构。我们用独有的一套cDNA集进行了整装原位杂交。所有信息以及对900RNAI表型的描述都存储在我们的万维网数据库“NEXTDB”&lt；http://nematode.lab.nig.ac.jp&gt；.中我们基于数据库中的数据进行了许多合作。2)我们研究了母体mRNAs的翻译调控机制，找到了GLD-1、Pos-1和SPN-4基因产物对GLP-1mRNA翻译的组合调节和Poly-A长度的微调。3)我们对另一种线虫Diploscapter sp.进行了EST/基因组分析，该线虫在原肠发育阶段具有不同的细胞切割和排列模式。我们有兴趣比较这些不同发育系统之间的基因表达和功能。从70,000个克隆中鉴定出10,000个EST簇，其中5,800个簇与线虫同源。我们还对这种蠕虫进行了低覆盖率(1倍)的全基因组鸟枪测序，发现了另外1000个同源物。所有结果也被纳入NEXTDB。4)细胞排列对发育过程中细胞命运的决定很重要。我们使用可变形和可分割的多面体构建了线虫胚胎直到原肠胚阶段(28细胞期)的物理模型。我们进一步实现了微管和中心体，并进行了计算机模拟分析，得到了重现野生型和突变型胚胎表型的参数。5)基于反应-扩散模型，阐明了动物皮肤自主图案形成的机制。

1) We obtained 130,000 ESTs of the nematode C.elegans, from which we identified the gene structures of 14,000 unique cDNAs. We performed whole mount in situ hybridization with the unique cDNA set. All the information together with the description of RNAi phenotypes of 900 genes was stored and opened at our WWW-based database "NEXTDB" <http://nematode.lab.nig.ac.jp>. We have performed many collaborations based on the data in the database.2) We studied on the translational control mechanism of maternal mRNAs, finding the combinatorial regulation of the translation of glp-1 mRNA by gld-1, pos-1 and spn-4 gene products and the fine tuning by poly-A length.3) We performed EST/genome analysis of another nematode Diploscapter sp., which has a different cell cleavage and arrangement pattern until gastrulation stage. We are interested to compare gene expression and function between these different developmental systems. From 70,000 cDNA clones, 10,000 EST clusters were identified, of which 5,800 clusters had homologs to C.elegans. We also performed a low coverage (1X) whole-genome shotgun sequencing of this worm and found additional 1,000 homologs. All the results were also incorporated to NEXTDB.4) Cellular arrangements are important for cell-fate determination in development. We constructed a physical model for C.elegans embryo up to gastrulation stage (28 cell stage) using deformable and dividable polyhedrons. We further implemented microtubles and centrosomes, and we performed computer simulation analysis to get the parameters that reproduced the phenotype of wild type and mutant embryos.5) Based on the reaction-diffusion model, a mechanism for autonomous pattern formation in the animal skin has been elucidated.