【作者】 邓晔；

【导师】 李德葆； 董海涛；

【作者基本信息】 浙江大学 ， 生物化学与分子生物学， 2007， 博士

【摘要】 微阵列技术中生物信息的利用和挖掘本文分别对两个相对独立的微阵列研究中，生物信息的利用和挖掘进行了阐明。首先是通过对尖孢镰刀菌微阵列的制备、杂交和分析过程的研究，勾勒出微阵列技术中生物信息的挖掘基本过程；然后从微生物功能基因微阵列中gyrB和错配探针微阵列的设计、制备以及实验数据的分析中，进一步阐述微阵列技术中信息利用和数据挖掘的过程。首先，从尖孢镰刀菌黄瓜专化型菌株ATCC16416的cDNA分生孢子发育文库中共获得6448条表达序列标签(EST)，并且把它们拼接成3372条推测独立的转录本(TUT)。随后我们构建了含有3158条cDNA序列的尖孢镰刀菌微阵列，用以分析分生孢子发育过程中的基因表达状况。很多核糖体蛋白基因本身就在我们的文库中高度冗余，同时还被检测到在发育中的表达量在孢子和芽管中高丰度表达。一个时钟调控基因显示在孢子萌发的阶段表达量上升，而信号基因ras却在菌丝体中表达量最高。这些结果都提示ras相关基因的主要功能是调节菌丝体的生长，而很可以它和其它信号基因，如时钟调控基因，共同作用才引发了分生孢子的萌发，并导致了蛋白合成量的加大。其次，在设计新一代微生物功能基因微阵列的过程中，通过收集和整理现有细菌和古细菌gyrB基因的序列资源，设计了由寡核苷酸探针(50nt)构成的gyrB微阵列，并使用互联网网站技术实现信息的共享。同时，也通过对错配探针微阵列预备实验数据的研究，构建了改进的最临近法在微阵列体系中的数据分析模型，并由此提出了错配探针的设计方法，为提高微阵列的特异性和灵敏度做好了理论准备。更多还原

【Abstract】 Through two individual microarray studies, the utilization and data mining in microarray technology were discussed in this thesis. In former Fusarium oxysporum microarray research, the basic process of bioinformatical data mining was described. Through latter designing, synthesis and analysis of gyrB and mismatch probe microarrays, the utilization and data mining were deeply discussed.Firstly, from 6448 expressed sequence tags (ESTs) from a cDNA library representing Fusarium oxysporum f. sp. cucumerinum transcripts, and assembled them to 3372 tentative unique transcripts (TUTs). Then a cDNA array with 3158 of the TUTs was produced to analyze the gene expression profiles in conidial development processes. Many ribosomal protein genes were highly redundant in our library and some of them fluctuated across development. A clock-controlled signaling gene (ccg) showed increased expression across developmental stages following conidial germination, while the signaling gene ras was expressed at higher levels in mycelia than in earlier two stages. These findings suggest that the main function of ras-related genes is to regulate hyphal growth. Furthermore, it is plausible that ras and other signaling genes, such as ccg, may initiate the conidial germination stages cooperatively by increasing protein synthesis.Besides, in construction of microbiology functional gene array (FGA), we designed gyrB oligo probes (50nt) after collecting and assembling gyrB sequences and all information was shared through internet. Meanwhile, in research of mismatch probe microarray, we constructed the modified nearest neighbor model to analyze data from mismatch probes and offer a method to further design mismatch probes which can be used to improve the specificity and sensitivity of FGA.更多还原