Streptococcus mutans gcp gene knockout strains expression profile gene chip

doi:10.3969/j.issn.2095-4344.2013.33.014

Abstract

Abstract:

BACKGROUND: Previous studies have confirmed the presence of bis-(3'-5')-cyclic dimeric guanosine monophosphate signaling pathway in Streptococcus mutans, which construct the streptococcus mutans gcp gene knockout strains.
OBJECTIVE: To compare the gene expression differences between Streptococcus mutans wild strains and gcp mutant strains, and to screen the biofilm-related genes from them for the follow-up study.
METHODS: The total RNA of two kinds of strains were extracted and stained with cy3 and cy5 respectively after reverse transcription. The gene chip was scanned after hybridization and the differential gene were obtained through the data analysis. The different expression genes were verified by real-time PCR.
RESULTS AND CONCLUSION: Differential genes were mainly relative about glucose metabolism and biofilm formation. We selected two genes for real-time PCR verification. The PCR results were consistent with the microarray results. After Streptococcus mutans gcp gene knockout, the gene expressions of gcp mutant strains were upregulated and the gene expressions of phosphotransferase system were downregulated, this result suggested that two different genes were related with the c-di-GMP signal pathway downstream.

Key words: tissue construction, cytology experiment in tissue construction, Streptococcus mutans, gene chip, c-di-GMP signal pathway, ahpC, phosphotransferase system, National Natural Science Foundation of China

CLC Number:

R318

Xie Miao-miao, Hu Xiao-cong, Wu Bu-ling, Yan Wen-juan. Streptococcus mutans gcp gene knockout strains expression profile gene chip[J]. Chinese Journal of Tissue Engineering Research, doi: 10.3969/j.issn.2095-4344.2013.33.014.

Figures/Tables 3

2.1 使用DEVA软件进行数据分析及标准化处理首先将芯片对其网格，使用缩略图或者通过软件自带的“调整对齐”功能来查看手动对齐的效果，检查芯片的角落位置。从DEVA“项目管理器”对话框中选择“RMA分析功能”(多阵列分析功能)。用“RMA分析对话框”选择数据文件，设置计算方法和目标文件夹，点击“RUN”来进行数据分析。DEVA软件会自动运行每一个应用程序的默认分析，当分析工作完成后，可以查看结果。DEVA软件使用Bolstad描述的“位数正常化”的方法对表达的数据进行标准化。通过标准化消除空间偏移误差后，这两列数据表示的就是实际表达水平。 2.2 上下调基因分析差异基因的筛选标准为国内外基因芯片实验的常用标准Ratio’=2和Ratio’=0. 5，Ratio’值大于2或小于0.5的点被认为是有显著表达差异的基因。实验以G’ i和R’ i为横纵坐标绘制杂交信号散点图，见图1，图中每个点的斜率代表该点的Ratio’值。分别以实验组数据和对照组数据为横纵坐标，根据自身比较和相互比较的结果绘制杂交信号散点图。通过标准化消除空间偏移误差后，这两列数据表示的就是实际表达水平。图1A和图1D分别显示的是实验组数据和对照组数据自身比较的结果，两组数据基本集中在对角线上，自身偏移小。图1B显示了实验组数据和对照组数据比较后的结果，大部分数据分布在左下角分值较小的区域，同时可以看到在对角线以上分布的数据较均匀，对角线以下分布的数据较离散，说明有个别基因表达下调的程度较高。图1C显示了对照组数据和实验组数据比较后的结果，同图1B相似，大部分数据分布在左下角分值较小的区域，但是与图1B不相同的是，在对角线以上分布的数据较离散，对角线以下分布的数据较均匀。"

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