建構抗菌藥物之網路蛋白質資料庫

蛋白質體學是廣泛研究蛋白質體的學問，而二維聚丙烯醯胺膠體電泳(2-D PAGE) 是研究蛋白質體的主要的核心技術。它可用來觀察在藥物的影響下或者是在不同生長條件下，生物體內蛋白質的作用路徑及其活性改變的情形。因此我們將用來討論比較已知與未知藥物機制的作用下，細菌細胞內的蛋白質表現差異。由於二維聚丙烯醯胺膠體電泳所獲得的資料量非常多，我們需要架構一資料庫來儲存與整理所獲得的資料。因此本論文目的在建構一個名為「Antibiotic 2D-PAGE」的資料庫來儲存抗菌藥物的二維電泳資料及蛋白質質譜的資料。我們參考了Open2Dprot的架構，並使用開放原始碼的資料庫管理系統「MySQL」來建構。接著我們藉由廣泛使用於一般用途的描述語言「PHP: Hypertext Preprocessor(PHP)」來建立一個方便使用者使用的網路管理介面。在這個網路管理介面內，我們可上傳二維聚丙烯醯胺膠體的電泳資料、下載標誌圖形檔案格式的影像圖片，並且我們可以很容易的藉由如：蛋白質的名稱（Peptide）、NCBI的登錄號碼（NCBI Accession Number）、圖像（Map）、膠片所使用的物種（Organisms）、蛋白質的等電點值與分子量範圍（pI/Mw range）、膠片使用的抗生素或化合物（Drug/Compound）以及實驗操作者（Operator）等條件來搜尋二維聚丙烯醯胺膠體電泳資訊。

關鍵字

蛋白質體學；抗生素；二維聚丙烯醯胺膠體電泳； MySQL ； PHP

並列摘要

Proteomics is a large-scale study of protein expression. Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) is the proteomics core technology. It is being used to monitor the external activation of proteins participating in biological pathways under the condition of the condition without drugs. We use the method to study protein expression of bacterial cells under the comparision of different drugs and from which the mechanismstic action of drugs are interpretated. Because the data obtained by 2-D PAGE is very large, we construct the database to store and organize the data. This thesis aims to construct the database to store the antibacterial 2-D PAGE data and the mass Spectrometry data. We call this database “Antibiotic 2D-PAGE.” Our framework is referring to Open2Dprot and we use MySQL that is the most popular SQL database management system of Open Source to construct the antibiotic 2-D PAGE database. We built the web-based control page by Hypertext Preprocessor(PHP) which is a widely-used for general-purpose scripting language, to have a user-friendly interface. At the web-based control page, it is able to upload our 2-D PAGE data and download the Tag Image File Format (TIFF) image. The 2-D PAGE data can be searched easily by limitation such as Peptide, NCBI Accession number, Map, Organisms, pI/Mw range, Drug/Compound, and Operator.

並列關鍵字

proteomics ； antibiotic ； 2-D PAGE ； MySQL ； PHP

參考文獻

[1] Hardiman Gary, "Introduction to proteomics:tools for the new biology," Proteomics, vol.1, no. 1, 2004, pp. 9-10.

[2] Huang San-Yuan, Lin Jyh-Hung, Chen Yu-Huey, Chuang Chin-Kai, Lin En-Chung, Huang Mu-Chiou, Sun Hsiao-Fang Sunny, Lee Wen-Chuan, "A reference map and identification of porcine testis proteins using 2-DE and MS." Proteomics , vol.5, no. 16, 2005, pp. 4205-4212.

[6] Naaby-Hansen S., Waterfield M.D., Cramer R. ,"Proteomics--post-genomic cartography to understand gene function." Trends in Pharmacological Sciences , vol.7, no. 22, 2001, pp. 376-384.

[8] Klose J. ,"Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. " Humangenetik , vol.7, no. 26, 1975, pp. 231–43

[11] Vihnen Mauno ,"Bioinformatics in proteomics." Biomolecular engineering, vol.5, no. 18, 2001, pp. 241-248.

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建構抗菌藥物之網路蛋白質資料庫

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