Drosobrain: Drosophila interactive database of memory related proteins and two dimensional gels

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研究生：	林國森 Wono Sardono
論文名稱：	Drosobrain: Drosophila interactive database of memory related proteins and two dimensional gels Drosobrain: 果蠅記憶相關蛋白質與二維電泳膠圖之互動式資料庫
指導教授：	呂平江 Lyu, Ping Chiang
口試委員:
學位類別：	碩士 Master
系所名稱：	生命科學暨醫學院 - 生物資訊與結構生物研究所 Institute of Bioinformatics and Structural Biology
論文出版年：	2009
畢業學年度：	97
語文別：	英文
論文頁數：	60
中文關鍵詞：	果蠅、資料庫、二維電泳膠圖、記憶
相關次數：	點閱：1 下載：0
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Drosophila melanogaster is one of the most studied eukaryotes model that being used to study many cellular processes such as neurodegenerative diseases, infections, and development of the cell. Based on World 2D-PAGE, there is no up to date D. melanogaster 2D-PAGE database today. 2D-PAGE is the center of proteome technique that can enable separation of protein mixtures in their isoelectric points (pI), for the first dimension, and subsequently by their molecular weight (MW) for the second dimension.
In order to establish a high-throughput platform for identification of memory related gene expression changes in D. melanogaster, we first constructed a website containing a high resolution D. melanogaster brain proteomes. To know the amount of protein expression level and the difference spots pattern, we have built an analytical tool to align or superimpose two different gel images. Our database enables users to upload, annotate, and compare their own 2D-PAGE image with our reference map.
As a result, the standard reference map and protein identification have been conveniently maintained as 2D-PAGE based D. melanogaster brain database accessible as image maps via World Wide Web (WWW) server. The constructed database will offer D. melanogaster brain clickable 2D-PAGE maps, spot ID, spot MW, spot pI, accession number, protein functions, bibliographical references and linked to other bioinformatics websites. The standard reference map can be used to compare different experimental conditions. A web service has been set up, which is available at: http://140.114.98.63/~drosobrain/flybrain/fb.html/.

果蠅 (Drosophila melanogaster) 是其中最常被拿來作為原核模式生物之一，研究者常常用此生物體研究各種不同的細胞機轉，例如：神經退化疾病、細菌感染以及細胞發育。基於在二維電泳的領域裡面，目前為止並沒有專屬果蠅 (Drosophila melanogaster) 的資料庫，我們致力於發展新的資料庫。二維電泳是一種蛋白質體學的工具，它可以藉由等電點 (isoelectric points)做第一維的蛋白質分離，接著利用蛋白質本身的分子量 (molecular weights) 差異來做第二維的分離。
為了要建立一個能夠檢出記憶相關基因改變的高產率平台，我們開始著手建立一個網站，其中囊括了果蠅的高解析度蛋白質體電泳資訊。為了要研究不同的電泳圖在蛋白質表現的差異，我們建立了兩片電泳圖的圖譜堆疊比較分析工具。我們的資料庫可讓使用者上傳、註釋以及與我們的參照電泳圖和他們所上傳的電泳圖進行比較。
因次，藉由網頁呈現一個果蠅二維電泳的資料庫大大地增加了標準的參照電泳圖的保存和蛋白質檢索的進行。其中的資訊包涵了可點選的果蠅大腦電泳圖、點圖譜序號、分子量、等電點、SWISS_PROT序號、蛋白質功能、文獻參考以及連結到其他資料庫的超連結等等。標準的參照電泳圖可以被用來和不同的實驗條件所得到的電泳圖做比較。網頁服務的資訊如下: http://140.114.98.63/~drosobrain/flybrain/fb.html/

Chapter 1 – Introduction    1
1.1 Proteomics and Proteome    1
1.2 Two-Dimensional Electrophoresis Gel    1
1.3 Mass Spectrometry    2
1.4 Proteomics and Bioinformatics Framework    4
    1.4.1 Proteomics Database    4
    1.4.2 Proteomics Software    4
1.5 Drosophila melanogaster    5
1.6 Motivation of This Study    6
Chapter 2 – Materials and Methods    8
2.1 Hardware    8
2.2 Software    8
2.3 Database and Web-Based Tools    8
2.4 2D PAGE Images and Spots Information    11
2.5 Construction of Drosobrain    12
Chapter 3 – Results and Discussions    15
3.1 Usage of the Web Service    15
3.2 Memory Related Protein    15
    3.2.1 Superfamily    19
    3.2.2 Swissmodel    20
    3.2.3 User update    20
3.3 Clickable 2D-PAGE    21
3.4 Searching Tools    22
3.5 Analytical Tools    23
    3.5.1 Image Alignment    23
    3.5.2 Image Annotation and Comparison    24
3.6 Advantages of Drosobrain    25
Chapter 4 – Conclusions    27
References    28
Attached Appendixes and Figures    32


List of appendix and figures
Appendix I.     Two-dimensional electrophoresis gel    33
Appendix II.    Flow chart of 2D-difference gel electrophoresis (2D-DIGE) and protein spot quantification and identification.    34
Appendix III.     Main components of mass spectrometer    35
Appendix IV.         A framework between bioinformatics (dry lab) and proteomics (wet lab) in protein analysis    36
Appendix V.     Online proteomics resources    37
Appendix VI.     Peptide Fragmentation Fingerprint (PFF) software and source    38
Appendix VII. Drosophila transgenic models of neurodegenerative disease    39
Figure 1.     Database overview on the web server.    40
Figure 2.     Web site of the Drosobrain database    41
Figure 3.     Navigation of Drosobrain database    42
Figure 4.     User interface of the protein property    43
Figure 5.     User interface of the secondary structure prediction was obtained from PSIPRED    44
Figure 6.     User interface of the transmembrane prediction    45
Figure 7.     User interface of the peptide cutter.    46
Figure 8.     User interface of the PANTHER pathway    47
Figure 9.     User interface of the protein-protein interaction    48
Figure 10.    Protein information from one of the node in OSPREY protein-protein interaction    49
Figure 11. Superfamily list of protein related to serotonin generated by NCBI’s Conserved Domain Database     50
Figure 12.    Swiss-model list of protein related to long term memory generated by SWISS-MODEL    51
Figure 13. Flowchart of the user update    52
Figure 14. The summarized of protein information from the selected spot    53
Figure 15. The list of signed spot and protein information    54
Figure 16. The clickable 2D gel    55
Figure 17. The total amount of signed spots pattern on a gel    56
Figure 18. The large scale of 2D gel image    57
Figure 19. Head Proteomes from male and female D. melanogaster were analyzed using 2D-PAGE    58
Figure 20. Head proteome of wild-type Drosophila (white) and serotonin (dSERT55) were analyzed using our analytical tools    59
Figure 21. Image comparison between the new uploaded gel with standard 2D gel    60

                                

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