研究生: |
余祖鈞 Yu, Tsu-Chun |
---|---|
論文名稱: |
利用系統化方法於大腸桿菌細胞族群控制裂解基因電路設計 Systematic Approach to Escherichia coli Cell Population Control by Lysis Genetic Circuit |
指導教授: |
陳博現
Chen, Bor-Sen |
口試委員: |
莊永仁
藍忠昱 林澤 王禹超 |
學位類別: |
碩士 Master |
系所名稱: |
電機資訊學院 - 電機工程學系 Department of Electrical Engineering |
論文出版年: | 2013 |
畢業學年度: | 102 |
語文別: | 英文 |
論文頁數: | 71 |
中文關鍵詞: | 合成生物學 、裂解基因電路 、基因演算法 |
外文關鍵詞: | Synthetic biology, Lysis genetic circuit, Genetic algorithm |
相關次數: | 點閱:3 下載:0 |
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細胞族群控制被使用於調控其細胞族群密度和維持特定的細胞族群密度。在本研究中,我們利用了從Biobricks裡的BBa_K11700元件來裂解宿主大腸桿菌。BBa_K11700是藉由在抑制型TetR調控的啟動子-核糖體元件或促進型LuxR調控的啟動子-核糖體元件下的裂解基因電路來調控其細胞族群密度。在這裡,我們提供了有效的設計方法學來設計裂解基因電路達成想要的細胞族群密度控制。我們首先建構了裂解基因電路。基於裂解電路的穩態模型,裂解電路的能力是被用於描述啟動子-核糖體元件和誘導物濃度之間的關係,從此關係我們可以觀察出主要影響細胞族群密度的因子,然後,良好特性化的啟動子-核糖體元件結合位元件庫被建立以及裂解速率從實驗的量測數據裡被識別出來。最後,依據使用者的設計規範,一個系統化設計方法被提出來達成強健的穩態細胞族群密度控制,藉由從啟動子-核糖體元件結合位元件庫選擇出一組適當的啟動子-核糖體元件組合和相對應的適當可執行範圍的誘導物濃度來提供合成生物學家達到想要的細胞族群密度調控。因此,根據本文的設計流程,我們相信我們所提出的使用者為導向的設計方法來達成想要的細胞族群密度控制,將提供於快速成長的合成生物領域,一個有用的設計指引來設計日漸複雜的基因調控網路。
1. Ellermeier CD, Hobbs EC, Gonzalez-Pastor JE, Losick R: A three-protein signaling pathway governing immunity to a bacterial cannibalism toxin. Cell 2006, 124(3):549-559.
2. Gardner A, West SA, Buckling A: Bacteriocins, spite and virulence. Proceedings of the Royal Society of London Series B: Biological Sciences 2004, 271(1547):1529-1535.
3. You L, Cox RS, Weiss R, Arnold FH: Programmed population control by cell–cell communication and regulated killing. Nature 2004, 428(6985):868-871.
4. Shetty RP, Endy D, Knight Jr TF: Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering 2008, 2(1):1-12.
5. Canton B, Labno A, Endy D: Refinement and standardization of synthetic biological parts and devices. Nature biotechnology 2008, 26(7):787-793.
6. Morita M, Asami K, Tanji Y, Unno H: Programmed Escherichia coli cell lysis by expression of cloned T4 phage lysis genes. Biotechnology progress 2001, 17(3):573-576.
7. Pasotti L, Zucca S, Lupotto M, Cusella De Angelis M, Magni P: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release. Journal of biological engineering 2011, 5(8).
8. Chak K-F, Kuo W-S, James R: Cloning and characterization of the ColE7 plasmid. Journal of general microbiology 1991, 137(1):91-100.
9. Cavard D, Baty D, Howard S, Verheij H, Lazdunski C: Lipoprotein nature of the colicin A lysis protein: effect of amino acid substitutions at the site of modification and processing. Journal of bacteriology 1987, 169(5):2187-2194.
10. CHAK K-F, JAMES R: Localization and characterization of a gene on the ColE3-CA38 plasmid that confers immunity to colicin E8. Journal of general microbiology 1984, 130(3):701-710.
11. Inukai M, Ghrayeb J, Nakamura K, Inouye M: Apolipoprotein, an intermediate in the processing of the major lipoprotein of the Escherichia coli outer membrane. Journal of Biological Chemistry 1984, 259(2):757-760.
12. PUGSLEY AP, COLE ST: An unmodified form of the ColE2 lysis protein, an envelope lipoprotein, retains reduced ability to promote colicin E2 release and lysis of producing cells. Journal of general microbiology 1987, 133(9):2411-2420.
13. Cavard D: Synthesis and functioning of the colicin E1 lysis protein: comparison with the colicin A lysis protein. Journal of bacteriology 1991, 173(1):191-196.
14. Lin LJ, Liao CC, Chen YR, Chak KF: Induction of membrane permeability in Escherichia coli mediated by lysis protein of the ColE7 operon. FEMS microbiology letters 2009, 298(1):85-92.
15. Cascales E, Buchanan SK, Duché D, Kleanthous C, Lloubes R, Postle K, Riley M, Slatin S, Cavard D: Colicin biology. Microbiology and Molecular Biology Reviews 2007, 71(1):158-229.
16. Wu C-H, Zhang W, Chen B-S: Multiobjective H2/H [infinity] synthetic gene network design based on promoter libraries. Mathematical biosciences 2011, 233(2):111-125.
17. Wu C-H, Lee H-C, Chen B-S: Robust synthetic gene network design via library-based search method. Bioinformatics 2011, 27(19):2700-2706.
18. Chen B-S, Wu C-H: A systematic design method for robust synthetic biology to satisfy design specifications. BMC systems biology 2009, 3(1):66.
19. Johansson R: System modeling & identification: Prentice-Hall, Inc.; 1993.
20. Alon U: An introduction to systems biology: design principles of biological circuits, vol. 10: Chapman & Hall/CRC; 2007.
21. Chen B-S, Chang C-H, Wang Y-C, Wu C-H, Lee H-C: Robust model matching design methodology for a stochastic synthetic gene network. Mathematical Biosciences 2011, 230(1):23-36.
22. Lo T-M, Tan MH, Hwang I-Y, Chang MW: Designing a synthetic genetic circuit that enables cell density-dependent auto-regulatory lysis for macromolecule release. Chemical Engineering Science 2013.
23. Saeidi N, Wong CK, Lo TM, Nguyen HX, Ling H, Leong SSJ, Poh CL, Chang MW: Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen. Molecular systems biology 2011, 7(1).
24. Green DR: Means to an end: apoptosis and other cell death mechanisms: Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY:; 2011.
25. Ross P, Mayer R, Benziman M: Cellulose biosynthesis and function in bacteria. Microbiological Reviews 1991, 55(1):35-58.
26. Elmore S: Apoptosis: a review of programmed cell death. Toxicologic pathology 2007, 35(4):495-516.
27. Leveau JHJ, Lindow SE: Predictive and interpretive simulation of green fluorescent protein expression in reporter bacteria. Journal of bacteriology 2001, 183(23):6752-6762.
28. Albano CR, Randers-Eichhon L, Chang Q, Bentley WE, Rao G: Quantitative measurement of green fluorescent protein expression. Biotechnology techniques 1996, 10(12):953-958.
29. Tuttle LM, Salis H, Tomshine J, Kaznessis YN: Model-driven designs of an oscillating gene network. Biophysical journal 2005, 89(6):3873-3883.
30. Selinger DW, Saxena RM, Cheung KJ, Church GM, Rosenow C: Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome research 2003, 13(2):216-223.
31. Alper H, Fischer C, Nevoigt E, Stephanopoulos G: Tuning genetic control through promoter engineering. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(36):12678-12683.