跳到主要內容

臺灣博碩士論文加值系統

(44.210.77.73) 您好!臺灣時間:2024/02/22 01:54
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果 :::

詳目顯示

: 
twitterline
研究生:葉鳴麗
研究生(外文):Ming-Li Yeh
論文名稱:描述代謝網路之層級式PetriNet模式
論文名稱(外文):Hierarchical Petri Nets for Modeling Metabolic Networks
指導教授:張玨庭張玨庭引用關係
指導教授(外文):Chuei-Tin Chang
學位類別:碩士
校院名稱:國立成功大學
系所名稱:化學工程學系碩博士班
學門:工程學門
學類:化學工程學類
論文種類:學術論文
論文出版年:2004
畢業學年度:92
語文別:中文
論文頁數:123
中文關鍵詞:基因調控代謝反應派屈網路
外文關鍵詞:operonregulonPetri Netmodulon
相關次數:
  • 被引用被引用:0
  • 點閱點閱:191
  • 評分評分:
  • 下載下載:13
  • 收藏至我的研究室書目清單書目收藏:1
  在本研究中我們利用派屈網(Petri net)發展出系統化建模策略來描述原核生物中包含基因控制機構的生化反應系統之行為。我們首先建構了不同的單元模組來表示細胞中的單元功能,再逐步依層級式結構將之組合而成系統模式。我們利用了幾個虛擬案例來展示了此一模式的用途,並利用四組文獻數據來驗證其正確性,並進一步預測反應系統的動態行為。
  A systematic strategy is developed in the present study to model biological reaction networks in prokaryotes with Petri nets. Component models are first developed to represent the cellular functional units in metabolic networks, i.e., operons, regulons, modulons and individual reactions. A step-by-step procedure is then presented to construct the hierarchical system models accordingly. The usefulness of the proposed model is demonstrated with a fictitious example. The model validity is shown by comparing simulation predictions with experimental data of four distinct systems in the literature.
目 錄
第一章 緒論……………………………………………1
第二章 代謝網路系統結構…………………………………4
2.1 代謝反應…………………………………………………4
2.2 基質輸送…………………………………………………8
2.3 基因表現…………………………………………………9
2.4 基因調控………………………………………………10
第三章 派屈網模式之建構………………………………18
3.1 派屈網路的基本元素…………………………………18
3.2 單元模組………………………………………………22
3.2.1 代謝反應……………………………………………22
3.2.2 基質輸送……………………………………………23
3.2.3 操縱組………………………………………………24
3.2.4 Modulon與Regulon…………………………………30
3.3建構派屈網模式之步驟………………………………32
3.4 虛擬系統之動態模擬…………………………………42
第四章 原核生物代謝系統模式之驗證……………………53
4.1 酥胺酸反應路徑(threonine pathway)………………53
4.2醣解作用與戊醣磷酸途徑………………………………62
4.3 乳糖操縱組……………………………………………86
4.4乳糖操縱組中的降解物抑制作用和誘導物排除作用103
第五章 結論與展望………………………………………119
5.1 結論…………………………………………………119
5.2展望……………………………………………………119
參考文獻……………………………………………………121
(1)Bailey, J. Toward a science of metabolic engineering. Science, 252, 1668-1673, 1991.
(2)Beckwith, J. The lactose operon. In Escherichia coli and Salmonella: Cellular and Molecular Biology, Vol. 2. F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, and H. E. Umbarger, editors. American Society for Microbiology, Washington, DC. 1444–1452, 1987.
(3)Bozinovski, S.; Müller, B.; Primio, F. di. Autonomous manufacturing systems and systems software. Report, http://www.gmd.de., 2000.
(4)Chassagnole, C.; Rai, B.; Quentin, E.; Fell, D.A.; Mazat, J.P. An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem. J., 356, 415-423, 2001.
(5)Chassagnole, C.; Fell, D.A.; Rai, B.; Kudla, S.B.; Mazat, J.P. Control of the threonine-synthesis pathway in Escherichia coli: a theoretical and experimental approach. Biochem. J., 356, 433-444, 2001.
(6)Chassagnole, C.; Naruemol Noisommit-Rizzi; Joachim W. Schmid; Mauch, K.; Reuss, M. Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol. Bioeng., 79, 53-73, 2002.
(7)David, R.; Alla, H. Petri net for modeling of dynamic systems - a survey. Automatica, 30(2), 175-202, 1994.
(8)Delgado, L.; Liao, L.C. Control of metabolic pathways by time-scale separation. Biosystems, 36, 55–70, 1995.
(9)Drath, R. Visual Object Net++, http://www.daimi.au.dk /PetriNets /tools/ complete_de.html, 1998.
(10)Flares, N.; Xiao, J.; Berry, A.; Bolivar, F.; Valle, F. Pathway engineering for the production of aromatic compounds in E. coli. Nat Biotech., 14, 620-623, 1996.
(11)Goodwin, B. C. Control dynamic of β-galactosidase in relation to the bacterial cell cycle. Eur. J. Biochem., 10, 515-522, 1969.
(12)Goss, P.J.E.; Peccouds, J. Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. PNAS, 6750, 1998.
(13)Hatzimanikatis, V.; Emmerling, M.; Saucer, U.; Bailey, J.E. Application of Mathematical tools for Metabolic design of microbial ethanol Production. Biotech. Bioengg. 58, 154-161, 1998.
(14)Hofestädt, R.; Thelen, S. Quantitative modeling of biochemical networks. http:/www. bioifo.de/isb/1998/01/006main/html/, 1998.
(15)Jacob F.; Monod J. Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology, 3, 318–356, 1961.
(16)Jamshidi, N.; Edwards, J. S.; Fahland, T.; Church, G. M.; Palsson, B. O. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics. 17, 286-287, 2001.
(17)Knorre, W. A. Oscillation of the rate of synthesis of β-galactosidase in Escherichia coli ML 30 and ML 308. Biochem. Biophys. Res. Commun., 30, 1248-1290, 1968.
(18)Koch, I.; Schuster; Heiner, M. Simulation and analysis of metabolic networks by time dependent Petri nets. Bioinformatics, http://www.bioinfo.de/isb/ gcb99/ poster/koch/, 1999.
(19)Kremling, A.; Jahreis, K.; Lengeler, J.W.; Gilles, E.D. The organization of metabolic reaction networks: A signal-oriented approach to cellular models. Metabolic Engineering, 2, 190-200, 2000.
(20)Lengeler, J. Metabolic Networks: a signal oriented approach to cellular models. Biological chemistry, 911-920, 2000.
(21)Mary K. Biochemistry, Campbell, Harcourt Asia Pte Ltd, 2001.
(22)Matsuno, H.; Doi, A.; Nagasaki, M.; Miyano, S. Hybrid Petri net representation of gene regulation network. Proceedings on Pacific Symposium on Bio-computing, 338-349, 2000.
(23)Millard, C.S.; Chao, V.P.; Liao, J.C.; Donnelly, M. Enhanced production of succinic acid by overexpression of phosphoenolpyruvate carboxylase in E coli. Appl Environ Microbial, 62:1808-l810, 1996.
(24)Nielsen, J. Metabolic Engineering. Applied. Biotechnology, 55, 263-283, 2001.
(25)Oehler, S.M.; Amouyal, P.; Kolkhof, B. von Wilcken-Bergmann; B. Mu¨ ller-Hill. Quality and position of the three lac operators of E. coli define efficiency of repression. EMBO J. 13, 3348–3355, 1994.
(26)Pardee A. B.; Jacob F.; Monod J. The genetic control and cytoplasmic expression of ‘inducibility’ in thr synthesis of β-galactosidase by E. coli. Jpurnal of molecular Biology, 1, 165-178, 1959.
(27)Pestka, S.; Daugherty B. L.; Hung V.; Hotta K.; Pestka R. K. Anti-mRNA: specific inhibition of translation of single mRNA molecules. Proc. Natl. Acad. Sci. USA. 81, 7525-7528, 1984.
(28)Peterson, J.L. Petrinet theory and the modeling of systems. Prentice Hall, 1981.
(29)Pissara P.N.; Nielsen J.; Bazin M.J. Pathway kinetics and metabolic control analysis of a high-yielding strain of fenicillium chrysogenum during fed batch cultivations. Biotechnol Bioeng, 51,168-l 76, 1996.
(30)Porro, D.; Brambilla, L.; Ranzi, BM.; Martegani, E.; Alberghina, L. Development of metabolically engineered Saccharomyces cerevisiae cells for the production of lactic acid. Biotech. Progress, 11, 294-298, 1995.
(31)Ramakrishna, R.; Edwards, J.S.; McCulloch, A.; Palsson, B.O. Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. Am J Physiol Regulatory Integrative Comp Physiol 280: R695-R704, 2001.
(32)Reddy, V.N.; Libeman, M.N.; Mavrovouniotis, M.L. Qualitative analysis of biochemical reaction systems. Computational. Biology Medicine, 9, 26-34, 1996.
(33)Santillán, M.; Mackey, M.C. Influence of catabolite repression and inducer exclusion on the bistable behavior of the lac operon. Biophysical Journal, 86, 1282-1292, 2004.
(34)Stephanopoulos, G..N. Metabolic fluxes and metabolic engineering, Metabolic Engineering, 1, 1-11, 1999.
(35)Stephanopoulos, G.N. Metabolic engineering: perspective of chemical engineer, AIChE J. 48, 920-926, 2002.
(36)Stephanopoulos, G..N.; Aristidou, A.A.; Nielsen, J. Metabolic Engineering, Academic Press, NY, 1998.
(37)Ullmann, A. Escherichia coli lactose operon. Encyclopedia of Life Sciences. http://www.els.net, 2001.
(38)Wong, P.; S. Gladney; J. D. Keasling. Mathematical model of the lac operon: inducer exclusion, catabolite repression, and diauxic growthon glucose and lactose. Biotechnol. Prog. 13, 132–143, 1997.
(39)Yildirim, N.; Mackey, M.C. Feedback regulation in the lactose operon: A mathematical modeling study and comparison with experimental data. Biophys. J., 84, 2841-2851, 2003.
QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top
無相關論文
 
1. 王文宇,”從信託法原理論共同基金之規範,”月旦法學雜誌,82,pp.65-79, 。
2. 王文宇,”信託法應如何定位三位一體之信託法律關係,”法令月刊,29(12),pp.46-67, 。
3. 王文宇,”不動產證券化法制評析,”法令月刊,53(5),pp. 28-39。
4. 王文宇,”信託法運用於金融市場的幾個爭議問題,”證券暨期貨管理,19(8),pp 1-25。
5. 王文宇,”不動產證券化條例之評析與前瞻”月旦法學雜誌,101,pp.62-71。
6. 王志誠,”論商事信託之功能與法制發展,”律師雜誌,268,pp.16-36。
7. 王志誠,”特殊目的信託與受益人之保護機制,”存款保險資訊季刊,15(3),pp.107-129。
8. 方嘉麟,”利害關係人交易問題探討—兼論信託財產運用之限制,”月旦法學雜誌,90,8-33。
9. 方嘉麟,”信託架構下利益衝突交易及其管制模式之經濟分析,”政大法學評論,56,pp.187-210。
10. 林世淵,”美、日兩國投資信託現狀及改革方向,”證交資料,425,pp.19-28。
11. 邱榮輝,”金融資產證券化的經濟利益和投資者保護,”月旦法學雜誌,88,pp.170-178。
12. 胡智忠,”不動產證券交易的資訊公開,”全國律師,6(7),pp.44-48。
13. 游啟璋,”不動產證券化法制解析,”月旦法學雜誌,88,pp.151-161。
14. 陳春山,”證券投資信託基金之法律地位,”證券公會,1,pp.2-13。
15. 葉賽鶯,”我國信託法析要暨其相較於日韓信託法之特色,”法學叢刊,42(3),pp.1-14。