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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 魏安祺(An-Chi Wei) | |
| dc.contributor.author | Shao-Ting Chiu | en |
| dc.contributor.author | 邱紹庭 | zh_TW |
| dc.date.accessioned | 2022-11-23T09:27:33Z | - |
| dc.date.available | 2021-08-20 | |
| dc.date.available | 2022-11-23T09:27:33Z | - |
| dc.date.copyright | 2021-08-20 | |
| dc.date.issued | 2021 | |
| dc.date.submitted | 2021-08-04 | |
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/80126 | - |
| dc.description.abstract | 粒線體是一種存在於真核細胞中的半自主性胞器，擔任細胞的能量工廠和代謝樞紐，其功能仰賴於細胞核基因體的供給與維護。因此粒線體對細胞核的傳訊過程在修補粒線體上扮演重要的角色。文獻上的研究著重於傳訊過程參與的蛋白質種類，與在不同狀態下對於基因體的定性調控。然而對於此粒線體網路的通訊 性質仍所知甚少。本篇論文採取控制系統的角度，以酵母菌為模式生物，整合粒線體往細胞核傳訊的分子機制，其中包含蛋白質結合與轉錄因子進入細胞核的過程。透過酵素動力學理論，以常微分方程系統來探討粒線體訊號傳遞的過程。本論文分成三個部分，第一部分為粒線體傳訊的布林模型; 第二部分為常微分模型; 第三部分為隨機系統模型。模擬出蛋白分子濃度在粒線體損害的動態過程包含波型、頻率響應及在雜訊影響下的可靠性。進一步的模擬與演算顯示，粒線體傳訊網路為近似於一個雙穩態系統，並附加三個區域性的穩態點。此外，訊號蛋白競爭型結合的過程，是提升敏感度的機制。透過隨機模擬亦發現訊號噪訊比會隨著粒線體損傷訊號增強而減少。本論文提出了粒線體傳訊的數學模型，以定量的角度思考資訊傳遞的過程。這不僅能夠更了解粒線體往細胞核傳訊的機制，也可能應用於致病性酵母的藥物研發與投藥策略。 | zh_TW |
| dc.description.provenance | Made available in DSpace on 2022-11-23T09:27:33Z (GMT). No. of bitstreams: 1 U0001-0407202119023200.pdf: 3571882 bytes, checksum: a652ebb8e1e50847b64874554c1afd5a (MD5) Previous issue date: 2021 | en |
| dc.description.tableofcontents | "Contents Verification Letter from the Oral Examination Committee i Acknowledgements iii 摘要 v Abstract vii Contents ix List of Figures xiii List of Tables xv Denotation xvii Chapter 1 Introduction 1 1.1 Mitochondria quality control An overview 1 1.2 Mitochondrial retrograde signaling in yeast 2 1.3 Mitochondrial signaling as a communication system 3 1.4 An ordinary differential equationbased model for mitochondrial retrograde signaling 4 1.5 Application of this Study 5 Chapter 2 Methods and Materials 7 2.1 The structure of the differential equationbased model of mitochondrial retrograde signalling in yeast 7 2.2 A Boolean model of mitochondrial network 8 2.3 The expression levels of RTG genes 10 2.4 From Boolean model to ordinary differential equationbased model 11 2.5 Parameter searching with the qualitative data of protein translocation 14 2.6 An ordinary differential equationbased model of mitochondrial retrograde signaling in yeast 17 2.7 Ultrasensitivity analysis with relative amplification approach 19 Chapter 3 Results 23 3.1 The steady states of 18 mitochondrialrelated conditions are verified by the qualitative studies. 23 3.2 The ultrasensitivity of Bmh/Mksp degradation causes the switchlike response of Rtg1/3p to mitochondrial damage 25 3.3 The competitive binding between Bmhp and Rtg2p with Mksp contributes to the ultrasensitivity of Bmh/Mksp degradation 27 3.4 Quantitative analysis of the activation layer 30 3.4.1 The analytical solution of the activation layer 30 3.4.2 The competitive binding of Bmhp and Rtg2p with Mksp is the source of the ultrasensitivity 31 3.5 Frequency modulation of mitochondrial retrograde signaling 34 3.6 Robustness analysis 38 Chapter 4 Discussion 41 Chapter 5 Concluding Remarks 45 5.0.1 Significance of this study 45 5.0.2 Limitation 46 5.0.3 Future perspective 47 References 49 Appendix A — Key Resources 63 Appendix B — Boolean model of mitochondrial retrograde signaling 65 B.0.4 Stress response and expression levels 65 B.0.5 Model with dynamical inputs 67 B.0.6 Rtg1/3p Translocation under Mulitple Conditions 72 B.0.7 Ordinary differential equationbased model of mitochondrial retrograde signaling 74 B.0.8 Fitted parameters 76 Appendix C — Package development 81 C.0.9 FindSteadyStates.jl A Julia package for searching steady states of ODE systems 83 List of Figures Figure 1.1 The workflow of the experimental design 6 Figure 2.1 Boolean equivalent circuit of Rtg1/3p translocation. 10 Figure 2.2 The circuit of mitochondrialtonucleus communication 19 Figure 3.1 Boolean decision in RTG signaling pathway 24 Figure 3.2 Step responses of Bmh/Mksp, Rtg1pn and Rtg3pn. 26 Figure 3.3 Ultrasensitivity of Bmh/Mksp heterodimer results from molecular titration 29 Figure 3.4 The frequency response of mitochondrial damage signal and RTG protein concentrations 36 Figure 3.5 The frequency analysis of Bmh/Mksp, Rtg1pn and Rtg3pn in respect of mitochondrial damage 37 Figure 3.6 Potential map of the Rtg1/3p translocation in response to mitochondrial damage signal 39 Figure 4.1 Mitochondrial retrograde circuit 44 Figure B.1 Expression levels of RTG proteins 66 Figure B.2 Pseudo time plots of yeast gene expression 66 Figure B.3 The retrograde response to mitochondrial damage with sigmoid. . 67 Figure B.3 The retrograde response to mitochondrial damage with square and sinusoidal waveforms. 68 Figure B.4 The inputoutput relation and Hill coefficient 69 Figure B.5 The square wave response of the proposed mitochondrial retrograde signalling model 69 Figure B.6 The steadystate of Mksp and its heterodimers 70 Figure C.7 Sample code for exploring steady states of an ODE model with FindSteadyStates.jl 84 List of Tables Table2.1 The expression level of RTG proteins from the quantitative Western blot 11 Table A.1 Key Resources 64 Table B.2 RTGassociated proteins 71 Table B.4 The Boolean model of mitochondrial retrograde signaling 73 Table B.5 Properties of Rtg1/3p translocation to nucleus 73 Table B.6 Parameter set of the proposed model 79 " | |
| dc.language.iso | en | |
| dc.subject | 常微分方程 | zh_TW |
| dc.subject | 數學模型 | zh_TW |
| dc.subject | 酵素動力學 | zh_TW |
| dc.subject | 粒線體逆向訊號 | zh_TW |
| dc.subject | 控制系統 | zh_TW |
| dc.subject | Ordinary differential equations | en |
| dc.subject | Control systems | en |
| dc.subject | Mathematical modeling | en |
| dc.subject | Enzyme kinetics | en |
| dc.subject | Mitochondrial retrograde signaling (RTG) | en |
| dc.title | 以微分方程系統解析粒線體對細胞核傳訊的系統特性 | zh_TW |
| dc.title | Understanding the System Dynamics of Mitochondrial Retrograde Signaling from a Differential Equationbased Framework | en |
| dc.date.schoolyear | 109-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 呂俊毅(Hsin-Tsai Liu),江介宏(Chih-Yang Tseng),黃宣誠,阮雪芬 | |
| dc.subject.keyword | 粒線體逆向訊號,酵素動力學,數學模型,控制系統,常微分方程, | zh_TW |
| dc.subject.keyword | Mitochondrial retrograde signaling (RTG),Enzyme kinetics,Mathematical modeling,Control systems,Ordinary differential equations, | en |
| dc.relation.page | 84 | |
| dc.identifier.doi | 10.6342/NTU202101265 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2021-08-05 | |
| dc.contributor.author-college | 電機資訊學院 | zh_TW |
| dc.contributor.author-dept | 生醫電子與資訊學研究所 | zh_TW |
| 顯示於系所單位： | 生醫電子與資訊學研究所 | |
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