在合成生物學中，為了達到更複雜的生物系統工程，過程中將會遇到一些困難及挑戰。第一，在基因電路中，因受限於基因元件的數量限制，欲表現多種特定功能在單一分子中是有困難的。第二，單一分子不容易達到分子和分子間溝通配合的行為。在此篇研究中，利用搜索元件庫方法來設計並達到強健性的多分子通訊系統。首先，我們為多分子通信系統建立數個良好特性的啟動子-核醣體結合位元件庫。
接著，我們從對應的啟動子-核醣體結合位元件庫選擇出一組最適當的啟動子-核醣體結合位元件來完成多分子通信系統中設計者所需的檢測能力和傳導能力及敏感度，並有效地提高了系統性能及衰減內部擾動和通道干擾對系統的影響。再來我們提出利用搜索元件庫的方法來解決合成生物學對於多分子通信系統中多目標設計的問題。最後，透過數個設計實例與實驗結果來說明其設計的步驟及過程，並確認我們所提出的系統化設計方法在多分子通信系統中確實完成設計者所需要的規格。

In synthetic biology, there are several challenges to deal with for more complex biological systems. First, it is difficult to behave all specific functions in single-celled organisms because of the limitation of component numbers in genetic circuit. Second, it is not easy to achieve a coordinated behavior among single-celled organisms through cell-to-cell communication. In this study, a library-based searching approach is designed for multicellular molecular communication system with some desired system performance. Several well-characterized promoter-RBS libraries are constructed at first for systematic design of multicellular molecular communication system. Then, we select the most adequate set of promoter-RBS components from the corresponding promoter-RBS libraries to design a multicellular molecular communication system with desired detection capability, transduction ability and system sensitivity to efficiently improve the system performance and attenuate the effect of intrinsic random fluctuations and channel noises. A library-based searching method is also proposed to solve the multi-objective design problem of multicellular molecular communication system in synthetic biology. Finally, several design examples with experiment results are given to illustrate the design procedure and to confirm the system performance of multicellular molecular communication system by the proposed systematic design method.

摘 要…………………………………………………………………………………………………i
Abstract………………………………………………………………………………………ii
誌謝……..…………………………………………………………………………………………iii
Content……………………………………………………………………………………………iv
List of Figures………………………………………………………………………v
List of Tables…………………………………………………………………………vi
Introduction………………………………………………………………………………1
1.1 Background…………………………………………………………………………1
1.2 Introduction of multicellular molecular communication system………………………………5
Construction of the promoter-RBS libraries for multicellular molecular communication system …8
2.1 Construction of the component libraries for copper biosensor genetic circuit in sender cell…9
2.2 Construction of the component libraries for synthtic genetic circuit in receiver cell………10
2.3 Dynamic models of sender cell with copper biosensor circuit………………………………11
2.4 Dynamic models of receiver cell……………………………………………14
2.5 Design methodology for the multicellular molecular communication system………………16
Design specifications and procedure of multicellular molecular communication system…………20
3.1 Design Specifications for the multicellular molecular communication system……………21
3.2 Design Procedure for the multicellular molecular communication system……………23
3.3 Synthetic gene design examples for multicellular molecular communication system in silico and verification via experiment in vivo…………………………………………………………24
3.4 Performance comparison for multicellular molecular communication system in silico and in vivo……………………32
Discussion………………………………………………………………………………………34
Conclusion…………………………………………………………………………………36
Reference……………………………………………………………………………………38
Figures…………………………………………………………………………………………43
Tables……………………………………………………………………………………………53
Supplementary Information…………………………………………61
A. Dynamic equation of catalysis process…61
B. Supplementary Figures……………………………………………63
C. Material and Method…………………………………………………64

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