光可以取代化學試劑來調控細菌基因按需表達。但是目前，即便是如測量光基因電路表達水準這樣基本的檢測專案，現有儀器工具的操作仍然很麻煩且勞動密集。我們提出了一套微型光生物反應器陣列來監測細菌內光基因電路對光的響應。該陣列可以進行自動化即時活體並行監測與大腸桿菌中CcaS-CcaR光感測系統反應的測量。每個生物反應器均可測量光密度和螢光強度，並應用外部光幹預來控制基因的表達。該生物反應器陣列由CcaS-CcaR光感測系統進行驗證。微生物生長與光基因表達之間的相互依賴性在控制三種微生物生長影響因素（碳源，曝氧和抗生素濃度）的實驗中得到證實。在不同碳源與曝氧程度下的生長情況可以從資源配置平衡的角度來解釋。

Light can replace the chemical effector for programming on-demand gene expression in bacteria. Existing tools for optogenetic bacterial circuits remain cumbersome and labor intensive even for simple tasks, such as measuring growth-related gene expression. We present an array of min photobioreactors that monitors the response of optogenetic bacterial circuits to light. The array enables automated, in vivo parallelizable monitoring in real-time and enable the measurement of the host circuit interaction for a synthetic optogenetic circuit, CcaS-CcaR light sensing system in Escherichia coli. Each bioreactor measures the optical density and fluorescence and applies light-source intervention of the gene expression control. The bioreactor array is demonstrated on the CcaS–CcaR light sensing system in Escherichia coli. The interdependence between microbial growth and optogenetic gene expression is confirmed in a growth experiment with three effectors of microbial growth (carbon source, oxygenation, and antibiotic drug concentration). Growth under different carbon sources and oxygenation levels can be explained in the context of resource allocation trade off picture.

誌謝 III
中文摘要 IV
Abstract V
目錄 VI
一、緒論 1
1-1研究動機 1
1-2文獻回顧 3
1-2-1可逆光致變色色素與基因表達過程 3
1-2-2低成本生物反應器 7
二、材料及方法 9
2-1感光大腸桿菌樣本 9
2-2系統設置 12
2-2-1 系統結構概述 12
2-3-2機械結構 17
2-3-3硬體電路 19
2-3-4 軟體控制 25
2-4選件與系統校正 31
三、實驗結果 33
3-1實驗前準備步驟 33
3-2實驗步驟 34
3-3實驗結果 34
四、結論及討論 40
附錄 41
A-1 生物反應器與壓克力盒設計圖 41
A-2 生物反应器阵列程式码 47
參考文獻 116

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