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In science, crafting theoretical models can help understand, predict and improve experiments and their interpretation. In our project, acid stress is often encountered during industrial fermentation as a result of the accumulation of acidic metabolites. Acid stress is often encountered during industrial fermentation as a result of the accumulation of acidic metabolites. Acid stress increases the intracellular acidity and can cause DNA damage and denaturation of essential enzymes, thus leading to a decrease of growth and fermentation yields[1]. We hope to change the acid tolerance of E. coliMG1655 by regulating the expression of genes gadB, gadC, yabS and katA.

First, we constructed a transcriptional regulatory pool with an outbound capacity of 10000. And we changed the promoter strength of four genes and recorded the final OD600 of strains under the same initial growth conditions. Then we find the optimal promoter strength combination through mathematical modeling. To this end, we established the GA-BP model.

Genetic algorithm is a global optimization algorithm, being capable of finding the globally optimal solution in complex, multi-crest, non-differentiable vector spaces. Utilizing genetic algorithm to search for the initial weights of the BP neural network could guarantee a relatively high probability to obtain the global optima, and therefore the initial search by the genetic algorithm is a preferred means to overcome the shortcoming of BP neural network. It is proved that the BP model optimized by GA is superior to the pure BP model.

Depending on the problem we're trying to solve, the input vector is the strength of four promoters, and output vector is the final OD600 of strains. Combined with genetic algorithm, the model has the characteristics of both local precise search and global search.

[1] Xianxing Gao, Xiaofeng Yang et al. (2018). Engineered global regulator H‑NS improves the acid tolerance of E. coli.
[2] Li Zhuo,Jing Zhang,Pei Dong,Yingdi Zhao,Bo Peng. An SA–GA–BP neural network-based color correction algorithm for TCM tongue images[J]. Neurocomputing,2014,134.


Parts Table
BBa_K3100001 Regulatory T7 Promoter T7-1  Zheng Yiyuan 23
BBa_K3100002 Regulatory T7 Promoter T7-2 Zheng Yiyuan 23
BBa_K3100003 Regulatory T7 Promoter T7-3 Zheng Yiyuan 23
BBa_K3100004 Regulatory T7 Promoter T7-4 Zheng Yiyuan 23
BBa_K3100005 Regulatory T7 Promoter T7-6 Zheng Yiyuan 22
BBa_K3100006 Regulatory T7 Promoter T7-8 Zheng Yiyuan 23
BBa_K3100007 Regulatory T7 Promoter T7-10 Zheng Yiyuan 23
BBa_K3100008 Regulatory T7 Promoter T7-15 Zheng Yiyuan 23
BBa_K3100009 Regulatory T7 Promoter T7-24 Zheng Yiyuan 23
BBa_K3100010 Regulatory T7 Promoter T7-38 Zheng Yiyuan 23
BBa_K3100011 Regulatory toehold switch A Zheng Yiyuan 90
BBa_K3100012 Regulatory toehold switch C Zheng Yiyuan 90
BBa_K3100013 Regulatory Trigger DNA A Zheng Yiyuan 129
BBa_K3100014 Regulatory Trigger DNA B Zheng Yiyuan 129
BBa_K3100015 Regulatory Trigger DNA C Zheng Yiyuan 65
BBa_K3100016 Regulatory Trigger DNA D Zheng Yiyuan 65
BBa_K3100017 Coding gadB (antiacid gene) Zheng Yiyuan 1401
BBa_K3100018 Coding gadC (antiacid gene) Zheng Yiyuan 1536
BBa_K3100019 Coding katA(antiacid gene) Zheng Yiyuan 48
BBa_K3100020 Coding ybaS(antiacid gene) Zheng Yiyuan 933
BBa_K3100021 Terminator rrnBT Zheng Yiyuan 247
BBa_K3100022 Regulatory T7 promoter variants family member Zheng Yiyuan 19
BBa_K3100023 Regulatory T7 promoter variants family member Zheng Yiyuan  
BBa_K3100024 Regulatory T7 promoter variants family member Zheng Yiyuan  
BBa_K3100025 Regulatory T7 promoter variants family member Zheng Yiyuan  
BBa_K3100026 Regulatory T7 promoter variants family member Zheng Yiyuan  
BBa_K3100027 Regulatory T7 promoter variants family member Zheng Yiyuan  
BBa_K3100028 Regulatory T7 promoter variants family member Zheng Yiyuan  
BBa_K3100029 Regulatory T7 promoter variants family member Zheng Yiyuan  
BBa_K3100030 Regulatory T7 promoter variants family member Zheng Yiyuan  
BBa_K3100031 Regulatory T7 promoter variants family member Zheng Yiyuan  
BBa_K3100100 Regulatory T7 Promoter T7-1_Trigger DNA A_T7 terminater Zheng Yiyuan 216
BBa_K3100101 Regulatory T7 Promoter T7-1_Trigger DNA A_T7 terminater Zheng Yiyuan 216
BBa_K3100102 Regulatory T7 Promoter T7-3_Trigger DNA A_T7 terminater Zheng Yiyuan 216
BBa_K3100103 Regulatory T7 Promoter T7-4_Trigger DNA A_T7 terminater Zheng Yiyuan 216
BBa_K3100104 Regulatory T7 Promoter T7-6_Trigger DNA A_T7 terminater Zheng Yiyuan 215
BBa_K3100105 Regulatory T7 Promoter T7-8_Trigger DNA A_T7 terminater Zheng Yiyuan 216
BBa_K3100106 Regulatory T7 Promoter T7-10_Trigger DNA A_T7 terminater Zheng Yiyuan 216
BBa_K3100107 Regulatory T7 Promoter T7-15_Trigger DNA A_T7 terminater Zheng Yiyuan 216
BBa_K3100108 Regulatory T7 Promoter T7-24_Trigger DNA A_T7 terminater Zheng Yiyuan 216
BBa_K3100109 Regulatory T7 Promoter T7-38_Trigger DNA A_T7 terminater Zheng Yiyuan 216
BBa_K3100110 Regulatory T7 Promoter T7-1_Trigger DNA B_T7 terminater Zheng Yiyuan 283
BBa_K3100111 Regulatory T7 Promoter T7-2_Trigger DNA B_T7 terminater Zheng Yiyuan 216
BBa_K3100112 Regulatory T7 Promoter T7-3_Trigger DNA B_T7 terminater Zheng Yiyuan 216
BBa_K3100113 Regulatory T7 Promoter T7-4_Trigger DNA B_T7 terminater Zheng Yiyuan 216
BBa_K3100114 Regulatory T7 Promoter T7-6_Trigger DNA B_T7 terminater Zheng Yiyuan 215
BBa_K3100115 Regulatory T7 Promoter T7-8_Trigger DNA B_T7 terminater Zheng Yiyuan 216
BBa_K3100116 Regulatory T7 Promoter T7-10_Trigger DNA B_T7 terminater Zheng Yiyuan 216
BBa_K3100117 Regulatory T7 Promoter T7-15_Trigger DNA B_T7 terminater Zheng Yiyuan 216
BBa_K3100118 Regulatory T7 Promoter T7-24_Trigger DNA B_T7 terminater Zheng Yiyuan 216
BBa_K3100119 Regulatory T7 Promoter T7-38_Trigger DNA B_T7 terminater Zheng Yiyuan 216
BBa_K3100120 Regulatory T7 Promoter T7-1_Trigger DNA C_T7 terminater Zheng Yiyuan 218
BBa_K3100121 Regulatory T7 Promoter T7-2_Trigger DNA C_T7 terminater Zheng Yiyuan 151
BBa_K3100122 Regulatory T7 Promoter T7-3_Trigger DNA C_T7 terminater Zheng Yiyuan 151
BBa_K3100123 Regulatory T7 Promoter T7-4_Trigger DNA C_T7 terminater Zheng Yiyuan 151
BBa_K3100124 Regulatory T7 Promoter T7-6_Trigger DNA C_T7 terminater Zheng Yiyuan 150
BBa_K3100125 Regulatory T7 Promoter T7-8_Trigger DNA C_T7 terminater Zheng Yiyuan 151
BBa_K3100126 Regulatory T7 Promoter T7-10_Trigger DNA C_T7 terminater Zheng Yiyuan 151
BBa_K3100127 Regulatory T7 Promoter T7-15_Trigger DNA C_T7 terminater Zheng Yiyuan 151
BBa_K3100128 Regulatory T7 Promoter T7-24_Trigger DNA C_T7 terminater Zheng Yiyuan 151
BBa_K3100129 Regulatory T7 Promoter T7-38_Trigger DNA C_T7 terminater Zheng Yiyuan 151
BBa_K3100130 Regulatory T7 Promoter T7-1_Trigger DNA D_T7 terminater Zheng Yiyuan 218
BBa_K3100131 Regulatory T7 Promoter T7-2_Trigger DNA D_T7 terminater Zheng Yiyuan 151
BBa_K3100132 Regulatory T7 Promoter T7-3_Trigger DNA D_T7 terminater Zheng Yiyuan 151
BBa_K3100133 Regulatory T7 Promoter T7-4_Trigger DNA D_T7 terminater Zheng Yiyuan 151
BBa_K3100134 Regulatory T7 Promoter T7-6_Trigger DNA D_T7 terminater Zheng Yiyuan 150
BBa_K3100135 Regulatory T7 Promoter T7-8_Trigger DNA D_T7 terminater Zheng Yiyuan 151
BBa_K3100136 Regulatory T7 Promoter T7-10_Trigger DNA D_T7 terminater Zheng Yiyuan 151
BBa_K3100137 Regulatory T7 Promoter T7-15_Trigger DNA D_T7 terminater Zheng Yiyuan 151
BBa_K3100138 Regulatory T7 Promoter T7-24_Trigger DNA D_T7 terminater Zheng Yiyuan 151
BBa_K3100139 Regulatory T7 Promoter T7-38_Trigger DNA D_T7 terminater Zheng Yiyuan 151
BBa_K3100140 Coding antiacid genes combination Zheng Yiyuan 4626

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