In this paper a method is developed to model the design process gene based on the extensible basic-element with the purpose of design process optimization and reuse. First, the principle of genetic engineering based d...In this paper a method is developed to model the design process gene based on the extensible basic-element with the purpose of design process optimization and reuse. First, the principle of genetic engineering based design process optimization and reuse is put forward and analyzed. Second, the extensible basic-element model of the design process gene is established based on the models of the design process base and the base pair through analyzing the concept and structure of the design process gene and the extensible basic-element as well as its extensibility. Third, the features of divergence and scalability of the extensible basic-element model of the design process gene are discussed for carrying out the extension translation to the design process gene by way of inserting, deleting and updating design process bases. Finally, an example of building extensible basic-element models for the design process base, base pair and design process gene in mechanical product design and the mutation process of the design process gene in airplane design is presented which demonstrates the application of the method proposed in this paper.展开更多
The idea of genetic engineering is introduced into the area of product design to improve the design efficiency. A method towards design process optimization based on the design process gene is proposed through analyzi...The idea of genetic engineering is introduced into the area of product design to improve the design efficiency. A method towards design process optimization based on the design process gene is proposed through analyzing the correlation between the design process gene and characteristics of the design process. The concept of the design process gene is analyzed and categorized into five categories that are the task specification gene, the concept design gene, the overall design gene, the detailed design gene and the processing design gene in the light of five design phases. The elements and their interactions involved in each kind of design process gene signprocess gene mapping is drawn with its structure disclosed based on its function that process gene.展开更多
A central goal of synthetic biology is to apply successful principles that have been developed in electronic and chemical engineering to construct basic biological functional modules, and through rational design, to b...A central goal of synthetic biology is to apply successful principles that have been developed in electronic and chemical engineering to construct basic biological functional modules, and through rational design, to build synthetic biological systems with predetermined functions. Here, we apply the reverse engineering design principle of biological networks to synthesize a gene circuit that executes semi-log dose-response, a logarithmically linear sensing function, in Escherichia coil cells. We first mathematically define the object function semi-log dose-response, and then search for tri-node network topologies that can most robustly execute the object function. The simplest topology, transcriptional coherent feed-forward loop （TCFL）, among the searching results is mathematically analyzed; we find that, in TCFL topology, the semi-log dose-response function arises from the additive effect of logarithmical linearity intervals of Hill functions. TCFL is then genetically implemented in E. coil as a logarithmically linear sensing biosensor for heavy metal ions [mercury （II）]. Functional characterization shows that this rationally designed biosensor circuit works as expected. Through this study we demonstrated the potential application of biological network reverse engineering to broaden the computational power of synthetic biology.展开更多
A structural gene (750 bp), which codes for a type I ribosome inactivating protein, trichosanthin, has been designed according to the codon usage of highly expressed gene in E. coli and chemically synthesized. In the ...A structural gene (750 bp), which codes for a type I ribosome inactivating protein, trichosanthin, has been designed according to the codon usage of highly expressed gene in E. coli and chemically synthesized. In the synthesized gene, twenty-seven unique restriction sites were evenly dispersed with an average distance between two adjacent sites less than 50 bp to facilitate a systematic investigation on structure-functional relationship of this protein by site-directed mutagenesis. To synthesize it, the whole gene was divided into three large fragments (EP, PN and NH) which were assembled from several chemical synthetic oligonucleotides by enzymatic method. The assembly of both the fragment EP from six oligonucleotides (A-F) and the fragment PN from four oligomers (G-J) was catalyzed by T-4 DNA ligase in using the single stranded DNA method [Chen, H.-B. et al., Nucl. Acids Res., 18, 871(1990)]. And fragment NH was formed from three duplexes K, L and M by the classical double stranded DNA method. Finally, each fragment was cloned into vector pUC18 in succession to form the plasmid, pC0TCS, to complete the whole gene synthesis, The sequencing data for the synthetic gene coincides with the designed one.展开更多
文摘In this paper a method is developed to model the design process gene based on the extensible basic-element with the purpose of design process optimization and reuse. First, the principle of genetic engineering based design process optimization and reuse is put forward and analyzed. Second, the extensible basic-element model of the design process gene is established based on the models of the design process base and the base pair through analyzing the concept and structure of the design process gene and the extensible basic-element as well as its extensibility. Third, the features of divergence and scalability of the extensible basic-element model of the design process gene are discussed for carrying out the extension translation to the design process gene by way of inserting, deleting and updating design process bases. Finally, an example of building extensible basic-element models for the design process base, base pair and design process gene in mechanical product design and the mutation process of the design process gene in airplane design is presented which demonstrates the application of the method proposed in this paper.
文摘The idea of genetic engineering is introduced into the area of product design to improve the design efficiency. A method towards design process optimization based on the design process gene is proposed through analyzing the correlation between the design process gene and characteristics of the design process. The concept of the design process gene is analyzed and categorized into five categories that are the task specification gene, the concept design gene, the overall design gene, the detailed design gene and the processing design gene in the light of five design phases. The elements and their interactions involved in each kind of design process gene signprocess gene mapping is drawn with its structure disclosed based on its function that process gene.
基金This work is part of the project for the 2010 team of Peking University in the international genetically engineered machine （iGEM） competition. H. Zhang. designed the project, performed the experiments and modeling simulation, and wrote the manuscript. Y. Sheng., A. Liu, and Q. Wu performed the experiments. Y. Lu and Z. Yin performed the modeling simulation. Y. Cao and W. Zeng performed the modeling simulation and wrote the manu- script. Q. Ouyang designed the project and wrote the manuscript. We would like to thank F. Hao, X. He, W. Wei, C. Xu, and L. Ji for their technical assistance the BioBrick Foundation for providing DNA materials and Anne O. Summers for supplying the plasmid carrying MerR gene. We thank Peking University for its financial support. This work is also partially supported by the National Nature Science Foundation of China （Nos. 10721463, 110740 09）, the National Basic Research Program of China （Nos. 2009CB918500, 2012AA02A702）, and the National Science Fund for Talent Training in Basic Science of China （Nos. J1030310, J1103205）.
文摘A central goal of synthetic biology is to apply successful principles that have been developed in electronic and chemical engineering to construct basic biological functional modules, and through rational design, to build synthetic biological systems with predetermined functions. Here, we apply the reverse engineering design principle of biological networks to synthesize a gene circuit that executes semi-log dose-response, a logarithmically linear sensing function, in Escherichia coil cells. We first mathematically define the object function semi-log dose-response, and then search for tri-node network topologies that can most robustly execute the object function. The simplest topology, transcriptional coherent feed-forward loop （TCFL）, among the searching results is mathematically analyzed; we find that, in TCFL topology, the semi-log dose-response function arises from the additive effect of logarithmical linearity intervals of Hill functions. TCFL is then genetically implemented in E. coil as a logarithmically linear sensing biosensor for heavy metal ions [mercury （II）]. Functional characterization shows that this rationally designed biosensor circuit works as expected. Through this study we demonstrated the potential application of biological network reverse engineering to broaden the computational power of synthetic biology.
基金Project supported by grants from the High Technology Development Program of China.
文摘A structural gene (750 bp), which codes for a type I ribosome inactivating protein, trichosanthin, has been designed according to the codon usage of highly expressed gene in E. coli and chemically synthesized. In the synthesized gene, twenty-seven unique restriction sites were evenly dispersed with an average distance between two adjacent sites less than 50 bp to facilitate a systematic investigation on structure-functional relationship of this protein by site-directed mutagenesis. To synthesize it, the whole gene was divided into three large fragments (EP, PN and NH) which were assembled from several chemical synthetic oligonucleotides by enzymatic method. The assembly of both the fragment EP from six oligonucleotides (A-F) and the fragment PN from four oligomers (G-J) was catalyzed by T-4 DNA ligase in using the single stranded DNA method [Chen, H.-B. et al., Nucl. Acids Res., 18, 871(1990)]. And fragment NH was formed from three duplexes K, L and M by the classical double stranded DNA method. Finally, each fragment was cloned into vector pUC18 in succession to form the plasmid, pC0TCS, to complete the whole gene synthesis, The sequencing data for the synthetic gene coincides with the designed one.
