Although the principles of synthetic biology were initially established in model bacteria,microbial producers,extremophiles and gut microbes have now emerged as valuable prokaryotic chassis for biological engineering....Although the principles of synthetic biology were initially established in model bacteria,microbial producers,extremophiles and gut microbes have now emerged as valuable prokaryotic chassis for biological engineering.Extending the host range in which designed circuits can function reliably and predictably presents a major challenge for the concept of synthetic biology to materialize.In this work,we systematically characterized the cross-species universality of two transcriptional regulatory modules—the T7 RNA polymerase activator module and the repressors module—in three non-model microbes.We found striking linear relationships in circuit activities among different organisms for both modules.Parametrized model fitting revealed host non-specific parameters defining the universality of both modules.Lastly,a genetic NOT gate and a band-pass filter circuit were constructed from these modules and tested in non-model organisms.Combined models employing host non-specific parameters were successful in quantitatively predicting circuit behaviors,underscoring the potential of universal biological parts and predictive modeling in synthetic bioengineering.展开更多
The existing research of sequential zoning system and simultaneous zoning system mainly focuses on some optimization problems such as workload balance,product assignment and simulation for each system separately.But t...The existing research of sequential zoning system and simultaneous zoning system mainly focuses on some optimization problems such as workload balance,product assignment and simulation for each system separately.But there is little research on comparative study between sequential zoning and simultaneous zoning.In order to help the designers to choose the suitable zoning policy for picker-to-parts system reasonably and quickly,a systemic selection method is presented.Essentially,both zoning and batching are order clustering,so the customer order sheet can be divided into many unit grids.After the time formulation in one-dimensional unit was defined,the time models for each zoning policy in two-dimensional space were established using filling curves and sequence models to link the one-dimensional unit grids.In consideration of ＂U＂ shaped dual tour into consideration,the subtraction value of order picking time between sequential zoning and simultaneous zoning was defined as the objective function to select the suitable zoning policy based on time models.As it is convergent enough,genetic algorithm is adopted to find the optimal value of order picking time.In the experimental study,5 different kinds of order/stock keeping unit（SKU） matrices with different densities d and quantities q following uniform distribution were created in order to test the suitability of sequential zoning and simultaneous zoning to different kinds of orders.After parameters setting,experimental orders inputting and iterative computations,the optimal order picking time for each zoning policy was gotten.By observing whether the delta time between them is greater than 0 or not,the suitability of zoning policies for picker-to-parts system were obtained.The significant effect of batch size b,zone number z and density d on suitability was also found by experimental study.The proposed research provides a new method for selection between sequential zoning and simultaneous zoning for picker-to-parts system,and improves the rationality and effi展开更多
Backgrounds:As an increasing number of synthetic switches and circuits have been created for plant systems and of synthetic products produced in plant chassis,plant synthetic biology is taking a strong foothold in agr...Backgrounds:As an increasing number of synthetic switches and circuits have been created for plant systems and of synthetic products produced in plant chassis,plant synthetic biology is taking a strong foothold in agriculture and medicine.The ever-exploding data has also promoted the expansion of toolkits in this field.Genetic parts libraries and quantitative characterization approaches have been developed.However,plant synthetic biology is still in its infancy.The considerations for selecting biological parts to design and construct genetic circuits with predictable functions remain desired.Results:In this article,we review the current biotechnological progresses in field of plant synthetic biology.Assembly standardization and quantitative approaches of genetic parts and genetic circuits are discussed.We also highlight the main challenges in the iterative cycles of design-build-test-learn for introducing novel traits into plants.Conclusion:Plant synthetic biology promises to provide important solutions to many issues in agricultural production,human health care,and environmental sustainability.However,tremendous challenges exist in this field.For example,the quantitative characterization of genetic parts is limited;the orthogonality and the transfer functions of circuits are unpredictable;and also,the mathematical modeling-assisted circuits design still needs to improve predictability and reliability.These challenges are expected to be resolved in the near future as interests in this field are intensifying.展开更多
基金National Natural Science Foundation of China,Grant/Award Number:12090054National Key Research and Development Programof China,Grant/Award Numbers:2020YFA0906900,2021YFF1200500。
文摘Although the principles of synthetic biology were initially established in model bacteria,microbial producers,extremophiles and gut microbes have now emerged as valuable prokaryotic chassis for biological engineering.Extending the host range in which designed circuits can function reliably and predictably presents a major challenge for the concept of synthetic biology to materialize.In this work,we systematically characterized the cross-species universality of two transcriptional regulatory modules—the T7 RNA polymerase activator module and the repressors module—in three non-model microbes.We found striking linear relationships in circuit activities among different organisms for both modules.Parametrized model fitting revealed host non-specific parameters defining the universality of both modules.Lastly,a genetic NOT gate and a band-pass filter circuit were constructed from these modules and tested in non-model organisms.Combined models employing host non-specific parameters were successful in quantitatively predicting circuit behaviors,underscoring the potential of universal biological parts and predictive modeling in synthetic bioengineering.
基金supported by National Natural Science Foundation of China (Grant No. 50175064)China Scholarship Council (Grant No. 2008622078)Material Handling Industry of America (Grant No. 12251)
文摘The existing research of sequential zoning system and simultaneous zoning system mainly focuses on some optimization problems such as workload balance,product assignment and simulation for each system separately.But there is little research on comparative study between sequential zoning and simultaneous zoning.In order to help the designers to choose the suitable zoning policy for picker-to-parts system reasonably and quickly,a systemic selection method is presented.Essentially,both zoning and batching are order clustering,so the customer order sheet can be divided into many unit grids.After the time formulation in one-dimensional unit was defined,the time models for each zoning policy in two-dimensional space were established using filling curves and sequence models to link the one-dimensional unit grids.In consideration of ＂U＂ shaped dual tour into consideration,the subtraction value of order picking time between sequential zoning and simultaneous zoning was defined as the objective function to select the suitable zoning policy based on time models.As it is convergent enough,genetic algorithm is adopted to find the optimal value of order picking time.In the experimental study,5 different kinds of order/stock keeping unit（SKU） matrices with different densities d and quantities q following uniform distribution were created in order to test the suitability of sequential zoning and simultaneous zoning to different kinds of orders.After parameters setting,experimental orders inputting and iterative computations,the optimal order picking time for each zoning policy was gotten.By observing whether the delta time between them is greater than 0 or not,the suitability of zoning policies for picker-to-parts system were obtained.The significant effect of batch size b,zone number z and density d on suitability was also found by experimental study.The proposed research provides a new method for selection between sequential zoning and simultaneous zoning for picker-to-parts system,and improves the rationality and effi
基金supported by the National Key Research and Development Program of China(No.2018YFA0900600)the Strategic Priority Research Program“Molecular mechanism of Plant Growth and Development”of Chinese Academy of Science(No.XDB27020202)+6 种基金the National Natural Science Foundation of China(Nos.22077129,32070328 and 41876084)the Natural Science Foundation of Shanghai Municipal Science and Technology Committee(No.21ZR1470900)the Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project(No.TSBICIP-KJGG-002-15)the Program of Shanghai Academic Research Leader(No.20XD1404400)financially supported by the Construction of the Registry and Database of Bioparts for Synthetic Biology of the Chinese Academy of Science(No.ZSYS-016)the International Partnership Program of Chinese Academy of Science(No.153D31KYSB20170121)the National Key Laboratory of Plant Molecular Genetics,SIPPE,Chinese Academy of Science.
文摘Backgrounds:As an increasing number of synthetic switches and circuits have been created for plant systems and of synthetic products produced in plant chassis,plant synthetic biology is taking a strong foothold in agriculture and medicine.The ever-exploding data has also promoted the expansion of toolkits in this field.Genetic parts libraries and quantitative characterization approaches have been developed.However,plant synthetic biology is still in its infancy.The considerations for selecting biological parts to design and construct genetic circuits with predictable functions remain desired.Results:In this article,we review the current biotechnological progresses in field of plant synthetic biology.Assembly standardization and quantitative approaches of genetic parts and genetic circuits are discussed.We also highlight the main challenges in the iterative cycles of design-build-test-learn for introducing novel traits into plants.Conclusion:Plant synthetic biology promises to provide important solutions to many issues in agricultural production,human health care,and environmental sustainability.However,tremendous challenges exist in this field.For example,the quantitative characterization of genetic parts is limited;the orthogonality and the transfer functions of circuits are unpredictable;and also,the mathematical modeling-assisted circuits design still needs to improve predictability and reliability.These challenges are expected to be resolved in the near future as interests in this field are intensifying.
