Attributions
Human practice: Liu Kaiwen planned a survey of human practice in Xuwen County. Li Yanjun, Qiao Hao, Yin Ziqi and other students participated in this practical activity. Qiu Hao was in charge of contacting the academicians，Robert Landick and he put forward a lot of useful suggestions for the experiment. Under the leadership of Mr. Fu Chunhua, Li Beibei went to the degumming factory for a visit and investigation.
Support for Human practice: thanks to Su Shiming, head of the Xuwen County Party Committee Secretariat, He qiang，researcher of the Xu Wen Academy of Sciences, and Director Yu Min for their support to human practice in Xu wen county,。The Robert Landick, an Academician, give us numbers of fantastic idea.
Experiment: In Yan Yunjun's laboratory, Li Beibei, Yang Hongboyu, Wen Jingkai, Liu Bingbing, Shi Jiacheng and other students led by Yin Ziqi, Liu Kaiwen and Zeng Yizhe have made a lot of contributions to the electric transfer of yeast.Also, Wang Bohan, Liang Yuanhao and Pan Chunxiu, led by Rao Xinran and Qiao Hao, express the pelA, SLAC and VP in Pichia pastoris. Other students also participated in the expression of Pichia pastoris later, and Yang Yingying's group was responsible for the expression of VP. The Wang Bohan’s group is responsible for the expression of SLAC, and the Zeng Yizhe’s group is responsible for the expression of pelA.
Support: Professor Yan Yunjun provide us adequate financial support, as well as the laboratory support, Pro. Ningkang and Pro. XieShangxian also support us with their lab. There is also support from the School of Life Sciences and Technology represented by Mrs. Kong Shu.
Advisor: Pro. Yan Yunjun, Pro. Ning Kang and Pro. Robert Landick, Mr. Zhanyi, Pro. Xie Shangxian have provided theoretical and experimental skills for our experiments.
Model: Zhang Xianglei led Zhang Dongfang, Ye Yaoxiong and others to simulate the experimental data, their model construction provides a strong guidance for the experiment.
Art design: Zhan Yi teacher and Li Yanjun are responsible for our poster design, team uniform design and wiki interface planning.
Paper: Qiu Hao, Yin Ziqi, Shi Jiacheng, Liu Bingbing, Fan Changxin and other experimental group students, they looked up a lot of literature, so that every step of our experiment has source to follow.
Support for Human practice: thanks to Su Shiming, head of the Xuwen County Party Committee Secretariat, He qiang，researcher of the Xu Wen Academy of Sciences, and Director Yu Min for their support to human practice in Xu wen county,。The Robert Landick, an Academician, give us numbers of fantastic idea.
Experiment: In Yan Yunjun's laboratory, Li Beibei, Yang Hongboyu, Wen Jingkai, Liu Bingbing, Shi Jiacheng and other students led by Yin Ziqi, Liu Kaiwen and Zeng Yizhe have made a lot of contributions to the electric transfer of yeast.Also, Wang Bohan, Liang Yuanhao and Pan Chunxiu, led by Rao Xinran and Qiao Hao, express the pelA, SLAC and VP in Pichia pastoris. Other students also participated in the expression of Pichia pastoris later, and Yang Yingying's group was responsible for the expression of VP. The Wang Bohan’s group is responsible for the expression of SLAC, and the Zeng Yizhe’s group is responsible for the expression of pelA.
Support: Professor Yan Yunjun provide us adequate financial support, as well as the laboratory support, Pro. Ningkang and Pro. XieShangxian also support us with their lab. There is also support from the School of Life Sciences and Technology represented by Mrs. Kong Shu.
Advisor: Pro. Yan Yunjun, Pro. Ning Kang and Pro. Robert Landick, Mr. Zhanyi, Pro. Xie Shangxian have provided theoretical and experimental skills for our experiments.
Model: Zhang Xianglei led Zhang Dongfang, Ye Yaoxiong and others to simulate the experimental data, their model construction provides a strong guidance for the experiment.
Art design: Zhan Yi teacher and Li Yanjun are responsible for our poster design, team uniform design and wiki interface planning.
Paper: Qiu Hao, Yin Ziqi, Shi Jiacheng, Liu Bingbing, Fan Changxin and other experimental group students, they looked up a lot of literature, so that every step of our experiment has source to follow.
Collaborations
1.Hosting the Central China Regional Exchange Conference
This year, many teams in central China are still working hard to prepare for the iGEM competition. Every team has made some progress and some doubts. We all need an all-round and large-scale exchange to adjust our thinking and learn from each other. In order to make the teams understand each other's projects and progress, put forward their opinions and questions, and prepare for the final exhibition more fully, we invited several teams in Central China to hold an "iGEM Exchange in Central China in 2019" on August 30. And it will serve as a channel to promote iGEM teams cooperation in central China.
Following is a brief introduction of the other teams and their projects participating in the conference：
HZAU-China 2019：In order to memory odor. E. coli can convert different attractive odors into other metabolites that can be stored in its body. Wondering the bacteria has just smelled, please add an inducer and E. coli will release the odor it has remembered.
WHU-iGEM：In order to help silk restoration. putting silk in machine and adding engineering bacteria. And Scanning product red light to Reinforce. Then washing, drying, and sterilizing.
HBUT-China: In order to Absorb Ni2+ from wastewater, treating it to make use in factory application.
HUBU-WUHAN：In order to make use of Waste cartons. We Improve isobutanol production module. Adding engineering bacteria culture into Waste cartons cut up. And then we can use it in PHB and Biofuels.
In this exchange, each team made a detailed introduction of their own projects, simulated the exhibition of the match day. After listening carefully to the introduction, the other team members raised their own questions about project and put forward different opinions and suggestions. The project of Huazhong University of Science and Technology and Huazhong Agricultural University has been discussed for a long time, and many valuable suggestions have been put forward. After we introduced the problems encountered in the project, the students from other teams provided us with their solutions, many of which gave us inspiration and helped us complete the following experiments.
Finally, the teams discussed the relevant rules of this year's competition and solved the problem of understanding the rules.
It is worth mentioning that we have also reached a deeper cooperation with Hubei University of Technology.
Following is a brief introduction of the other teams and their projects participating in the conference：
HZAU-China 2019：In order to memory odor. E. coli can convert different attractive odors into other metabolites that can be stored in its body. Wondering the bacteria has just smelled, please add an inducer and E. coli will release the odor it has remembered.
WHU-iGEM：In order to help silk restoration. putting silk in machine and adding engineering bacteria. And Scanning product red light to Reinforce. Then washing, drying, and sterilizing.
HBUT-China: In order to Absorb Ni2+ from wastewater, treating it to make use in factory application.
HUBU-WUHAN：In order to make use of Waste cartons. We Improve isobutanol production module. Adding engineering bacteria culture into Waste cartons cut up. And then we can use it in PHB and Biofuels.
In this exchange, each team made a detailed introduction of their own projects, simulated the exhibition of the match day. After listening carefully to the introduction, the other team members raised their own questions about project and put forward different opinions and suggestions. The project of Huazhong University of Science and Technology and Huazhong Agricultural University has been discussed for a long time, and many valuable suggestions have been put forward. After we introduced the problems encountered in the project, the students from other teams provided us with their solutions, many of which gave us inspiration and helped us complete the following experiments.
Finally, the teams discussed the relevant rules of this year's competition and solved the problem of understanding the rules.
It is worth mentioning that we have also reached a deeper cooperation with Hubei University of Technology.
2.Helping Team HBUT-China with modelling
We helped HBUT to model their gene pathway’s expression and by the convection dispersion model we thoroughly predicted the absorption of in a three-dimensional homogenous space occupied by Ni
PART I: gene expression model
they designed 4 gene pathways as below
for the process of DNA to Protein, we use mass-action model to describe. Firstly, it’s there are many copies of DNA in the cell the number of copies is n, we assume that some gene are repressed others are activated, then the activated DNA can be transcript to mRNA with a coefficient, then to be translated to Protein with another coefficient. For mRNA and Protein, they can both degrade with different coefficient. By the law of mass action, we can obtain a basic model of the gene expression.
PART I: gene expression model
they designed 4 gene pathways as below
for the process of DNA to Protein, we use mass-action model to describe. Firstly, it’s there are many copies of DNA in the cell the number of copies is n, we assume that some gene are repressed others are activated, then the activated DNA can be transcript to mRNA with a coefficient, then to be translated to Protein with another coefficient. For mRNA and Protein, they can both degrade with different coefficient. By the law of mass action, we can obtain a basic model of the gene expression.
We can use ordinary differential equation the describe this.
Since the copy of gene and the activation and repression of gene is constant compared to the transcription process, we can assume that λ[ X_1]= C_r,which is the constitutive transcription rate.
The results is as below. At last it will reach a homeostasis which reaches to 55804.
PART II :
The absorption of Ni2+
To simplify the model of the real world, we can take only one well-grown cell into our consideration. At first the space was full of Ni2+,but in the cell, there is none, with channel protein and Hex-His on the plasmid, Ni2+ diffuse into the cell and are adsorbed by the Hex-His group. Then the Ni2+ concentration in the environment decrease gradually.
Using the results of PART I, we regard that there are 55804 active molecules on the plasmid.
For Hex-His Group, we can ignore the time for chelate reaction, and only consider the adsorption, for the ion channel, we can ignore how Ni2+ be absorbed.
Then, according to Stokes-Einstein equation
The absorption of Ni2+
To simplify the model of the real world, we can take only one well-grown cell into our consideration. At first the space was full of Ni2+,but in the cell, there is none, with channel protein and Hex-His on the plasmid, Ni2+ diffuse into the cell and are adsorbed by the Hex-His group. Then the Ni2+ concentration in the environment decrease gradually.
Using the results of PART I, we regard that there are 55804 active molecules on the plasmid.
For Hex-His Group, we can ignore the time for chelate reaction, and only consider the adsorption, for the ion channel, we can ignore how Ni2+ be absorbed.
Then, according to Stokes-Einstein equation
By convection diffusion equation
Laplace operator, N is a function of x,y,z,t, which we defined to be the number density of Ni2+.
We define a cell occupied a globular space V, so the initial state of the system must be
We define a cell occupied a globular space V, so the initial state of the system must be
For the absorption and adsorption, it depends on the diffusion and we can consider the Ni2+ number density in plasmid is always 0 to simplify the model.
1. U. Alon. An Introduction to Systems Biology. Desing Principles of Biological Circuits. Champan and Hall/CRC, Edition, 2007.
2. Jinzhi Lei. Systems Biology Modeling Analysis Simulation. Shanghai Science and Technology Press, 2011.
3.Golding I, Paulsson J, Zawilski S M, el al. Real-Time Kinetics of Gene Activity in Individual Bacteria.
Cell, 2005, 123:1025-1036.
4. Shahrezeai V, Ollivier J, Swain P. Colored extrinsic fluctuations and stochastic gene expression. Molecular Systems Biology, 2008, 4:1-9
2. Jinzhi Lei. Systems Biology Modeling Analysis Simulation. Shanghai Science and Technology Press, 2011.
3.Golding I, Paulsson J, Zawilski S M, el al. Real-Time Kinetics of Gene Activity in Individual Bacteria.
Cell, 2005, 123:1025-1036.
4. Shahrezeai V, Ollivier J, Swain P. Colored extrinsic fluctuations and stochastic gene expression. Molecular Systems Biology, 2008, 4:1-9