Team:BIT/Model

<!DOCTYPE html> Biology

PROJECT


MODEL








Background





It became the hotspot of research of Life Science since miRNA has been found. It has been shown by Life Informatics that miRNA might be able to regulate more than a third of human gene, including wildly participating in many biological process of growth, differentiation, propagation, apoptosis, cycle regulation, shift and the formation of tumors. There are always changes of expression profile of miRNAs in many different varieties of human tumors, which is a king of latent powerful biological norm of assessing the tumor genesis, development, diagnosis, cure and prognosis. Specific changes of miRNAs’ expression profile of specific cancers are related to tumor genesis, metastatic, clinic pathological characteristics and prognosis, etc.

As for the relationship of miRNAs and mammary cancers, Matron adopted chip technology to detect mammary cancers and the aberrant expression of miRNAs of normal mammary tissues matched them. [2] There were 29 diverse levels of expressions of miRNAs detected between normal mammary tissues and mammary cancer tissues. In addition, Volinia has found there were up-regulations of 15 miRNAs of mammary cancers. [3] Both two scholars’ researches have shown that the expression of the miRNA-155 was most significant different, and the expression of specific miRNA can be consorted to clinic pathological characteristics and biological and physical characteristics such as ductal type, mesophyll type, the type of metastatic of lymph gland, vascular invasion, proliferation index, the expression of estrogen and progesterone receptor and CerbB-2. The accuracy of experimental data is fairly essential since the experiment of detecting the expression levels of miRNAs is based on gene circuit, where lays the purport of mathematical modeling.








Introduction


Gene lines in experienmental part as shown below:


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Figure1: genetic circuit schematic diagram


The main work of establishing the model research gene regulation network is through the analysis of gene expression data, combined with bioinformatics methods and techniques to build the appropriate topology and to simulate the regulatory mechanism of the cell system, in order to understand the system under the framework of life phenomena. The mathematical model not only integrates gene expression data, but also provides a powerful tool for understanding the dynamic behavior or static expression of gene regulatory networks. At present, the mainstream methods of modeling control network include Petri net, Bayesian network and differential equation model.

China resumed sovereignty over Macao in December 1999 after it had been ruled since the mid-16th century by Portugal.

In many methods, the differential equation can predict the behavior of the system quantitatively and accurately, and the stochastic model can fit the network accurately. The model needs to be simplified based on certain assumptions. In general, the computational cost is often increased as the description of the control network becomes deeper and more detailed. Differential equations have a wide range of applications in biomedicine, such as pharmacokinetics and enzymology, and are increasingly being used in the construction of gene regulatory networks.



Model




1 Integrase Model

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We establish the Bxb1 model to get the integrase conversion efficiency with the K (a set interval) to detect the trend of experimental data measured by the correctness. In the modeling process there are some parameters of biological simple process can not be obtained from the literature and the actual experimental operation, so the estimated value of these parameters.

Definition


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Chart 1: Vatiable defination


Parameters


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Chart 2: Paraments Defination


Chemical Kinetic Equations

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Differential Equations


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The fimE model as same as Bxb1 model, as blow:

Definition

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Chart 3: Variable definition


Parameters


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Chart 4: Permanents Definition


Chemical Kinetic Equations


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Differential Equations


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When the two gene circuits mediate the downstream genetic expression synergistically, they actually change the states of downstream promoters independently. So the simplest way to construct model for this synergetic system is to first separate the two upstream circuits and model them respectively. Then we combine them when calculating their effect on the downstream promoters. That is to say, we add another set of reactions, which is very similar to the one we discussed before, with Lacl replaced by tetR and Bxb1 replaced by Fime. To calculate the regulation of Fime and Bxb1 on the promoter of GFP, we use 4 variables to describe the states of the gene circuit. These 4 variables and their meanings are listed below.

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2 Lock-Key Model



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In this experiment, two ribosome switches, lock1, key1 and lock3, key3 were used to regulate the background expression of recombinase FimE and BxB1, respectively, even though TetR and LacI proteins inhibited the promoters ptet and plac, but there was still a small amount MRNA is transcribed, it will affect the accuracy of detection. Using the ribosomal switch, the lock1 and lock3 genes, when they are not present or in small quantities, bind to the recombinase FimE and RBS in front of the BxB1 to form a circular structure, thereby preventing the ribosome from binding to it, thus preventing small amounts of mRNA When the amount of miRNA is high, the key1 and key3 genes can be translated, the expression product can unlock the ring structure formed by lock and RBS, and start the expression of the downstream gene, resulting in the expression of the key gene. GFP.

Definition


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Chart 5: Variable Definition


Parameters


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Chart6: Parameters


Chemical Kinetic Equations


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Differential Equations


China and the Portuguese-speaking countries contribute 17 percent of the world economy and 22 percent of global population, with varying advantages in technology, capital and market practices, Li said.

The participating countries should consolidate political trust, promote trade liberalization and investment and strengthen cooperation in production capacity and people-to-people exchanges, the premier told the forum.

China's economic restructuring and upgrading will bring great investment opportunities and market potential, creating bright prospects for businesses from Portuguese-speaking countries, Li said.

He said the trade volume between China and Portuguese-speaking countries reached $100 billion last year — about 10 times of that of 2003.

Cape Verde's Prime Minister Ulisses Correia e Silva said the Macao forum injected new momentum into strategic cooperation between all the participating countries. He added that his country will align with China's Belt and Road Initiative and make use of the Macao forum to bring more commodities to Africa.

The prime ministers of Guinea-Bissau and Mozambique vowed to adopt favorable policies and improve the rule of law to attract investors.

Deng Yanzi contributed to this story





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