Team:TPHS San Diego/Model
Key Terms
RNA/protein Ratio: This specific ratio is seen in many graphs specifically the Y-Axis. In E. Coli most of the RNA is folded in ribosomes, so the ribosomes are one very important part in the project. The papers talk a lot of ribosome synthesis.
Nutrients: The nutrient quality is also very important. There are lots of equations regarding the nutrient used, and depending on the quality of nutrients over the time, the graph becomes linearly or exponentially different.
Main Bacteria used: E Coli.
Abstract
The goal of this paper is to understand the physiological functions of endogenous genetic circuits. However, in order to do this, we have to study the rate of cell proliferation and the level of gene expression. Their main bacteria that we used E Coli. The nutrient influx and translation-inhibiting antibiotics seem to play a huge role in this study. Then, we use equations and graphs to model the direction in which mutation will go in.
Background
Introduction: Engineering of genetic circuits is extremely important. Recent studies show how protein expression and much more can affect the cell’s physiological state. We have to respect growth laws, which provide a framework for the design of robust synthetic systems.
Empirical growth rate dependence: Monod had a discovery between the growth rate of a culture and the concentration of nutrient in the growth medium. In balanced exponential growth, every constituent in the cell is going to double at the same pace. They found this exact same discovery in the work of Salmonella, which is a bacteria in the human body. After his work, Helmstetter and Cooper studies E Coli and found that the cell mass has a direct effect on the growth rate. Monod also had very important equations for his growth relation theory. He theorizes that the nutritional capacity and the translational capacity can be estimated from the composition of exponentially growing bacteria under the conditions of translation and nutrient limitation.
Quantitative models of bacterial physiology: This part emphasizes growth rate maximization. Growth rate is strongly dependent on many independent factors and many experiments seem to have limitations to them. The growth rate can be altered many ways as these experiments have shown. For example, there is ribosome limiting factors, temperature, and a lot more.
Bacterial growth laws: This is where the RNA/Protein ratio take a big part within the experiment. In E Coli a lot of the make up is RNA(85%). Therefore, the RNA/Protein ratio is directly proportional to the mass fraction of ribosomes in the cell. There is also a linear relationship in these models. In terms of nutrient quality, there is a linear relationship between the ribosome content and the growth rate.
| Name | Equation | Extra equations within original equation | Variable Equations |
| Monod’s growth equation | λ = λm*[S’/([S]+Km) | Λ=λm*(Kn/(Kn+Kt)) | λ is the specific growth rate of the microorganisms λm is the maximum specific growth rate of the microorganisms S is the concentration of the limiting substrate for growth Ks is the "half-velocity constant"—the value of S when μ/μmax = 0.5 |
We use this equation to determine the growth rate of a Ecoli. This suggests that factors such as the RNA in E.coli matters in cell density.
Caption: this is a banana!
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