Difference between revisions of "Team:Austin UTexas/Model"

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<h2 style="font-family: verdana; font-size: 35px">Why Model?</h2>
  
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<p style="font-family: verdana">Scientific models are mathematical renditions of real-world systems. In synthetic biology, models are often used to define the kinetics of biochemical systems to aid in the visualization of information, and can be used to predict the behavior or outcome of biological systems.
  
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The goal of our model is to simulate the expected behavior of our transformed <i>Lactobacillus plantarum</i> after consumption.
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We focused on modeling the binding reaction of glutamate decarboxylate and L-glutamate, dependent on the cofactor pyridoxal- 5"phosphate (PLP). We looked specifically at how our <i>Lactobacillus plantarum</i> would encode the <i>gadB</i> gene to produce higher levels of glutamate decarboxylate and increase the uptake of GABA by the ENS.
  
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<h2 style="font-family:verdana; font-size: 25px"> Why Model? </h2>
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Scientific models are mathematical renditions of real-world systems. In synthetic biology, models are often used to define the kinetics of biochemical systems to aid in the visualization of information, and can be used to predict the behavior or outcome of biological systems. </p>
 
  
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<h2 style="font-family:verdana; font-size: 25px">Our Model</h2>
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<h2 style="font-family: verdana; font-size: 35px">Our Model</h2>
  
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<p style="font-family:verdana">The goal of our model is to simulate the expected behavior of our transformed <i>Lactobacillus plantarum</i> after consumption.
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We focused on modeling the binding reaction of glutamate decarboxylate and L-glutamate, dependent on the cofactor pyridoxal- 5"phosphate (PLP). Plp binds to the C-terminal domain of the <i>gadB</i>. We looked specifically at how our <i>Lactobacillus plantarum</i> would encode the <i>gadB</i> gene and encode glutamate decarboxylate. </p>
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<p style="font-family: verdana"> In our model, we aimed to compare the rates of GABA uptake by the ENS at differing concentrations dependent on an increased production of glutamate decarboxylate from over expression of the GadB gene. Our model assumes a first-order dosing type and an enzymatic elimination type.
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[[File:T--Austin UTexas--Gmodel2017.png|thumb|center|800px|Figure 1. Diagram of our model including species (blue), reactions (yellow), and parameters (green).]]
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<p style="font-family: verdana">We turned to literature to acquire a better understanding of GABA uptake in the gut and to find parameters for the uptake reaction in our model. GABA produced in the gut is proposed to accumulate in glial cells throughout the ENS(1). Enteric ganglia exist in the submucosal and myenteric plexuses beneath epithelial cells lining the intestinal wall(2). GABA uptake by epithelial Caco-2 cells at pH 6.0 was recorded as 6.6 pool.cm^-2 min^-1 (44% uptake). (3)
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<h2 style="font-family: verdana; font-size: 35px">Results </h2>
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<p style="font-family: verdana">The simulation of our model provided a graphical output showing the increase in uptake by epithelia cells of GABA as a result of increased Glutamate Decarboxylate.</p>
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[[File:T--Austin UTexas--uptakeofgaba.png|thumb|center|800px|Figure 2. GABA uptake over time at varying glutamate decarboxylate concentrations]]
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<p style="font-family: verdana">We compared the results of our modeling with results from literature examining other factors contributing to GABA production by lactobacillus strains. According to a 2015 article published in Microbial Biotechnology, GABA production was shown to increase as glutamic acid concentration increased up to 520mM in conjunction with optimal pH, 525 mM in conjunction with optimal temperature (4). The significance of the glutamate decarboxylase concentration as a factor for GABA production led us to look into a constitutive promoter that could overexpress the GadB gene.</p>
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<h2 style="font-family: verdana; font-size: 35px">References</h2>
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<li>Jessen, KR. GABA and the enteric nervous system. A neurotransmitter function? <i>Mol Cell Biochem</i>. 38: 69-76 (1981).</li>
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<li>Yu Y-B, Li Y-Q. Enteric glial cells and their role in the intestinal epithelial barrier. <i> World Journal of Gastroenterology : WJG.</i> 2014;20(32):11273-11280.  </li>
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<li>Thwaites DT, Basterfield L, McCleave PMJ, Carter SM, Simmons NL. Gamma-aminobutyric acid (GABA) transport across human intestinal epithelial (Caco-2) cell monolayers. <i>British Journal of Pharmacology.</i> 2000;129(3):457-464. </li>
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<li>Tajabadi N, Baradaran A, Ebrahimpour A, Rahim RA, Bakar FA, et al. Overexpression and optimization of glutamic decarboxylase in Lactobacillus plantarum Taj-Apis362 for high gamma-aminobutyric acid production. <i> Microb Biotechnol </i> .2015. </li>
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Revision as of 17:32, 30 October 2017


Why Model?

Scientific models are mathematical renditions of real-world systems. In synthetic biology, models are often used to define the kinetics of biochemical systems to aid in the visualization of information, and can be used to predict the behavior or outcome of biological systems. The goal of our model is to simulate the expected behavior of our transformed Lactobacillus plantarum after consumption. We focused on modeling the binding reaction of glutamate decarboxylate and L-glutamate, dependent on the cofactor pyridoxal- 5"phosphate (PLP). We looked specifically at how our Lactobacillus plantarum would encode the gadB gene to produce higher levels of glutamate decarboxylate and increase the uptake of GABA by the ENS.

Our Model


In our model, we aimed to compare the rates of GABA uptake by the ENS at differing concentrations dependent on an increased production of glutamate decarboxylate from over expression of the GadB gene. Our model assumes a first-order dosing type and an enzymatic elimination type.



Figure 1. Diagram of our model including species (blue), reactions (yellow), and parameters (green).



We turned to literature to acquire a better understanding of GABA uptake in the gut and to find parameters for the uptake reaction in our model. GABA produced in the gut is proposed to accumulate in glial cells throughout the ENS(1). Enteric ganglia exist in the submucosal and myenteric plexuses beneath epithelial cells lining the intestinal wall(2). GABA uptake by epithelial Caco-2 cells at pH 6.0 was recorded as 6.6 pool.cm^-2 min^-1 (44% uptake). (3) .



Results

The simulation of our model provided a graphical output showing the increase in uptake by epithelia cells of GABA as a result of increased Glutamate Decarboxylate.



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Figure 2. GABA uptake over time at varying glutamate decarboxylate concentrations



We compared the results of our modeling with results from literature examining other factors contributing to GABA production by lactobacillus strains. According to a 2015 article published in Microbial Biotechnology, GABA production was shown to increase as glutamic acid concentration increased up to 520mM in conjunction with optimal pH, 525 mM in conjunction with optimal temperature (4). The significance of the glutamate decarboxylase concentration as a factor for GABA production led us to look into a constitutive promoter that could overexpress the GadB gene.



References

    m
  1. Jessen, KR. GABA and the enteric nervous system. A neurotransmitter function? Mol Cell Biochem. 38: 69-76 (1981).
  2. Yu Y-B, Li Y-Q. Enteric glial cells and their role in the intestinal epithelial barrier.  World Journal of Gastroenterology : WJG. 2014;20(32):11273-11280.
  3. Thwaites DT, Basterfield L, McCleave PMJ, Carter SM, Simmons NL. Gamma-aminobutyric acid (GABA) transport across human intestinal epithelial (Caco-2) cell monolayers. British Journal of Pharmacology. 2000;129(3):457-464.
  4. Tajabadi N, Baradaran A, Ebrahimpour A, Rahim RA, Bakar FA, et al. Overexpression and optimization of glutamic decarboxylase in Lactobacillus plantarum Taj-Apis362 for high gamma-aminobutyric acid production. Microb Biotechnol  .2015.