Difference between revisions of "Team:NCKU Tainan/Analysis"

 
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        <h1 class="head">CO<sub>2</sub> utilization result analysis</h1>
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                <h1 class="head">CO<sub>2</sub> Utilization Result Analysis</h1>
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                <h6 class="subtitle">Let Numbers Talk</h6>
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                                 <div id="Analysis">
 
                                 <div id="Analysis">
 
                                     <h3>Analysis</h3>
 
                                     <h3>Analysis</h3>
                                     <p class="pcontent">There are three major questions we have answer in result analysis</p>
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                                     <p class="pcontent">There are three major questions we have answered in result analysis</p>
 
                                     <ol>
 
                                     <ol>
 
                                         <li class="licontent"><a class="link" href="#CO2_uptake">How much CO<sub>2</sub> (air) uptake by engineering <i>E. coli</i>?</a></li>
 
                                         <li class="licontent"><a class="link" href="#CO2_uptake">How much CO<sub>2</sub> (air) uptake by engineering <i>E. coli</i>?</a></li>
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                                             </div>
 
                                             </div>
 
                                             <div class="col-12">
 
                                             <div class="col-12">
                                                 <p class="pcenter">Fig 2. result of xylose and pyruvate under A, B, C, time interval</p>
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                                                 <p class="pcenter">Fig 2. Result of xylose and pyruvate under A, B, C, time interval</p>
 
                                             </div>
 
                                             </div>
 
                                         </div>
 
                                         </div>
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                                                 <tr>
 
                                                 <tr>
 
                                                     <th colspan="1">Time interval</th>
 
                                                     <th colspan="1">Time interval</th>
                                                     <th colspan="1">Rubp produced rate (mM/s)</th>
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                                                     <th colspan="1">RuBp produced rate (mM/s)</th>
 
                                                     <th colspan="1">3PGA produced rate (mM/s)</th>                                                         
 
                                                     <th colspan="1">3PGA produced rate (mM/s)</th>                                                         
 
                                                 </tr>
 
                                                 </tr>
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                                             <p class="pcontent">a:3PGA generated from the central pathway</p>
 
                                             <p class="pcontent">a:3PGA generated from the central pathway</p>
 
                                             <p class="pcontent">b:CO<sub>2</sub> fixed by the CO<sub>2</sub> bypass pathway</p>
 
                                             <p class="pcontent">b:CO<sub>2</sub> fixed by the CO<sub>2</sub> bypass pathway</p>
                                             <p class="pcontent">c:mol of 3PGA<sub>0</sub> into downstream</p>
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                                             <p class="pcontent">c:mole of 3PGA<sub>0</sub> into downstream</p>
                                             <p class="pcontent">d : mol of 3PGA’ into downstream</p>
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                                             <p class="pcontent">d : mole of 3PGA’ into downstream</p>
 
                                         </div>
 
                                         </div>
 
                                     </div>
 
                                     </div>
 
                                     <p class="pcontent">To define the MFI<sub>CO<sub>2</sub></sub>, we use CO<sub>2</sub> fixed by the CO<sub>2</sub> bypass pathway,  
 
                                     <p class="pcontent">To define the MFI<sub>CO<sub>2</sub></sub>, we use CO<sub>2</sub> fixed by the CO<sub>2</sub> bypass pathway,  
 
                                         noted as b, divided by the 3PGA generated from the central pathway,  
 
                                         noted as b, divided by the 3PGA generated from the central pathway,  
                                         noted as a. We also assume c is mol of 3PGA¬0 and d is mol of 3PGA’ that channels into downsteam metabolism.  
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                                         noted as a. We also assume c is mole of 3PGA¬0 and d is mole of 3PGA’ that channels into downsteam metabolism.  
                                         After metabolism, (a+b) mol of 3PGA<sub>0</sub> and b mol of 3PGA’ are generated.
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                                         After metabolism, (a+b) mole of 3PGA<sub>0</sub> and b mole of 3PGA’ are generated.
 
                                     </p>
 
                                     </p>
 
                                     <p class="pcontent">Besides, X and Y represent the actual 3PGA detected from the original pathway and CO<sub>2</sub> bypass pathway,  
 
                                     <p class="pcontent">Besides, X and Y represent the actual 3PGA detected from the original pathway and CO<sub>2</sub> bypass pathway,  
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                                     <p class="pcontent">$${MFI(Metabolic \ flux \ index) = {b \over a} = {{0.97y-0.03x} \over {1.03x-0.97y}}}$$</p>
 
                                     <p class="pcontent">$${MFI(Metabolic \ flux \ index) = {b \over a} = {{0.97y-0.03x} \over {1.03x-0.97y}}}$$</p>
 
                                     <p class="pcontent">As a result, we only need the amount of 3PGA<sub>0</sub> and 3PGA’ to calculate MFI<sub>CO<sub>2</sub></sub>.  
 
                                     <p class="pcontent">As a result, we only need the amount of 3PGA<sub>0</sub> and 3PGA’ to calculate MFI<sub>CO<sub>2</sub></sub>.  
                                         Through modelling, we supply 0.4% xylose and 5% CO<sub>2</sub> to get the data of 3PGA<sub>0</sub> and 3PGA’,  
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                                         Through modelling, we supply 4 (g/l) xylose and 5% CO<sub>2</sub> to get the data of 3PGA<sub>0</sub> and 3PGA’,  
 
                                         which helps us to adjust the rate between xylose and CO<sub>2</sub> sources.
 
                                         which helps us to adjust the rate between xylose and CO<sub>2</sub> sources.
 
                                     </p>
 
                                     </p>
 
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                                     <div id="centerimg">
 
                                         <img class="oneimg" src="https://static.igem.org/mediawiki/2018/c/cd/T--NCKU_Tainan--analysis_3PGA.png">
 
                                         <img class="oneimg" src="https://static.igem.org/mediawiki/2018/c/cd/T--NCKU_Tainan--analysis_3PGA.png">
                                         <p class="pcenter">Fig 6. The result of 3PGA produced form PP pathway (original metabolism) and from CO<sub>2</sub> bypass pathway.</p>
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                                         <p class="pcenter">Fig 5. The result of 3PGA produced form PP pathway (original metabolism) and from CO<sub>2</sub> bypass pathway.</p>
 
                                     </div>
 
                                     </div>
 
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                                        <table>
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                                      <p class="pcenter">Table 3 MFI<sub>CO<sub>2</sub></sub> at different time</p>
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                                        <table>
 
                                             <tr>
 
                                             <tr>
 
                                                 <th colspan="1">Time</th>
 
                                                 <th colspan="1">Time</th>
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                                             </tr>
 
                                             </tr>
 
                                         </table>
 
                                         </table>
                                         <p class="pcenter">Table 3 MFI<sub>CO<sub>2</sub></sub> at different time</p>
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                                     </div>
 
                                     </div>
  
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                                         <div id="centerimg">
 
                                             <img class="oneimg" src="https://static.igem.org/mediawiki/2018/e/e6/T--NCKU_Tainan--kinetic_law_fig6.png">
 
                                             <img class="oneimg" src="https://static.igem.org/mediawiki/2018/e/e6/T--NCKU_Tainan--kinetic_law_fig6.png">
                                             <p class="pcenter">Fig 7. pyruvate produced under different CO<sub>2</sub> uptake condition (model result)</p>
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                                             <p class="pcenter">Fig 6. pyruvate produced under different CO<sub>2</sub> uptake condition (model result)</p>
 
                                         </div>
 
                                         </div>
 
                                         <div id="centerimg">
 
                                         <div id="centerimg">
 
                                             <img class="oneimg" src="https://static.igem.org/mediawiki/2018/1/12/T--NCKU_Tainan--analysis_p3_cell_growth.png">
 
                                             <img class="oneimg" src="https://static.igem.org/mediawiki/2018/1/12/T--NCKU_Tainan--analysis_p3_cell_growth.png">
                                             <p class="pcenter">Fig 8. cell growth under different CO<sub>2</sub> conditions (experimental data)</p>
+
                                             <p class="pcenter">Fig 7. cell growth under different CO<sub>2</sub> conditions (experimental data)</p>
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                                            <p class="pcenter" style="font-size: 15px;">* LXSPC = Engineered <i>E. coli</i> contains PRK, Rubisco, and CA</p>
 +
 
 
                                         </div>
 
                                         </div>
 
                                         <p class="pcontent">The final goal of our project is to prove that our engineered <i>E. coli</i> could  
 
                                         <p class="pcontent">The final goal of our project is to prove that our engineered <i>E. coli</i> could  
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                                     <h3>References</h3>
 
                                     <h3>References</h3>
 
                                     <ol>
 
                                     <ol>
                                        <li class="smallp">Fuyu G, Guoxia L, Xiaoyun Z, Jie Z, Zhen C and Yin L. Quantitative analysis of an engineered CO<sub>2</sub>-fixing <i>Escherichia Coli</i> reveals great potential of heterotrophic CO<sub>2</sub> fixation. Gong et al. Biotechnology for Biofuels, 2015, 8:86.</li>
+
                                                                                <li class="smallp">Michaelis Menten Kinetics in bio – physic wiki, web : http://www.bio-physics.at/wiki/index.php?title=Michaelis_Menten_Kinetics</li>
 
                                         <li class="smallp">citric acid cycle from Brenda, web : https://www.brenda-enzymes.org/pathway_index.php?ecno=&brenda_ligand_id=Alpha-ketoglutarate&organism=Escherichia+coli&pathway=citric_acid_cycle&site=pathway</li>
 
                                         <li class="smallp">citric acid cycle from Brenda, web : https://www.brenda-enzymes.org/pathway_index.php?ecno=&brenda_ligand_id=Alpha-ketoglutarate&organism=Escherichia+coli&pathway=citric_acid_cycle&site=pathway</li>
                                         <li class="smallp">Uwe Sauer, Bernhard J. E. The PEP—pyruvate—oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiology Reviews, Volume 29, Issue 4, 1 September 2005, Pages 765–794.</li>
+
                                         <li class="smallp">U. Sauer, J. E. Bernhard, The PEP—pyruvate—oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiology Reviews, Volume 29, Issue 4, 1 September 2005, Pages 765–794.</li>
                                         <li class="smallp">Mugihito O, Hideaki S, Yukihiro T, Noriko M, Tatsuya S, Masahiro O, Ayaaki I, and Kenji S. Kinetic modeling and sensitivity analysis of xylose metabolism in Lactococcus lactis IO-1. Journal of Bioscience and Bioengineering VOL. 108 No. 5, 376–384, 2009.</li>
+
                                         <li class="smallp">O. Mugihito, S. Hideaki, T. Yukihiro , M Noriko, S. Tatsuya, O. Masahiro, I. Ayaaki, S. Kenji, Kinetic modeling and sensitivity analysis of xylose metabolism in Lactococcus lactis IO-1. Journal of Bioscience and Bioengineering VOL. 108 No. 5, 376–384, 2009.</li>
                                         <li class="smallp">Akira W., Keisuke N., Tomohiro H., Ryohei S. & Toshio I. Reaction mechanism of phosphoribulokinase from a cyanobacterium, Synechococcus PCC7942. Photosynthesis Research 56: 27–33, 1998</li>
+
                                         <li class="smallp"> W. Akira, N. Keisuke, H. Tomohiro, S. Ryohei, Reaction mechanism of phosphoribulokinase from a cyanobacterium, Synechococcus PCC7942. Photosynthesis Research 56: 27–33, 1998</li>
                                         <li class="smallp">Guillaume G. B., Tcherkez, Graham D. Farquhar, and T. John Andrews. Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized Proc Natl Acad Sci U S A. 2006 May 9; 103(19): 7246–7251.</li>
+
                                         <li class="smallp">G. B. Guillaume, D. F. Graham, T. J. Andrews, Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized Proc Natl Acad Sci U S A. 2006 May 9; 103(19): 7246–7251.</li>
                                         <li class="smallp">Yun L. and Keith A. M. Determination of Apparent Km Values for Ribulose 1,5- Bisphosphate Carboxylase/Oxygenase (Rubisco) Activase Using the Spectrophotometric Assay of Rubisco Activity. Plant Physiol. (1991) 95, 604-609</li>
+
                                         <li class="smallp"> L. Yun, A. M. Keith, Determination of Apparent Km Values for Ribulose 1,5- Bisphosphate Carboxylase/Oxygenase (Rubisco) Activase Using the Spectrophotometric Assay of Rubisco Activity. Plant Physiol. (1991) 95, 604-609</li>
 
                                         <li class="smallp">Rong-guang Z, C. Evalena A., Alexei S., Tatiana S., Elena E., Steven B., Cheryl H. A., Aled M. E., Andrzej J., and Sherry L. M. Structure of <i>Escherichia Coli</i> Ribose-5-Phosphate Isomerase: A Ubiquitous Enzyme of the Pentose Phosphate Pathway and the Calvin Cycle Structure, Vol. 11, 31–42, January, 200</li>
 
                                         <li class="smallp">Rong-guang Z, C. Evalena A., Alexei S., Tatiana S., Elena E., Steven B., Cheryl H. A., Aled M. E., Andrzej J., and Sherry L. M. Structure of <i>Escherichia Coli</i> Ribose-5-Phosphate Isomerase: A Ubiquitous Enzyme of the Pentose Phosphate Pathway and the Calvin Cycle Structure, Vol. 11, 31–42, January, 200</li>
 
                                         <li class="smallp">Inês L., Joana F., Christine C., Sandra M., Nuno S., Nilanjan R., Anabela C., and Joana T. Ribose 5-Phosphate Isomerase B Knockdown Compromises Trypanosoma brucei Bloodstream Form Infectivity PLoS Negl Trop Dis. 2015 Jan; 9(1): e3430.</li>
 
                                         <li class="smallp">Inês L., Joana F., Christine C., Sandra M., Nuno S., Nilanjan R., Anabela C., and Joana T. Ribose 5-Phosphate Isomerase B Knockdown Compromises Trypanosoma brucei Bloodstream Form Infectivity PLoS Negl Trop Dis. 2015 Jan; 9(1): e3430.</li>
 
                                         <li class="smallp">Singh2006 TCA mtu model1. SBML2LATEX. Web : http: //www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX</li>
 
                                         <li class="smallp">Singh2006 TCA mtu model1. SBML2LATEX. Web : http: //www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX</li>
                                         <li class="smallp">Jun Shen, Modeling the glutamate–glutamine neurotransmitter cycle, Front. Neuroenergetics, 28 January 2013</li>
+
                                         <li class="smallp">J. Shen, Modeling the glutamate–glutamine neurotransmitter cycle, Front. Neuroenergetics, 28 January 2013</li>
                                         <li class="smallp">Xueyang Feng and Huimin Zhao, Investigating xylose metabolism in recombinant Saccharomyces cerevisiae via 13C metabolic flux analysis, Microb Cell Fact. 2013; 12: 114.</li>
+
                                         <li class="smallp">X. Feng, H. Zhao, Investigating xylose metabolism in recombinant Saccharomyces cerevisiae via 13C metabolic flux analysis, Microb Cell Fact. 2013; 12: 114.</li>
                                         <li class="smallp">David Runquist, Bärbel Hahn-Hägerdal and Maurizio Bettiga, Increased expression of the oxidative pentose phosphate pathway and gluconeogenesis in anaerobically growing xylose-utilizing Saccharomyces cerevisiae, Microbial Cell Factories 2009, 8:49</li>
+
                                         <li class="smallp">D. Runquist, M. Bettiga, Increased expression of the oxidative pentose phosphate pathway and gluconeogenesis in anaerobically growing xylose-utilizing Saccharomyces cerevisiae, Microbial Cell Factories 2009, 8:49</li>
 
                                         <li class="smallp">Kalle Hult rev 2005, 2007 Linda Fransson Department of Biotechnology KTH, Stockholm, Enzyme kinetics, An investigation of the enzyme glucose-6- phosphate isomerase</li>
 
                                         <li class="smallp">Kalle Hult rev 2005, 2007 Linda Fransson Department of Biotechnology KTH, Stockholm, Enzyme kinetics, An investigation of the enzyme glucose-6- phosphate isomerase</li>
 
                                         <li class="smallp">Model name: “Mosca2012 - Central Carbon Metabolism Regulated by AKT”, SBML2LATEX. Web : http: //www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX</li>
 
                                         <li class="smallp">Model name: “Mosca2012 - Central Carbon Metabolism Regulated by AKT”, SBML2LATEX. Web : http: //www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX</li>
                                         <li class="smallp">Ettore M., Roberta A., Carlo M., Annamaria B., Gianfranco C. and Luciano M., Computational modeling of the metabolic states regulated by the kinase Akt, Front. Physiol., 21 November 2012</li>
+
                                         <li class="smallp">M. Ettore, A. Roberta, M. Carlo, B. Annamaria, C. Gianfranco, M. Luciano, Computational modeling of the metabolic states regulated by the kinase Akt, Front. Physiol., 21 November 2012</li>
                                         <li class="smallp">Jacqueline E. G., Christopher P. L., Maciek R. A., Comprehensive analysis of glucose and xylose metabolism in <i>Escherichia Coli</i> under aerobic and anaerobic conditions by 13C metabolic flux analysis, Metabolic Engineering Volume 39, January 2017, Pages 9-18</li>
+
                                         <li class="smallp">E. G. Jacqueline, P. L. Christopher, R. A. Maciek, Comprehensive analysis of glucose and xylose metabolism in <i>Escherichia Coli</i> under aerobic and anaerobic conditions by 13C metabolic flux analysis, Metabolic Engineering Volume 39, January 2017, Pages 9-18</li>
                                         <li class="smallp">N. Nuray Ulusu, Cihangir Şengezer, Kinetic mechanism and some properties of glucose-6- phosphate dehydrogenase from sheep brain cortex, Türk Biyokimya Dergisi [Turkish Journal of Biochemistry–Turk J Biochem] 2012; 37 (4) ; 340–347</li>
+
                                         <li class="smallp">N. N. Ulusu, C. Şengezer, Kinetic mechanism and some properties of glucose-6- phosphate dehydrogenase from sheep brain cortex, Türk Biyokimya Dergisi [Turkish Journal of Biochemistry–Turk J Biochem] 2012; 37 (4) ; 340–347</li>
                                         <li class="smallp">Stefania H., Katy M., Carlo C., Morena M., and Franco D., 6-Phosphogluconate Dehydrogenase Mechanism EVIDENCE FOR ALLOSTERIC MODULATION BY SUBSTRATE, J Biol Chem. 2010 Jul 9; 285(28): 21366–21371.</li>
+
                                         <li class="smallp">H. Stefania, M. Katy, C. Carlo, M. Morena, D. Franco, 6-Phosphogluconate Dehydrogenase Mechanism EVIDENCE FOR ALLOSTERIC MODULATION BY SUBSTRATE, J Biol Chem. 2010 Jul 9; 285(28): 21366–21371.</li>
                                         <li class="smallp">K. Nielsen, P.G. Sørensen, F. Hynne, H.-G. Busse, Sustained oscillations in glycolysis: an experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations, Biophysical Chemistry 72 (1998) 49–62</li>
+
                                         <li class="smallp">K. Nielsen, P.G. Sørensen, F. Hynne, H. G. Busse, Sustained oscillations in glycolysis: an experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations, Biophysical Chemistry 72 (1998) 49–62</li>
 
                                         <li class="smallp">UniProtKB - A0RV30 from web : https://www.uniprot.org/uniprot/A0RV30</li>
 
                                         <li class="smallp">UniProtKB - A0RV30 from web : https://www.uniprot.org/uniprot/A0RV30</li>
 
                                     </ol>
 
                                     </ol>
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Latest revision as of 02:16, 18 October 2018

CO2 Utilization Result Analysis

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