Difference between revisions of "Team:ECUST China/Model"

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<link rel="stylesheet" href="https://2019.igem.org/wiki/index.php?title=Template:ECUST_China/ecustbox.css&action=raw&ctype=text/css"/> 
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<div id="ecust-box" > 
  
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<div class="img-main-box">
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<img class="img-main" src=https://static.igem.org/mediawiki/2019/b/b7/T--ECUST_China--awards_main.jpg"/>
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<img class="img-mask" src="https://static.igem.org/mediawiki/2019/5/55/T--ECUST_China--model_mask.png">
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</div>
  
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      <div class="mininav-left">
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<ul class="circle">
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<li>01
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<a class="mininav-item"  href="#main1" style="padding-top: 15px;">Market analyzes</a>
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</li>
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<li>02
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<a class="mininav-item"  href="#main2">Industry outlook</a>
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<div class="sec-minninav-box">
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<a class="sec-mininav-item"  href="#main2_1">- Paper Industry</a>
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<a class="sec-mininav-item"  href="#main2_2">- Food Industry</a>
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<a class="sec-mininav-item"  href="#main2_3">- Medical Industry</a>
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<a class="sec-mininav-item"  href="#main2_3">- Acoustic Equipment</a>
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</div>
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</li>
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<li>03
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<a class="mininav-item"  href="#main1">Application scenario</a>
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</li>
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<li>04
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<a class="mininav-item"  href="#main1">Project benefit</a>
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</li>
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<li>05
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<a class="mininav-item"  href="#main2" style="padding-bottom: 15px;">What is scale-up of fermenter?</a>
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</li>
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</ul>
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</div>
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<div class="mian-text-box">
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  <div class="attri-box"> <h1 style="font-size: 34px;padding-bottom: 50px;font-weight: 900;">Project long-term planning</h1>
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    <img class="img-com" src="img/表格.png"/>
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    <h1 id="main1">Expression and Reaction of endocellulase & exocellulase</h1>
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    <p>Genes of endocellulase and exocellulase expressed conducted by λ promoter at first.Without inhibition for λ promoter,genes of endocellulase and exocellulase transcribed and translated as E.coli strain grew.So we aimed to incubate E.coli at liquid medium and predicted the concentration of bacteria and activity of enzymes with Logistic equation and Luedeking-Piret equation.As a result,we assumed the relationship between concentration of E.coli and enzymes was semi-relative and predicted how much we could get enzymes.</p>
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    <img src="#"/>
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    <p>Then,with results of activity of enzymes and concentration of cellulose,we had used Langmuir adsorption equation and modeled Michaelis-Menten equation to predict concentration of cellobiose.Langmuir adsorption equation was commonly used for enzyme adsorption to solid substrate.Especially,for cellulose,just when enzymes adsorbed long chains of cellulose they could work.Michaelis-Menten equation was a classical equation for enzyme reaction,but because of inactivity in process of enzyme adsorption,it was modified to match the actual enzyme reaction rate.To calculate the concentration of cellobiose,we applied the empirical second exponential decay equation which could predict the maximum concentration of cellobiose under different concentrations of cellulose.We found the most suitable concentration of cellulose was 20g/L and time of fermentation was 24hours</p>
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    <img src="#"/>
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    <h1 id="main2">Regulation model</h1>
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    <p>For the former was hydrolysis reaction and the latter was synthesis reaction,we considered the difference of the enzymes under different pH and temperature to avoid the conflict which cellulase catalyzed the bacteria cellulose.So we comprehensively considered the effect of pH and temperature to cellulase and bacterial cellulose synthase to ensure suitable fermentation condition.The best condition for bacterial cellulose synthase was that pH is 6.0 and temperature was 28℃,but for E.coli growth and cellulase synthesis,we set 37℃ and pH 7.0.After changing pH and temperature,the enzyme activity of cellulase was down to 15% and 10% of original activity of cenA and cex.</p>
 +
    <img src="#"/>
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    <p>When Lac promoter worked,the gene of CI expressed CI protein as inhibitor for λ promoter.So we aimed to know about effect of the concentration of IPTG to λ promoter.To realize the close of λ promoter and latter enzymes expression,we had to clear what concentration was suitable for our experiment. </p>
 +
    <h2>Reaction of Cellobiose Phosphorylase and Bacterial Cellulose Synthesis</h2>
 +
    <p>When cellobiose in fermentation liquor entered E.coli,with expression of Cellobiose Phosphorylase and Bacterial Cellulose Synthase,the strain began to produce bacterial cellulose utilizing cellobiose.So,we analyzed the metabolic pathways from glucose to UDPG and from UDPG to bacteria cellulose,predicting the varieties of the concentration of cellobiose and bacteria cellulose.</p>
 +
    <h2>Bio-manufacturing by fermentation</h2>
 +
    <p>how we make paper transformer work and maximize our profit by recycling and reuse waste paper,so we build a factory to produce bacteria cellulose according to recent statue of waste paper utilization.</p>
 +
    <p>By investigation, we find pretreated waste-paper pulp contains 65% cellulose and its pH is 2~3 and after adjustment,it can act as substrate for fermentation.So we design a set of 500L fermentor as a factory model to produce bacteria cellulose.We use waste-paper pulp and industrial molasses as substrate for E.coli to produce and in the early fermentation we use airlift fermentor to keep strain grow and maintain suitable level of cellulase concentration for catalyzing cellulose to cellobiose.When the concentration of cellobiose does not change,we change fermentation liquor condition and control the temperature and pH to open later-stage fermentation switch by adding lactose as a inducer to synthesize BC.</p>
 +
    <p>But how to ensure the concentration of cellulose and get maxium quality of cellobiose,we build logistic model for strain growth,cellulase enzymatic reaction equation model and the mathematical models for transformation from cellulose to cellobiose.Finally,we consider the concentration of cellulose is 20g/L and can get 6g/L cellobiose after 24-hr fermentation under 37℃ in the first fermentation.Then,we analyze the metabolic pathway of UDPG which transfers about 5% cellobiose and other sugar to BC and will get 1.3g/L cellobiose in the end.To avoid to destroy the length and diameter of BC,we decline the ventilation in the airlift fermentor for latter process.      </p>
 +
    <p>We analyze the expense of all materials and items to evaluate economic benefits,if we build a factory and have such a produce process in 200 m3 fermentor ,we can make a profit 8062780 dollars per year,decrease waste water 412200 ton ,reduce waste paper pulp 2061 ton,so environmentally friendly and economical!</p>
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  </div>
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</div></div>
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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2019.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2019.igem.org/Judging/Awards"> award listed below</a>. </p>
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<h1> Modeling</h1>
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
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<h3> Gold Medal Criterion #3</h3>
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Convince the judges that your project's design and/or implementation is based on insight you have gained from modeling. This could be either a new model you develop or the implementation of a model from a previous team. You must thoroughly document your model's contribution to your project on your team's wiki, including assumptions, relevant data, model results, and a clear explanation of your model that anyone can understand.  
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The model should impact your project design in a meaningful way. Modeling may include, but is not limited to, deterministic, exploratory, molecular dynamic, and stochastic models. Teams may also explore the physical modeling of a single component within a system or utilize mathematical modeling for predicting function of a more complex device.
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<h3>Best Model Special Prize</h3>
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To compete for the <a href="https://2019.igem.org/Judging/Awards">Best Model prize</a>, please describe your work on this page  and also fill out the description on the <a href="https://2019.igem.org/Judging/Judging_Form">judging form</a>. Please note you can compete for both the Gold Medal criterion #3 and the Best Model prize with this page.  
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You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
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<h3> Inspiration </h3>
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<p>
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Here are a few examples from previous teams:
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</p>
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<ul>
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<li><a href="https://2018.igem.org/Team:GreatBay_China/Model">2018 GreatBay China</a></li>
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<li><a href="https://2018.igem.org/Team:Leiden/Model">2018 Leiden</a></li>
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<li><a href="https://2016.igem.org/Team:Manchester/Model">2016 Manchester</a></li>
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">2016 TU Delft</li>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">2014 ETH Zurich</a></li>
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">2014 Waterloo</a></li>
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</ul>
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</div>
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</html>

Revision as of 16:14, 16 October 2019

Project long-term planning

Expression and Reaction of endocellulase & exocellulase

Genes of endocellulase and exocellulase expressed conducted by λ promoter at first.Without inhibition for λ promoter,genes of endocellulase and exocellulase transcribed and translated as E.coli strain grew.So we aimed to incubate E.coli at liquid medium and predicted the concentration of bacteria and activity of enzymes with Logistic equation and Luedeking-Piret equation.As a result,we assumed the relationship between concentration of E.coli and enzymes was semi-relative and predicted how much we could get enzymes.

Then,with results of activity of enzymes and concentration of cellulose,we had used Langmuir adsorption equation and modeled Michaelis-Menten equation to predict concentration of cellobiose.Langmuir adsorption equation was commonly used for enzyme adsorption to solid substrate.Especially,for cellulose,just when enzymes adsorbed long chains of cellulose they could work.Michaelis-Menten equation was a classical equation for enzyme reaction,but because of inactivity in process of enzyme adsorption,it was modified to match the actual enzyme reaction rate.To calculate the concentration of cellobiose,we applied the empirical second exponential decay equation which could predict the maximum concentration of cellobiose under different concentrations of cellulose.We found the most suitable concentration of cellulose was 20g/L and time of fermentation was 24hours

Regulation model

For the former was hydrolysis reaction and the latter was synthesis reaction,we considered the difference of the enzymes under different pH and temperature to avoid the conflict which cellulase catalyzed the bacteria cellulose.So we comprehensively considered the effect of pH and temperature to cellulase and bacterial cellulose synthase to ensure suitable fermentation condition.The best condition for bacterial cellulose synthase was that pH is 6.0 and temperature was 28℃,but for E.coli growth and cellulase synthesis,we set 37℃ and pH 7.0.After changing pH and temperature,the enzyme activity of cellulase was down to 15% and 10% of original activity of cenA and cex.

When Lac promoter worked,the gene of CI expressed CI protein as inhibitor for λ promoter.So we aimed to know about effect of the concentration of IPTG to λ promoter.To realize the close of λ promoter and latter enzymes expression,we had to clear what concentration was suitable for our experiment.

Reaction of Cellobiose Phosphorylase and Bacterial Cellulose Synthesis

When cellobiose in fermentation liquor entered E.coli,with expression of Cellobiose Phosphorylase and Bacterial Cellulose Synthase,the strain began to produce bacterial cellulose utilizing cellobiose.So,we analyzed the metabolic pathways from glucose to UDPG and from UDPG to bacteria cellulose,predicting the varieties of the concentration of cellobiose and bacteria cellulose.

Bio-manufacturing by fermentation

how we make paper transformer work and maximize our profit by recycling and reuse waste paper,so we build a factory to produce bacteria cellulose according to recent statue of waste paper utilization.

By investigation, we find pretreated waste-paper pulp contains 65% cellulose and its pH is 2~3 and after adjustment,it can act as substrate for fermentation.So we design a set of 500L fermentor as a factory model to produce bacteria cellulose.We use waste-paper pulp and industrial molasses as substrate for E.coli to produce and in the early fermentation we use airlift fermentor to keep strain grow and maintain suitable level of cellulase concentration for catalyzing cellulose to cellobiose.When the concentration of cellobiose does not change,we change fermentation liquor condition and control the temperature and pH to open later-stage fermentation switch by adding lactose as a inducer to synthesize BC.

But how to ensure the concentration of cellulose and get maxium quality of cellobiose,we build logistic model for strain growth,cellulase enzymatic reaction equation model and the mathematical models for transformation from cellulose to cellobiose.Finally,we consider the concentration of cellulose is 20g/L and can get 6g/L cellobiose after 24-hr fermentation under 37℃ in the first fermentation.Then,we analyze the metabolic pathway of UDPG which transfers about 5% cellobiose and other sugar to BC and will get 1.3g/L cellobiose in the end.To avoid to destroy the length and diameter of BC,we decline the ventilation in the airlift fermentor for latter process.

We analyze the expense of all materials and items to evaluate economic benefits,if we build a factory and have such a produce process in 200 m3 fermentor ,we can make a profit 8062780 dollars per year,decrease waste water 412200 ton ,reduce waste paper pulp 2061 ton,so environmentally friendly and economical!