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| | + | {{RDFZ-China}} |
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| − | <link rel="edit" title="Edit" href="/wiki/index.php?title=Team:RDFZ-China/Model&action=edit" /> | + | <ul> |
| − | <link rel="shortcut icon" href="/favicon.ico" /> | + | <li><a href="#section1">Expression Burden</a></li> |
| − | <link rel="search" type="application/opensearchdescription+xml" href="/wiki/opensearch_desc.php" title="2018.igem.org (en)" /> | + | <li><a href="#section2">Capacity Monitor</a></li> |
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| − | <link rel="copyright" href="http://creativecommons.org/licenses/by/3.0/" /> | + | <li><a href="#section5">References</a></li> |
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| + | <h1>Measurement</h1> |
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| + | <h3>Expression Burden</h3> |
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| + | <p>In synthetic biology, a common issue in integrating exogenous sequences into host cells is that heterologous gene expression can cause significant metabolic burden. Typically, this gene expression burden is implied by a declining growth rate of bacteria, which is unfavorable for fermentation industry because it lowers yields and profits. According to Ceroni et al. (2015), a fluorescence-based method allows to measure gene expression capacity of cells, by inserting a “capacity monitor”.</p> |
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| + | <h3>Capacity Monitor</h3> |
| − | </head> | + | <p>The “Capacity Monitor” consists of a superfold GFP with a strong constitutive promoter, which is constantly expressed in the bacterial genome. Thus, any alternation in fluorescence intensity can reflect in overall resource availability in the cell. Particularly, with expression of synthesized genes, the expression of GFP will decrease, thus reporting a reallocation of cellular resources. </p> |
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| + | <h3>VioABDE</h3> |
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| + | <p>After applying capacity monitor, we compared the fluorescence of E. coli with an empty vector and E. coli with VioABDE inserted and expressed. Both strains were incubated for 24 hours with fluorescence and OD constantly monitored. However, the OD of bacteria with VioABDE increased faster than the bacteria without Vio expression, which contradicts our initial expectation.</p> |
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| + | <p>We co transformed the TlpA39-VioABDE into the capcatiy monitor component cell which was made by beyotime component cell kit. </p> |
| − | | + | <p>Then the Capacity Monitor and Capacity Monitor-Vio were incubicated in microshaker in 39 degree Celsius, then they were added to the 96 well plates. |
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| − | | + | <div class=" topic- title" id=" section4"> |
| − | <div id= 'top_menu_under' class='noprint'></ div> | + | <h3>Alternative Device</h3> |
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| + | <p>Since we target to modify bacteria used in fermentation industry, which primarily are used for material synthesis and production, our sequence inserts should occupy as limited resources in bacteria as possible to avoid significant expression burden. In order to reduce this expression stress, we designed another device for fermentation which used a LuxR repressive promoter (Peking-S, 2011) and the “Cold Box” in 5’UTR region of CspA (Ionis Paris, 2017). With only one transcriptional regulator, less energy will be consumed, which is beneficial for fermentation industry.</p> |
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| − | | + | <h3>References</h3> |
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| + | <p>Ceroni, F., Algar, R., Stan, G. B., & Ellis, T. (2015). Quantifying cellular capacity identifies gene expression designs with reduced burden. Nature methods, 12(5), 415.</p> |
| − | <div id="content" class=" mw- body" role=" main"> | + | <p>Ionis Paris. (2017). Biological thermo-responsive solution, that reduces the plant’s thermal stresses. Available from: https://2017.igem.org/Team:IONIS-PARIS.</p> |
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| + | <p>Peking-S iGEM. (2011). A Chemical Wire Toolbox for Synthetic Microbial Consortia. Avaible from: https://2011.igem.org/Team:Peking_S.</p> |
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| − | <h1> Modeling</h1>
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| − |
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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>
| |
| − | <p>
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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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| − | <br><br>
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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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| − | </p>
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| − |
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| − | <p>
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| − | Please see the <a href="https://2018.igem.org/Judging/Medals"> 2018
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| − | Medals Page</a> for more information.
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| − | </p>
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| − | </div>
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| − |
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| − | <div class="column two_thirds_size">
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| − | <h3>Best Model Special Prize</h3>
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| − |
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| − | <p>
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| − | To compete for the <a href="https://2018.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://2018.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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| − | <br><br>
| |
| − | 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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| − | </p>
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| − |
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| − | </div>
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| − |
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| − | <div class="column third_size">
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| − | <div class="highlight decoration_A_full">
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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://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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| − | </div>
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