Difference between revisions of "Team:UFSCar-Brasil/modelling.html"

 
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             Modelling
 
             Modelling
 
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           <h2>What we do</h2>
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           <h2>The mathematical explanation of our results, and how we can provide desired information</h2>
 
           <a href="#overview" class="ui huge inverted primary basic button">Overview<i class="right arrow icon"></i></a>
 
           <a href="#overview" class="ui huge inverted primary basic button">Overview<i class="right arrow icon"></i></a>
 
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           <h3 class="ui header" id="overview">Overview</h3>
 
           <h3 class="ui header" id="overview">Overview</h3>
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           <p>Diseases transmitted by insect vectors, such as malaria and dengue, affect significantly the Brazilian population. In our city, São Carlos, this year in summer the public health organ featured a big number of cases. Working in this problem,
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           <div class="row">
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            our project consists in the development of an alternative repellent of that currently sold in the market and more or equally effective in preventing mosquitoes bites transmitted diseases. The main compound in current repellents is DEET (N,
+
           <p>Our main purpose with modeling was to determine how deeply connected the collected data are and starting from this to make some previsions and take decisions. For this purpose, we have used several mathematical tools, since: analytic geometry, complex systems calculations to final tridimensional solutions. We hope that our previsions and mathematical models help the next teams and groups work better and harder, despite of course answer important questions of our current work.</p>
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            N-diethyl-m-toluamide), a toxic molecule which at certain concentrations could be lethal, and therefore must have strict control on their use in products. The main characteristic of our repellent is the long duration when compared to other
+
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            products and the replacement of the compound DEET by D-limonene. Instead, the D-limonene has low toxicity, is highly volatile and present a pleasant smell.</p>
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           <p>Our proposal is building a bacteria carrying out the production of D-limonene via limonene synthase. To enable long term storage at room temperatures, the bacterial cells that make up the repellent will be plasmolyzed, with suspended metabolism,
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            considered a dormant state. The maintenance of this state will be obtained by a solution of polyethyleneglycol (PEG) that will raise the osmotic pressures. Once in contact with the skin, the PEG solution will be diluted by sweat, inducing
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            an osmotic shock in cells. Then the universal stress protein promoter (UspA) will be activated and will induce the expression of limonene synthase. Beyond PEG, other compounds such as glycerol and metal ions in low concentrations will compose
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            our insect repellent cream, in order to sustain the bacteria to the required metabolites building and posterior enzyme activities. In this way, the distribution of our repellent may become feasible, allowing its use.</p>
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          <p>To overcome those problems with limonene synthase folding, we used constitutive promoters for the expression of chaperones from all Escherichia coli available classes (like ClpB, DnaK and IbpA / IbpB). It will reinforce the stockpile of chaperones
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            naturally produced during osmotic shocks (heat-shock proteins) in bacteria. Our goal is to improve protein solubility, indirectly creatinga toolkit for protein solubility enhancement for future iGEM teams. . Besides, reducing the occurrence
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            of insoluble bodies and improving the production of limonene.</p>
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          <p>Finally, a way to ensure the biosafety in the use of our repellent and keep a control of bacterial cells is the use of a system of programmed death or Kill Switch. This system will work with two suicide genes: Killer red, a protein which trigger
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            oxidative species generation destroying the DNA (plasmid and chromosomal) allied to a potent RNAse which will avoid any contribution of RNA to host or normal microbiota. These genes will be switch on through an association with a zinc sensitive
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            promoter triggered by zur proteins which associate with zinc and avoid the expression of them allowing the bacterial growing. After long periods of repellent action, bacteria activities will decrease zinc concentration in medium, which allows
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            the gene activation and cells death.</p>
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           <h3 class="ui header" id="parts">Parts</h3>
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           <h3 class="ui header" id="parts">Plasmolysis</h3>
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           <p>Diseases transmitted by insect vectors, such as malaria and dengue, affect significantly the Brazilian population. In our city, São Carlos, this year in summer the public health organ featured a big number of cases. Working in this problem,
+
           <p>This section proposes to determine what would be the longest time of bacterial maintenance with lowest possible percentage of PEG 6000. Plasmolysis experiments were performed in microbiology laboratory for some weeks. Collected data were processed and analyzed for best-fit model to those points. After that, using this model, it was built a simulated surface and specific values were found. Finally, we found tangent lines to the surface where our point of interest could be found. This study was of great significance when we realize that our project belongs to manufacturing tracking. Since it results in a product, and it should be found in stores, this analysis makes possible to predict the validity of the product and of its storage process.
−
            our project consists in the development of an alternative repellent of that currently sold in the market and more or equally effective in preventing mosquitoes bites transmitted diseases. The main compound in current repellents is DEET (N,
+
</p>
−
            N-diethyl-m-toluamide), a toxic molecule which at certain concentrations could be lethal, and therefore must have strict control on their use in products. The main characteristic of our repellent is the long duration when compared to other
+
 
−
            products and the replacement of the compound DEET by D-limonene. Instead, the D-limonene has low toxicity, is highly volatile and present a pleasant smell.</p>
+
 
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         </div>
 
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           <h3 class="ui header" id="result">Result</h3>
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           <h3 class="ui header" id="result">Protein solubilization toolkit</h3>
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           <p>Diseases transmitted by insect vectors, such as malaria and dengue, affect significantly the Brazilian population. In our city, São Carlos, this year in summer the public health organ featured a big number of cases. Working in this problem,
+
           <p>Desenvolvemos uma abordagem estatística para o estudo da eficiência das chaperonas no enovelamento da limoneno sintase. Com o intuito de criar uma método que melhor descreva a combinação de chaperonas com base nos dados de rendimento, criamos um dendograma que ilustra o agrupamento delas com base na distancia estatística dos seus rendimentos. Depois foi resolvido um sistema linear com todas as relações e encontrou-se constantes estatísticas de cada componente.</p>
−
            our project consists in the development of an alternative repellent of that currently sold in the market and more or equally effective in preventing mosquitoes bites transmitted diseases. The main compound in current repellents is DEET (N,
+
 
−
            N-diethyl-m-toluamide), a toxic molecule which at certain concentrations could be lethal, and therefore must have strict control on their use in products. The main characteristic of our repellent is the long duration when compared to other
+
−
            products and the replacement of the compound DEET by D-limonene. Instead, the D-limonene has low toxicity, is highly volatile and present a pleasant smell.</p>
+
 
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         </div>
 
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           <h3 class="ui header" id="judging">Judging Criteria</h3>
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           <h3 class="ui header" id="judging">Kill Switch</h3>
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           <p>Diseases transmitted by insect vectors, such as malaria and dengue, affect significantly the Brazilian population. In our city, São Carlos, this year in summer the public health organ featured a big number of cases. Working in this problem,
+
           <p>One of our prime objective is to describe the activity of uspA promoter ( Universal Stress Protein A promoter) when exposed to osmotic chock compared with J23101 promoter. To quantify more precisely this behavior we adjust experimental points with general exponential functions and also related PEG concentration’s date with osmotic pressure. With the proper fitted curves, we modeled the concentration’s fall of Zn 2+ from external environment by import the metal to intracellular environment and gradually build up the smtA protein aiming estimate the approximate time for begin the death cell process, that initiate with the release of our killswitch’s promoter region due to the absence of Zn in cellular environmental to maintain the zur factor repressing ufscarA promoter. With the unblocked promoter, the transcription of death genes starts, metabolism and cell integrity is compromised leading to cell death.</p>
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            our project consists in the development of an alternative repellent of that currently sold in the market and more or equally effective in preventing mosquitoes bites transmitted diseases. The main compound in current repellents is DEET (N,
+
 
−
            N-diethyl-m-toluamide), a toxic molecule which at certain concentrations could be lethal, and therefore must have strict control on their use in products. The main characteristic of our repellent is the long duration when compared to other
+
 
−
            products and the replacement of the compound DEET by D-limonene. Instead, the D-limonene has low toxicity, is highly volatile and present a pleasant smell.</p>
+
<h3 class="ui center aligned header">Our amazing sponsors!</h3>
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<img class="ui centered massive image" src="https://static.igem.org/mediawiki/2015/archive/0/0e/20150908223157!UFSCar-Brasil_logos.png">
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Latest revision as of 14:14, 16 September 2015

Home
Project
Overview
Issue Plasmolysis and Limonene synthase Protein Solubilization Toolkit Kill Switch
Team
Our Team Attributions
Achievements
Overview
Parts Results Judging Criteria
Policy & Practices
Overview
Political Social Educational Safety/Security Meetings Fundraising
Modeling
Overview
Plasmolysis Protein Solubilization Toolkit Kill Switch
Notebook
Protocols Problems Collaborations Safety Acknowledgements

Modelling

The mathematical explanation of our results, and how we can provide desired information

Overview

Overview

Our main purpose with modeling was to determine how deeply connected the collected data are and starting from this to make some previsions and take decisions. For this purpose, we have used several mathematical tools, since: analytic geometry, complex systems calculations to final tridimensional solutions. We hope that our previsions and mathematical models help the next teams and groups work better and harder, despite of course answer important questions of our current work.

Plasmolysis

This section proposes to determine what would be the longest time of bacterial maintenance with lowest possible percentage of PEG 6000. Plasmolysis experiments were performed in microbiology laboratory for some weeks. Collected data were processed and analyzed for best-fit model to those points. After that, using this model, it was built a simulated surface and specific values were found. Finally, we found tangent lines to the surface where our point of interest could be found. This study was of great significance when we realize that our project belongs to manufacturing tracking. Since it results in a product, and it should be found in stores, this analysis makes possible to predict the validity of the product and of its storage process.

Protein solubilization toolkit

Desenvolvemos uma abordagem estatística para o estudo da eficiência das chaperonas no enovelamento da limoneno sintase. Com o intuito de criar uma método que melhor descreva a combinação de chaperonas com base nos dados de rendimento, criamos um dendograma que ilustra o agrupamento delas com base na distancia estatística dos seus rendimentos. Depois foi resolvido um sistema linear com todas as relações e encontrou-se constantes estatísticas de cada componente.

Kill Switch

One of our prime objective is to describe the activity of uspA promoter ( Universal Stress Protein A promoter) when exposed to osmotic chock compared with J23101 promoter. To quantify more precisely this behavior we adjust experimental points with general exponential functions and also related PEG concentration’s date with osmotic pressure. With the proper fitted curves, we modeled the concentration’s fall of Zn 2+ from external environment by import the metal to intracellular environment and gradually build up the smtA protein aiming estimate the approximate time for begin the death cell process, that initiate with the release of our killswitch’s promoter region due to the absence of Zn in cellular environmental to maintain the zur factor repressing ufscarA promoter. With the unblocked promoter, the transcription of death genes starts, metabolism and cell integrity is compromised leading to cell death.

Our amazing sponsors!

Our amazing sponsors!

Links

iGEM UFSCar

About

Team

Thanks for reading our wiki!

Come Again :)