Difference between revisions of "Team:Calgary/Software"

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<h1 class="page-title">Software</h1>
 
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<div class="col-lg-6 col-md-6 col-sm-12 col-xs-12 expand-on-hover" > <a target="blank" href="https://2019.igem.org/Team:Calgary/iGAM">
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                 <div class="container__sources">
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                    <img src="https://static.igem.org/mediawiki/2019/6/61/T--Calgary--GixieChix.png" width="100%" style="margin-left: auto; margin-right: auto; display: block;"/>
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                <img style="width: 100%" src="https://static.igem.org/mediawiki/2019/3/33/T--Calgary--DynaGixWhite.gif" />
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                <p>iGAM</p>
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                        <h3 style="text-align:center">Protein Production</h3>
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            </div><div class="col-lg-6 col-md-6 col-sm-12 col-xs-12"><a href="https://2019.igem.org/Team:Calgary/BOT">
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                        <p style="text-align:center">Production of 6GIX, our WSCP</p>
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                 <img style="width: 100%" src="https://static.igem.org/mediawiki/2019/3/33/T--Calgary--DynaGixWhite.gif" />
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                    </div>
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                <p>BioBrick Optimization Tool - synthesis</p>
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<p>We built a tool that could easily and quickly optimize sequences so synthetic biologists can focus on their experiments not ordering.</p></a>
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            <h1>Inspiration</h1>
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            <h2>iGAM</h2>
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                </div></a>
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            <b>Proteins are widely used in the iGEM community,</b> but there is very little iGEM teams can do to understand their protein’s atomic behaviour. At iGEM Calgary we wanted to generate a quantitative way to allow other teams to characterize each amino acid of their proteins.
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<div class="col-lg-6 col-md-6 col-sm-12 col-xs-12 expand-on-hover" > <a target="blank" href="https://2019.igem.org/Team:Calgary/EmulsifiedBindingProteinProcess">
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                    <img src="https://static.igem.org/mediawiki/2019/3/31/T--Calgary--ternaryPhaseGIF.gif" width="56%"style="margin-left: auto; margin-right: auto; display: block;"/>
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                    <div class="sources--cms">
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                        <h3 style="text-align:center">Protein Emulsification</h3>
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                        <p style="text-align:center">Characterizing the properties of 6GIX in emulsion</p>
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            <h1>Measurement</h1>
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            <h2>WHAT DID WE QUANTIFY?</h2>
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<h1>Chlorophyll Repurposing</h1>
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            <b>To assist in the dynamic characterization by other teams</b> we looked to develop a methodology that allows for the calculation and aggregation of Brownian motion measurements for each amino acid in a sequence. The Brownian motion measurement chosen was the Root Mean Square Fluctuation(RMSF) calculated for every atom of a protein in ten picosecond intervals.
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            <b>The RMSF data</b> was calculated from a nanosecond Molecular Dynamic Simulation(MDS) completed within GROMACS, an industrial MDS software.  These values were then averaged over each amino acid, this ensured that the unit of measurement was observed on a scale that was modifiable by teams. This resulted in a series of curves that quantitatively expressed the dynamics for each amino acid.
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<p style="margin-bottom:5vh">After removing chlorophyll from green seed canola oil, our team looked to ways in which we could repurpose chlorophyll to create a valuable commercial product. Our team investigated the enzymatic conversion of chlorophyll into pheophorbide a, and its use as an anti-fungal agent. </p>
  
  
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            Above is a complete view of the movement attributed to every amino acid of a protein. Having all of the curves present at the same time can be quite confusing. The true power of this measurement can be harnessed when amino acids are displayed in smaller clusters. Below is the dynamics of the 25th, 80th, and 90th amino acid of the 6GIX protein.
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<div class="col-lg-6 col-md-6 col-sm-12 col-xs-12 expand-on-hover"> <a target="blank" href="https://2019.igem.org/Team:Calgary/RepurposingChlorophyll">
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                    <img src="https://static.igem.org/mediawiki/2019/c/ce/T--Calgary--ICARUC.gif" width="90%"style="margin-left: auto; margin-right: auto; display: block;"/>
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                        <h3 style="text-align:center">Repurposing Chlorophyll</h3>
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                        <p style="text-align:center">Enzymatic degradation of chlorophyll into pheophorbide a </p>
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                </div></a>
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                 <h1>Functionality</h1>
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                <h2>WHAT CAN RMSF ACCOMPLISH</h2>
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                    <img src="https://static.igem.org/mediawiki/2019/c/ca/T--Calgary--Pheophorbide.png" width="58%"style="margin-left: auto; margin-right: auto; display: block;"/>
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                        <h3 style="text-align:center">Anti-Fungal</h3>
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                        <p style="text-align:center">Pheophorbide a as an anti-fungal agent</p>
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                <h1>Appendix A</h1>
 
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                <h2>Procedure of data collected <i>in vitro</i></h2>
 
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Revision as of 05:53, 20 October 2019

Software

Protein Production

Production of 6GIX, our WSCP

Protein Emulsification

Characterizing the properties of 6GIX in emulsion

Chlorophyll Repurposing

After removing chlorophyll from green seed canola oil, our team looked to ways in which we could repurpose chlorophyll to create a valuable commercial product. Our team investigated the enzymatic conversion of chlorophyll into pheophorbide a, and its use as an anti-fungal agent.

Repurposing Chlorophyll

Enzymatic degradation of chlorophyll into pheophorbide a

Anti-Fungal

Pheophorbide a as an anti-fungal agent
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