Difference between revisions of "Team:NRP-UEA-Norwich/Results"

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<h2> Project Results</h2>
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<p>Here you can describe the results of your project and your future plans. </p>
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<h5>What should this page contain?</h5>
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<li> Clearly and objectively describe the results of your work.</li>
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<li> Future plans for the project </li>
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<li> Considerations for replicating the experiments </li>
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                                    <li ><a href="/Team:NRP-UEA-Norwich">Home</a></li>
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                                    <li ><a href="/Team:NRP-UEA-Norwich/Team">Team</a></li>
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Description">Overview</a></li>
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Project">Background</a></li>
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Approach">Approach</a></li>
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Results">Results</a></li>
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Parts">Parts</a></li>
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Protocols">Protocols</a></li>                                 
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Software">Glyco2D</a></li>
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Modeling/3D">3D Models</a></li>
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                                        <li ><a href="/Team:NRP-UEA-Norwich/Modeling">Kinetic Model</a></li>                                
  
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                                    <li  ><a href="/Team:NRP-UEA-Norwich/Attributions">Attributions</a></li>
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                                    <li  ><a href="/Team:NRP-UEA-Norwich/Achievements">Achievements</a></li>                                   
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    <h1 class="title1">Modelling and Software</h2>
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    <p class="space20">While we were bringing all the parts together in the lab, a lot of unanswered questions started to raised: How does glycogen and starch look like in real life? How will GlgX and GlgB expression affect the glycogen global structure? How this branching and debranching process take place? And,
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how will the acyltransferases add the acyl group into the glycogen/starch molecule and in which position? Will this addition affect the functionality of the molecule? </p>
  
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<h4> Project Achievements </h4>
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<p>Thanks to computers, software and maths, we were able to predict the outcome of all this processes to help us understanding what was going to happen in the lab. </p>
  
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<p>You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.</p>
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    <h3 class="title">Software: Glyco2D</h2>
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We used glycogen as a model system to gain a better understanding of the parameters involved in carbohydrate structure, branching and modification. </p>
  
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<p>We built Glyco2D based on the mathematical model that described the structural properties of glycogen based on different parameters such as chain length, branching degree and the number of tiers<sub><a data-id="ref" class="scroll-link" style = "color: #002bb8;">1</a></sub>. </p>
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<li>A list of linked bullet points of the successful results during your project</li>
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<li>A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.</li>
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</ul>
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        <p class="space20">Then we used the software to model the putative changes in glycogen structure depending on the location of the modification.  Our aim was to produce carbohydrate molecules with 5-10% of the residues modified since this level of butrylation (achieved by chemical modification) has positive benefits to the colons of rats <sub><a data-id="ref" class="scroll-link" style = "color: #002bb8;">2</a></sub>.</p>
  
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<p class="space20">You can learn more by clicking on the image to the right.</p>
  
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<h4>Inspiration</h4>
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<p>See how other teams presented their results.</p>
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<ul>
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    </div>
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<li><a href="https://2014.igem.org/Team:TU_Darmstadt/Results/Pathway">2014 TU Darmstadt </a></li>
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    <div class="col-md-5 col-md-offset-1  col-sm-offset-1 space30 text-center">
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<li><a href="https://2014.igem.org/Team:Imperial/Results">2014 Imperial </a></li>
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                    <div class="success-work science">
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<li><a href="https://2014.igem.org/Team:Paris_Bettencourt/Results">2014 Paris Bettencourt </a></li>
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                        <div class="success-work-desc">
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</ul>
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                        <img src="https://static.igem.org/mediawiki/2015/f/fb/NRP-UEA-Norwich-modelling-unmodified-structure.png" class="img-responsive" style="width:400px; height=300px;">
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                          <a title="Glyco2D"  href="https://2015.igem.org/Team:NRP-UEA-Norwich/Software" class="btn outlinebtn  space50">
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                            Read More
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                          </a>
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    <h3 class="title">3D models</h2>
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    <p class="space20">We build 3D models of carbohydrates (glycogen and the 2 components of starch -amylopectine and amylose-) to get a better understanding of the effect of branching degree and chain length on the real structure. We used the <href="http://www.glycosciences.de/modeling/sweet2/doc/index.php">SWEET </a> software to build them. </p>
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        <p class="space20">We developed a pipeline to 3D print these molecules. After several attempts, we managed to have our own 3D printed glycogen! </p>
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<p class="space20">You can learn more by clicking on the image on the right.</p>
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    <div class="col-md-5 col-md-offset-1  col-sm-offset-1 space30 text-center">
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                    <div class="success-work project">
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                        <div class="success-work-desc">
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                        <img src="https://static.igem.org/mediawiki/2015/b/b6/NRP-UEA-Norwich-3d-printing-overview.png" class="img-responsive ">
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                          <a title="3D models"  href="https://2015.igem.org/Team:NRP-UEA-Norwich/Modeling/3D" class="btn outlinebtn  space50">
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                            Read More
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                          </a>
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                        </div>
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    </div>
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<div class="row">
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    <h3 class="title">Kinetic modelling</h2>
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    <div class="space30"></div>
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    <p class="space20">To analyse the efficiency of the branching (GlgB) and debranching (GlgX) enzymes in glycogen production, we generated a set of differential equations to explain glycogen biosynthesis. We also incorporated all the enzymes involved in the pathway starting from taking the glucose from the medium <sub><a data-id="ref" class="scroll-link" style = "color: #002bb8;">3</a></sub>.</p>
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        <p class="space20">This model helped us understanding the outcome of overexpressing GlgB and GlgX in the lab in an <i>E. coli</i> cell. </p>
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<p class="space20">You can learn more by clicking on the image on the right.</p>
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    <div class="col-md-5 col-md-offset-1  col-sm-offset-1 space30 text-center">
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                    <div class="success-work">
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                        <div class="success-work-desc">
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                        <img src="https://static.igem.org/mediawiki/2015/e/e1/NRP-UEA-Norwich-kinetic-pathway-copy.png" class="img-responsive ">
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                          <a title="Kinetic model"  href="https://2015.igem.org/Team:NRP-UEA-Norwich/Modeling" class="btn outlinebtn  space50">
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                            Read More
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                          </a>
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    <h2 class="title1" id="ref">References</h2>
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    <p><a name="1"></a>1. Meléndez-Hevia E., Waddell T.G., and Shelton E.D., 1993, <i> Optimization of molecular design in the evolution of metabolism: The glycogen molecule </i>, Biochem Journal, 295, p. 477–83 </p>
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<p><a name="2"></a>2. Bajka B.H., Clarke J.M., Topping D.L., Cobiac L., Abeywardena M.Y., and Patten G., 2010, <i> Butyrylated starch increases large bowel butyrate levels and lowers colonic smooth muscle contractility in rats </i>, Nutrition Research, 30, p. 427–34</p>
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<p><a name="3"></a>3. Wilson WA, Roach PJ, Montero M, Baroja-Fernández E, Muñoz FJ, Eydallin G, Viale AM, Pozueta-Romero J (2010) <i>Regulation of glycogen metabolism in yeast and bacteria.</i> FEMS Microbiology Reviews 34:952–85</p>
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      <!-- start sponsors section -->
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                    <h2 class="gray">MANY THANKS TO OUR SPONSORS</h2>
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                    <h3>Useful Links</h3>
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                    <h3>Contact Us</h3>
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                        <li>nrpuea.igem2015@gmail.com</li>
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                        <li>Norwich Research Park,</li>
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                        <p class="fsize18 space10">We are the NRP-UEA-Norwich 2015 iGEM Team. </p>
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Revision as of 10:58, 16 September 2015

House of Carbs

Modelling and Software

While we were bringing all the parts together in the lab, a lot of unanswered questions started to raised: How does glycogen and starch look like in real life? How will GlgX and GlgB expression affect the glycogen global structure? How this branching and debranching process take place? And, how will the acyltransferases add the acyl group into the glycogen/starch molecule and in which position? Will this addition affect the functionality of the molecule?

Thanks to computers, software and maths, we were able to predict the outcome of all this processes to help us understanding what was going to happen in the lab.

Software: Glyco2D

We used glycogen as a model system to gain a better understanding of the parameters involved in carbohydrate structure, branching and modification.

We built Glyco2D based on the mathematical model that described the structural properties of glycogen based on different parameters such as chain length, branching degree and the number of tiers1.

Then we used the software to model the putative changes in glycogen structure depending on the location of the modification. Our aim was to produce carbohydrate molecules with 5-10% of the residues modified since this level of butrylation (achieved by chemical modification) has positive benefits to the colons of rats 2.

You can learn more by clicking on the image to the right.

Read More

3D models

We build 3D models of carbohydrates (glycogen and the 2 components of starch -amylopectine and amylose-) to get a better understanding of the effect of branching degree and chain length on the real structure. We used the SWEET software to build them.

We developed a pipeline to 3D print these molecules. After several attempts, we managed to have our own 3D printed glycogen!

You can learn more by clicking on the image on the right.

Read More

Kinetic modelling

To analyse the efficiency of the branching (GlgB) and debranching (GlgX) enzymes in glycogen production, we generated a set of differential equations to explain glycogen biosynthesis. We also incorporated all the enzymes involved in the pathway starting from taking the glucose from the medium 3.

This model helped us understanding the outcome of overexpressing GlgB and GlgX in the lab in an E. coli cell.

You can learn more by clicking on the image on the right.

Read More

References

1. Meléndez-Hevia E., Waddell T.G., and Shelton E.D., 1993, Optimization of molecular design in the evolution of metabolism: The glycogen molecule , Biochem Journal, 295, p. 477–83

2. Bajka B.H., Clarke J.M., Topping D.L., Cobiac L., Abeywardena M.Y., and Patten G., 2010, Butyrylated starch increases large bowel butyrate levels and lowers colonic smooth muscle contractility in rats , Nutrition Research, 30, p. 427–34

3. Wilson WA, Roach PJ, Montero M, Baroja-Fernández E, Muñoz FJ, Eydallin G, Viale AM, Pozueta-Romero J (2010) Regulation of glycogen metabolism in yeast and bacteria. FEMS Microbiology Reviews 34:952–85

MANY THANKS TO OUR SPONSORS

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  • nrpuea.igem2015@gmail.com

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  • Norwich, NR4 7UH, UK.

We are the NRP-UEA-Norwich 2015 iGEM Team.

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