Difference between revisions of "Team:Valencia UPV/Modelling"

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<h2>Valencia UPV</h2>
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<p>Be patient, we are under construction</p>
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<h2><b>Modelling</b></h2>
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<p>Be patient, we are under construction</p>
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<li><a href="#main" class="button">Abstract</a></li>
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<li><a href="https://www.youtube.com/watch?v=D9Nx-kyEsO0"  id="button02" class="button" target="blank">Video</a></li>
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<li><a href="#scroll1" class="button">First steps</a></li>
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<li><a href="#scroll2" class="button">The circuit</a></li>
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<li><a href="#scroll3" class="button">Expression levels</a></li>
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<h2>AladDNA<br />
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Conventional production methods require huge and specialized infrastructures, making the establishment of new production facilities in remote locations complicated. What if we could just send information that could unfold on site? AladDNA is a new revolutionary system able to process genetic information and give a response based on the user’s needs just like a genie in a lamp! This system uses DNA to store information inside a plant seed, acting as a miniaturized and flexible biofactory capable of producing a myriad of bioproducts such as interferon alpha or anti-choleric vaccines. Equipped with a multiplexed-optogenetically controlled circuit, AladDNA can activate the production of different high-added value products upon the reception of external signals based on combinations of light stimuli. AladDNA allows bioproduction in any condition avoiding prohibitive costs due to infrastructures. No matter where you are or what you need, just ask your wish! Because AladDNA has no frontiers!
 
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<h3>Project overview</h3>
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<p>What is our project about? Which are the parts? What have we done? Check here to meet our biological circuit</p>
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<h2>First steps<br />
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<h3>Minecraft</h3>
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<p style="height:90px">The treasure of our policies and practices. The interactive platform has a lot of things to offer to you... Do you want to know more?</p>
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<p>We started by figuring out how it should work in a tree diagram, keeping the idea simple:</p><br/>
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<div class="row no-collapse 50% uniform" style="padding: 1em 1em 1em 1em;">
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<img class="image left" style="width:19em" src="https://static.igem.org/mediawiki/2015/a/a8/Alpha.png" alt="simple circuit" /></span>
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<img style="width:28em" class="image right" src="https://static.igem.org/mediawiki/2015/e/e5/Valencia_upv_tablaverdad.jpg" alt="truth table" /></span>  
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<p style="text-align:center;font-weight:bold">
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2 pulses <br/>
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4 possible combinations <br/>
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4 different products <br/>
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</p>
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<h3 style="text-align:left">Overview<br />
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<div style="text-align: center;"><img width=600em src="https://static.igem.org/mediawiki/2015/9/93/Valencia_upv_blackboxcircuit.png" usemap="#dnamap"></div>
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<p style="text-align:center;font-size:big">Our idea is to model a biological multiplexor that responds to two different light pulses.</p>
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<h2>The circuit<br />
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<h3>The device</h3>
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<p style="margin-bottom:1em;height:90px;">Discover our magic lamp, the device that makes the magic to put the biological circuit to work</p>
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<div style="text-align: center;"><img width="900em" src="https://static.igem.org/mediawiki/2015/0/00/Valencia_upv_wholecircuit.png" usemap="#circuitmap"></div>
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<area shape="rect" coords="0,0,120,120" alt="dna" href="https://2015.igem.org/Team:Valencia_UPV/Modelling#scrollsect1">
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<area shape="rect" coords="130,10,2046,190" alt="dna" href="https://2015.igem.org/Team:Valencia_UPV/Modelling#scrollsect3">
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<div style="text-align: center;"><img width="700px" height="600px" src="https://static.igem.org/mediawiki/2015/a/a6/Valencia_upv_circuitkey.png"></div>
 
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<img src="https://static.igem.org/mediawiki/2015/e/e6/Valencia_upv_circuit_thumb.png" href="https://2015.igem.org/Team:Valencia_UPV/Modelling" alt="model circuit example" />
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<h3>Modelling</h3>
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<h2>Expression levels<br />
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<p style="height:90px">A great multiplexed circuit needs a great modelling. So we did. Here the results!</p>
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<h3 style="text-align:left">Constitutive expression<br />
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<img src="https://static.igem.org/mediawiki/2015/2/26/Valencia_upv_goldmedal.png" href="https://2015.igem.org/Team:Valencia_UPV/Achievements" alt="gold medal" />
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<h3>Achievements</h3>
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<p style="height:90px">After months of hard work, here we show you what we've managed to do and why it is really important</p>
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<img class="resize" style="float: left; margin: 0px 15px 15px 0px; width:15em;" src="https://static.igem.org/mediawiki/2015/8/8a/Valencia_upv_equation1.png" />
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Proteins A, B, C and D, are used to control the expression of next level. As they keep being produced before light pulses are given to the organism, we will assume that their concentrations have reached their balanced values. This assumption lets us simplify several expressions from this first level, as we will demonstrate in the development of the mathemathical model.
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</p> <br/>
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<div style="text-align: center;"><img width=600em src="https://static.igem.org/mediawiki/2015/6/61/Valencia_upv_equation2.png"></div>
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<p style="text-align:right;font-size:big">same for B,C,D and E.</p>
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<div style="text-align: center;"><img width=400em src="https://static.igem.org/mediawiki/2015/7/77/Valencia_upv_equation3.png"></div>
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<p id="scrollsect4" style="color:white">.</p>
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<div style="text-align:right"><a left href="https://2015.igem.org/Team:Valencia_UPV/Modelling#scrollsect2" class="button alt">Back to circuit</a></div>
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<h3 style="text-align:left">Regulated expression: 2nd level<br />
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<span class="image right"><img width="500em" src="https://static.igem.org/mediawiki/2015/e/e5/Valencia_upv_equation4.png"></span>
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<div style="margin-right:40px">When A (E-PIF6), B (PhyB-VP16), C (Gal4-KDronpa) and D (NDronpa-VP16) are pro- duced, they interact with the operator binding sites OBD1 (in gE, gF and gG) and OBD2 (in gH, gI and gJ). Thus, proteins produced in previous levels, regulate the expression of the following ones. Light induced transcription, is due to the activacion of proteins B and D, whose structures change according to a certain light wavelenght. Theoretically, only if B* (activated) binds A (which is already attached to the genes), proteins E, F and G will be produced. On the other hand, it occurs similarly with D*, C and proteins H, I and J. The symbol ”+”, makes reference to those genes which can be transcripted because recombinases have not bind to them. </div> <br/>
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<a href="https://2015.igem.org/Team:Valencia_UPV/Modelling#scrollsect2" class="button alt">Back to circuit</a>
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Revision as of 20:15, 12 September 2015

Link title Valencia UPV iGEM 2015

First steps

We started by figuring out how it should work in a tree diagram, keeping the idea simple:


simple circuit truth table

2 pulses
4 possible combinations
4 different products


Overview

dna

Our idea is to model a biological multiplexor that responds to two different light pulses.

The circuit

dna dna dna

Expression levels

.

Constitutive expression

Proteins A, B, C and D, are used to control the expression of next level. As they keep being produced before light pulses are given to the organism, we will assume that their concentrations have reached their balanced values. This assumption lets us simplify several expressions from this first level, as we will demonstrate in the development of the mathemathical model.


same for B,C,D and E.

.

Regulated expression: 2nd level

When A (E-PIF6), B (PhyB-VP16), C (Gal4-KDronpa) and D (NDronpa-VP16) are pro- duced, they interact with the operator binding sites OBD1 (in gE, gF and gG) and OBD2 (in gH, gI and gJ). Thus, proteins produced in previous levels, regulate the expression of the following ones. Light induced transcription, is due to the activacion of proteins B and D, whose structures change according to a certain light wavelenght. Theoretically, only if B* (activated) binds A (which is already attached to the genes), proteins E, F and G will be produced. On the other hand, it occurs similarly with D*, C and proteins H, I and J. The symbol ”+”, makes reference to those genes which can be transcripted because recombinases have not bind to them.

Back to circuit