Difference between revisions of "Team:William and Mary/Description"

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<h1>Description</h1>
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<p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
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<h1 style="color:green;text-align:center;">Background</h1>
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<div style = 'padding-left: 8%; padding-bottom: 10px;font-size: 25px' ><b>Motivation</b></div>
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A fundamental goal of synthetic biology is to be able to effectively interface with natural systems. No matter where you look, from synthetic organs to the production of biomaterials, synthetic systems are constantly closely interacting with the biological systems they serve. This means that synthetic systems must share in the capabilities and principles of their natural counterparts.</div>
  
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<h3>What should this page contain?</h3>
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However, when it comes to signal processing, synthetic biology lacks a in a crucial way: there is no existing system that can decode dynamic information. In nature, countless systems rely on decoding dynamic inputs (giving different outputs depending on how the signal is encoded). Take, for instance, the p53 tumor suppressor gene. Depending on the type of DNA damage the cell undergoes, p53 will be activated in a transient or sustained manner. These two inputs lead to vastly different outputs: cell death or apoptosis.ADD FIGURE OF TRANSIENT V SUSTAINED</div>
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<li> A clear and concise description of your project.</li>
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Until synthetic systems can similarly decode dynamic signaling, biologists will be unable to meaningfully interact with p53 and other dynamic biological systems.To address this problem, our team set out to create a circuit that can decode time-based inputs, opening up the field to more applied research in signal processing. </div>
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<h3>Inspiration</h3>
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<p>See how other teams have described and presented their projects: </p>
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<li><a href="https://2016.igem.org/Team:Imperial_College/Description">2016 Imperial College</a></li>
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<li><a href="https://2016.igem.org/Team:Wageningen_UR/Description">2016 Wageningen UR</a></li>
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<li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> 2014 UC Davis</a></li>
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<li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">2014 SYSU Software</a></li>
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<div style = 'padding-left: 8%; padding-bottom: 10px;font-size: 25px' ><b>The IFFL</b></div>
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In nature, a great number of systems that decode dynamic information have a similar genetic architecture: the incoherent feedforward loop (IFFL). IFFLs code for a protein and its inhibitor. </div>
  
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Figure 1: Schematic of an Incoherent Feed Forward Loop architecture. An activator (green) activates the production of a reporter/output (purple) as well as an inhibitor of the reporter (blue).
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<h3>Advice on writing your Project Description</h3>
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Based on abstract mathematical modeling, IFFLs are predicted to be temporal distinguishers, meaning their output is different depending on how the input was delivered. When subjected to a continuous input, the output is expected to be a pulse. When subjected to a pulsatile input, we expect to see a stepwise output. (cite plos)</div>
  
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We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be concise, accurate, and unambiguous in your achievements.  
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The p53 tumor suppressor gene mentioned earlier is built on an IFFL motif, as are many other relevant systems, such as ERK in determining cell fates. Clearly, IFFLs play a unique and critical role in biology, so bringing their decoding abilities into SynBio could offer boundless research opportunities.</div>
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<div style = 'padding-left: 8%; padding-bottom: 10px;font-size: 25px' ><b>Our Project</b></div>
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<h3>References</h3>
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<p>iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you thought about your project and what works inspired you.</p>
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Our team created an IFFL mathematical model tuned specifically to our system. Based on our modeling, we designed and constructed various IFFL circuits. We then investigated how these circuits responded to varying temporal inputs. Our results can be found here: link.</div>
  
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By researching the dynamics of genetic circuits, we are opening the doors to new possibilities in synthetic biology relating to dynamic signaling, thus broadening the ability of synthetic biologists to interact with natural systems. Through building and characterizing a diverse set of IFFL circuits, we have given every iGEM team access to the unique abilities of this genetic motif. We hope that teams will continue with our foray into the advancing field of dynamics within SynBio. </div>
  
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Revision as of 03:54, 17 October 2018

Page Title

Background

Motivation
A fundamental goal of synthetic biology is to be able to effectively interface with natural systems. No matter where you look, from synthetic organs to the production of biomaterials, synthetic systems are constantly closely interacting with the biological systems they serve. This means that synthetic systems must share in the capabilities and principles of their natural counterparts.
However, when it comes to signal processing, synthetic biology lacks a in a crucial way: there is no existing system that can decode dynamic information. In nature, countless systems rely on decoding dynamic inputs (giving different outputs depending on how the signal is encoded). Take, for instance, the p53 tumor suppressor gene. Depending on the type of DNA damage the cell undergoes, p53 will be activated in a transient or sustained manner. These two inputs lead to vastly different outputs: cell death or apoptosis.ADD FIGURE OF TRANSIENT V SUSTAINED
Until synthetic systems can similarly decode dynamic signaling, biologists will be unable to meaningfully interact with p53 and other dynamic biological systems.To address this problem, our team set out to create a circuit that can decode time-based inputs, opening up the field to more applied research in signal processing.
The IFFL
In nature, a great number of systems that decode dynamic information have a similar genetic architecture: the incoherent feedforward loop (IFFL). IFFLs code for a protein and its inhibitor.
Figure 1: Schematic of an Incoherent Feed Forward Loop architecture. An activator (green) activates the production of a reporter/output (purple) as well as an inhibitor of the reporter (blue).
Based on abstract mathematical modeling, IFFLs are predicted to be temporal distinguishers, meaning their output is different depending on how the input was delivered. When subjected to a continuous input, the output is expected to be a pulse. When subjected to a pulsatile input, we expect to see a stepwise output. (cite plos)
The p53 tumor suppressor gene mentioned earlier is built on an IFFL motif, as are many other relevant systems, such as ERK in determining cell fates. Clearly, IFFLs play a unique and critical role in biology, so bringing their decoding abilities into SynBio could offer boundless research opportunities.
Our Project
Our team created an IFFL mathematical model tuned specifically to our system. Based on our modeling, we designed and constructed various IFFL circuits. We then investigated how these circuits responded to varying temporal inputs. Our results can be found here: link.
By researching the dynamics of genetic circuits, we are opening the doors to new possibilities in synthetic biology relating to dynamic signaling, thus broadening the ability of synthetic biologists to interact with natural systems. Through building and characterizing a diverse set of IFFL circuits, we have given every iGEM team access to the unique abilities of this genetic motif. We hope that teams will continue with our foray into the advancing field of dynamics within SynBio.