Difference between revisions of "Team:BostonU/Design"

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<div id = "design" style = "font-size:300%; padding:75px 50px 25px 50px; text-align:center; color:#0071A7;">Design</div>
  
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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2016.igem.org/Judging/Awards#Special_Prizes"> design special prize</a>. </p>
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<br><br><center style = "font-size:225%; color:#0071A7;">Phase 1:</center><br>
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<center style = "font-size:200%; color:#0071A7;">Gene Activation Component</center>
  
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<p> Delete this box in order to be evaluated for this medal. See more information at <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions"> Instructions for Pages for awards</a>.</p>
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<p style = "font-size:150%; padding:25px 150px 20px 150px; color:#0071A7;">In order to make genes activate in response to certain signals, our system first needed a method to activate genes in general. We chose CRISPR/dCAS9-VPR as an activator. We chose  dCAS9 due to its ease of use and its ability to target specific DNA sequences. dCAS9-VPR targets specific sequences by binding to specialized RNA. Part of this RNA (gRNA) contains 20 base pairs that will act as a guide, guiding the dCAS9 to the complimentary 20 base pairs found upstream of a gene one wishes target. This can be seen in the info-graphic below:</p>
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<center><img src = "https://static.igem.org/mediawiki/2016/3/37/T--BostonU--ProjectDescription_dCas9_explanation.png" style = "padding:0px 0px 50px 0px; width:80%;"></center>
  
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<br><br><br><center style = "font-size:225%; color:#0071A7;">Phase 2:</center><br>
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<center style = "font-size:200%; color:#0071A7;">Analog Expression System</center>
  
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<p style = "font-size:150%; padding:25px 150px 20px 150px; color:#0071A7;">Once we were able to activate genes, we then expanded our system to activate genes to different levels, thereby achieving the graded analog expression level that we desired from our system. To accomplish this, we multermerized the 20 base pair target sequence, placing multiple copies
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of the target sequence upstream of the gene. By varying the number of copies, we were able to create a gradient of expression. The more target sequences we added, the more the gene was activated. This is illustrated in the image below:</p>
  
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By talking about your design work on this page, there is one medal criterion that you can attempt to meet, and one award that you can apply for. If your team is going for a gold medal by building a functional prototype, you should tell us what you did on this page.
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<br><br><br><center style = "font-size:225%; color:#0071A7;">Phase 3:</center><br>
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<center style = "font-size:200%; color:#0071A7;">Signal Integration Components</center>
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<p style = "font-size:150%; padding:25px 150px 20px 150px; color:#0071A7;">Finally, once we completed phase one and two, we expanded our system once again. Using recombinase based circuits, we were able to control which gRNA was produced. gRNA 1 corresponded to a reporter with one target sequence, and gRNA 2 corresponded to the same gene but with two of the target sequence. Releasing gRNA 1 turned the gene on to a small degree, and gRNA two turned it on to a large degree. We then incorporated two more gRNA's flanked by two more recombinase recognition sites, allowing the system to have a smoother, four point analog expression level increase. Since the recombinase circuits that release the different gRNA is completely digital, (the recombinases are activated by the digital prescience or absence of a signal such as a hormone and once activated, are extremely efficient) the system was a merger of digital signals giving rise to different levels of analog gene expression, as stated in our goal. A diagram of these circuits can be found below:</p>
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<center><img src = "https://static.igem.org/mediawiki/2016/0/06/T--BostonU--RealRecombinase.png" style = "padding:0px 0px 50px 0px;; width:80%;"></center>
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<p>This is a prize for the team that has developed a synthetic biology product to solve a real world problem in the most elegant way. The students will have considered how well the product addresses the problem versus other potential solutions, how the product integrates or disrupts other products and processes, and how its lifecycle can more broadly impact our lives and environments in positive and negative ways.</p>
 
<p>This is a prize for the team that has developed a synthetic biology product to solve a real world problem in the most elegant way. The students will have considered how well the product addresses the problem versus other potential solutions, how the product integrates or disrupts other products and processes, and how its lifecycle can more broadly impact our lives and environments in positive and negative ways.</p>
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<p>Teams who want to focus on art and design should be in the art and design special track. If you want to have a sub-project in this area, you should compete for this award.</p>
 
<p>Teams who want to focus on art and design should be in the art and design special track. If you want to have a sub-project in this area, you should compete for this award.</p>
 
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Revision as of 19:43, 17 August 2016



Design




Phase 1:

Gene Activation Component

In order to make genes activate in response to certain signals, our system first needed a method to activate genes in general. We chose CRISPR/dCAS9-VPR as an activator. We chose dCAS9 due to its ease of use and its ability to target specific DNA sequences. dCAS9-VPR targets specific sequences by binding to specialized RNA. Part of this RNA (gRNA) contains 20 base pairs that will act as a guide, guiding the dCAS9 to the complimentary 20 base pairs found upstream of a gene one wishes target. This can be seen in the info-graphic below:




Phase 2:

Analog Expression System

Once we were able to activate genes, we then expanded our system to activate genes to different levels, thereby achieving the graded analog expression level that we desired from our system. To accomplish this, we multermerized the 20 base pair target sequence, placing multiple copies of the target sequence upstream of the gene. By varying the number of copies, we were able to create a gradient of expression. The more target sequences we added, the more the gene was activated. This is illustrated in the image below:




Phase 3:

Signal Integration Components

Finally, once we completed phase one and two, we expanded our system once again. Using recombinase based circuits, we were able to control which gRNA was produced. gRNA 1 corresponded to a reporter with one target sequence, and gRNA 2 corresponded to the same gene but with two of the target sequence. Releasing gRNA 1 turned the gene on to a small degree, and gRNA two turned it on to a large degree. We then incorporated two more gRNA's flanked by two more recombinase recognition sites, allowing the system to have a smoother, four point analog expression level increase. Since the recombinase circuits that release the different gRNA is completely digital, (the recombinases are activated by the digital prescience or absence of a signal such as a hormone and once activated, are extremely efficient) the system was a merger of digital signals giving rise to different levels of analog gene expression, as stated in our goal. A diagram of these circuits can be found below:

This is a prize for the team that has developed a synthetic biology product to solve a real world problem in the most elegant way. The students will have considered how well the product addresses the problem versus other potential solutions, how the product integrates or disrupts other products and processes, and how its lifecycle can more broadly impact our lives and environments in positive and negative ways.

If you are working on art and design as your main project, please join the art and design track. If you are integrating art and design into the core of your main project, please apply for the award by completing this page.


Teams who want to focus on art and design should be in the art and design special track. If you want to have a sub-project in this area, you should compete for this award.

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