Difference between revisions of "Team:Edinburgh UG/Medal Criteria"
Sam Grainger (Talk | contribs) |
|||
| (12 intermediate revisions by 2 users not shown) | |||
| Line 77: | Line 77: | ||
<a class="nav-link" href="https://2018.igem.org/Team:Edinburgh_UG/Safety">Safety <span class="sr-only">(current)</span></a> | <a class="nav-link" href="https://2018.igem.org/Team:Edinburgh_UG/Safety">Safety <span class="sr-only">(current)</span></a> | ||
</li> | </li> | ||
| − | <li class="nav-item | + | <li class="nav-item active"> |
| − | <a class="nav-link | + | <a class="nav-link" href="https://2018.igem.org/Team:Edinburgh_UG/Human_Practices">Human Practices <span class="sr-only">(current)</span></a> |
| − | + | </li> | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | </li> | + | |
<li class="nav-item dropdown"> | <li class="nav-item dropdown"> | ||
<a class="nav-link dropdown-toggle" href="#" id="navbarDropdownMenuLink" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> | <a class="nav-link dropdown-toggle" href="#" id="navbarDropdownMenuLink" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> | ||
| Line 109: | Line 104: | ||
<div class="row"> | <div class="row"> | ||
<div class="col-lg-8 mx-auto"> | <div class="col-lg-8 mx-auto"> | ||
| − | <h1 class="brand-heading">Medal Criteria</h1> | + | <h1 class="brand-heading" align="center">Medal Criteria</h1> |
<p class="intro-text"></p> | <p class="intro-text"></p> | ||
</div> | </div> | ||
| Line 138: | Line 133: | ||
<thead> | <thead> | ||
<tr> | <tr> | ||
| − | <th> | + | <th>Previous parts we have improved </th> |
<th>Description</th> | <th>Description</th> | ||
<th>Supporting information</th> | <th>Supporting information</th> | ||
| Line 210: | Line 205: | ||
<p style="text-align:left"> <b>#2 Collaboration</b></p> | <p style="text-align:left"> <b>#2 Collaboration</b></p> | ||
| − | <p style="text-align:left"> We have done <a href="https://2018.igem.org/Team:Edinburgh_UG/Modelling_Collaboration"> Modelling Collaboration </a> with team Vilnius-Lithuania. | + | <p style="text-align:left"> We have done <a href="https://2018.igem.org/Team:Edinburgh_UG/Modelling_Collaboration"> Modelling Collaboration </a> with team Vilnius-Lithuania. We have attended meetups and hosted one of our own (<a href="https://2018.igem.org/Team:Edinburgh_UG/Collaborations">see here</a>).</p> |
| Line 232: | Line 227: | ||
<h2 style="text-align:left"><font color="gold">Gold</font> Medal Criteria</h2> | <h2 style="text-align:left"><font color="gold">Gold</font> Medal Criteria</h2> | ||
<p style="text-align:left"> <b>#1 Integrated Human Practices</b></p> | <p style="text-align:left"> <b>#1 Integrated Human Practices</b></p> | ||
| − | <p style="text-align:left"> The Edinburgh UG project looks to solve a fundamental problem facing synthetic biology | + | <p style="text-align:left"> The Edinburgh UG project looks to solve a fundamental problem facing synthetic biology – the lack of a chassis for safe environmental release – by developing a novel chassis. We had to ensure our chassis had all the basic characteristics that a synthetic biologist would require. Therefore, we consulted with a number of active researchers in synthetic biology in order to gauge what they would require in an ideal chassis. These consultations became a basis of our project design as a whole, and often changed the direction of large parts of our work. We recorded these consultations and decisions on a timeline (<a href="https://2018.igem.org/Team:Edinburgh_UG/Human_Practices">see here</a>) so that anyone may follow and understand the progression of our project.</p> |
<p style="text-align:left"> <b>#2 Improve a Previous Part or Project </b></p> | <p style="text-align:left"> <b>#2 Improve a Previous Part or Project </b></p> | ||
| − | <p style="text-align:left"> We have improved <a href="https://2018.igem.org/Team:Edinburgh_UG/Improve"> | + | |
| + | <p style="text-align:left">We have improved upon the sequence of the previous part BBa_K914009 which contains a kanamycin resistance gene with one serine codon -> amber STOP codon mutation. We have increased the number of serine -> amber STOP codon mutations up to 5 in our part BBa_K2725012 and so it now confers decreased kanamycin resistance in the absence of a suppressor tRNA, i.e. we have reduced the leakiness of the gene. See | ||
| + | <a href="https://2018.igem.org/Team:Edinburgh_UG/Improve">here</a> for more information. | ||
| + | </p> | ||
| + | |||
| + | |||
<div class="container"> | <div class="container"> | ||
<table class="table"> | <table class="table"> | ||
<thead> | <thead> | ||
<tr> | <tr> | ||
| − | <th>Parts | + | <th>Parts </th> |
<th>Description</th> | <th>Description</th> | ||
<th>Supporting information</th> | <th>Supporting information</th> | ||
| Line 246: | Line 246: | ||
</thead> | </thead> | ||
<tbody> | <tbody> | ||
| − | |||
| − | |||
| − | |||
| − | |||
<tr> | <tr> | ||
<td> <a href="http://parts.igem.org/Part:BBa_K914009">BBa_K914009</a></td> | <td> <a href="http://parts.igem.org/Part:BBa_K914009">BBa_K914009</a></td> | ||
<td>P1003* Ser133->Amber Codon</td> | <td>P1003* Ser133->Amber Codon</td> | ||
| − | <td> | + | <td>We have improved the characterisation of this part</td> |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td> <a href="http://parts.igem.org/Part:BBa_K2725012"> BBa_K2725012</a></td> | <td> <a href="http://parts.igem.org/Part:BBa_K2725012"> BBa_K2725012</a></td> | ||
| − | <td>P1003 Cassette with 5 amber | + | <td>P1003 Cassette with 5 amber STOP codons</td> |
| − | <td> | + | <td>This is our new part which is an improvement on the previous part <a href="http://parts.igem.org/Part:BBa_K914009">BBa_K914009</a></td> |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
</tr> | </tr> | ||
| Line 277: | Line 263: | ||
<p style="text-align:left"> <b>#3 Model Your Project </b></p> | <p style="text-align:left"> <b>#3 Model Your Project </b></p> | ||
| − | <p style="text-align:left"> Rational design of biobrick parts and protocols is an iGEM | + | <p style="text-align:left"> Rational design of biobrick parts and protocols is an iGEM principle that Team Edinburgh UG have embraced this year through mathematical modelling. The mechanistic modelling of our DNA degrading killswitch was used to check for the viability of our project and to decide which promoters and ribosome binding sites to use in the final build of our system. |
| + | We created a model which would tell us how often our semantic containment system would theoretically fail and allow horizontal gene transfer. This allowed us to be more informed when approaching the human practices side of out project. | ||
| + | We also trained an ordinal logistic regression classifier to be able to take growth curve data and identify which of our Semantic Containment parts was present within an organism. This provided a quick way to diagnose instances of Semantic Containment failure. For more information please read | ||
| + | <a href="https://2018.igem.org/Team:Edinburgh_UG/Model">here</a>.</p> | ||
<p style="text-align:left"> <b>#4 Demonstration of Your Work </b></p> | <p style="text-align:left"> <b>#4 Demonstration of Your Work </b></p> | ||
<p style="text-align:left"> All aspects of our project combine to provide a novel chassis for Synthetic Biology: Maxicells. These maxicells are easy to use and can be safely deployed into the environment through the use of our Triple Lock System <a href="https://2018.igem.org/Team:Edinburgh_UG/Demonstrate"> (link) </a> </p> | <p style="text-align:left"> All aspects of our project combine to provide a novel chassis for Synthetic Biology: Maxicells. These maxicells are easy to use and can be safely deployed into the environment through the use of our Triple Lock System <a href="https://2018.igem.org/Team:Edinburgh_UG/Demonstrate"> (link) </a> </p> | ||
Latest revision as of 01:50, 18 October 2018
Medal Criteria
Bronze Medal Criteria
#1 Registration and Giant Jamboree Attendance
We had a great iGEM season and see you all at the Giant Jamboree!
#2 Competition Deliverables
While reading our wiki, we hope you are excited to see our poster and presentation as well! We have also submitted a Judging form.
#3 Attributions
Our team is proud to state that we conceived the idea for Maxed OOT and subsequently designed and carried out all experiments ourselves. That said, there are many advisors who we would like to thank for helping to provide continuous advice and support, because, without them, we would not have been able to have achieved our goals. You can read more about people, teams and companies who helped us here.
#4 Characterization / Contribution
We successfully participated in InterLab study (see here). We performed and obtained successful results after performing both plate Reader and CFU and Flow Cytometry protocols.
Also, we characterised two parts from iGEM 2012 Paris Bettencourt. You can find out more about our improved parts here.
| Previous parts we have improved | Description | Supporting information |
|---|---|---|
| BBa_K914009 | P1003* Ser133->Amber Codon | contain a kanamycin resistance gene with one two serine -> amber codon mutation |
| BBa_K914018 | P1003** Kan resistant gene with 2 Amber Codon | contain a kanamycin resistance gene with two serine -> amber codon mutations |
Silver Medal Criteria
#1 Validated Part / Validated Contribution
Our validated parts:
| Parts Validated | Description | Supporting information |
|---|---|---|
| BBa_K2725016 | J23108 - SupD | Serine amber suppressor tRNA gene under J23108 Anderson promoter |
| BBa_K2725004 | FabV + Low expression cassette | Triclosan resistance gene from Vibrio fischeri |
| BBa_K2725013 | KanR 10* | P1003 kanamycin resistance with 10 amber stop codons |
#2 Collaboration
We have done Modelling Collaboration with team Vilnius-Lithuania. We have attended meetups and hosted one of our own (see here).
#3 Human Practices
(See gold medal criteria #1 Integrated Human Practices)
Gold Medal Criteria
#1 Integrated Human Practices
The Edinburgh UG project looks to solve a fundamental problem facing synthetic biology – the lack of a chassis for safe environmental release – by developing a novel chassis. We had to ensure our chassis had all the basic characteristics that a synthetic biologist would require. Therefore, we consulted with a number of active researchers in synthetic biology in order to gauge what they would require in an ideal chassis. These consultations became a basis of our project design as a whole, and often changed the direction of large parts of our work. We recorded these consultations and decisions on a timeline (see here) so that anyone may follow and understand the progression of our project.
#2 Improve a Previous Part or Project
We have improved upon the sequence of the previous part BBa_K914009 which contains a kanamycin resistance gene with one serine codon -> amber STOP codon mutation. We have increased the number of serine -> amber STOP codon mutations up to 5 in our part BBa_K2725012 and so it now confers decreased kanamycin resistance in the absence of a suppressor tRNA, i.e. we have reduced the leakiness of the gene. See here for more information.
| Parts | Description | Supporting information |
|---|---|---|
| BBa_K914009 | P1003* Ser133->Amber Codon | We have improved the characterisation of this part |
| BBa_K2725012 | P1003 Cassette with 5 amber STOP codons | This is our new part which is an improvement on the previous part BBa_K914009 |
#3 Model Your Project
Rational design of biobrick parts and protocols is an iGEM principle that Team Edinburgh UG have embraced this year through mathematical modelling. The mechanistic modelling of our DNA degrading killswitch was used to check for the viability of our project and to decide which promoters and ribosome binding sites to use in the final build of our system. We created a model which would tell us how often our semantic containment system would theoretically fail and allow horizontal gene transfer. This allowed us to be more informed when approaching the human practices side of out project. We also trained an ordinal logistic regression classifier to be able to take growth curve data and identify which of our Semantic Containment parts was present within an organism. This provided a quick way to diagnose instances of Semantic Containment failure. For more information please read here.
#4 Demonstration of Your Work
All aspects of our project combine to provide a novel chassis for Synthetic Biology: Maxicells. These maxicells are easy to use and can be safely deployed into the environment through the use of our Triple Lock System (link)
• We have assessed various methods of maxicell production and have concluded that they are easy to make through UV exposure and homing endonuclease action.
• The Triple Lock System - Colicin E2 kill switch, semantic containment and triclosan resistant plasmid backbone was produced
Contact EdiGEM18
Feel free to leave us a comment on social media!