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| | + | $('#animation').css({marginTop: '+=150px'}); |
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| − | <h2>Notebook</h2>
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| | + | </script> |
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| | + | <img id="Banner" alt="Banner By Natascha Muller" src="/wiki/images/0/03/Banner_Pretoria_UP.png" style="width:30%; padding-top:7.5%;"/> |
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| − | <!--*******************************************************************************************--> | + | <!--<h4 id="description">SYNCHRONIZED, CONDITIONAL, GENETIC CHEMOTAXIS PROGRAMMING</h4>--> |
| − | <!--******************************************SLIDESHOW****************************************--> | + | <h2 id="description"> Synchronized, Conditional, Genetic Chemotaxis Programming </h2> |
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| | + | <img id="animation" alt="Animation by Schae Ind" src="/wiki/images/1/15/Up_animation.gif" /> |
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| | + | </div> |
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| | + | <div align="center" style="width:100%; padding-right:6%;"> |
| | + | <h3 style="clear:both;"> Project Description </h3> |
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| | + | <p> |
| | + | The Pretoria UP iGEM team of 2015 have proposed a design for intelligent motile bacteria based on a combination of DNA modules that confer different functions. The synchronous behaviour of the bacteria will be achieved through a quorum sensing module allowing the population to behave as a swarm instead of independent units. A conditional response to an environmental signal is conferred through a post transcriptional control mechanism known as riboswitching, thus the bacterial swarm may recognise and respond to a chemical attractant. Since the system makes use of several modular components, an AND gate is required to process the various signals which in turn would trigger a genetic switch in the bacterial chemotaxis. The irreversible change is programmed by a DNA recombination switch which inverts the directionality of a promoter through the Cre-loxP pathway. We invite you to explore the various aspects of the project on this site. |
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| − | <th class="AJR_TH"> </th>
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| − | <th class="AJR_TH"> <h4 style="width:160px; text-align: center;">Date</h4> </th>
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| − | <th class="AJR_TH"> <h4 style="text-align: center;"> Activity</h4> </b></th>
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| − | <th class="AJR_TH"> <h4 style="text-align: center;">Participants </h4> </b></th>
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| − | <tr class="" ><td class="AJR_TD" ><img id="Banner" alt="Hand" src="/wiki/images/3/3e/Up_design.png" /></td> <td class="AJR_TD" > 2015-03-03 </td> <td class="AJR_TD" > Introduction to iGEM by advisor Steven Hussey.
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| − | Examples of successful iGEM projects were discussed.
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| − | Started to think about project ideas. </td> <td class="AJR_TD" > Interested parties and advisor Steven Hussey </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ><img id="Banner" alt="Hand" src="/wiki/images/3/3e/Up_design.png" /></td> <td class="AJR_TD" > 2015-03-24 </td> <td class="AJR_TD" > Participation criteria for iGEM team discussion.
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| − | Attendance by 19 interested students, final team size will be 8.
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| − | Applications for Pretoria UP iGEM team by 13 April. </td> <td class="AJR_TD" > Interested parties and advisor Steven Hussey </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" >
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| − | <img id="Banner" alt="Hand" src="/wiki/images/c/c6/Up_lab.png" /></td> <td class="AJR_TD" > 2015-04-21 </td> <td class="AJR_TD" > The iGEM kit arrived </td> <td class="AJR_TD" > </td> </tr>
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| − |
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| − | <tr class="" ><td class="AJR_TD" ><img id="Banner" alt="Hand" src="/wiki/images/3/3e/Up_design.png" /></td> <td class="AJR_TD" > 2015-04-24 </td> <td class="AJR_TD" > Selection of final team members:
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| − | Axel Ind
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| − | Ricu Claassens
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| − | Vaughn Barendsen
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| − | Nomakula Zim
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| − | Thabang Msimango
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| − | Modjadji Makwela
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| − | Gert Pietersen
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| − | Brad Querl </td> <td class="AJR_TD" > Interested parties and advisor Steven Hussey </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ><img id="Banner" alt="Hand" src="/wiki/images/3/3e/Up_design.png" /></td> <td class="AJR_TD" > 2015-04-28 </td> <td class="AJR_TD" > First meeting as the UP iGEM team 2015
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| − | Registration of team with iGEM HQ
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| − | Shortlisting of project ideas from which we would choose the best one to work on as a team
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| − | Introduction to BioBricks and how the repository works </td> <td class="AJR_TD" > Interested parties and advisor Steven Hussey </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ><img id="Banner" alt="Hand" src="/wiki/images/3/3e/Up_design.png" /></td> <td class="AJR_TD" > 2015-05-09 </td> <td class="AJR_TD" > Brainstorming workshop
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| − | We decided to build on WITS_CSIR’s Chemotactic “Biotweet” design
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| − | Discussed 5 potential improvements we could add:
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| − | 1) E.coli torrents (information collation)
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| − | 2) Travel history
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| − | 3) ”Mob-coli”
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| − | 4) Trade routes visualisation of motile E. coli
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| − | 5) Conditional “Reply Tweet” </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" >
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| − | <img id="Banner" alt="Hand" src="/wiki/images/c/c6/Up_lab.png" /></td> <td class="AJR_TD" > 2015-05-19 </td> <td class="AJR_TD" > 2015 iGEM project proposal
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| − | Prototype Circuit design:
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| − | </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ><img id="Banner" alt="Hand" src="/wiki/images/3/3e/Up_design.png" /></td> <td class="AJR_TD" > 2015-05-30 </td> <td class="AJR_TD" > Split the team into smaller groups to work in parallel on each functional module in the prototype, researching previous iGEM projects with similar components and browsing the iGEM BioBrick repository for desired BioBricks </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ><img id="Banner" alt="Hand" src="/wiki/images/c/c6/Up_lab.png" /></td> <td class="AJR_TD" > 2015-06-05 </td> <td class="AJR_TD" > The team was now at the stage where it could decide on which components to test and how
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| − | Recap on the different BioBrick assembly methods
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| − | Developed procedure for characterising our constructs deciding on aspects such as choice of vector, experimental conditions and competition requirements.
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| − | Refinement of switch: adoption of a permanent genetic switch
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| − | </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ><img id="Banner" alt="Hand" src="/wiki/images/3/3e/Up_design.png" /></td> <td class="AJR_TD" > 2015-06-12 </td> <td class="AJR_TD" > Decided on focusing our efforts on two modules and split the team in two groups to work on the separate modules:
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| − | Cre recombinase switch
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| − | AND gate
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| − | Whatsapp and Facebook groups were created for communication purposes.
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| − | A Google drive account was also created for the team to store all the work in one place.
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| − | Identified possible complications with the Cre recombinase system. </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ><img id="Banner" alt="Hand" src="/wiki/images/3/3e/Up_design.png" /></td> <td class="AJR_TD" > 2015-06-25 </td> <td class="AJR_TD" > The two initial designs for the modules that are being characterised:
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| − | AND logic gate
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| − | Recombinase Switch design </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <img id="Banner" alt="Hand" src="/wiki/images/7/73/Up_human.png" /><td class="AJR_TD" > 2015-06-29 </td> <td class="AJR_TD" > Discussed the possibility of attending the jamboree and how we could go about acquiring funding before September. </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td>
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| − | <img id="Banner" alt="Hand" src="/wiki/images/c/c6/Up_lab.png" /><td class="AJR_TD" > 2015-06-30 </td> <td class="AJR_TD" > Discussed the inverter switch mechanism and confirmed our design of the parts required to characterise this module.
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| − | BioBrick specifications were discussed in context of the assembly standard 10. </td> <td class="AJR_TD" > </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" >
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| − | <img id="Banner" alt="Hand" src="/wiki/images/c/c6/Up_lab.png" /></td> <td class="AJR_TD" > 2015-07-02 </td> <td class="AJR_TD" > Concerns raised about which plasmids to use for the experimental work to follow – multiple antibiotic resistance genes would be required.
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| − | It was decided that the parts would be cloned into pSB plasmids for the characterisation.
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| − | Decided that we would not have time to test the “AND” gate </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-07-06 </td> <td class="AJR_TD" > Discussed obtaining team shirts
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| − | Logo discussed to represent our team
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| − | Experimental procedures, as well as which track we are going to complete in in the jamboree. </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-07-20 </td> <td class="AJR_TD" > Finished compiling the sequences for gBlock synthesis and placed the order at IDT. </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-07-21 </td> <td class="AJR_TD" > The whole team is back from the holidays and ready for the final stretch before the Jamboree </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-07-28 </td> <td class="AJR_TD" > A budget for travel, residence, living expenses and registration for the Jamboree was compiled </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-07-29 </td> <td class="AJR_TD" > Email was sent to our iGEM HQ representative about the progress we are making and the current status of our project. </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-07-31 </td> <td class="AJR_TD" > The teams financial position and important decisions regarding the future directions
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| − | · Funding for the whole team to attend the giant jamboree would be impossible for 2015
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| − | · Two representatives and our academic representative would attend the jamboree
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| − | · A formal nomination and election process was held to chose representatives
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| − | gBlock synthesis order placed from IDT - promotion
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| − | Much of the wiki content already developed offline </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-08-01 </td> <td class="AJR_TD" > First labwork completed: transformations for the GFP and RFP positive control constructs
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| − | Finally decide on a team name for our project: ”Switch Coli” </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-08-07 </td> <td class="AJR_TD" > Submission of abstract for the team’s project </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-08-14 </td> <td class="AJR_TD" > Our team logo with the help of a qualified graphic designer – Marilyn Ekoka.
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| − | Prioritised content for the wiki </td> <td class="AJR_TD" > UP iGEM team 2015 and graphic designer Marilyn Ekoka </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-08-28 </td> <td class="AJR_TD" > Completed the iGEM safety form
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| − | Developed a survey which will be completed as part of the human practices aspect of our project </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-08-29 </td> <td class="AJR_TD" > We received our six gBlocks fragments and started cloning our BioBricks </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-09-04 </td> <td class="AJR_TD" > We participate in our first community outreach, at Lehlabile secondary School in Mamelodi. Gave a presentation on synthetic biology to Grade 11 science pupils, discussed synthetic biology innovation, and asked them to fill out our survey. </td> <td class="AJR_TD" > Lehlabile secondary School in Mamelodi grade 11 pupils and UP iGEM team 2015 </td> </tr>
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| − | <tr class="" ><td class="AJR_TD" ></td> <td class="AJR_TD" > 2015-09-06 </td> <td class="AJR_TD" > First set of content added to wiki </td> <td class="AJR_TD" > UP iGEM team 2015 </td> </tr>
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