iGEM 2016 — Team Pretoria_UP

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# Team:Pretoria UP/Notebook

WATTS-APTAMER - PRETORIA\_UP iGEM

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[PRETORIA\_UP 2016](https://2016.igem.org/Team%3APretoria_UP)

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* [Project Description](https://2016.igem.org/Team%3APretoria_UP/Description)
* [Parts](https://2016.igem.org/Team%3APretoria_UP/Parts)
* [Results](https://2016.igem.org/Team%3APretoria_UP/Results)
* [Medal Criteria](https://2016.igem.org/Team%3APretoria_UP/Medal_Criteria)
* [Proof of Concept](https://2016.igem.org/Team%3APretoria_UP/Proof)
* [Human Practices](https://2016.igem.org/Team%3APretoria_UP/HP/Silver)
* [Engagement](https://2016.igem.org/Team%3APretoria_UP/Engagement)
* [Collaboration](https://2016.igem.org/Team%3APretoria_UP/Collaborations)
* [Modelling](https://2016.igem.org/Team%3APretoria_UP/Model)
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* [Attributions](https://2016.igem.org/Team%3APretoria_UP/Attributions)
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* [Team](https://2016.igem.org/Team%3APretoria_UP/Team)

WATTS-APTAMER - UP\_PRETORIA iGEM

Our Notebook

On this page you can view the work we did each month, from February through October.

![...](https://static.igem.org/mediawiki/2016/9/92/T--Pretoria_UP--Notebook_Photo_4.jpg)
### February

Click for details.

![...](https://static.igem.org/mediawiki/2016/4/4b/T--Pretoria_UP--Notebook_Photo_5.jpg)
### March

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![...](https://static.igem.org/mediawiki/2016/4/45/T--Pretoria_UP--Notebook_Photo_6.jpg)
### April

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![...](https://static.igem.org/mediawiki/2016/e/e6/T--Pretoria_UP--Notebook_Photo_7.jpg)
### May

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![...](https://static.igem.org/mediawiki/2016/f/f3/T--Pretoria_UP--Notebook_Photo_8.jpg)
### June

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![...](https://static.igem.org/mediawiki/2016/f/f3/T--Pretoria_UP--Notebook_Photo_9.jpg)
### July

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![...](https://static.igem.org/mediawiki/2016/f/ff/T--Pretoria_UP--Notebook_Photo_1.jpg)
### August

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![...](https://static.igem.org/mediawiki/2016/d/d6/T--Pretoria_UP--Notebook_Photo_2.jpg)
### September

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![...](https://static.igem.org/mediawiki/2016/8/89/T--Pretoria_UP--Notebook_Photo_3.jpg)
### October

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# February

* Introduction to iGEM by instructor Dr. Steven Hussey
* Team member roles were discussed
* We looked at previous successful iGEM projects
* Vaughn presented slides on photo-bioelectrochemical cells as the basis of a potential 2016 iGEM project
* A general discussion and brainstorming session followed the presentation
* Dr Hussey would be contacting individual students to ascertain their interest in being a 2016 team member, before the final selection will take place
* We looked at three iGEM teams with photosynthesis-related projects. These are iGEM McGuire, iGEM Brown-Stanford and iGEM Harvard
* Discussion on bioelectrical and photoelectochemical cell prototypes
* Suggestion of designing aptamers to identify a conserved protein on chloroplasts. Aptamers also designed to be attracted to graphene.
* Presented at Sappi head office, Braamfontein, Johannesberg to request funding for 2016

![](https://static.igem.org/mediawiki/2016/8/8a/T--Pretoria_UP--Notebook_Photo_13.jpg)

# March

* Presentation to Department of Science and Technology for funding (10 March).

![](https://static.igem.org/mediawiki/2016/f/f0/T--Pretoria_UP--Notebook_Photo_12.jpg)

# April

* Discussions with Prof. Manyala and his students at the Carbon Technology and Materials Research Group, University of Pretoria (14 April) about manufacturing graphene electrodes. It was during these discussions that we decided to use graphene foam formed on nickel as the basis for our electrodes.

![](https://static.igem.org/mediawiki/2016/b/bf/T--Pretoria_UP--Notebook_Photo_11.jpg)

# May

* Discussed target proteins on thylakoid membrane CP43, CP47, D1 and D2 for which aptamers can be designed
* Decided to use MAWS software (Heidelberg iGEM team, 2015) to design aptamers
* Decided on using laccases as the reducing enzyme to recycle water at the cathode
* Reflected on our team hoodie designs!
* Had Project proposal on 20 May
* Met with Katie Barnhill, a postgraduate social scientist at North Carolina State University and who was visiting the University of Pretoria, for advice on how to communicate our project to a lay audience
* Tried using MAWS software (Heidelberg iGEM team, 2015) to design aptamers by replicating their experiments
* We met with Dr. Michal Gwizdala, Department of Physics, about physico-chemical considerations influencing the choice of target proteins for our aptamer in Photosystem II crystal structures
* Simon gave an extensive presentation on the engineering side of the project and highlighted some issues, including cell size, selectively permeable membrane, and making use of magnets.

![](https://static.igem.org/mediawiki/2016/3/34/T--Pretoria_UP--Notebook_Photo_10.jpg)

Pretoria\_UP after their project defense to the Department of Genetics (20 May).

# June

* We compiled a survey for PBEC experts toward our Integrated Human Practices portfolio. The Survey was hosted on Surveymonkey and sent out to 14 experts in the PBEC field that we identified from the literature. Unfortunately we got only one reply!
* Heidelberg 2015 iGEM team predicted one DNA aptamer against PSII. We synthesized this candidate along with a random oligo control for assessment of its ability to bind to PSII.

# July

* FMG/iGEM photoshoot with EyeScape photographers
* We filmed our project description video
* Due dates for iGEM: project description, about our lab and about our project forms submitted

![](https://static.igem.org/mediawiki/2016/c/c2/T--Pretoria_UP--Team_2.jpg)

Read more on our team composition on our [Team page](https://2016.igem.org/Team%3APretoria_UP/Team).

# August

* Brad mastered the art of thylakoid extractions
* We received offers to collaborate with Ain\_Shams-Egypt, Aix-Marseille, Groningen
* Initiated our SELEX experiments to develop a graphene-binding aptamer, starting with determining the washing buffer stringency
* Designed binding test for candidate aptamers designed using MAWS
* Started adding content to our Wiki
* Interview with Dr Karen Surridge-Talbot
* Identified and synthesised Eucalyptus grandis laccases with IDT
* iGEM due dates: track selection, title and abstract, Giant jamboree registration

![](https://static.igem.org/mediawiki/2016/e/ee/T--Pretoria_UP--Interview_Dr_Karen.jpg)

Read more on our engagement with Dr. Surridge-Talbot in our [Human Practices section](https://2016.igem.org/Team%3APretoria_UP/HP/Gold).

# September

* In early September we held the ACGT/IGEM synthetic biology workshop at the University of Pretoria
* Pretoria\_UP exhibition at the Women in Energy Business Summit
* Pretoria\_UP reached out to secondary school students through the UP with Science program
* Instant fame! Pretoria\_UP was invited by Tuks FM radio for an interview
* Lab work: binding tests, cloning of laccases (synthesised and existing laccases in the distribution kit)
* Met iGEM due date: team rosters
* Assisted team Macquarie by making a graphical user interface on MatLab

# October

* Presentation at SANEDI
* Lab work (LOTS of lab work)
* Filmed a short documentary for Aix-Marseille on how alternatives to platinum mining may affect the industry in SA
* Presentation to Genetics department
* Preparing for the iGEM Giant Jamboree presentation
* Working on poster
* BOSTON iGEM Giant Jamboree (YAY!)
* iGEM due dates: safety and judging forms, part submissions, wiki freeze

WATTS-APTAMER - PRETORIA\_UP iGEM

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2016  Pretoria\_UP iGEM

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