WATTS-APTAMER - UP_PRETORIA iGEM

Human Practice for Silver Medal:

First step: We want to spread awareness among medical students and staff at AinShams University, Faculty of Medicine about Synthetic biology and its applications in the medical field, and to encourage them to think outside the box and participate in such competitions and researches. Also we believe that we should work on children and raise them early on understanding the importance of science and research.

How: We started by questioning random students at the faculty of medicine Ain Shams University about simple facts regarding synthetic biology. The lack of knowledge about the subject encouraged us to meet up with the college’s dean to talk about spreading awareness among both students and staff. Upon his immediate approval, flyers were made containing simple information about iGEM, synthetic biology and its applications in medicine as well as other fields. This was performed through a small event at the faculty of medicine Ain Shams University. The event was a success; both students and staff alike were very interested at what we had to say and they kept asking for more information especially concerning the field of synthetic biology. Such enthusiasm only served to encourage us to extend our human practice beyond university doors.

This was performed in 2 high schools in Cairo where we sat down with a number of students in a class room and explained some fun facts about biology and shifted to the rising field of biology which is synthetic biology, we were very happy to see such a positive response from those amazing young people.

Second step: Our aim is to spread awareness beyond medical staff, researchers and hospital, hoping to reach all youth in Egypt and worldwide. How: This was performed by starting a series of animated web videos on our YouTube channel. These videos talk about synthetic biology in a simple and visually attractive way. We started this series to serve as a basic introduction to the wonderful world of synthetic biology. You can find our channel by clicking Here .

Human Practice for Golden Medal :

Aim is to spread awareness and knowledge among researchers and physicians at 57357 Hospital about Synthetic biology and to get their feedback and suggestions about our work.

How: An educational session was scheduled at 57357 Hospital. The whole team was there for the session, we started by setting up our poster, setting up the presentation and everything was good to go.

The session started by introducing team members, iGEM and the aim of our work. Then we went on to explain synthetic biology and our plan to use it along with bioinformatics to fulfill our aim.

We were considering using either nano particles or bacteria for the delivery of our circuit. Since our ultimate goal is reach a treatment that can be used by physicians for HCC, we asked the physicians attending our session about their preference for the vehicle to deliver our circuit. We explained the advantages and disadvantages of both ways.We found out that the majority of them preferred nano particles to bacteria for delivery. We also found out that the researchers as well displayed more interest in nano particles to be used in synthetic biology research.We integrated their opinions in our project and decided to use nano particles instead of bacteria this year. The session was concluded by answering the staff’s questions and their wishes of good luck.

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

March

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

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.

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.

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

Read more on our team composition on our Team page.

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

Read more on our engagement with Dr. Surridge-Talbot in our Human Practices section.

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