Team:Pretoria UP/Collaborations
Collaborating with other teams We collaborated with three different teams in the 2016 iGEM season.
We assisted team Macquarie by making a graphical user interface on MatLab showing how the concentration of various intermediates including ALA (Y-axis) changes over time (X-axis) in chlorophyll.
We created a documentary for team Aix-Marseille focusing on the socio-economic and political issues facing the current platinum sector, including the Marikana strikes.
Team Heidelberg 2015 ran their MAWS software to provide us with a target specific aptamer, in exchange for numerous candidate PDB files for them to test their system on, as well as valuable feedback about how well their aptamer performed in our thylakoid binding experiments.
Furthermore, surveys from iGEM Evry, iGEM Groningen and iGEM UPO-Sevilla were posted on our social media pages, and we also provided content to iGEM XMU-China for their compilation of the iGEM Newsletter.
Collaboration with Aix-Marseille University South Africa is regarded as having the largest platinum reserves in the world. The Merensky Reef stretching from southern Zimbabwe through to Rustenburg and Pretoria is the centre of platinum mining in South Africa. AMPLATS is the leader in platinum mining in South Africa, producing 40% of the total group platinum group metals. The Aix-Marseille University iGEM team identified problems faced by the mining sector which include limited sources, the use of hazardous chemicals to eliminate impurities, the disregard of safety measures and the lack of methods to recycle platinum next to highways.The solutions they came up with are to concentrate the platinum accumulated from roadside soil by phytoremediation plants and to transform it into nanoparticles. We assisted them by creating a documentary focusing on the socio-economic and political issues facing the current platinum sector, including the Marikana strikes. We also looked at the possible implications of their 2016 project. We had a discussion with Dr. Bertie Meyer, a senior lecturer in the Department of Mining Engineering in the Faculty of Engineering at the University of Pretoria. Dr. Meyer holds a degree in BEng Mining, MSc, Phd and Pr. Eng. We also had a discussion with Mr Ronald Henwood, a lecturer in the Department of Political Sciences in the Faculty of Humanities at the University of Pretoria. Mr. Henwood is a political commentator who holds a BA(Hons) from the University of Pretoria.
Interview with Dr Meyer at the University of Pretoria for team Aix-Marseille.
Interview with Mr Henwood at the University of Pretoria for team Aix-Marseille.
Collaboration with Macquarie University We assisted team Macquarie by making a graphical user interface (GUI) on MatLab. The GUI that was made is a graph which shows how the concentration of various intermediates including ALA (on the Y-axis) changes over time (X-axis) in chlorophyll. Team Macquarie provided a list of specifications for the interactive graph they wanted. These specifications include:
1. Creating an interactive display that plots the Chlorophyll concentration as a function of time.
The GUI was created using Matlab’s built in app, GUIDE (GUI development environment). GUIDE was ideal for this problem as it allowed for complete customisation of the of the interactive graph according to the specifications of team Macquarie.
The GUIDE interface allows the programmer to easily place plots, sliders, texts and buttons, amongst other handles, in the exact position that is needed. Figure 1 shows the GUIDE interface as well as the layout that was designed for Macquarie according to their team’s specifications. These included allowing the user to enter the initial total enzyme concentration as well as the ALA concentration. The user can also set the number of days using the slider. The plot is then generated automatically upon each input.
Figure 1: GUIDE interface with layout of GUI handles, including a set of axes, two "edit text" boxes, a "slider" and eight "static text" boxes. Saving this layout generates a skeleton code.
Once the desired layout was achieved, Matlab generates a skeleton code upon saving which can then be used to assign the various functions to the various handles. Attached is the code as well as the GUIDE layout structure that was used to generate the interactive graph. Three additional functions were added to the code. The first function, “plotter”, was used to generate the actual graph. This function requires three inputs, the total duration of time (in days), the total enzyme concentration as well as the ALA concentration. The second and third functions were required to model the actual concentration changes as a function of time and were provided by team Macquarie.
The two “edit text” handles were then programmed to allow the user to enter their desired enzyme and ALA concentrations. The slider was also programmed to extend or reduce the time duration (X-axis) of the plot. Lastly one of the “static text” handles was programmed to inform the user of the position of the slider, namely a value between 1 and 16 days. A zooming toolbar was also added to the GUI to allow the user to zoom into sections of the plot.
Running the code starts the newly programmed GUI with which the user can now change the various variables and see the effect it has on the concentrations. Figure 2 is a few screenshots of the GUI in action. Due to the nature of Macquarie`s experiments the graph was crucial to make an accurate conclusion about their results. We also helped them to solve coding problems on MatLab.
Figure 2-4: Screen shots of the GUI showing the plotter in action.
2. Increase or decrease the time duration with the help of a slider.
3. The maximum duration of time should be 16 days.
4. Users should be able to zoom in and out of plot.
Collaboration with Heidelberg University
Team Heidelberg was the second runner up during the finals in the 2015 iGEM competition. In our project we needed to design an aptamer that would specifically bind to a target site of a protein present in the Photosystem II (PSII) complex of the thylakoid membrane. Normally the only way to developget target specific aptamers is through the process of SELEX (Systematic evolution of ligands by exponential enrichment). However, SELEX would not indicate to us clearly what the target protein is, and overall is a very challenging and time consuming process. Fortunately for us, Team Heidelberg-2015 developed a software tool known as MAWS (Making Aptamers Without SELEX) which requires a PDB (Protein Data Bank) input file to generate an aptamer that binds specifically to a target site.
We decided to use this software to design our thylakoid aptamer as it would allow us to not only choose a specific protein in the PSII protein complex but also to choose which area of our target protein to use in the analyses and design an aptamer for. We attempted to use the MAWS software but ran into some difficulties, afterwhich we contacted the Heidelberg team and decided on a mutually beneficial collaboration. As team Heidelberg is still developing and improving the software they agreed to run the analysis for us on their systems, and give us an output file. In exchange we would provide them with numerous candidate PDB files for them to test their system on, which would allow them to determine possible shortcomings, e.g. one of which was that there is a limit to the size of the PDB input file for the system to work. We were also able to provide valuable feedback about how well their aptamer performed in our thylakoid binding experiments.
Animation depicting a single-stranded DNA aptamer bound to luminal side of thylakoid protein: CP47.
MAWS designed aptamer binding to luminal side of CP47.
MAWS generated aptamer.
