Team:TU-Delft/novel approach

Novel approaches on Human Practice

In the iGEM competition certain regions/continents (e.g. Africa and Latin America) have few teams and this over the past recent years. One of the reasons for this may be the lack of lab equipment for characterization. In our view, being able to participate in the iGEM competition should be accessible to everyone and the cost of equipment should not come to hinder creativity all over the world.
Therefore we took a noval approach in the Human Practive to open op synthetic biology by designing a DIY lab device, a low cost fluorescent scanner, the Zephyr. The Zephyr is more affordable than the exciting fluorescence scanner Tyhpoon (1500 dollar vs. 120,000 dollars). Furthermore, we designed it in such a way that it is easy for everyone to build. This way research is made possible in places where people don't have access to the expensive instruments (ownership) and encourages the idea of resource and knowledge sharing.

In iGEM projects safety is usually 'added'. We took the new approach by changing the natural part itself to become more safe. Signiferin, the antimicrobial peptide used, is at a concentration of 100-150 μM toxic to simian cells. We as the team 'Peptidor' were curious and enthusiastic to make our own novel peptide that is less toxic to simian cells. This way the use of these peptides would be safer, since the toxicity for humans would be less. We then used machine learning on antimicrobial peptides (AMP) databases. This model then derived rules by which we manually designed 3 novel peptides. They were also tested on COS-1 cells to prove that they are less not toxic to mammals than signiferin. This way the safety is improved by altering the biological part (the antimicrobial peptide), which is a noval approach on combining modeling, human practice and lab-work.

Implications of project

Our project has several implications on environment, security and safety. The main aim of our project is to develop a novel approach to combat MRSA (Methicillin Resistant Staphylococcus aureus). This clearly suggests that the safety, security and environmental issues that might arise, should to be addressed in an convincing manner.

The safety and security issues were considered for choosing some bacterial strains that were in need for our project. We had a detailed discussion with our Bio safety Officer (BVF), as we need to fight MRSA. She suggested us to use closely related species on the BSL-1 permit, as we have only the permit to work with BSL-1 strains. We decided to use the closely related species S. delphini (DSMZ 20771) which was listed in BSL-1 permit to carry out our minimum inhibitory concentration (MIC) tests.

The security of the people working in lab was considered as at most high priority while choosing to work with natural peptides. They were chosen not to harm the people working with it and the surroundings. The environmental security was considered to be the most crucial feature of our project. The ultimate application of our project will be a 'Band Aid' having our engineered bacteria. This rises plenty of environmental safety & security concerns on the use and disposal of genetically modified organisms (GMO). To address these concerns, we used a kill switch, BBa_K112808 that was engineered by UC Berkley 2008 iGEM team. The cells undergo autolysis once the required target protein is produced in required quantities.