Team:Sydney Australia/Medals
Medals
We have accomplished many things throughout this project. Click on the tabs below to see how our work meets the bronze, silver and gold medal criteria!
| Bronze Criteria | Pages that Contribute | How |
|---|---|---|
| Attributions | Attributions Page | We have described what work our team has done and how other people have helped us. |
| Project Inspiration and Description | Project Description | We have documented what inspired our iGEM project and why we feel it is a useful application of Synthetic Biology |
| Part Characterisation | Characterisation Page | We have characterised the thermal stability of the existing iGEM part, sfGFP. |
| Registration and Judging Form | Judging Form | We have registered for the Jamboree and completed the judging form. |
| Silver Criteria | Pages that Contribute | How |
|---|---|---|
| Collaborations | Collaborations | We have collaborated with three teams: Macquarie University, UNSW, and Dusseldorf University. We did lab work, gave a talk, and made a postcard for these collaborations. |
| Human Practices | Human Practices | We have engaged with the social context of our project through literature reviews and interviews with experts. |
| Validated part | Registry parts: Results page: Characterisation of PsiD/K/M in vitro | We have contributed the RFC10 compatible BioBricks PsiD and PsiK. We have confirmed that these parts work as expected in vitro, using purified proteins, and in vivo, with a resting cell assay containing the PsiD/K/M gene cluster. |
| Gold Criteria | Pages that Contribute | How |
|---|---|---|
| Integrated Human Practices | Human Practices | Our silver human practices work has allowed us to reflect on how to adapt our project to better serve society. We have changed the design of our project to use a two plasmid system as part of the integration of human practices. We have also generated a Scale Up plan. This is a plan for implementing our project in the real world, which has been shaped from our human practices work. |
| Improve a Previous Part/Project | Improve | We have improved an existing part, a Vivid blue light sensor, to create a strongly fluorescent Vivid protein. |
| Demonstration of Your Work | Demonstrate | We have proved that two of the four parts of our project work under realistic conditions, using a resting cell assay. |
| Model your project | Modelling | Using our codon harmonisation software, the Codonator 3000, we produced a number of codon harmonised sequences using different harmonisation methods, and applied the concept of information entropy to gauge the difference in entropy between the input and output sequences. Based on the results of our modelling, we predicted that a “nearest frequency” harmonisation model would be the best harmonisation approach for a given gene sequence, which we verified experimentally. |
Integrated Human Practices
When you aim to synthesise a prohibited substance, you need to make sure that you’re going to bring more benefit into the world than harm. We owe it to ourselves and to the community to make sure that our work is accessible to those who need this novel therapy while remaining socially and ethically responsible. To do so, we have integrated our own knowledge and expert suggestions into all aspects of our project, including current work and future avenues for investigation. We have explored the question “Why are we doing this?” through investigating the history, and the ‘what and how’ of psilocybin. We have answered the question “should we do this?” by investigating the safety of psilocybin and talking to the clinicians who would make use of our product. We have integrated suggestions and concerns through the design of our two-plasmid system, and through our proposed Bacillus subtilis shuttle vector. We believe that we have gone above and beyond to showcase how our therapeutic will be good for the world, and how we desire to mitigate any potential harm that could be caused by our project.
Software
Heterologous expression of proteins is a cornerstone of synthetic biology, but sometimes moving a gene from one organism to another doesn’t go down so well. Part of the reason is that codon usage may vary greatly from one chassis to the next: a relatively common codon in one organism could be rare in another, or vice versa — and often this is reflected by the availability of tRNA. Protein folding can be adversely affected when translation is too fast (or too slow), and tRNA availability is a strong mediator of the rate of protein translation. We have built the Codonator 3000, a program that takes a nucleic acid input and conducts codon harmonisation and codon optimisation for any source and destination chassis that has available coding sequences on NCBI. Optimisation replaces each codon with the most frequently used codon for that amino acid, whereas harmonisation attempts to match the codon frequencies of the source organism through either absolute rank or relative frequency methods. To our knowledge, no other such tool is publicly available with both the scale of choice in species, and in the implementation of multiple harmonisation algorithms.