Team:UNSW Australia/Medals

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Project

Description Design

Experiment

Overview Scaffold PAM AND TYCA LXYL-P1-2 AND DBAT Protocols Notebook Safety

Modelling

Overview Creating 3D Structure Files Molecular Dynamics Analysis Enzyme Kinetics

Human Practices

Overview Cancer Sustainability Commercialisation Integrated

People

Team Collaborations Attributions

Awards

Entrepreneurship Education & Public Engagement Medals Judging Form

unsw.igem@gmail.com

/unswigemteam

@unsw_igem

Medals

Overview

We have provided a list showing how we have met each of the various components of the medal judging criteria. Additionally, there are links to the corresponding pages if more information is required. Click on the icons below to see how we've met each criteria.

Bronze

Criteria	Description
Registration and Giant Jamboree Attendance.	Our team, UNSW Australia is registered, and we have 7 team members and one PI attending the conference.
Competition Deliverables	You are currently on the wiki look around to see how we have used the wiki to document our project. Our presentation and poster session are on the Friday of the Giant Jamboree! You can find our judging form here.
Attributions	We have summarised all the support received during this project. See our page here.
Project Inspiration and Description	We have discussed what inspired us as well as, described our project here.
Characterization	We successfully created RFC10 compatible BioBricks linked to our project. They have been sequenced and characterised experimentally. These parts can be attached to the Assembalse scaffold via the Snoop Catcher-Tag system. The BioBrick we are submitting for bronze is BBa_J45014.

Silver

Criteria	Description
Validated Part	We successfully, created the RFC10 compatible part DBAT-SnoopT. It has been sequenced and characterised experimentally. We have validated that this part works as expected through calculating kinetic values using the Ellman's Reagent assay. DBAT-SnoopT can be found in the BioBrick Registry as BBa_K3075001 .
Collaboration	We collaborated with different iGEM teams from all around the world across 4 collaboration efforts available here . We collaborated with University of British Columbia, Aalto Helsinki and Ku Leuven creating a business plan template that has been used by 7 igem teams to create a business plan. We also collaborated with the Macquarie University, Sydney University and Melbourne university team by inviting them to present at our symposium.
Human Practices	We incorporated our UNSW HP framework; consideration, engagement and integration to selectively understand the problem faced by our community surrounding Paclitaxel manufacturing. Through exploring a myriad of diverse perspectives, we could create the necessary changes to our Assemblase Scaffold that would maximise the outcome for the community. To find out more click here.

Gold

Criteria	Description
Integrated Human Practices	Our human practices elements have directed the design and experimental methodologies of the Assemblase scaffold. Consultations with various stakeholders allowed us to understand the need for an adaptable multi modular protein scaffold. This informed our lab design undertaking pathway A, B and FRET to demonstrate these qualities. Additionally, modelling work was performed to allow us to model the commercially viability of our co-localisation design and potential recovery methods for our system in a manufacturing setting. Different academics and companies expressed the need for a thermally stable and chemically inert substance as a result we utilised different hosts and structures to ensure this concern was mitigated. Other concerns were centred around sustainability and the environment resulting in pathway B that utilises a cofactor recycling method. Additionally, a guide was created to educate and improve Yew tree farming, which is the primary feedstock in Paclitaxel production. Overall thought and consideration allowed the Assemblase scaffold to meet stakeholders’ needs by addressing any concerns. This provided a maufacturing process that will prove useful for the world at large.
Improve a Previous Part	We successfully, created RFC10 compatible BioBricks linked to our project. They have been sequenced and characterised experimentally. We added a snoop tag and 6xhis-tag allowing our protein to bind to a snoop-catcher system. The BioBricks we are submitting for Gold is BBa_K3075004 which, is an improvement on BBa_J18930.
Model Your Project	Our modelling work informed our project predominately by validating the design of our Assemblase scaffold. The Molecular Dynamic analysis performed on our system gave us three measures. Firstly, the scaffold part’s flexibility was observed from the MD simulation and supplemented with Normal Mode analysis to validate our decision to attach larger enzymes to our structure. Secondly, the distance between the active sites of enzymes in our system was measured and utilised by a Diffusion and Kinetic model developed by a previous iGEM team. The results of this model verified our design hypothesis that co-localisation would increase the reaction yield of Paciltaxel. Finally, the size dimensions of our Assemblase system were approximately measured and used to inform the appropriate pore size that would hypothetically be used for a cross-flow filtration recovery of our system in an in-vitro bioreactor. We believe our modelling efforts are highly versatile and have been well-documented and by extension provide a helpful learning resource for future iGEM teams wishing to reuse our methodology and approach using molecular dynamics to their own projects.

Awards

Criteria	Description
Education and Public Engagement	Our team consistently prioritised community dialogue, with core values of mutual learning, respect and engagement informing our commitment to responsible science. Many of our activities centred around informing the general public of synthetic biology and the context in which it has arisen, such as within our symposium, which also allowed us to understand community perceptions and opinions on the value of SynBio. We applied this insight to create tools including a myth-busting video series that enabled academic and non-academic communities (including numerous iGEM teams) to engage with, and raise awareness of, SynBio - and thus increase their contribution to SynBio lab and policy work. These tools were carefully crafted following multi-way dialogues with various cross-sections of the community to best allow for interdisciplinary understanding and learning, and address concerns which were raised (like accessibility from non-biology majors). We also took steps to ensure accessibility across racial, geographical, age and educational lines.
Entrepreneurship	We have built a strong business case surrounding Assemblase which has culminated in a pre-seed investment of $100,000 from a private investor and interest from 9 firms. Stakeholder analysis has formed the foundations of our business case having analysed the market and interviewed pharmaceutical companies, VC firms and government. Our customer discovery led to an understanding of the market. This informed our customer need hypothesis suggesting there was a necessity for systems that could improve biochemical manufacturing lines. Assemblase aims to solve this problem through improving yield; impacting cost, reaction time and sustainability in the process. This hypothesis led to the creation of a promising Minimum Viable Product improving yield by 6x. Furthermore, we created a business plan and pitchbook used to share our business value when pitching to 4 investment firms. These resources have also mapped out the next 36 months for Assemblase with a clear market entry strategy.
Integrated Human Practices	We have integrated human practices to inform the direction of our manufacturing system design throughout the year, consistently refining our invented Paclitaxel manufacturing system to meet stakeholder requirements. Initial industry consultation and research informed our decision to use the Assemblase scaffolding system, given its industrially useful thermostability and self-assembly. Consultation throughout the year then helped lead system refinement, with Australian Government Pharmaceutical Benefits Scheme meetings redirecting the system’s focus from just production cost reduction to also prioritising environmental sustainability, given this is unmet by current Paclitaxel manufacturing. We also met with climate activists, and scientists from two separate green chemistry centres, who reinforced the need for sustainability and reaction waste management. This led to our inclusion of a second, sustainability-focused Paclitaxel synthesis pathway. Thus, our final system is two separate Paclitaxel synthesis pathways on Assemblase that work in conjunction (using each other’s by products and recycling material) to increase sustainability and decrease production cost.
Modelling	The modelling work done by our team is a testament to the engineering aspects of both iGEM and Synthetic Biology. Our Molecular Dynamics analysis accomplished our goals of measuring the distance between the active sites of our device as well as the flexibility of our scaffold part and the total size of our device. Moreover, we incorporated a model from a previous iGEM team, using our distance measurement to verify our co-localisation design in the absence of demonstrating the system worked. The methodology we detail for achieving our aims are versatile and hence provide a helpful resource for future iGEM teams to utilise and model their projects. Certainly, we focused on inspiring future iGEM teams to make use of molecular dynamic simulations so that they can better their understanding the of the function and operation of their projects.
Manufacturing	Our project proves revolutionary for all biochemical manufacturing processes. The adaptable nature as well as, the strong business case surrounding Assemblase will ensure our scaffold is incorporated into a plethora of manufacturing processes. This will remove inefficiencies in biochemical manufacturing lines in Australia as well as globally. Thus, reducing costs whilst, improving yield and environmental sustainability.