Our team has worked very hard to try and attain as many
objectives as possible. Here we have summarized all the medal criteria we achieved to meet.
We have written and completed the Attributions page for our Wiki. We described what work our team members carried out, as well as what other people did for our project. More precisely, we specified what teams were created (logistics, communication, human practices, dry lab and wet lab), and how each member contributed to the project throughout the iGEM season. We have also listed all external people who helped us throughout the season: instructors, advisors, wiki coders and designers, artistic designers, translators, people who provided technical support at the lab, and others.
We have written and completed the Description page for our Wiki. We described the current global context, that led us to work on this project: a biological tool that can make some bacteria produce luminescence. We provided more information about how the project works and the biochemical pathways, in a clear and concise way. We described our project goals, and how we achieved them. We gave the characteristics of FIAT LUX, and how it could be used, as well as its potential. We described how and why we chose this project (answering a major concern of our century: food security), and wrote about the iGEM teams and research that inspired our project. We showed how our project was an application of synthetic biology, and how it could be used to tackle global problems. We used schemes to illustrate the biochemical pathways behind our tool. Finally, the description is complete with references.
We have written and completed the Contribution page for our Wiki. We know how important it is to contribute to the iGEM community: that is why we thrived to do so. We created and documented new parts, and added them to the Parts registry. By doing so, we provided future iGEM teams with a new and efficient reporter gene. We described tips and troubleshooting for the experiments part, and provided a plasmid stability test protocol. We provided future teams with a new open-source software to detect and analyze bioluminescence. We also provided them with an affordable prototype (as well as the instructions for the construction of this hardware). They will thus be fully able to use our reporter gene, and analyze it with our open-source software and hardware. Finally, we created an open-source card game, for any teams wanting to promote iGEM, synthetic biology and its applications.
Part Numbers: BBa_K4239008, BBa_K4239009, BBa_K4239010
We have written and completed the Engineering Success page for our Wiki. Our project has followed the whole engineering cycle, multiple times, to achieve our major goal: create a bioluminescence tool that allows bacteria to be tracked in situ. We have explained how we iterated the cycle several times. Indeed, the first example is the construction of our ilux operon in an iGEM Biobrick format: we had designed a strategy by mutagenesis (Design), assembled the genetic material we needed (Build), tested it according to our protocol (Test), and realized that it had not worked after performing an electrophoresis gel (Learn). We could thus develop another method during another iteration of the engineering cycle, by having part of the operon synthetized, for example. We finally obtained the Biobrick format of our construction, thanks to this second iteration of the engineering cycle.
Part Numbers: BBa_K4239006, BBa_K4239007
We have written and completed the Collaboration page for our Wiki. We explained and described the different and meaningful collaborations we did with teams throughout the iGEM season. They included thorough article writing and reviewing for a journal in collaboration with other teams, urgently helping out a team with IDT synthesis, a card game, and many virtual or real team meetups to discuss the project and give feedback/advice on the project and the presentation. We organized a call with a team from Greece, to go over the human practices. We wrote about how these collaborations helped our team, but also benefited the other teams.
We wrote and completed the Human Practices page. The issue of food security and responsible agriculture was always something we had in mind. We considered how our project could influence society in a positive and responsible way, and this was the principal value we had in mind when designing the project, but also at each stage of our project. After relying on our personal reflections, we also conducted lots of research and learnt to surround ourselves with experts and adapt our experiments to their opinions. Beyond the scientific aspect, contacting numerous specialists, from different environments like biotech industries or agricultural entities, as well as consumers, gave us a new perspective on the challenges and possibilities offered by the progression of our project. Their feedback encouraged us in our research and evidently showed that our project is responsible and good for the world. We expanded this logic into Integrated Human Practices.
We have written and completed the Proposed Implementation page for our Wiki. We have considered the end-user analysis to explain how people could benefit from it: the scientific community (a new tool for research), agroindustries (new products for agriculture), farmers (drop in crop loss and higher quality harvest) and the population (higher quality food). A scheme of our end-users analysis was done. We also put forward our vision of others using our project (with a scheme), namely research teams, future iGEM teams and potentially farmers. We also explained how our project would be implemented in the real world. We have discussed the matters of intellectual property, legislation and the process of commercialisation. Finally, we have also presented the safety measures that should be implemented and the global challenges our project is facing (providing a turnkey tool, extending the tool to many hosts, bacteria that can’t be cultivated, etc).
We wrote the Integrated Human Practices page. The conducted interviews gave us an insight on the potential impact of our tool in the agricultural industry, but it also concretely affected the construction of FIAT LUX. Discussions with agricultural research experts provided information on the phytopathogens we could study and led us to choose a more adaptable plasmid than what was originally wanted, making our tool more versatile for different crops diseases. By exchanging with advisors, scientific partners and other teams, we set priorities to our design, and prioritized the values of accessibility, environmental impact control, while also providing an innovative tool for future teams. We compromised to make our tool as efficient as possible, while still being aligned with our values, safety and technical issues. Finally, we managed to produce a safe, adaptable, useful and environmentally-friendly tool thanks to our Human Practice’s work.
We completed the Project Modeling page. The model developed is designed to verify possible effects of our plasmid on bacterial growth. We detailed the model’s assumptions. We analyzed the growth of bacteria transformed with our plasmids in presence of different antibiotic concentrations to model the optical density as a function of time. Hence allowing us to compare our design to models like Gompertz, Verhlust and Baranyi. According to the AIC criteria, we chose the model that best fitted our conditions. We chose parameters to conduct a several statistical analysis, to characterize the significant difference between them, and thus extrapolate conclusions about the growth. Furthermore, we studied the luminescence over optical density ratio to correlate the luminescence with the number of bacteria. The results are concisely presented. This substantial modeling enabled us to gain insight into how our tool functioned and how to adapt our experiments to the plasmid’s effect.
We have written and completed the Proof of Concept page for our Wiki. Our goal was to demonstrate that our project was likely to work in the real world. To do so, after engineering our parts in E.coli, we transferred our construction into phytopathogenic bacteria and infected plants. We assessed that transformed Dickeya solani was able to produce light thanks to our plasmid constructions, our software and hardware, thus proving the use of our tool. We focused on Dickeya solani, as this bacteria is responsible for causing the blackleg disease on potato tubers: our proof of concept is hence perfectly applicable to a real-life situation and emerging global problems. Thanks to this proof of concept, we were able to show that our project could honestly be a part of the solution to protect crops and secure a brighter future for global nutrition. We also extended the tool to other bacteria.
We wrote the Education-Communication page. Throughout the iGEM season, we made it a priority to develop and implement education and science education, to as many target audiences as possible, all the while following safety policies and adapting the material to the audience, to encourage open dialogue. We intervened in a summer camp for children, where we promoted synthetic biology through various fun activities, and in a middle school to present our project, microbiology and iGEM. We created a card game aimed at children, science lovers and experts, and worked on scientific popularization on social media to explain lab techniques, raise awareness about pesticides and biocontrol methods, to reach as many people as possible. We promoted iGEM and the applications of biology within our college, under different formats. Finally, we presented a seminar in our host lab to confront our project to experienced researchers and communicate around our tool.
Furthermore, we would like to enter the competition for the
following Special Prizes.
Our project is driven by our desire to address today’s threat to food security. FIAT LUX was designed with the aim of positively impacting society, agricultural practices, the environment and economy. To do so, we collaborated closely with many different stakeholders (biotech industries, agricultural organizations, law makers, consumers) and used their input to guide us throughout our project. We understood that pesticides were not a sustainable solution, thus inspiring our project purpose. Our exchanges with inov3PT (a research entity, specialized in seeds and crop protection) and the input and data they gave us, led to thorough ethical considerations from our team and drove the choice of the bacterium for our proof of concept (Dickeya solani). We thoroughly documented our thoughtful approach and project evolution throughout the iGEM season, hoping to inspire future teams. Our work shows that FIAT LUX is a project that is responsible and good for the world.
We quickly noticed that companies took interest in our project, as the existing solutions don’t meet today’s needs. inov3PT (FN3PT research entity, the French agricultural professional organization for potato seeds), to which we pitched our project to, showed interest in pursuing it after iGEM and funded the experimental part, giving credibility to FIAT LUX. We quickly understood the potential our tool had, especially as our proof of concept showed that the project was inventive and applicable. We conducted a thorough economical, market and risk analysis. We wanted to make sure that as many labs as possible could use our tool: we developed our own software and built our own hardware. We approached Kubii (an electronics supplier) who was eager to help us financially. We imagined a business plan, thought about “after” steps (an incubation by the entrepreneurship structure at INSA Lyon), and about the positive/negative long-term impacts of our solution.
We developed softwares to track the luminescence produced by bacteria directly in plants (a direct need for our project). Our desire was to generate an open-source code that is easier to use than existing standards, and accessible to all. It could be used as a basis for future innovation by iGEM teams. It has been validated by experimental work, and is well documented. We have two distinct parts to our software, encoded using Python: an autonomous data processing part, and a completely interactive part. The interactive part consists of importing the data in a user-friendly way, coupled with visualization of the data. It works on Linux, Windows, Mac, and is machine-independent. The whole code was written to make sure it can be embedded in new workflows. It is: open-source, cross-platform, interactive and efficient. We have also developed a user-friendly interface to control the Raspberry Pi camera for our hardware.
Listed in the Sustainable Development Goals by the UN, Zero hunger (#2) is an ambition that we must meet in order to secure a future where everyone has access to adequate nutrition. Our project will definitely help get us closer to this goal, by providing an efficient tool to search for treatments against phytopathogenic bacteria. We incorporated feedback from researchers from inov3PT (engineers specialized in biocontrol and pathogenic diseases), and they insisted on the fact that our tool would considerably prevent crop and economic losses, thus contributing to developing solutions towards meeting this SDG. They also confirmed that this tool will allow the development of biocontrol and more responsible agricultural practices by reducing the use of pesticides, thus contributing to the Responsible consumption and production goal (#12) and to the Climate action goal (#13) as well. We have documented our work, to allow future teams to build upon it.
We quickly realized, when exchanging with researchers, that an affordable and accessible machine was needed to analyze bioluminescence, compared to the expensive machines that currently exist. We learned from their feedback, and designed and constructed a prototype. We tested it with infected plants, and it was a great success. In the framework of open-source, the design and construction process is available in our Wiki, to enable reproduction by other teams. This proofer allows us to measure inner-temperature and humidity and detect bioluminescence when coupled to a high-resolution camera, or even to a simple smartphone, making it customizable to any circumstance. Furthermore, this device for less than $400 permits the tracking of luminescence, contributing to making it accessible to all, only with wood and electronic components. We hope that this hardware will help future teams to efficiently characterize their biobricks throughout time, with ilux as reporter gene.
Our ultimate goal was to promote synthetic biology and its applications, to as many people as possible. These people included children, middle, high school and university students, researchers and the general public. The format was adapted to each public, to promote mutual learning, such as: playful activities, a card game we designed, seminars, etc. The aim of these different formats was to include many people in shaping synthetic biology, thus engaging in a mutual dialogue, by taking the time to exchange with them. By engaging with so many different actors, we were given the opportunity to promote public values and the science behind synthetic biology, but also be influenced by these actors. We hope that these interventions encouraged people to contribute to the synthetic biology sector, as we have learned so much from these interventions. We hope that the work we documented on our wiki will inspire future teams.
Here is our best part: BBa_K4239008
We have generated a collection of parts that all work together towards our goal: creating a biotechnological tool that allows any bacteria to produce luminescence, in order to track their propagation in situ in real time. Our parts form a system of genetic constructions that allows:
- constitutive luminescence emission by any bacteria
- selective pressure of the plasmid in situ thanks to both our toxin/antitoxin systems
- its transfer between different bacteria when put in a conjugative plasmid thanks to the biobrick format
- the use as a reporter gene when the promoter is removed
All of these functional parts are fully documented on the Registry, showing how each Basic Part interacts with the others to form Composite Parts. This part collection can be very useful to future iGEM teams thanks to the documentation we provided as well as the modeling we performed.
Find our whole collection on the Parts page.
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