Our team's resolve to contribute to the iGEM community stems from the commitment of wanting to provide for future iGEM teams. As an iGEM team we were profoundly inspired by previous iGEM projects and the wealth of knowledge and practices they shared, which also aided in forming our own project “Euphoresis”. In the spirit of paying it forward, we set out to give back and elevate the iGEM experience for teams to come.
During the making of our project, our team incorporated the principles of circular economy and sustainability in various aspects, with one of them being the development of a software. This software is based on optimizing resource utilization and waste reduction. Ultimately, it would work as an app where different companies, industries and businesses would be able to sign up and choose whether they are interested in discarding their waste or reclaiming the waste of another company. The companies that intend to discard their waste would have to fill a corresponding form that would contain the required information about the waste, like the type of waste, the quantity and the availability date. Then, this form is immediately listed in a database. On the other hand, the businesses that are interested in utilizing the waste of another company, will have access to a page that will have all the existing waste information that is acquired in the database and they will be able to navigate and decide on the waste that is more suitable for their desired use. Upon deciding, the software will provide the business with the other company’s details so they can carry on with the transaction. This software has the potential to revolutionize and facilitate the way businesses and industries communicate and operate, regarding resource efficiency. Moreover, it promotes collaboration and data sharing among stakeholders, fostering a circular ecosystem where materials, products, and information are shared with the ultimate purpose of reducing environmental impact, enhancing economic viability and actually contributing to a more sustainable and environmentally responsible future. We are hoping that the upcoming iGEM teams can utilize the code we created to conduct their own ideas or reformulate it accordingly to assist their own project needs.
After deciding to work with cyanobacteria on our project, our team noticed that they are not used as often as other microorganisms in synthetic biology (by iGEM Teams), resulting in a lack of standardization. Therefore, we aspired to provide some helpful insight on using cyanobacteria in synthetic biology, that derived from our own experimental experience and bibliographic research. In the handbook, under the supervision of our PI Mr Gkelis, we incorporated genetic and genomic information about cyanobacteria, while focusing on providing an insight on the recent advancements in genome editing and modeling in these microorganisms. The creation of “CyanoPedia: your guide to cultivating innovation” constitutes our team’s commitment to provide crucial information about the utilization of cyanobacteria in synthetic biology, aiming to encourage more teams to choose them for their iGEM projects and explore their potential.
Upon research, we came across useful information about how to design our desired genetic parts. New parts in iGEM encompass both basic elements, such as standalone functional DNA units like promoters or protein-coding regions that cannot be further subdivided, and composite parts, which are assemblies of basic parts capable of executing more intricate functions. After conducting a thorough review of the literature to identify unique sequences that would best meet the requirements of our microorganisms, we decided to design the following parts. These parts have been documented in the Registry of Standard Biological Part. We hope that future iGEM teams can incorporate these parts into their projects and elevate their research. Visit our parts page for more.
As new researchers in the field of synthetic biology, we understand that the engineering of groundbreaking biological systems is not an easy and smooth process, but it demands a deep understanding of the lab's complexity and a structured approach to problem-solving. Our team wishes to emphasize that troubleshooting is definitely not a sign of failure, in contrast, it demonstrates the tenacity and resilience that characterize scientific exploration and improvement.Below, we share our troubleshooting experiences and insights. We hope these resources will be valuable for future iGEM teams as they conduct their own experiments, tackle their problems, and overcome their obstacles.
When we were in the stage of assembly, we had trouble with the recombination of our plasmid with our genes of interest. We have included in our parts the prefix and suffix sequences so that they are compatible with the requirements of BioBrick assembly. On our first attempt, we followed the protocol of New England Bioline (NEB) for the double digestion using restriction enzymes and the protocol of NEB for the ligation using T4 DNA ligase, but both protocols had low success rate. The results of gel electrophoresis showed that the plasmids had not incorporated our parts, so we repeated the assembly with a different protocol.
The efficiency of Golden Gate Assembly compared to Biobrick was the reason we troubleshooted with a modified protocol. We based it on the Golden Gate Protocol from our instructor Mr. Giannakopoulos, and we replaced BsaI-HFv2 enzyme with the restriction enzymes E.coRI and PstI. The results from gel electrophoresis revealed the success of the protocol and almost all of our parts were inserted into the plasmid vector. We even accomplished a triple assembly since three parts were incorporated into the plasmid vector in one circle.
Our contribution doesn’t regard only the iGEM community, but affects the global community in general. Forest fires each year plague not only Greece, but the majority of the countries worldwide with enormous consequences to plant and animal ecosystems, global economy, and human well-being. The restoration of these disastrous fires is a slow process and never reaches the level of the initial balance. We believe that Euphoresis has the potential to evolve into a catalyst expedited and optimal restoration of burned soil after forest fires.
