As with the scientific scenario as a whole, the iGEM competition demands interaction between different research groups, so that well-established partnerships can provide robust results for both parties involved. We established two very significant partnerships for the development of the work, based on the sharing of common interests and objectives. Contact with these teams occurred throughout the construction process of our project, through messages, virtual meetings, and even activities implemented in person.
The collaboration with the Ui_Oslo team gave rise to Celluminatti, a mutual support group in aspects of Human Practices, exchange of experiences on experimental design and mathematical modeling, as we share our efforts in studies of bacterial cellulose production and knowledge dissemination.
The USP-EEL team was also of great importance for the development of the project, allowing the establishment of a partnership focused on education and outreach activities, evidencing the shared concern of the teams with human practices.
With a bacterial cellulose production project, by an organism of the same genus as the bacteria used by our team, Ui_Oslo seeks to produce a co-polymer of cellulose and chitin, trough a co-culture assay, that can be used for a large number of applications. Considering our common goals and aiming to contribute to future teams, together we built Celluminati
With the dissemination of our project and activities developed on Instagram, Ui_Oslo noticed that our team was also working with bacterial cellulose production and coincidentally with an organism of the same genus (Komagataeibacter sp.). The social network was, therefore, an important means of communication, through which the partner team got in touch with us. It was how we scheduled the first, of many, online meetings to discuss projects, desires, and possible contributions.
A demand raised by our team was the urgency to find alternatives to deal with the delay in the delivery of crucial custom parts for the development of our project. From then on, we collaborated through fruitful discussions and elaborated alternatives for the absence of a gene of interest to Cellulopolis. In this context, Ui_Ui_Oslo contributed to the Troubleshooting, presenting advice on how to get our gene, through the establishment of a protocol for DNA assembly.
The gene they were missing was LexRO. LexRO is essentially a fusion protein in which the DNA-binding domain, LexA408 repressor of mutated Escherichia coli is fused with the blue light sensory domain RsLOV from Rhodobacter sphaeroides (purple bacteria). The Ui_Oslo Team´s suggestion was to: 1. fuse the LexA408 repressor with RsLOV by molecular biology methods, design specific primers with linker regions that overlap. Gene 1 3'end overlaps with 5'end of gene 2.Reverse primer of gene 1 (3'end for RsLOV) containing restriction enzyme site/GS-linker forward prime of gene 2 (5'end for LexA408) containing restriction enzyme site/GS-linker. 3. Isolate gDNA from Rhodobacter sphaeroides and mutated Escherichia coli K12 mutant and PCR amplify gene 1 and 2 using the designed primers. 4. Digest PCR product with the designed restriction enzymes. 5. Ligate it into the same enzyme-digested vector containing the first gene, E. coli vector.
Source: https://2022.igem.wiki/uioslo-norway/team
Our efforts were motivated by the desire to create a substantial education contribution, both about our iGEM projects in particular and in a more general sense about synthetic biology. Since our projects share the common attribute of working with a cellulose producing genus of bacteria (Komagataeibacter), we decided that it would be useful to draw a straightforward and pedagogically entertaining lesson about molecular biology around this theme. Using an experimental demonstration of bacterial cellulose synthesis and with the aid of an infographic, we can teach an interesting lesson for the students about how bacteria can synthesize polymers (like cellulose) from monomers (like glucose).
In order to help the students understand the science we’re demonstrating, as well as provide them with a means of retaining the information they learned that day, we created infographics for elementary and high school students. English and Norwegian high school level was used for education collaboration. The education partnership used the high school level and two versions were created: one in English and one in Norwegian. From Oslo’s team, we received the English version to use for educational outreach.
In one of our meetings, the Ui_Ui_Oslo team raised its interest in the possibility of exploring a mathematical model that could predict changes in the growth and cellulose production due to changes in the composition of the culture medium, thus being able to evaluate the efficiency of production of your copolymer of interest.
The team from Norway uses the bacterium Komagataeibacter xylinus for the development of its project, an organism of the same genus as the strain adopted in Cellulopolis, which has genetic and metabolic similarities. Therefore, our team, which was already working on metabolic modeling for cellulose production optimization analysis, proposed the development of models capable of answering the questions established by Ui_Ui_Oslo.
Using the Genomic Scale Model - GEM, it is possible to change the uptakes conditions and use this to understand the minimum requirements for the culture media. The production of chitin, part of their copolymer, uses nitrogen. So, to better understand the needs of cultivation, different cultivation conditions are simulated, evidencing how much NH4 the Komagataeibacter itself needs for its development. Ammonium becomes essential in the culture media once is consumed by E. coli, wich is growing in co-culture to produce the chitin, and also by Komagataeibacter, who needs for vital functions in the metabolism. In this scenario, it is possible to uncover the minimum of NH4 is needed by K. xylinus to grow that in the medium.
Besides, Komagataeibacter is an obligate aerobic bacteria, so oxygen presence in the media is mandatory. Therefore, the model was used to test different media conditions, changing not only the concentration of NH4 but also the O2 available, with the purpose of analyzing the minimum for cell growth and cellulose production.
Education is considered a very important aspect for Celluminatti teams, so several collaborations were built for this purpose. Among them, we emphasized the development of a game that presents the metabolism of Komagataeibacter for educational purposes. The app proposes the interaction of the player with metabolic control over cell growth and cellulose production, so that it is possible to change some of its metabolic parameters and observe the triggered phenotypic effects.
Working with no model organism can be a bit challenging, considering the difficulty of finding relevant information about the specie and even to adapt protocols and procedures para better response of our chassis. Taking this into account, the Ui_Ui_Oslo team found some obstacles in the Komagataeibacter transformation, which our team was troubleshooting. In this case, our action was to advise them on different concentrations of antibiotics that could be tested the growth of the bacteria and enable the team the organism transformation.
The jamboree is a highly awaited moment by the iGEM teams, but it can also be a period that generates some trepidation, based on the expectations of being able to present with quality all the work developed during the competition. In view of these aspirations, and in an attempt to contribute to improving our pitches, the proposal is that cellu-minatti teams collaborate with each other, recreating the performance of the iGEM judges. We arranged that in the next few days, after the WIKI freeze, both teams will coach each other, evaluating the group's performance in various aspects and providing tips and advices to improve the final presentation.
We gained more in-depth knowledge of the USP-EEL team project through the LATAM meeting, in which we already observed potential intersection points of our projects. Again social media was crucial for arranging first contact with USP-EEL, through which we arranged our first meeting to present our projects and consider possibilities of collaboration. After establishing this connection, throughout the competition the teams were in contact.
During our second meeting, we identified some difficulties regarding the mathematical modeling that our team was developing and USP-EEL, by exposing their models and sharing knowledge and ideas in the area, could help us to resolve this question.
One of the goals of our project is to enable the production of cellulose in a sustainable way, based on the use of alternative culture media for Komagataeibacter rhaeticus AF1. In this scenario, the USP-EEL team worked by contacting professors from their university to collect information that led to the cultivation of the bacteria in sugarcane bagasse residues.
If there is a thing that both teams shared, it is the passion for making knowledge accessible. With this in mind, our team traveled to the city of Lorena, where we held a presentation of our project and had a chat about the iGEM competition and its possibilities. The event, which was open to the public was only possible with the support of USP-EEL.
Outreach is another important aspect of our collaboration, USP-EEL was responsible for hosting a "Synthetic Biology Tournament" in an ETEC (technical school) in Lorena, where we contributed as judges of the event and shared information about our project.
The construction of WIKI is a fundamental part of the competition. The collaboration with USP-EEL allowed the teams to work together to develop a clear and cohesive group identity. This is not always an easy task, as it requires programming knowledge and care in exposing information. In this context, our team was responsible for assisting USP-EEL in changing the fonts used on the website.