Notebook

On February 7th, we had a team leader orientation, followed by a team orientation session on February 8th conducted over Zoom. Additionally, we organized a team hangout on February 9th, providing an opportunity for team members to connect and strengthen our relationships.

The subtrack teams started contacting last year’s members and organizing the workshops to clarify the different tasks and responsibilities. Each member had to do some research to get ideas for the topic of the project.

During this week, we engaged in an in-depth exploration of potential project tracks and reviewed the initial ideas that were contributed to the Flinga page. From these discussions, we identified several promising leads put forth by team members.
These included:
1. Investigation into the impact of unhealthy lifestyle choices on overall health and well-being.
2. Exploring the development and implementation of rapid testing methods to enhance efficiency and accuracy in various domains.
3. Advancements in enhancing food taste and additives to improve overall consumer experience and satisfaction.
4. Utilizing synthetic biology techniques for food production, aiming to revolutionize the industry by developing innovative and sustainable solutions.
After a voting process, two ideas were selected from each category for further consideration and exploration. Our team also worked together to update the Hilife proposal, making the necessary changes to keep it relevant and accurate. We also planned a workshop day to focus on human practices, where we can gain valuable insights for our project.

This week we presented a few potential project ideas briefly. Potential ideas:
1- Antibiotic treatments and gut microbiota disruption
2- Sugar craving and addiction, leading to metabolic syndrome
3- Optimization of the production process for a therapeutic protein
4- Rapid testing and at-home STD tests
5- Lab-on-a-chip, microfluidics for cheap diagnostic tests
6- Biodiversity Loss and sustainable protein production
7- Biological solution to plastic pollution
8- Lack of diversity and taste in vegan food
9- Energy generation from microbes
10- Drug delivery enhancement
11- Developing a biosensor for water system contamination detection
Voting was conducted via Telegram with each person selecting their top 5 ideas.

We focused on reviewing and refining the iGEM proposal during our progress review. To enhance our human practices section, we arranged a meeting with Zsófia, who participated in iGEM 2022. Zsófia's insights and recommendations were sought, and specific questions were prepared to facilitate productive discussions. In the meeting with our PIs, we discussed focusing on topics aligned with Aalto and the University of Helsinki’s research expertise. Good topics identified were: antibiotics (specifically antimicrobial peptides), a biological solution for plastic pollution, and improving the taste of vegan food. Markus approved these topics, considering available resources. We aimed to finalize the topic by next week through further research and contacting key individuals.

This week, effective communication with faculties was established about salaries and contracts, fundraising efforts were organized, presentation materials were developed, and the process of creating a logo was initiated.

This week, the team prepared presentation material for the deans of various faculties. Work was divided among team members. Productive brainstorming sessions were conducted to generate ideas and ultimately to reach a consensus on the logo design. Additionally, the team took the initiative to begin website development and activate social media efforts.

The aim was to present the project concepts to FIMAR, Onego Bio, and Rahul Mangayil. Collaboration with the ABOA iGEM team was also brought up. Individual meetings between the leaders and team members were planned for a later date. In terms of administrative tasks, a revised version of the sponsorship one-pager was to be created for distribution, and the iGEM registration deadline was noted. Contact with Heureka and finalizing the website, pending the logo, were also discussed. Finally, plans for team holidays and organizing fun activities were initiated. Importantly, we had a meeting with the School of Electrical Engineering at Aalto University regarding summer job positions.

The project, titled "PET-2-Protein: Revolutionizing Plastic Recycling and Protein Production," was discussed. Topics included the selection of plastic for degradation, the availability of enzymes such as PETase and MHETase, the use of HPLC for monitoring degradation progress, the potential use of scaffolds, and the feasibility of utilizing the end products as food for organisms. The team also addressed the possibility of combining the entire pipeline into a single system. The next steps included working on expression systems for PETase and MHETase, testing PET degradation using existing enzymes, and ordering the end products TPA and EG.
On Saturday 22.4 Cleopatra attended Harvard OpenBio Team’s online “Future of Synthetic Biology Conference”. There were many speeches by esteemed guests, such as Pamela Silver, Ph.D who is one of the founders and on the Board of iGEM and Marc Facciotti who had mentored 11 iGEM teams in the States. During the conference, there were also two workshop slots. Cleopatra attended the "Reimagining A Century of Synthetic Biology: From GMOs to Cyborgs and Beyond!" and "Being a Leader in the Research World" workshops, both of which were thought-provoking.
Lastly, we met with the School of Chemical Engineering and the School of Engineering of Aalto University regarding summer job positions.

A meeting was held with Nesli Sözer and Kari Koivuranta from VTT. Points of discussion included UV pre-treatment of plastic bottles, usage of enzymes for degradation, and the potential of Pseudomonas putida for utilizing the end products.
Additionally, we took part in a workshop hosted by Brendan Battersby at the Univeristy of Helsinki on the topic of mentoring, leadership and project management. From this meeting, we got in touch with Shameer Kodambiyakamenna, and Alesia Levanova, who would later act as an instructor for the team.

Social media and logo updates were shared. Collaboration efforts were initiated, and other iGEM teams were contacted. Decisions were made to prioritize collaboration and meeting with IBO Finland 2023 was scheduled. Search for relevant wet lab protocols was also initiated.

This week our discussions focused on the Human Practices aspect of our project. Furthermore, we decided to propose hosting a collaborative educational workshop at Heureka with the ABOA iGEM team. Finally, we also had a social event at Aalto Design Factory.

This week, we planned to meet with the Faculty of Agriculture and Forestry at the University of Helsinki to discuss our project. We also explored options for assistance with cloning and reached out to contacts for strains relevant to plastic degradation. We scheduled meetings with Thermo Fisher Scientific regarding a sponsorship deal, and with the previous Aalto-Helsinki iGEM team for advice. We also hosted a class for 6th graders at the Maunula Elementary School. Furthermore, we presented our project in Merja Penttilä's class at Aalto University. Lastly, we attended another mandatory laboratory safety session at Aalto University.

We had a meeting with the Faculty of Biological and Environmental Sciences from the University of Helsinki regarding summer job positions. We also had a meeting with Alesia Levanova where we discussed our initial insert designs and the cloning strategy. On the sponsorship side, we had meetings with Kemianteollisuus ry and Thermo Fisher Scientific. Work on the iGEM impact grant was begun. Lastly, this was our first week of full-time work.

This week, our team made significant progress in our research and development endeavors. We began working on our biweekly newsletter, updated our website and confirmed the suitability of our parts for optimized protein expression. We also placed orders for the necessary primers and inserts. Furthermore, we engaged in collaborative discussions, submitted sponsorship applications, and held a meeting discussing the financial situation of the team. Additionally we designed, planned, and printed our team T-shirts at the Iso Omena library.

Village selection for our project was made. In the dry lab, we ordered oligos, validated SpyCatcher/SpyTag designs, and integrated plastic degradation-related metabolic reactions. Updates were made to aaltohelsinki.com. We furthermore ordered primers for conducting colony PCR related to the SpyCatcher/SpyTag inserts.

This week, we began working in the wet lab, completed ligation, and performed metabolic modeling in the dry lab. We had a productive meeting with Bioethicist Heikki Saxen, integrated his advice into our project, and developed bioethics guidelines based on his notes and the recommendations make by the 2022 UCopenhagen iGEM team. We published project updates on social media, finalized the project description, and maintained a daily lab diary. We contacted VTT and Kemianteollisuus, and secured collaboration with Terkko Health Hub. Additionally, we booked tickets for the upcoming Nordic iGEM Conference, and the European Meet-Up.

Last week, we achieved significant milestones in the lab, generating E. coli T7 electrocompetent cells and completing crucial experiments involving restriction enzyme digestion, gel purification, and ligation. Our metabolic modeling work showed potential growth without extra amino acids, with co-expression of the fucO and aldA genes playing a vital role in EG utilization. Additionally, we had a productive meeting with Solar Foods' Susanna Mäkinen and Juha-Pekka Pitkänen, discussing alternative food sources.

Last week, significant progress was made in both the wet and dry labs. In the wet lab, we successfully conducted electrotransformation of new vectors (pRSFDuet-1 and pET-28a) in Top10 cells and prepared media (LB and M9). Additionally, new FAST-PETase and MHETase inserts were ordered, and we designed fucO and aldA inserts for pRSFDuet-1. Translation rate issues were addressed, and protein folding on Puhti was set up, with SpyCatcher/SpyTag design optimization underway. In human practices, we had a productive meeting with stakeholders in Bangladesh. Graphic design also progressed, including the publication of a comic chapter, the completion of a brochure, the progress being made towards a project poster.

We also had a valuable Zoom meeting with Ting Lu, receiving feedback on protein production and metabolic optimization for plastic degradation and bioconversion. He suggested bottleneck identification through HPLC analysis and conducting an adaptive lab evolution experiment.

In the dry lab, the team discussed the feasibility of SpyTag/SpyCatcher interaction with Sesilja Aranko. Initial findings suggest a moderate interaction strength for the construct. Further analysis will precede any order, with no rush.

With a focus on R. opacus due to Stephen's recommendation and literature, we're aiming to propose a growth hypothesis related to a specific pathway for our project presentation.

Conducting BLAST searches for the tph operon and tpaK in R. opacus DSM 43205, we folded relevant ORFs from hits.

Shifting to the wet lab, R. opacus and C. testosteroni were cultured in EG, TPA, and TPA + EG conditions, both individually and together. Broths and microbial stocks were duly prepared.

Lastly, we attended the iGEM Nordic Conference in Odense hosted by the SDU-Denmark iGEM team over the weekend.

In the Viikki lab, we prepared M9 medium with both EG and TPA, and both broth and agar for the plates. We cultured R. opacus and C. testosteroni with M9 + PET monomers and left them for overnight incubation. The following day when starting bioconversion, we noticed that after centrifugation, there were no pellets from the overnight culture. We decided to leave them in incubation for the duration of our upcoming trip. Our team had a great opportunity to attend Junior Jam - the European Meet-up conference in Münster hosted by the UniMünster iGEM team over the weekend.

In the wet lab, R. opacus and C. testosteroni were grown in laboratory evolution for the HPLC analysis. Insert digestion, gel purification and ligation had to be repeated. This step was repeated because the previous time the inserts were not cleaned and did not run in the gel. We did some troubleshooting and tried some minor protocol changes to make the protocol. After working, we did transformation, plating and restreaking from those transformation plates.

Meanwhile in the dry lab, primers for PCR were designed and ordered. We predicted ddG and selected the top 10 most negative candidates. We also used AlphaFold and looked into docking. We started to go through our survey data and cleaned up the data.

This week we started to record our promotional video and the voice-overs that we were going to use in it.

We also had a meeting with Finnish plastic agency called Suomen Uusiomuovi Oy. It was a great opportunity to talk and learn about plastic recycling in Finland and also hear their thoughts about our project.

In the wet lab in Viikki, we got training for the use of HPLC, after which we got results from R. opacus and C. testosteroni bioconversion. The results were good for R. opacus but we decided to repeat the bioconversion to see if some modification could also give better results for C. testosteroni. We also received the PCR primers ordered previously and conducted PCR amplification of our PETase and MHETase inserts.

The last biweekly newsletter for the summer was finished and sent out this week.

In the wet lab, we noticed that P. putida can grow on M9+30mM of TPA and M9+10gr/l of EG. We got good results from the transformation and were finally able to send our pRSFDuet-1 FAST-PETase construct for sequencing.

We worked on our wiki texts and started to transfer our survey data into a graphical form.

We shot the clips for our promotional video all over the Aalto campus. We got some good video footage and began editing the video.

We also organized the first Heureka workshop with the ABOA team this week. We were able to teach visitors about DNA, RNA, proteins and the field of synthetic biology in general.

We received promising results from the Sanger sequencing by Eurofins Genomics. The sequencing quality was excellent, and for one of the colonies, there was a perfect match between both reads. In the case of the other colony, both reads showed a single silent mutation, but it is worth noting that this mutation occurred in a specific peak with a relatively low intensity. This week in the wet lab we started a plastic degradation test and enzyme purification.

This week in the laboratory, we conducted Bradford protein assays on R. opacus bioconversion samples. We also took steps to prepare our samples for SDS-PAGE analysis.

We gave two presentations, one for Master's students and one for Bachelor's students. We aimed to introduce iGEM and our project while looking for potential members for next year's team.

This week, we also began to shift our focus toward writing wiki texts.

In the wet lab, we induced FAST-PETase expression by adding IPTG and attempted to confirm enzyme expression by SDS-PAGE analysis. Unfortunately, the result did not meet our expectations in terms of quality, so we decided to perform a second SDS-PAGE analysis.

Additionally, on Saturday, we had the Science Basement talk in collaboration with the ABOA team at the Oodi Library in Helsinki.

During our weekly meeting, we once again focused on wiki writing tasks and their deadlines.

We repeated the SDS-PAGE protocol, this time leaving it for two consecutive nights to destain. This time, the image of the gel showed some improvement. However, due to the absence of a control, we cannot definitively confirm that the observed band corresponds to our product.

We also had another meeting with Nesli Sözer because we were finishing the experiments and we followed her advice on merging the two initial ideas, which were enzymatic plastic depolymerization and microbial protein production. We asked for her expertise in biotechnology and food production to discuss and refine our approach.

This week, our goal was to complete all the wiki texts so that by the next week, they would be ready for publication on our wiki pages. After that our next step was to focus on the Grand Jamboree.

This week was spent on moving all of the completed texts to the wiki before the freeze on the 12th of october. Additionally, the registry pages were double-checked and finalized, and the attribution and judging forms were filled.

Our team participated in the Grand Jamboree in Paris, where we engaged in different workshops and presentations. We had our project presentation as well as the judging session. In the finale, we were thrilled to be nominated for the Best Environment Project, Best Wiki, Best Integrated Human Practices, and Best Education and proudly secured a gold medal!

We initiated the recruitment process for the Aalto-Helsinki 2024 team. The job description and application form were finalized, and we begun reaching out to Aalto University and the University of Helsinki to advertise our recruiting efforts. Furthermore, we have shared these updates on our social media platforms.

The wiki was proofread once more and updated with some mistakes fixed. Lastly, the achievement page was added before the final freeze day on the 14th of December.