Logbook

The Team Member Recruitment interviews came to an end and we, the new team members, were informed about the selection results personally by email.

Team co-leaders met each other over a coffee and got in contact with Heli Viskari, our Primary PI. On Thursday 15th, our team was registered officially to the iGEM competition and payment was received the day after. On Friday, our team met up and got to know each other better. We discovered that everyone has passion for the medical field. Further, a meeting was scheduled with our long-time sponsor HiLIFE.

During this week, our team members from Helsinki University had personal meetings, so called “one on one's”, with the team co-leads. We discussed everyone's expectations of the project and talked about everyone's strengths and hopes to divide us into sub teams. The team co-leaders also contacted our advisor Yin Yin to discuss the topic ideation and to meet with the team. We also met with Olli Pietikäinen from HiLIFE to introduce ourselves.

Our team members from Aalto University had their personal meetings with the co-leaders. After all the meetings, the co-leaders once again met over a coffee to discuss the initial division of the tasks. We also got in contact with Hanna Juutilainen from Heureka to discuss our contribution to the Children's Medicine Day. We also met up to discuss the topic, and divided some areas that each one covered on their own, and afterwards met up again to discuss how to proceed.

Our co-leaders met with the primary PI Heli to discuss iGEM rules and timelines. The fundraising team decided how to proceed. We also asked Markus Linder officially to be our secondary PI. We took our first official portraits and met with Yin to discuss the project ideation. After the meeting, we narrowed our topic ideation down to utilizing bio-adhesives, either for:

• 1. Drug delivery, for example via gels or films to treat chronic wounds or burn injuries in challenging conditions such as oral
• 2. Advanced Diagnostics, by developing a probe to detect specific biomarkers associated with e.g., melanoma

During this week, the human practices (HP) and education -team prepared presentation material for the Children's Medicine Day -event, as well as went to Aalto asking volunteers who spoke Finnish to help with the workshop. The fundraising team had a workshop hosted by the previous team and worked on a proposal for HiLIFE to apply for funding. This consisted of for example, creating a budget and financing plan, project timeline and planning scientific communication and community outreach.

The week started by creating different drafts for our logo. In the middle, the fundraising team finalized and submitted the proposal for HiLIFE. The human practices and education -team prepared the physical teaching material for the Children's Medicine Day -event and made sure everything was ready. Finally on Saturday, the team had a long but rewarding day teaching children about DNA structure and basic laboratory skills.

In the beginning of the week our team received a nice email from TEK, asking if we would be interested in acting as a Jury for TuKoKe -competition. We said yes and started planning. We also created our first one-page flier to support fundraising. The fundraising team met with HiLIFE to properly introduce ourselves to the board and by the end of the week secured the funding. We also approached different departments of Aalto University regarding sponsorship and collaborations. Additionally, our team signed up for Nordic iGEM Conference (NIC).

April started by us selecting a jury for Tukoke -competition amongst ourselves and discussing the details in a meeting with Tuula Pihlajanmaa from TEK. Our team also had a meeting with Yin, where we discussed our recent literature research. We especially talked about bio-adhesive patches and their usages, for example regarding wound dressings, bacterial and biomarker detection, and bone fracture treatment. We also discussed some material compositions, and brought up biological logic gates as a topic but realized that it wouldn't necessarily suit our purposes. At the end of the week, a couple of us went to clean the lab with previous team members.

The two-day TuKoKe competition occurred at the beginning of the week, where some of our team members were acting as juries. Regarding topic ideation and research, we talked about our findings regarding the previously divided topics. Based on this, we created a presentation for Yin and Heli to finalize our topic idea. We also emailed more possible sponsors and bought our team tickets for the jamboree.

We were honoured to participate in the Leadership and Mentoring -course, hosted by Brendan Battersby at the University of Helsinki. We also opened our iGEM distribution kit after the course! We also decided that some of our members should participate in the BFH European Meet-Up, so we planned the trip and made the bookings. The Wiki team had a workshop with previous iGEM team. They ended up discussing writing as well, along with logo ideas.

Our team met with Yin and Heli to talk about our current progress. Regarding the hydrogel patch, we discussed how we could produce it, and one possibility was 3D printing. During this meeting we also brought up our idea of MFP-inspired drug delivery, and especially with Doxorubicin to reduce side effects. We decided to carry on with this topic.

May started by holding a meeting with the previous team to legally change the authority for Aalto-Helsinki Synthetic Biology Ry -organization, and therefore access our bank account. We also had rest of the workshops for each sub team, hosted by the previous team.

After settling down with our topic, we started more in-depth research and identifying different problems we might need help to solve. Therefore, our team contacted research scientists, and

potential companies for collaboration and sponsorships. We divided our team members to work with collaboration proposal for Thermo Fisher, material for the BFH European Meet-Up and iGEM Safety Forms as well as Promega funding. Our travel planning team finalized and booked the Grand Jamboree flight tickets. We ended the week by brainstorming the project name together.

We started and ended the week with weekly meetings to discuss the project details and set up schedules for meeting up with our sponsors. We updated our supervisors Heli and Yin about the project progression. As the BFH-meet up and meeting with Thermo Fisher were approaching, we refined the current deliverables. The fundraising team met with the deans of different faculties of the University of Helsinki for sponsorship and a couple of us met up with Heureka to discuss future collaborations. One highlight of the week was the laboratory safety introduction as we were eager to access the labs!

The week got off to a bit of a mixed start, as one of our team members stepped down from the project to chase another good opportunity besides iGEM. However, we got back on track quite fast and discussed the new allocation of work.

Regarding sponsorships, part of our team met up with Sirpa Riistama-Laari and Tiina Karla from Thermo Fisher and secured sponsorship. While waiting for lab work to officially start, a couple of our Aalto team members with permits to enter the labs sorted out our chemical inventory. They also met with Ville Takio to discuss dry lab and our construct designing more in detail. At the end of the week, we finalized and sent the BFH meet-up deliverables to Germany, along with Nisa and Mahin!

This week we had our laboratory safety tours, hosted by the invaluable lab technicians Ulla Åhman and Mikael Hytti. We wanted to contact experts working in the drug delivery field, so we scheduled a meeting with the pharmacy department of the University of Helsinki. We gained a lot of insight and more contacts for our research. One major thing this week was compiling our safety forms, among preparing applications for different grants, such as Jenny and Antti Wihuri Foundation and Promega.

This week, our team had a series of important meetings, including weekly -, Aalto lab -, Synbio meeting, and a meeting with Virpi Talman from University of Helsinki regarding cardiovascular pharmacology and drug discovery and her experience with Doxorubicin. She gave us more contacts, whom with we scheduled meetings.

Our main goal for this week was to complete the Safety Forms, and to familiarize ourselves properly with the Judging Handbook. Based on the book and the iGEM website, we discussed villages and different medal criteria. We discussed mandatory deliverables regarding iGEM, such as project description and human practices. To showcase our project, we worked on social media posts and designs along with drafting an update presentation for Heli. For team building, we organized a team barbecue activity!

This week, we focused extensively on refining our project description, advancing wet lab work, and designing our website. The team worked on social media content, created templates, and planned posts to enhance our online presence. Email communication was active, involving administrative work, corresponding with sponsors, and handling fundraising efforts. A project logo (Coales) was drafted, an unboxing video filmed for ThermoFisher, and work continued with wiki and the Aalto-Helsinki website. Human practices were a consistent focus, involving planning and implementation across various activities. Team engaged in programming tasks and handling funding aspects. A weekly meeting was held to discuss project updates, and we began preparations for the following week. We documented our wet lab progress in the lab notebook.

This week, we held our weekly meeting and several individual meetings to align our goals and progress. We continued to work on both dry and wet lab tasks, including writing lab protocols and instrument training session. Administrative efforts included invoicing, budget planning, and filling in reimbursement forms. The team worked on promotional content, newsletter and finalized content for social media platforms, including Instagram posts and introductory posts. Our outreach included follow-up emails regarding human practices and contacting research groups for meetings. Significant progress was made with visuals, our project logo, website and wiki design. The administrative aspects of the project continued, as well as machine learning and MATLAB tasks.

For upcoming events, we planned our trip to Turku for the Nordic iGEM conference, including budget estimates and material planning. We started preparing a poster and presentation for Turku and began organizing for the Grand Jamboree in Paris, including ticket arrangements. We engaged in meetings with Markus Linder to discuss various project elements. Additionally, we reviewed the judge handbook and discussed its contents again.

This week we started planning materials for the Nordic iGEM Conference. As a part of our human practises, we reached out to different stakeholders and experts and planned on making a survey. We sent our first newsletter to our collaborators and sponsors and met up with Hanna Hyyryläinen from Kemianteollisuus. Regarding writing, we discussed and distributed sections for each person to write for the wiki. In the lab, we got training to use the ÄKTA go protein purification system and PCR machine. We kept constructing our plasmids.

This week we finished making the materials for the Nordic Conference and finalized our discussions on medals and special prizes. We had a meeting with Senz Velasco Alba to discuss protein chemistry. We worked on finishing the initial survey and discussed it with the whole team in depth. In the lab we continued to verify our plasmids using PCR for example and transformed bacteria. We also did plasmid isolation to mention.

The week started by practising our presentation for the Nordic Conference and making sure the rest of the material was done. In the lab we send some of our constructs for sequencing, continued amplifications and got to visualize some of our samples. We were also problem solving our SDS-page's. At the end of the week, we attended the Nordic Conference in Turku.

After returning from our trip to Turku, we resumed work in the lab. With our major plasmids successfully transformed, we prepared samples for sequencing, from couple of which we also obtained the results, and moved on to the next logical step: prepping for protein production. We also had to catch up on a lot of emails and administrative tasks, such as reimbursements, which had piled up while we were away. Meanwhile, we continued our work on the surveys and prepared for our upcoming meeting with the Association of Cancer Patients in Finland.

The week ended on a high note with a really informative meeting with our advisor, Dr. Shiqi Wang, who provided us with valuable insights on how to proceed with Phase II of our project, which involves doxorubicin conjugation through a pH-sensitive linker. Additionally, Nea Möttönen, a researcher at Aalto University assisted us in the wet lab by providing Ni-NTA spin columns, allowing us to fast-track our protein purification steps while we awaited our order from BioNordika.

This week, we focused on advancing our project and preparing for upcoming events. We started by finalizing our Germany deliverables, including the Project Description, Short Introduction Video, Team Poster, and Presentation, and submitted them on time. Simultaneously, we worked on creating animations for our Wiki page to better explain our project.

In the lab, we performed plasmid isolation and repeated some transformations to ensure adequate protein production. This was essential as we planned to retry purification with Michael's assistance after returning from Germany. We also finalized and opened our surveys, printing QR codes to distribute during our trip to boost participation.

Before heading to Germany, we confirmed our meeting with Michael for the following Tuesday. Later, during our time at Junior Jam, we presented our project to other iGEM teams and judges, gathering invaluable feedback for our project. Being in Germany also boosted our confidence as we realized that many teams were facing the same challenges as us. Additionally, during this week, we also initiated the planning process for the 10-year anniversary of Aalto-Helsinki by creating the necessary groups and reaching out to alumni.

This week, we got back from Germany and jumped right into our lab work. Since our last protein purification attempts didn't go so well, we spent a lot of time with Michael Jeltsch, who guided us on how to properly use the FPLC and make better SDS-PAGE gels. The gels we were making before had issues like leaking or not letting the samples run properly, but with his help, we've made good progress. However, due to some unknown reason, protein purification was still unsuccessful leading us to sit down and back track the possible problems.

We also received a big order from ThermoFisher, which was our second order from them which would help us progress with our lab work with more ease since we could now try out our new resin since it could have been a potential cause of our failure. On the collaboration side, we had a productive meeting with the ABOA Turku team about how we can work together to promote synthetic biology. We also worked with TSB on our communication collaboration and had a great introductory meeting to discuss the details of the episode we're planning, plus the idea of writing a blog post for them.

Throughout the week, we focused on distributing our survey to get as many responses as possible, and we spent some time compiling data for our Wiki updates. On the administrative side, we made sure all the reimbursements were taken care of and held a team meeting to discuss our educational goals and ensure we're on track for the special prize. We also received our merchandise for the Grand Jamboree, which was really exciting as we prepare for the event.

This week, we stayed busy with a mix of lab work, meetings, and preparations. We started by holding our weekly team meeting in which we discussed the remaining timeline of the project and also our progress so far. We made a checklist of the remaining tasks and distributed them; we also had a discussion involving our social media presence and how to go ahead with our wiki. Additionally, we finalized our safety forms and sent them for review to our PI. Meanwhile, we worked on preparing our FPLC Columns which arrived just in time with our new resin so we could resume our attempts at protein purification, hoping that the issue was in the previous resin we were using. Simultaneously, we ran crude extracts to confirm the presence of our proteins after our successful transformations. On the project side, we had a discussion about the parts registry and how to proceed with it. We assigned and distributed the tasks so that both the writing and the experimental work could go on side by side.

We continued promoting our surveys by distributing informative leaflets across the campus (Aalto) to receive the maximal number of responses. A proper meeting for the 10-year anniversary also came about and the planning team made progress with its details. Further, towards the end of the week, we had a detailed update meeting with our secondary PI Heli Viskari, to inform her of our progress of the summer and also get her input on how to proceed considering our lab times were coming to an end. On the administrative side of things, we continued with completing our reimbursements and ensuring everything was within budget.

Continuing from last week, we had our pre-recording meeting with the team of TSB to fine-tune the narrative of our podcast episode and to get down the basic structure of how they record and what we should expect. We also discussed how to use their platform to educate people on the integration of synthetic biology in various different fields. We also set up a meeting for discussing how we could contribute to their blog for next week.

Since the week ending meant that we no longer had complete access to our office and lab spaces, some dedicated time was spent clearing up both the spaces and moving our things to the designated area since the semester was resuming and teaching was set to begin. Relevant people were also contacted to make sure that our lab extension time was approved, and our lab accesses would be in order starting next week. Overall, we had a productive week as we balanced lab work, collaboration, and administrative tasks.

As we neared the end of our iGEM cycle, the upcoming week was set to be incredibly busy. In the wet lab, we began purifying our proteins. Despite encountering several errors and troubleshooting challenges during the purification process, we were fortunate to receive assistance from Michael Jeltsch of the Pharmacy Department at the University of Helsinki. His support in troubleshooting and guiding us through the overall purification process was invaluable.

Additionally, we actively promoted our survey across all our social media platforms, emphasizing the importance of gathering as many responses as possible. Meanwhile, some of our team members met with The Science Basement team to do a final recording on a podcast series focused on synthetic biology.

This week, we conducted an interview with Jenni, the Executive Director of the Finnish Cancer Association. We also held a collaborative meeting with the ABOA iGEM 2024 team to plan for the upcoming Heureka event. Additionally, we confirmed our participation in the pitching event with Y Science 2024. In preparation for the BioArts event, we developed the necessary protocols, did the plates for the kids and finally on Friday went and hosted the first part of the workshop. Simultaneously, we dedicated many hours to analyzing and cleaning the data collected from our cancer surveys. Meanwhile, some team members focused on writing other content for our Wiki.

In the wet lab, we continued our work on protein purification and troubleshooting, making progress despite some challenges had begun the conjugation of the drug with Yin's plasmid as we had not purified ours due to time constraints.

Most of our team members were busy writing various sections for our Wiki, including parts registry, education, and Human Practices. The analysis on surveys kept going, since to our surprise there was a lot more of data that could also be compared with each other in many different ways, within and amongst the surveys. A lot of things came to an end, with Education we hosted the second Heureka workshop on 24th together with ABOA iGEM 2024, and second part of Bioarts on Wednesday. That same say, 25th, experiments in the wet lab got finalized. Simultaneously, we were thinking how we wanted our project description video to look like.

In the final days before the Wiki freeze, we'd be lying if we said we weren't feeling overwhelmed. Everyone was busy finishing their sections, while one of our team member was diligently coding the Wiki to ensure all the information was online.