Welcome to the Notebook of the Aalto-Helsinki team, where we briefly summarise our weekly doings and accomplishments. For information about the wet lab, please check out our protocols and experiments.
Interviews for the 2022 team as well as selection of new members occurred, with 3.5 team Aalto students and 6.5 University of Helsinki students making the final cut (one team member studies at both!).
On 7th February, we all met for the first time over Zoom, a call which was also joined by members of the 2021 Team who selected us. We started off with a round of introductions and our two new leaders, Melissa and Veera, were revealed to us. Later that same week, we met up in person for our first social event at the sauna. Using a poll, we chose the most suitable weekly meeting time going forward, settling on Thursdays at 6-8pm.
The two new team leaders took up contact with last year's academic advisors: Sesilja Aranko, Heli Viskari, Markus Linder and Ville Paavilainen.
Our first 'proper' weekly meeting was held on 17th February. At this point, we were still operating remotely. We went over the different communication channels that had been created, such as Discord and a Whatsapp group, and introduced the initial sub-groups that the team would be sub-divided into: fundraising, writing, wet-lab, dry-lab, social media, human practices, graphic design & videography, and collaborations. The fundraising team had to get to work earlier than the rest as setting up a pool of sponsors was the first urgent task, so a fundraising kickoff meeting followed the regular team meeting. A Presemo page was also set up for team members to drop early leads and broad project ideas.
This week, we discussed the different track possibilities for our project and checked which initial ideas had been added to the Presemo page. Here is a selection of the early leads suggested by various team members:
2-3 members were assigned one of the above four ideas (which had received the most votes) to do further literature review and research by the following week. We went over the overall medal criteria on the iGEM website and set up a PI meeting photoshoot date, as we would need headshots to be displayed on our sponsorship material.
We started our March by meeting our PIs and presenting them the tracks we are interested in and potential topics we have previously thought about. Additionally, we confirmed with them that we will have lab spaces available and which prerequisite we would have to meet regarding safety instructions in order to work in the laboratory. After we met our PIs we limited our topics to six potential topics and also included an additional topic of antibody synthesis in yeast as a new potential topic. After brainstorming we were also able to take our first group picture and individual pictures for our web page. At the end of the week, we went ahead with our photoshoot as planned and took headshots for each team member. The fundraising team finalised the budget plan that we would use in order to apply for funding at HiLIFE.
This week we highly focused on the fundraising proposal that we passed to HiLIFE to apply for funding for the entire year. Furthermore, we continued brainstorming and limited our topics to three topics including “microbes generating energy”, “antibody production”, “targeting of biofilms” and divided our group according to this topic to perform further literature research.
We decided to just continue with two of our topics, because we saw the opportunity to combine two of our topics including biofilm inhibition and antibody production, but we excluded the topic of energy generating microbes. Additionally, we prepared for a course of Prof. Dr. Brendan Battersby that we took part in to find mentors.
We met with Prof. Dr. Alexander Frey to discuss our project and possible advances on synthetic production of antibodies. However, he did not recommend us to continue on this path, because of the anti-immune activity of biofilms. He rather recommended artificial binding molecules like DARPins or Lectins. We split our group into three literature research groups for biofilms, DARPins and Lectins. We also had our monthly social event for March, which was karate training with the team.
The first logo sketches were shared and we decided to focus more on DARPins and quorum quenching. In order to do this we were planning to research quorum sensing and DARPins in more detail for the next week.
Our PI Heli Viskari helped us to start the iGEM registration process this week, on 5th April. Team members then self-registered by 9th April.
We were happy to hear positive feedback about our proposed project topic from our PIs in general, and were told by Ville Paavilainen that DARPins are a good option as they are small enough to pass through the biofilms polysaccharide matrix. PIs advised us to now find a simple starting point for the potential research and to break it down into small steps.
During this week's team meeting, held on 7th, different members were assigned different research tasks to further refine the project idea. These pressing research topics included:
Made our 2022 Instagram debut by introducing the two team leaders on 12th and 14th April.
On 20th April, as suggested by our PI Markus Linder, we contacted Christopher Jonkergouw to discuss the biosensor that he previously built to detect AHL molecules (used in gram negative quorum sensing). On this same day, we also contacted Thermofisher regarding fundraising.
On the 21st, much of our team meeting was dedicated to making a Human Practices roadmap. We came up with a list of potential HP routes to go down, including contacting and interviewing clinicians and expert researchers, starting an education and human practice-focused podcast. The podcast could be done in collaboration with the Aalto Entrepreneurship Society (AaltoES), which has a podcast-dedicated recording room on campus.
We were happy to receive a positive reply from Thermofisher on the 22nd stating their interest in sponsoring us.
On the 25th, we had two important meetings. The first one was with TEK, in the morning. In the afternoon, we met with Jouni Lounasmaa, former CEO of the Startup Foundation in Finland, at the Terkko Health Hub of the University of Helsinki Faculty of Medicine. On the same day, we sent a sponsorship proposal to Synbio Powerhouse, which operates under VTT, one of Finland's leading state-owned research innovation institutions. On 28th, we met with the University of Helsinki's Faculty of Agriculture and Forestry. We were also happy to receive a positive response from Synbio Powerhouse on this day, specifically from their BioGarage branch. We were offered a 1500€ sponsorship, the opportunity to use labspaces for free at the brand new GMO lab, as well as hold an event in collaboration with them.
On the 3rd we met with Sesilja and Ville in order to discuss the DARPin design. We decided to rather use a ribosome display than a phage display for the affinity selection of the DARPins and we discussed the potential aims we want to focus on for our DARPin including either the AgrC receptor or the AIP itself. However, we were recommended to only focus on one target to simplify the project. Two days later on the 5th we were able to meet with our PIs and advisors and discuss the project in more detail. We decided that we want to establish our bioreporter in only one plasmid and that we will add a positive control to our ribosome display by utilising a known GFP targeting DARPin. After an intense meeting we had our social monthly event watching a movie. On the next day we met with the Faculty of Science at the University of Helsinki to discuss possible funding. We received feedback and worked towards a mutually beneficial collaboration between our team and the Faculty of Science. On the 7th the iGEM opening day took place and most of our team attended that event to learn what iGEM is all about.
On the 12th we had a meeting with Heureka. Heureka is a science centre in the Helsinki metropolitan area and we discussed our collaboration in further detail. Heureka gave us ideas of what they would anticipate the workshop that we would prepare to look like and we were able to grasp ideas from that to prepare an ideal workshop for several age groups. In our weekly meeting we finalised our funding and decided the salaries of the team members. Furthermore, we confirmed future meetings that everyone is able to attend. We continued working on our DARPin sequences and finalised our bioreporter.
This week we focused on our podcast starting the week with a podcast meeting on the 17th and podcast recording on the 20th interviewing our co-leaders. In between, we had a meeting with our advisors Sesilja and Ville to discuss the potential size of our DARPin library. We were recommended to rather order our DARPin library than assemble it in order to save time during our project. On the 19th we prepared our talk for the synthetic biology course in Aalto University. In our weekly meeting, we started to suggest names for our product and started to assemble lab protocols as well as reach out to other teams for potential collaborations. Additionally, the social media team started to be more active since the team introduction was finished. On the 21st we had our May social event, which involved going to Heureka, so that we could explore the facilities that would be available to us in order to prepare our workshop.
We started the week on the 23rd by presenting our project to the synthetic biology course at Aalto University. On the 24th we had a meeting with the Microbiology and Microbial Biotechnology (MMB) Master's programme social media team of the University of Helsinki. In this meeting, we decided which content the MMB programme would require for our collaboration. We had a funding meeting with Kemianteollisuus. In our weekly meeting, we decided upon the date to start the wet lab and have an introductory safety course to be allowed to access the Aalto School of Chemical Engineering building. We planned further meetings for the future and focused more on the collaborations again. On the 30th we were able to finalise QBlock as our project name.
This week, kicked off our first week of full-time iGEM work, which will continue over the whole summer period. Both our designated office space and our lab are located in the Aalto University School of Chemical Engineering, and all team members completed three compulsory safety training courses before beginning. We were kindly given a comprehensive lab tour by the department's two technicians, Mikael Hytti and Ulla Ahman, who gave clear instructions on where to find chemicals and supplies as well as how to notify staff when stocks need to be replenished. On the 2nd, we met with our PhD mentors as well as Esko Kankuri, regenerative medicine professor and wound healing researcher, to seek advice on our project workflow, methods and goals. At the end of the week, on 3rd, we met with GeneArt to discuss prices for our potential orders, though we did not end up using their services.
On 7th, 2021 iGEM team member Quique showed us around the laboratory a bit more. On the 8th, the whole team met at the Helsinki Conference Centre (Messukeskus) for the ChemBio event. Here, we spoke to many different companies, including Eppendorf, Thermofisher, and Immunodiagnostics Oy. For the latter, we were able to see the CODEX DNA synthesis machine in real life and negotiate our temporary use of the equipment in the summer. On 9th June, the team presented an overview of our project in the School of Chemical Engineering's lecture theatre to keep the other researchers and groups housed in the same building abreast of what we are hoping to achieve. We also tested the vinyl press available for printing our logo on team shirts at Helsinki central library, Oodi. On 10th, we published an educational Instagram post on what biofilms are.
On the 13th we met with the HUS Wound and Burn Care staff for the first time, explaining our project to them and seeking feedback on whether they'd be interested in our solution in the hospital setting - it was positively received. On 14th we began our first day in the lab with amplification of the pET28a-sfGFP plasmid, which we continued for the next two days with transformation and purification protocols. The expression and extraction of the pET28a-sfGFP plasmids were successful, and the highest yield, as well as purity, was achieved for pET28a-sfGFP plasmid 1. On the 15th, our project was also publicly revealed on Instagram. We also published the first, June edition of our newsletter. The mailing list includes our sponsors, PIs, and faculty members, as well as any other interested collaborators such as clinical staff and start-up founders. We
On 20th, we met with the Dresden team to discuss our shared wet-lab plan, primarily the introduction of our GFP DARPin into their hydrogel, and how we could send or transport our DARPin to them.
On the 21st, met with Anja, postdoc and research coordinator at the University of Helsinki institute for biotechnology. We also sent our application for the Impact Grant, in which we detailed the tremendous health economics as well as the quality of life costs of chronic wounds and how and why our solution plays into relieving society from some of this burden. On this day we also started our transformation of the pET28a-sfGFP plasmid into E. coli. As the pET28a-sfGFP plasmid contains GFP, our aim is for the plasmid to be expressed in BL21 E. coli cells amplified and the GFP expression induced. We continued this experiment using the Transformation protocol also on the following day. Also on the 22nd, we met via Zoom with the Latvia team - the first iGEM participants from the country - and presented our projects to each other while ideating how we could create a regional Baltic Collaboration. Also on the 22nd, we published the first episode of our podcast on Spotify and spoke about the upcoming Nordic Conference meet-up with the Linkoping, Sweden team.
On 23rd, we began with colony expansion and expression of GFP in the lab using our protein expression protocol. We tried to record the second episode of our podcast but due to equipment malfunction, recording stopped and data was wiped from our SD card when we were about to conclude the episode. Since there was no way to repair the machine within the next week, we decided to delay recording to early July. We also met with the CODEX and Immunodiagnostics Oy, who will be providing us with their BioXP DNA synthesis machine for a trial run in August, to synthesise 32 DARPins. On 24th we met with our sponsor, BioGarage.
On 27th, the team gathered at the University of Helsinki Viikki Campus, where the BioCentres are located. Here we met with Lars Paulin, NGS expert to advise us on how we can work together for our sequencing steps. On 28th, we wrote the 1-minute elevator pitch required for the European meet-up at the end of the week, met with our PI Heli Viskari, and with our two collaborators/sponsors CODEX DNA and BioGarage. Between 28 and 30th June we started GFP extraction and purification in the lab. After GFP was expressed and extracted it needed to be purified in order to be utilised as a target for the ribosome display. It was checked with an SDS-PAGE that mainly GFP was expressed. Additionally, buffers were prepared for the extraction of GFP.
On 29th, we had a meeting with Heidi Salonen from Aalto's engineering school, who was interested in hearing about our project progress. On 30th, several team members embarked on a trip to Hamburg for the European iGEM meetup.
In the lab, we repeated the SDS gel for the expressed GFP after adapting the protocol and successfully showed that we expressed GFP. Additionally, part of our team returned from the European iGEM Meetup and we had a meeting with Ville and Kah Ying Ng to discuss our ribosome display and arrange the possibility to perform the first in vitro transcription and translation in Ville's lab under the supervision of Kah Ying. On the next day, we had a meeting with IDT, because we needed to discuss the synthesis of our bioreporter parts. Our bioreporter showed issues in the synthesis, therefore, we met with IDT to adjust and discuss the synthesis. We also prepared buffers for the extraction of our expressed GFP and continued with the GFP purification via Ni-NTA spin purification for the next two days. Additionally, we started our promotion video preparation and had a meeting to discuss the script on the 7th and finished our second podcast episode recording on the 8th.
This week we started with the amplification of the second part of our bioreporter containing the AgrC and AgrA gene. However, due to false positives, we repeated the PCR several times replacing water and primers to identify the contaminant. The primers were successfully identified as the contaminating source of the PCR and the bioreporter part 2 was extracted. On Friday we measured the DNA concentration of both the NGFP plasmid and the bioreporter part 2 and digested them both with XbaI and PaeI.
This week we struggled with a successful ligation of our digests and realised at the end of the week that we assumed the plasmid size wrong and needed to recalculate the correct ratio of plasmid and digest in order to achieve a successful ligation. Additionally, we focused heavily on our dry-lab collab with Dresden and researched data points that are needed for the collaboration. Furthermore, we also set-up a wet-lab collaboration with Dresden, which involves transporting a GFP targeting DARPin from Helsinki to Dresden. The Dresden team will analyse the diffusion of the DARPin through their hydrogel. On Tuesday the 19th we had our July social event and went to Nuuksio and on Thursday the 21st we went to Turku to meet the Aboa Team. At this meeting, we exchanged the experience of our project work and also fundraising issues. The meeting was beneficial for both of us and we planned activities that we wanted to do in Heureka for our workshop targeting several age groups.
We repeated digestion and ligation twice and incubated the second ligation reaction longer than the first one. Additionally, we realised that we were not supposed to run the finished ligation product on an agarose gel for gel extraction due to supercoiling and transformed it into E. coli and observed three colonies on Friday that we put in the fridge over the weekend. On Tuesday, we also performed in vitro transcription and translation under Kah Ying’s supervision in Ville's lab, where we also stored our products until Ville returns.
We started our week with the weekly meeting and finalising our trip details for the Nordic iGEM conferences. On the 2nd of August we also had a meeting with our PI Heli to inform her about our progress and we had a meeting with the ImmunoDiagnostics Oy marketing team to come up with a social media strategy. On the 1st and 2nd August, amplification of the cloned plasmid was performed. We grew three of the four colonies overnight and made a PCR colony from these before performing a plasmid purification. The concentration of each plasmid was determined using the nanodrop. Unfortunately, no bands were observed in the colony PCR in which just colonies were picked from the plates indicating unsuccessful transformation. The colony PCR might have not worked due to inhibition of other components present in the E. coli, so we repeated a general PCR with the purified plasmid on the following day.
For this repeat, on the 3rd of August, the agarose gel showed three clear bands indicating that successful transformation and ligation of the plasmid took place. On the 3rd of August, we also published the 3rd episode of our podcast on Spotify, during which Zsofia spoke with last year's team leader Sally about the challenges and successes of the 2021 project. In the evening, 6 of our team members embarked on an overnight ferry adventure from Helsinki to Stockholm to attend the Nordic iGEM Conference in Linköping, Sweden. The conference lasted from Friday 5th to Sunday 7th and gave us the opportunity to practice our presentation skills for the Grand Jamboree.
After coming back from Linköping, we had a meeting with the Aboa team to discuss our workshop for Heureka. On the 10th of August we gave a presentation to the Finnish IBO team about our project and iGEM itself. We also had a meeting with our mentors to inform them on our progress. We also retrieved the plasmid for expressing the GFP-targeting DARPin for the TU Dresden Team. The next day the BioXPTM machine from Codex DNA was transported to our lab and we set it up. On the same day we had a meeting with the TU Dresden team discussing the modelling approaches of the DARPin passing through the biofilm.
In the lab we were busy with troubleshooting the amplification of bioreporter part 1 and also digested, ligated and transformed it into TOP10 E. coli.
On Monday 15th of August, our videographers Mari, Joose and Hanna met with the clinical staff at the HUS Wound and Burn Centre to film interviews and hospital shots for the promotion video. We also performed the ribosome display in Viikki on Monday with the help of Anja. Later on Tuesday we were supposed to continue with the RNA purification at Aalto, but we realised we were missing the RNA purification kit. We continued with the ligation and transformation of bioreporter part 1 during the week, and went through the feedback from the Nordic iGEM Conference with the whole team. On the 23rd, we had a zoom call with Turku and Heureka to introduce them and to prepare a plan for the workshop, and made a list of all needed equipment for the workshops. Additionally, we had a meeting with Codex DNA to discuss marketing.
We also started to amplify, digest, ligate and transform the GFP-targeting DARPin into the plasmid provided by Sami.
We started our week with the weekly meeting updating everyone on what has been going on in the previous weeks. On the 23rd, a few of the team went to Heureka to try out some of the materials we were going to use in the workshops, and in the lab we had an exciting day as we finally did the DARPin DNA synthesising run with the Codex DNA BioXp machine. We got the Immunodiagnostic Oy representative Anni Kivinen also with us onsite for the run and Codex DNA representative Andrew Jones online with us. The run went well and we stored the DNA fragments in the freezer until we were ready to start the next ribosome display run. On the 24th we had a call with Turku about the Science Basement presentation, where we planned the presentation slides and went through the content. On the 25th we also gathered and filmed a few team shots for the promotion video, which was fun. During the weekend 26-28th of August, one of our team members Zsófia also flew to Germany for the JuniorJam meetup in Münster, where she met our partnership iGEm team Dresden.
In the same week, we also continued with the purification and dry-freezing of the GFP-targeting DARPin. However, we were not able to see a band on the SDS-PAGE and realised then that the GFP-targeting DARPin presented the wrong start codon, which probably prevented expression. Therefore, we re-ordered the GFP-targeting DARPin with the correct start codon and restriction sites, because we received a different plasmid from our mentor Sami then expected.
During our last week working full time with iGEM, we had a small recap of what both wet-lab and dry-lab had done so far, to make sure that everyone was up to date and could explain both parts of the project if needed. We also took during the 30th new profile pictures and team photos for the wiki. We faced some struggles still with the transformation of bioreporter part 1 in the lab, and we tested a few different ratios of DNA to plasmid concentration to see if that would help get successful colonies after transformation. We ended the week with a movie night where we watched the Hamilton musical. During the week we also finalised our promotion video and sent it to iGEM. Additionally, we received the new GFP-targeting DARPin and cloned it into Sami's plasmid, grew and extracted the DARPin.
The week started with a meeting with Heidi Salonen. We updated her about our progress on the project and promised to send her our results, so that she can share them with the faculty for further internal communication about iGEM in Aalto University. On the same day, we had our weekly meeting in which we discussed mainly the presentation that we will present to the Science Basement and everyone checked that they were aware of their writing tasks. On Thursday we had our meeting with the Science Basement and the Aboa Team. We presented our presentation together and received a lot of helpful feedback from Noemi Gutierrez-Valdes and Noemi Turpin from the Science Basement. Furthermore, we met with the TU Dresden to discuss our dry-lab collaboration. The TU Dresden Team informed us that the DARPins would be only present for 30 minutes at the wound site and that the AIP concentration would change over time. On Saturday we were able to give our two workshops with the Aboa team in Heureka. The workshops were a lot of fun and the children, parents and we enjoyed it very much.
We also progressed in our wet-lab work. On Monday we both in vitro transcribed and translated our DARPins that we previously synthesised in the BioXPTM machine. We furthermore immobilised the AIP on the 96-well plate. However, the AIP showed trouble dissolving due to probably the increased hydrophobicity of the peptide. Therefore, we repeated the immobilisation on the next day and were able to affinity select on Wednesday followed by reverse transcription, and amplification of the DARPins. The affinity-selected DARPins were submitted for sequencing on Thursday at the Institute of Biotechnology. Additionally, we further worked on expressing the GFP targeting DARPin for Dresden by running the extracted and purified protein on an SDS-PAGE. The same steps without purification were repeated again at different temperatures Friday to Sunday to improve the DARPin expression, because most of the DARPin was present in the pellet after extraction.
This week we started with our weekly meeting and we focused mainly on writing tasks, the upcoming science basement presentation, and sitsit preparation. The alumni sitsit was held on Saturday and was a great success. We had fun games and were able to let the alumni relive iGEM memories and share our experiences. We also progressed further in the lab, because we were finally able to successfully ligate bioreporter part 1 into the plasmid containing GFP and bioreporter part 2. Furthermore, the ligate was successfully transformed into E. coli NEB alpha-5. The ligate was extracted and digested in order to be run on the gel to confirm successful cloning. Furthermore, the work on the GFP targeting DARPin expression did not stop. We changed IPTG concentration and further temperatures and settled that an overnight induction at 20 °C seemed to be most successful. Furthermore, we purified and deep-freezed all the GFP-targeting DARPin we had to at least have some DARPin to send to TU Dresden as soon as possible.
The week started with the weekly meeting and we discussed writing tasks for the wiki, science basement and the science basement presentation, which were able to successfully present on Saturday. On Wednesday Lilith presented our iGEM project and iGEM to the microbial biotechnology course in the University of Helsinki. Additionally, we changed the approach for the expression of the GFP-targeting DARPin and in vitro transcribed and translated it, because we realised that the previous expression was not successful. The successful protein synthesis could not been proven, because the gel was not successful, however due to observing white powder we deemed the synthesis as successful and informed TU Dresden and they decided that they were able to receive this GFP-targeting DARPin in this form without the final confirmation. We were able to transport it to Germany and send it via mail to Dresden. We also progressed in our bioreporter and successfully expressed the plasmid in BL21 E. coli. This allows us to express GFP more successfully upon sensing the AIP.
We started our week by participating in a workshop of Olle Bergman that was organised by Lund university, where we had the opportunity to listen to many iGEM presentations, but also present our own presentation. Amna presented for the entire team and received a lot of helpful feedback for both slide design and body language. We also had our weekly meeting on Monday, where we focused again on the wiki writing tasks and started planning our grand jamboree presentation for which we had an additional meeting on Wednesday. In the lab, we also progressed and finally tested our bioreporter in the presence of AIP. We also had controls with BL21 E. coli expressing the GFP-targeting DARPin, but no GFP to and no AIP presence to ensure that the fluorescent signal is only being expressed in the combination of the bioreporter and AIP.
During the last week before the wiki freeze we focused mainly on finishing the last writing tasks for the wiki. In wet-lab we analysed the data from the bioreporter measurements and concluded that there is some problem with the P2 promoter, either that it is leaky and active even if it is not induced or then our strong constitutive promoter is too strong and also starts transcription in the other direction. Further testing would be necessary if we would have the time for that. Otherwise the cell growth wasn't affected by the bioreporter and only our bioreporter cells emitted the GFP signal and not the controls, which was positive to see. The dry-lab continued to work on the sequencing data analysis and finalised our wiki pages. We also had a meeting on 4th to plan and discuss the Jamboree presentation and started working on the slides for that.