February
Week 6
Our team’s journey started on the 6th of February with our first meeting. We were all enthusiastic about the awesome iGEM experience we would share in this group and eager to find an awesome topic for this iGEM year.
This was officially our first week as the new iGEM Team of TU Darmstadt and we were extremely motivated to get started.
Prof. Jürgens from our university kindly offered to give us a talk about how to read and write scientific research papers. We were able to prepare well for the research ahead of us to find a project topic!
We started our research with a meeting on the 13th of February. We met on teams and went through a lot of SynBio papers to search for inspirations and ideas for our project. We collected a lot of amazing project ideas, such as an microbial alternative to wood, GMOs to prevent mite infections in honey bees, symbiotic rhizobacteriacea for improved crop growth and many more! We continued our research within the following weeks and met with our whole team each Saturday.
Week 7
We used the week to further elaborate our findings from the first research weekend. We met in small groups on teams, had great discussions and found a lot more information about our project ideas that could be presented on the next research weekend for the whole team. We still had a lot to organize in our freshly founded team and talked a lot about our general team structures and what we would do in the following iGEM year.
Week 8
This week we were again really busy with our research phase. Besides some general organization we mostly focused on scanning through research papers to elaborate our project ideas.
March
Week 9
This week we were working hard on our research phase again. Also, we had a lot of discussions about our team rules: Since we are a rather big iGEM Team we had to ensure that we can stay productive and function well as one unit. Therefore, we created a set of rules everyone in the team committed to, to work together respectfully in a fun atmosphere.
Also, we were getting closer and closer to the decision of our project, so we all were pretty excited.
Week 10
After our intense research phase we were able to have a discussion and vote between 6 amazing and well defined ideas:
- Bioconcrete as a biological engineered living material
- Bacteria for electrical pulse induced biosensors for HEV
- Bioleaching of rare elements
- Pathogen eradication using phages
- TU Bee
- Inoculating seeds with Rhizobacteria
We decided to continue our project with the topic Pathogen eradication using phages, tackling local and global problems of MDR bacteria, especially in extremely resistant biofilms. We were stoked to elaborate our amazing topic and really get going with iGEM 2021!
We started to work on our project sponsoring directly after deciding on a project topic on the 8th of march. We started by collecting awesome companies that might be willing to sponsor our iGEM Team and writing first drafts of contact forms.
Week 11
This week we had the kick off events for both our Modeling and HP work. We started by introducing both topics in our team meeting and continued with setting goals in these areas for the team.
We started our Human Practices work with an introduction of Human Practices and its importance for modern research. We were happy to contribute to a better understanding of synthetic biology in our society and to find applications of our project in the real world.
We started our Modeling team on the 15th of March on our team meeting. We were eager to contribute to our project with interesting in-silico experiments. Our first checkpoint was to get to know programming languages and bioinformatic environments such as Python or Rosetta.
Week 12
We were still pretty busy with researching our topic and getting more ideas for our iGEM project. We were also organizing our small groups for the research and project work ahead of us.
We were introduced into Python by Fran and Tom, members of 2019’s iGEM Team at TU Darmstadt. They are both experts in computational biology and were able to provide us with a lot of useful tips and tricks, for example regarding the biotite bioinformatics package for Python.
April
Week 13
This week we scheduled the kick off events for our research/lab groups. We were all motivated to get experts in our topics.
To illustrate our wiki and presentations we also started with an Inkscape workshop with some of the members from last years team.
We started talking about the iGEM medal criteria and general judging in the iGEM competition.
Also, Eileen came up with the idea to have a team plant, that we can watch grow together just as our project grows. We choose chard as our plant, since its easy to handle and could be used in a team cooking event to cook a delicious recipe.
Week 14
This week the research groups phage engineering, biosafety, detection and ECM degradation and killing presented their research topics in our weekly team meeting. We were able to collect a lot of good points and to discuss the problems or bottlenecks that could come with this topics.
We also finished our sponsoring portfolio, introducing our team and our topic to companies. We wanted to contact companies as soon as possible to get support for our project both outside and inside the lab.
To get ready to plan our part assembly we introduced SnapGene to the team and scheduled a SnapGene workshop held by one of our project coordinators.
To push our research phase and coordinate our progress in the research groups with the whole team we had our first project development meeting. We used these Saturday meetings to have a presentation by every research group and discuss their progress with the whole team. This way everyone in our team had a good overview over the whole project and we ensured the research would lead into the same direction.
Week 15
Besides the research in our research groups, we collected ideas how our Modeling team could support the project. We therefore scheduled a meeting with some iGEMers of the previous years at TU Darmstadt and discussed our ideas. We got a lot of inspirational feedback from recent research papers and their experience.
Since we got no lab access at least till July we discussed the idea from one of the ambassadors at the iGEM ambassador meeting to have a two phase project with two phases: Design and Model in the first year followed by Build and Test in the second year.
Week 16
We got into contact with a lot of experts in the fields of phages, biofilms, biosafety e.g. to find out if they can provide us any help with our project or give us any feedback. If you want to find out more about our Integrated Human Practices you can click here. We also got in contact with a lot of local stakeholders to talk about the relevance of our project or biofilms in general.
We also had an amazing talk with iGEM Monterrey from Mexico, since both our teams are interested in biofilms. We were able to share some ideas and scheduled another meeting.
We participated in the iGEM monument challenge by iGEM Kaiserslautern and shared some of the most popular attractions of Darmstadt with the iGEM community.
In our project development meeting we made huge steps forward by discussing the different approaches of the research groups in detail. We got a lot of inspirations for our research in the next few weeks but also had to discard some ideas. Also, we got some feedback from our advisors, that we have to focus our research, so we had a little bit of restructuration planned for the following weeks.
Last but not least we planted our team plant together in our team meeting.
Week 17
This week, we had to reschedule our weekly plan, since we got the feedback that we need to focus our research, because we were running in too many directions with our research. We therefore cancelled our small group meetings this week to define clear to-dos for our project.
Also, some of our teammates contributed at the Sustainable Research Symposium and we got a lot of interesting information about the sustainability of our project. We got so inspired, that we wanted to contribute in this sustainability discussion by having our “Greener Lab” workshop and sharing some of the information from the symposium with researchers at our university.
We also had a Biobrick workshop this week, talking about the iGEM Biobrick standard, assembly methods and plasmid construction. This workshop was really helpful for our experimental planning and the general understanding of some of the iGEM parts.
May
Week 18
To refocus the aims of our project we made a brainstorming week for the restructuration: We started by collecting the key elements, aims and goals of our project on a board and then discussed these points in the team. By this we wanted to work out the key elements of our project and focus completely on this part to have our project actionable and fun for the whole team. On Saturday we had breakfast together and further discussed the points on our board.
Our team plant started growing really tall so we had to move it to a new and nicer plant top.
Week 19
During the last week we collected awesome ideas how to fix our little issue with our project direction and condensed them to 3-4 main concepts which we could continue with: The first idea was to implement a second chromosome into a E. coli to produce a broad variety of different phages induced by different signaling factors, utilizing the high capacity of a second chromosome. Alternatively, we could use a similar system in our original host organism B. subtilis to have an immune like response to different invading pathogens. This system could even be used in combination with our last year’s project. As a second idea we thought of phages for the food industry as an alternative for harmful chemicals as cleaning agents for biofilms. We also talked about one of the ideas from our original research phase, using phages to introduce siRNA systems to gut bacteria of honey bees to protect them from invading mites. Lastly, we had the idea of implementing a system for the directed evolution of bacteriophages for example for an extended host range, extreme conditions such as pH or temperature and many more.
We decided to go for a final voting between the sleeper cell in B. subtilis detecting and killing invading pathogens and the phage directed evolution in our next team meeting to then continue with our research.
We had an amazing workshop on science communication held by Sascha from the science birds. We learned a lot about science slams, science communication in general, our role as young scientists and what we can do to contribute to a better understanding of science in society. See our wiki section about the workshop and also check out the science bird’s website if you are interested!
Our team was looking forward towards joining the first official iGEM event: The iGEM opening festival. We had an amazing time listening to interesting calls, having discussions with other scientist from the field of synthetic biology and taking about the iGEM experiences and projects of other teams! With this meeting, out team really caught the iGEM spirit and was motivated to work even harder for our project.
Week 20
We talked about the two directions for our project again and had our final vote: We decided to continue with the sleeper cells! We were really happy to have new goals set for the following research phase.
We also recapped the iGEM opening weekend, which was an amazing experience for us and a lot of fun!
Week 21
We continued with our research groups and shifted some of the topics because of our project restructuration: The biosafety group became the kill-switch group developing a kill-switch triggered by QS signals and the detection group continued with research about B. subtilis biofilms. We had to read a lot of new literature and thus were pretty busy.
To develop our project and find proof of concept experiments, we talked a lot about the DBTL cycle which we would implement into our planning.
June
Week 22
This week we were looking for applications of our project to include into our Modeling work.
We also finished the script for our first podcast episode, planned as an introduction of our team and synthetic biology in general.
We also contacted our uni’s INSPIRED team, a project about the colonialization of mars with an extraterrestrial greenhouse, to have a meeting together and talk about our projects.
We also talked about the project promotion video, which would be due in July and started a group responsible for the script.
For our wiki we started with a framework to put our texts in, to be as ready as possible for the wiki freeze which always comes sooner than expected.
Week 23
This week we really focused on collaborations with other iGEM Teams: We met with iGEM Team Aachen for our iJet collaboration, we scheduled our next meeting with iGEM Monterrey, designed our postcards for the postcard collaboration of iGEM Düsseldorf. We also met with the team from Bochum to talk about our projects and share some ideas together. In our first meeting with the iGEM Team from Chicago we talked about the model of our project B-TOX from 2020 and also got some feedback regarding our project, especially the genetic circuit modeling.
We also talked to iGEM Turku from Finnland about laccases, since we focused on them last year and they were also working with microbial laccases this year.
We prepared our applications for the iGEM safety and impact grants, lucky to get these great possibilities of funding for our project.
We collected name ideas for our project that we wanted to set till next week.
Our team wrote an article for the biotech and biology journal “Biospektrum” to introduce our iGEM Team to the german bio community.
Together with Stuttgart’s iGEM Team we finished this week with an amazing game night.
Week 24
We had an extended team meeting this week intensively discussing our progress with our advisors and the team. We got a lot of amazing feedback and made some really good progress in this meeting.
Our project promotion video team came up with a script for our video and searched for actors playing detectives and phages in our video. If you want to check the video out, just follow this link.
For some socializing in the team we had a pub quiz online together, which was really fun!
Week 25
This week we got the first results from our in-silico SnapGene planning. We finished the filming of our project promotion video and went ahead with the video production and some animations. We also talked a little bit about the story of our project and the application possibilities of our system.
We also were told, that it may be possible to enter the lab in August! We were really stoked about these news and focused on planning simple proof of concept experiments to be as productive as possible in the lab.
In this week we also had a project development meeting on Saturday, where all the small groups updated us about their progress. A lot of groups presented their SnapGene constructs and POC experiments, so this meeting really helped us on our way into the lab! Besides that, we talked about the medal criteria that we want to achieve and their current status in our team.
Week 26
We talked a lot about our parts and how we would order them to get ready for the lab as soon as possible. We decided to go for type IIs restriction enzymes and Golden Gate assemblies for our cloning because of their reliability and easy implementation.
For our project presentation video we were starting with our video editing and animations.
Another important point we talked about was the selection of our iGEM track: We discussed all tracks and old iGEM projects from these tracks with the team to raise our awareness for the track selection.
July
Week 27
This week we had a long team meeting intensively discussing our progress on the main research topics:
For the implementation of phages into a B. subtilis biofilm we discussed how we could mimic the specifically adapted expression system of bacteriophages in their host organism in our sleeper cells.
We had a major breakthrough in our research about biofilms with an expert interview with Dr. Bischofs-Pfeifer and Prof. Dr. Kovács: They recommended us strains for the formation of biofilms and told us that homogenous biofilms of different genotypes might already be possible without metabolic dependence etc.
We finalized the constructs for our kill-switch proof of concept experiments and started the planing of our pathogen sensing genetic circuit.
For our Modeling we decided to write a software to combine two models for metabolic dependency of two bacterial strains in a single interface. Additionally, we started modeling the response of our pathogen sensing circuits to AHLs to improve our future lab experiments in this part of the project.
In Human Practices we continued our podcast, worked in education by writing audiobooks for our Tonie-Boxes, talked to a lot of experts about ethics and policies and started planning a science slam for the german iGEM community.
Week 28
This week we talked about the design of our wiki page. We talked a lot about inclusivity and how we can make the wiki as barrier-free as possible. We also decided to have a “dark-mode” design and created a document, were we wrote down all the design principles for our wiki.
We were all excited to design our team hoodies, which turned out really nice in the end. We wanted to get fair-trade and sustainable merchandise for our team.
We also discussed the progress in our project research, HP and modeling since our last meeting on monday really intensively. Unfortunately, we also realized that the science slam can most likely not be hosted by our team, since not that many teams agreed to prepare a short slam for the meeting.
Week 29
This week we decided to pick New Application as our track for the iGEM competition. We had a vote based on the discussions and our Miro board regarding the track selection from the previous weeks. We were really happy with this choice and eager to further refine our project.
We also prepared a presentation about our project held in front of our uni’s faculty. By this we were looking forward to get some valuable feedback and input for our project.
Week 30
We came up with a novel genetic circuit for a proof of concept of lambda phage induction in E. coli using the native repressor/regulator systems cI and Cro. As a first readout a fluorescence measurement is supposed to be conducted but phage expression in E. coli cells with an integrated lambda prophage. We finished the second episode of our podcast, which we were really proud of!
We also were able to order Tonie-Boxes, which we could use in kindergartens to teach children basic scientific knowledge as part of our HP education work.
In our faculty presentation we presented our project to our uni’s biology faculty and experts of our team that we invited. We were able to give an awesome talk to all participants and get a lot of feedback regarding our project. We also decided to have a second faculty presentation after finishing our project presentation video to prepare for the judging session.
August
Week 31
This week we had a talk with our PI about the lab work. We were able to get into the lab but only under strong conditions due to the pandemic. We worked out a hygiene concept to give as many members of our team as possible the ability to work in the lab and get some experience. Some of them haven’t been in the lab since they started university so it was a great opportunity for all!
For the experiments in the lab, we decided to shift all experiments to E. coli as host organism. In agreement with our advisors and PIs it seemed to be the best possibility to provide proof of concept experiments in this short time in the lab with varying lab members each week. This meant a lot of replanning to adapt all experiments to E. coli for the next parts, to get ready to order our parts and begin with the lab work. We planned our assemblies using the GoldenBraid system, since its already established at our university.
We also discussed a lot of details about our iGEM lab with our team. In our hygiene concept we decided to have weekly Covid tests and to have four people simultaneously in the lab. We talked about the devices and instruments we have in the lab and the assembly plans for our team. We also had small groups that each prepared protocols for the experiments we had planned adapted to the materials we had in the lab.
Week 32
This week we were more than happy and really honored to receive the iGEM Team Grant.
We made plans for our lab schedule and organized our members for the several lab weeks, so everybody gets the experience to enter the lab at least once.
We presented the workflow and cloning plan for our first lab week using GoldenBraid again to the whole team and discussed it in detail.
To prepare for our project presentation video we scheduled presentation trainings for the whole team held by experienced ex-iGEMers from TU Darmstadt.
For our wiki we talked about the structure again and started to make the plans for all topics of our project. We discussed how we wanted to present our research, results and discussions and what pages we need for that.
We also had the interview with molecular cloud, check it out if you want to learn more about our team and our project.
For our final wiki phase we decided to have at least 4 weekends blocked for the whole team to work on our wiki together. We were really excited to finally present all our results to the iGEM community and collect everything we learned so far.
Week 33
We started this week with our safety training for our team, so everybody would be able to enter the lab starting from this week. We learned a lot about safety in the lab, general safety regarding GMOs and good laboratory practice.
We spoke about our assays in detail and came up with well-plate schemes for our assays that could be done within the next few weeks.
Akos T. Kovacs kindly provided us B. subtilis strains for biofilm formation. We wanted to use these fluorescence labeled cells to conduct first experiments regarding the homogeneity of our biofilms.
We continued to finish more podcast episodes and finished our survey about synthetic biology. Also, we prepared workshops for high school students in the next few weeks.
For our lab we transferred our materials and consumables into our iGEM lab and organized everything for the upcoming lab work. To organize everything and save our lab results or protocols we created a detailed notion page containing our lab inventory and a digital lab book.
We had the first presentation trainings this week with a lot of fun presentations. We were able to learn a lot and really improved our presentation skills. This would be especially useful for the final presentation video.
Week 34
We implemented our quorum sensing based Pseudomonas aeruginosa sensing circuit in a Python model. Additionally, we thought about adding a second module calculating the expected phage expression based on the AHL input generated by our circuit. For the model we discussed in the whole team how we could get parameters for our model and came up with a few promising solutions for that problem.
In the lab we prepared cryo-stocks of our biofilm forming B. subtilis strains, carried out a first golden gate test reaction and grew our first biofilms for our microscopy measurements of B. subtilis mKate GFP cocultures. We also tested our equipment with PCR reactions, agarose gels and first golden gate assemblies of test parts.
We talked about the design of our wiki and started with the first design of figures for our wiki.
Also, we ordered the T-Shirts and Hoodies for our team, which we were really looking forward to in the last weeks.
September
Week 35
This week we were excited to discuss our first results from the lab: We made fluorescence microscopy pictures of the biofilm monocultures and also established a first coculture of two differently marked B. subtilis transformants.
Also our parts arrived and we started the first Golden Gate assemblies of our QS based P. aeruginosa sensing genetic circuit. These assemblies would result in our first ⍺-level plasmids of our GoldenBraid approach, which then could later be combined to form 𝝮-level plasmids with our completed construct.
For our final wiki phase we scheduled wiki weekends beginning from the 11th of September. With these weekend meetings we wanted to gather the whole team (digitally) to productively work on our wiki texts together.
We began to film a short team introduction video for the promega instagram page. We wanted to introduce our research foci and explain our project for the broad audience of the instagram channel.
Week 36
This week we mainly focused on the first of our wiki weekends. We planned all texts we wanted to write for our wiki and distributed them to different authors from our team. On the first day of our wiki weekend we first met at a local park to take some photos for our wiki and then went home to start the writing and correction process.
We also finished the short introduction of each our team members for the promega video (external).
Additionally, we talked about the figures we wanted to include in our wiki. Since we focused on inclusion this year, we had to make sure they are easy to understand and that the colors are distinguishable for color blind people. If you want to find out more about that, check out our guide on inclusivity for websites, such as our wiki.
In the lab we continued with the assembly and sequencing of our first 𝝮-level plasmids. We had some trouble with some of the constructs and thus had to repeat some of the assemblies.
Week 37
One of our team members prepared an introduction into scientific writing, which we all profited from for our wiki texts. We further discussed how we wanted to structure our wiki pages and how we want to include our figures.
We also wrote an algorithm to analyze the appearance of biofilms in iGEM wikis within the last few years. We found out, that this topic gets increasingly relevant for the synthetic biology community, which also highlights the importance of our project introducing an additional safety layer to these systems.
In the lab we made first fluorescence measurements with the cloned 𝝮-level plasmids in our plate reader, but unfortunately no fluorescence was detected upon induction. We thus focused on the troubleshooting of our assays to figure out potential issues during the measurements.
Week 38
We still encountered problems with the IPTG induction of our BL21(DE3) cells and put a lot of focus on fixing this problem. We also worked on the safety data sheets of E. coli cells we got send from Prof. Dr. Węgrzyn to eventually use E. coli cells containing the lambda prophage for the measurement of our genetic circuit containing cI and a recA mutant for induction of its lytic state.
In the lab we focused on the assembly of the remaining 𝝮-level plasmids and the sequence verification of the assembled ones by both restriction digests and Sanger sequencing.
Week 39
This week all genetic parts for our project arrived in our lab and we started all assembly reactions for our plasmids. Dr. Rapp from our university helped us with the fluorescence microscopy of our biofilms and we got some amazing shots of our cocultures.
We also talked about upcoming deadlines and recapped the collabos we had within this iGEM year.
On our wiki weekend we wrote a lot of texts, created figures and continued with the creation of our website. We worked really productively and got a lot of texts done this week.
October
Week 40
We successfully cloned the Cre recombinase for our kill-switch assays into a production plasmid. We also managed to fix the problem we encountered with the IPTG induction of the T7 polymerase in BL21(DE3). The genetic circuit for our lambda phage lytic cycle induction was also started to get assembled, but we encountered some problems with this multiple-fragment golden gate reaction. Nevertheless, we got the plasmid assembled at the end of the week and were ready to measure all our constructs in the next week, which was really exciting for us.
We also wrote the script for our project presentation video and started to look for locations for us to film at. Like always in this final phase of iGEM we also talked about upcoming deadlines for the team and the challenges we still had in front of us.
Week 41
This week we successfully conducted the assays for the genetic circuit designed for the proof of concept of our phage induction construct. We were able to detect green fluorescence upon IPTG induction caused by the expression of recA730. For all other genetic constructs, we were unfortunately not able to measure our expected outputs. We were unable to perform troubleshooting on these constructs due to the lack of time with the wiki freeze ahead.
We were able to finalize our wiki on the last wiki weekend, finishing our wiki texts and figures. We also started filming our project presentation video.
Week 42
This week the final wiki freeze would take place. We were all excited to submit our wiki and still worked hard on our project presentation video.