Difference between revisions of "Team:Aachen/Collaborations"

When building a colony, cells communicate with one another through different methods, exchanging all sorts of molecules and therefore information, enabling them to coexist and grow as a whole. Inter teams’ collaborations in iGEM plays a very similar role in its community. The teams interact with the community, telling them what they need. The teams, as a singular cell, communicate how they can offer knowledge, experience and even gear to others that seek it. Once a beneficiary connection has been established, the teams share detailed information regarding their project and explain how the other team can help them accomplish it. This year, our team collaborated with the Köln / Düsseldorf iGEM Team.

Our task was to create a S. cerevisiae cell with lacked both PEX7 and PEX5 genes. We had the choice of either deleting PEX7 in a dPEX5 strain or deleting PEX5 in a dPEX7 strain. Knocking PEX5 could damage genes PRP28 (upstream) and MNN10 (downstream), having consequences we would not oversee. Therefore, our team decided to knock out PEX7 in the dPEX5 strain. Because of our experience performing different gene knock outs in our project, this process was much easier for us.

We used primer sequences flanked by overhangs, designing them in such a manner that they would bind the sequences outside of the PEX7 gene. The overhangs are homologue to the previously isolated selective marker gene KanMX (G418 resistance) + loxP sides. When transforming the dPEX5 yeast strain using this cassette (both homologue regions and the KanMX gene), the PEX7 cell is removed from chromosome IV and replaced for the selective marker. The cell is then plated on plates containing G418 resistance. Once fully-grown colonies were observable, the genetic information was isolated and a verification PCR, using new plasmids, was performed.

Results:
The PEX7 knock out transformation cells (dPEX5 S. cerevisiae) were spread on a plate containing the antibiotic G148 (geneticin). As observed in Image #1, several colonies showed an observable culture growth. After this, 3 different colonies were taken and their genome isolated. Image #2 shows the verification PCR performed on the isolated genomes from the dPEX7, dPEX5 mutated S. cerevisiae. The primer used for this process were designed to bind to the sides of the knock out cassette. Having this in mind, we used a ladder that fitted the length of our amplified sequence.

The plate contains several yeast colonies. A colony was randomly picked and analyzed through a microscope. No visible contamination was observable.

The ladder can be on column #1. The 2 PCR products (found in columns 2, 3) show a strong band situated at around 2000 bp. Using the software Geneious^®, we digitally constructed the dPEX7 knock out cassette, determining that its length should be around 2100 bp.

Discussion: The transformation was a success. The control plate presented no contamination on the controlled colony and the verification PCR showed the results we hoped for. The successfully mutated cells were prepared and delivered to our fellow iGEM Düsseldorf / Köln partners.

Once we finished this collaboration, our team realized its importance and the positive effect it had on our partner iGEM team's project. Keeping in contact with our friends in Cologne/Düsseldorf, we learned that the knockout we accomplished was a key transformation in their proyect. Getting rid of PEX5 and PEX7 genes would get rid of the own cellular protein import system of the peroxisomes. This important step would then allow our partners to integrate their own protein translocation system and therefore control the synthetic pathway that happens in the intercellular compartments. Through our experience and knowledge, we helped them overcome this obstacle which, as they explained, wouldn't have been possible by themselves.

In the research phase of our project, there was also an exchange with other iGEM teams who had decided to work in the field of environment and water pollution. During the first Skype talks with the iGEM Team Worcester it soon became clear that there were many overlaps between our projects.

At this time, the iGEM Team Worcester worked intensively on a biosensor system in which organisms can display the lead content in a body of water and can also absorb this lead to clean the water from heavy metals.

In the discussions we found out that both projects relate to a local problem in the region of the respective team. The question quickly arose as to whether this problem with the drainage of drinking water is also a problem in Germany and whether American waste water is contaminated with salts as well. Because both teams had difficulties with this research, which was also due to language barriers with German literature team Worcester needed, we opted for an investigation collaboration between our teams.

We investigated the contamination of drinking water with lead in Germany and translated, among other things, the German Drinking Water Ordinance, the government's information material to lead pipes in old buildings, and an opinion on the pollution of drinking water with lead in large German cities.

The iGEM Team Worchester collected information about the salt pollution of waters in the North East of the USA. They found that in many freshwater areas in these states the chloride concentration could reach a toxic level, if there should be no political initiative to reduce the burden. The main reason for the load was the use of salt-based de-icing on roads, as well as dense building and industrial pollution.

Through this collaboration, we realized that salinization of fresh water reserves is a problem not restricted to highly industrial regions in Europe, but a global challenge for the future.

The iGEM Team TU Dresden hosted the three-day German-wide iGEM Meet-Up from June 30th to July 3rd. Henri, Gerolamo and Fabian, three members of our team, joined this event representing the iGEM Team Aachen. The event gave us the opportunity to get in touch with the 14 other German teams present and to exchange knowledge with them. Since each team presented its project in a 20-minute session, we got an insight into the topics of the other German teams. In addition to that, we could also present our own project and identify the areas and problems of our project we still needed to work on together with the listeners during the subsequent questionnaire. In the free time on Sunday, we also had the opportunity to explore Dresden's historic town together with the other teams and to talk about collaborations. The weekend also included the presentation of the” iGEM goes green” initiative of the iGEM Team Dresden. In the workshop, detailed discussions about how each team can make the laboratory work more sustainable were conducted. Because we as a team are just as convinced of the importance of this topic, we decided to join the “iGEM goes green” movement and work together to minimize our carbon footprint (-> Read more).

At the Meet-Up, we not only found a lot of new friends and gathered new insights, but we were able to develop initial ideas with the iGEM Team Cologne-Dusseldorf, which resulted in our intense laboratory collaboration (->Read more). We would like to thank the iGEM Team TU Dresden for the great event and the excellent organization, which enabled us to get to know the other German teams and make important contacts for our further iGEM summer.

The iGEM Team York built a digital in-line holographic microscope (DIHM) this year. To validate its function, they used a number of different microorganisms that iGEM teams worked with this year. We provided the iGEM Team York with several mutants of our S.cerevisiae strain (Fig.).

For a successful project, a critical and objective review of the progress and problems is necessary. To ensure this objective view, we have conducted repeated discussions with the iGEM Team Knoxville. In addition, we held a mentoring session focused on the problems of iGEM Team Knoxville regarding the recruitment of a new team. We discussed ways to improve the this process in the future to form a larger team for the coming years.

In troubleshooting sessions, a detailed description of the problems of the respective projects was discussed. With the results obtained from these sessions, we improved our project several times and adapted our work so that our project is easier to understand and our laboratory work becomes faster. Especially our Project Presentation was really complicated and misleading in the beginning and has been improved a lot with the help of the iGEM Team Knoxville.

The Delft european meeting was our first international meet-up. This brought along a lot of positive effects on our whole team as a whole and on our working goals towards the Giant Jamboree.

At first, we arrived at a camping place after a long trek in the beautiful suburbs of Delft surrounded just by nature. In this camping place we got the opportunity to meet a few other members of the attending teams. Starting from there the whole experience was full of interchange with our iGEM peers. That night we went out and got to get a glimpse of the city and exchanged our ideas accompanied by the warmth of a good pub.

On the second day, we attended the scheduled symposium where we got to listen to three uppermost interesting presentations by Prof. Dekker, Dr. Stemering and last but not least Prof. Murphy.

Prof. Dekker as a pioneer in biophysics gave us a glimpse into his research on synthetic biology. We were really excited to see the extent of possibilities that exist nowadays.

Dr. Stemmering was a positive boost to our fading belief in the usage of our project. We thought that the introduction of our genetically-modified yeast in other countries or cultures would be difficult, if not impossible. In his presentation, he assured us that a GMO which is helpful and solves a problem would be accepted in other cultures as well.

Prof. Murphy brought to us to the idea of using data in a much better way, and how to try to connect the information technology creating gigantic throughputs of data with actual results that can be used. For us as young researchers, the work with these new data technologies is of extreme importance.

After the presentations and a great meal, we met up for a poster presentation from every attending team. This was by far the best opportunity to spark up collaborations with other teams. Through this poster presentation we finally got the idea that we could make an awesome Wet Lab collaboration with the iGEM Team Cologne/Duesseldorf.

Delft was all about making new friends, contacts and collaborations as well as just thriving on the awesome iGEM spirit. So all in all it was a really great experience.

We attended the European Practice Jamboree, organized by the iGEM Team KU Leuven as our last event before the Giant Jamboree in Boston.

After a short train ride, we arrived in the beautiful town of Leuven, Belgium.

At first we thought we were accidently beamed to New York City, because the conference centre from KU Leuven looks exactly like the Guggenheim museum in New York.

We were welcomed with snacks and coffee and a short introduction by the vice rector of Science, Engineering and Technology Professor Gerard Govers. Johan Robben, former PI from Team Leuven, held a short stand up Q&A about the history of iGEM at KU Leuven and the importance of asking for funding in the right places, since most professors have very limited funds. However, the higher up administrative staff might have access to bigger and different grants.

The first lecture was by Professor Jos Vander Sloten who talked about challenges in biomedical engineering. These challenges range from the design stage to the finished product and its application by customers. Professor Sloten emphasised that personalised medicine might be expensive but can improve the lives of all of us in the future.

After a short break, we were ready to have our talks, starting with Team Leuven and their idea to use pulsating cells as biosensors for drug monitoring.

Next was Team Munich with their novel way of using CRISPR Cas13a as a biosensor to diagnose a range of infectious diseases.

Team Paris IONIS presented us their very hands-on (and also very French) approach to protect vineyards from extreme weather conditions caused by global warming. In addition, they assured us that their project is also adaptable to other crops and vegetables.

The team from Amsterdam had an interesting talk about their modification of cyanobacteria to have an improved day and night cycle and engineering it to be able to produce fumarate, an important bulk chemical. Their “super cyanobacterium” will be able to use CO2 as its sole carbon source to reduce and even reverse the oil industries impact on the environment.

Last but not least, we listened to the very inspiring presentation of iGEM Leuven`s PI Johan Swinnen, who explained what it means to be a scientist from his personal live as a cancer researcher. On his long journey to Santiago de Compostela he raised awareness and funds for victims of cancer.

After a plentiful dinner and short poster session with valuable feedback about our talks and posters from the other attending teams we were ready to go back home.

The iGEM team Franconia is organizing an Augmented Reality game for smartphones at this year's Giant Jamboree. For this purpose, the team has developed an app. In Boston you have the possibility to find a QR code at our poster-stand, which can be used in the game. You can find more information about the game at Team Franconias WIKI page.