Difference between revisions of "Team:TU Darmstadt/Awards"

Revision as of 10:14, 12 December 2020

Best Education Best Integrated Human Practices Best Model Medals

While working on our project, we paid attention to many sub-components in order to create our finished overall system. Even if all parts were important to assemble our project, we put particular focus on some of them, like Human Practices and Modeling. It was also important to us to choose a project, contributing to cleaner water and therefore to the United Nations sustainable development goals. On this page we would like to concentrate on our innovative strategies to contribute to:

global challenges
educating people
integrating additional opinions/needs into our project
modeling our system for better experimental planning
designing a software tool for biofilm modeling in collaboration with the Hannover iGEM Team

The texts below should give you an overview about our award-worthy endeavors. The short versions of these texts can be found in the Judging Form. Furthermore, we summarize which medal criteria we fulfill and link you to the associated pages.

Best Education

Biotechnology is something that is a mystery to many in our society. Everybody has heard of it - but what does it actually mean?
We have made it our mission to change something about that: everything within the framework of our teams Science Communication. We have started various activities to bring the abstract topic of Synthetic Biology (SynBio) closer to the general public. Therefore, we aim for the special price Best Education.

In times of the COVID-19 pandemic human-to-human contact can be described as difficult to nearly impossible to carry out for non-school educational purposes. Defying these limiting circumstances, we developed methods that allowed us to communicate with the general public – by successfully doing all of this online. This way we made sure to remain safe and healthy and do our part to prevent the spread of the virus. We are aware that this digital approach to education is more likely to reach younger audiences, but we tried our best to include a wide range of age groups into our efforts, as described below.

To begin with, we started a survey to understand what kind of image SynBio has in today's society. We shared the survey on several platforms so that people from all walks of life could access the survey. This way we also learned new things by looking at the opinion and knowledge about SynBio within Germany: A major part of the respondents were not a hundred percent sure what to expect when presented with terms like genetically modified organism (GMO) or synthetic biology. Although some people may have concerns regarding implementing GMOs in areas like wastewater treatment, the majority sees a future for the use of GMOs. If you want to find more about the information we gained through the survey, you can visit our Human Practices Page. Based on the survey, we started a livestream with iGEM Kaiserslautern in which we talked about what we learned and drew some attention to the promising world of SynBio. The livestream has given us an opportunity to interact directly with people from all over Germany and establish a dialogue with new communities. In this way we were able to educate about general safety concepts and our kill switch, as well as get invaluable feedback about these topics. We found out that many viewers had a general interest in SynBio, but were lacking any deeper knowledge, which we tried to remedy as best as we could. For example, it wasn’t clear to some of our viewers, that waste water treatment plants are currently not able to filter out certain micropollutant without any problems. We chose German as the language of communication because we wanted to make a difference locally and the attitude towards biotechnology is often based on missing knowledge within Germany.

For the same reason, we also chose a German-language podcast. Using the title "Genomenal – Ein Haufen Zellen redet über Biotech" (Genomenal – a bunch of cells talks about biotech) we address topics such as ethics in biotechnology, legal issues or even iGEM as a competition in itself. We refer to our project as well as to other topics in synthetic biology by discussing the opportunities and above all the risks SynBio offers. It was important for us not only to report on the positive aspects of SynBio, but also to put any negative aspects into the right context. The podcast is published on Spotify because we wanted to create a medium that is easy to use and provides a permanent access even in the future. The podcast thus provides information for all interested parties who may become involved in the world of SynBio. It was important to us to include listener’s feedback and interact with our listeners, which is why we included a way of possible communication by listing our teams mail address in every episode description. Because we wanted to make our work as transparent and accessible for future generations who may want to continue our work or come up with their own podcast, we created a guideline on “how to podcast”, which helps with topics like the selection of technical equipment or how to build up your own RSS-feed.

Science is something for every member of our society, which is why we have thought of a way to give younger people access to SynBio. Together with Aleksa Zečević, we programmed a jump-and-run computer game called "The Genomal Adventures of Dr. W" in accordance with our podcast. The main character, a scientist, has to master seven levels in which he is confronted with tasks from everyday laboratory life. In this way, we playfully arouse interest, even among the youngest members of our society.

It was also particularly important for us to appeal to upper school students separately, as they are in a period of life that will have an extreme impact on their later professional life. For this reason, we worked together with the Kurt-Schumacher-School in Karben. We hosted a zoom call with an advanced course in biology at this school in which we introduced biotechnology as a subject of study. We answered questions about our studies, gave tips and tricks that we have collected in our daily study life and introduced iGEM and our project. In this way we paved the way for students to get involved in synthetic biology.

In addition to everything presented above, we have published our own article in the BIOspektrum, a German scientific journal. The BIOspektrum is linked to many German Societys such as the GBM, VAAM, GfG or DPGT and reaches around 15 000 readers monthly. This enabled us to reach out to established scientist or even just people who have a greater interest in SynBio, who we have never thought of contacting by ourselves, but who turned out to help us take our project even further. For example, Prof. Dr. Möller, astromicrobiologist at the German Aerospace Center, has reached out to us as a direct result from publishing in the BIOspektrum. If you want to find more about this, you can visit our Integrated Human Practices. We talked to him about possible implementation scenarios of our biofilm in aerospace and how we would have to adjust our project to enable the usage e.g. aboard the ISS (international space station).

Our efforts include teaching others about SynBio, but also learning ourselves: scientific knowledge is a valuable good and you don’t need to be a scientist to develop a deeper understanding and begin to shape a world of SynBio. We have built up a system of safe, informative and generations-spanning possibilities to enthuse others for science and establish new opportunities. And all this, despite facing a global pandemic and having restricted possibilities especially in human contact. We still managed to come up with ideas and enjoyed including feedback into our work (for example with our podcast or with other iGEM Team’s we have collaborated with), creating conversations and therefore mutual learning. The projects we built up are a basis for future iGEM generations, who may want to continue our work.

Best Integrated Human Practices

After vigorous research for our project idea and discussions about the implementation of our project, we came to write experts. With our project B-TOX we intervene into something man build in order to preserve the environment and wild life. Consistently, it is necessary for us to turn to society, stakeholders and experts in the field of wastewater treatment as well as purification to even consider an implementation of our project idea. We had informative and fascinating talks with multiple people from different professions, like professors from philosophy departments and sewage management, the head managers from local wastewater treatment plants, aquatic toxicologists and microbiologists amongst others. To our great advantage, most of the experts we contacted are working on comparable projects, utilizing either laccases or having worked on the filtration of wastewater in regard to diclofenac. We integrated many of their valuable ideas and suggestions into our project. But what exactly have we learned from our experts?

We have led conversations with various stakeholders who were able to stress their doubts and apprehensions about our project, especially regarding safety concerns. Considering that we are working with genetically modified organisms, it was important to ensure the containment of our biofilm system. To seize control over our biofilm, we developed a kill switch system in order to attain a secure use, as Dr. Ulrich Ehlers from the Federal Office for Consumer Protection and Food Safety suggested. For a complete review on the input he gave, please click here.

In the matter of safety and ethics, we also turned to experts in this field like Prof. Dr. Sibylle Gaisser from the department of industrial biotechnology at the Hochschule Ansbach. Following her recommendations, we created a safety form with the goal to prevent a misuse of our biofilm (dual use issue), and also constructed a safety sheet meant for the wastewater treatment employees in order to educate them for their safety. For a more detailed review of Prof. Dr. Gaisser’s input, click here.

With Prof. Dr. Alfred Nordmann and Prof. Dr. Andres Jürgens we investigated the question of how to develop an ethically justifiable project and the steps toward it. We summarized all of our ethical considerations on an extra page, click here.

Dipl. Ing. Udo Bäuerle, an engineer specialized on the planning of WWTPs, elucidated us on the reoccurring problems considering commonly used procedures like ozonolysis and the use of active carbon in wastewater treatment plants – assuring us that a project like ours would be helpful. Click here for more information on him.

Another aspect we focused on, besides safety, was the proper disposal of pharmaceuticals like diclofenac. There would be considerably less water contamination trough drugs if our society was aware of the proper disposal, to begin with. As we were told by Dr. Patrick Schröder from the German Environment Agency, private households are the primary and main source of drugs in wastewater treatment plants. Hence, we went on and translated the key aspects of the flyer regarding proper disposal of pharmaceuticals from the German Federal Agency into English to achieve a sensibility at an international level. We are convinced that this will also enhance the awareness towards other substances such as ibuprofen or hormones like estrogen, which in addition to diclofenac can be dismantled by our laccase. For a complete review of our interview with Dr. Patrick Schröder, please click here. Last but not least, Prof. Dr. Jörg Oehlmann, an aquatic ecotoxicologist from the Goethe University in Frankfurt, also called attention to other degradable substances like 17-alpha-estradiol and bisphenol A - in addition to carbamazepine and the few others, as mentioned before. To read more about his input, click here.

The input we gathered confirmed our initial perception of the danger diclofenac poses to the environment and that there is need of a project like ours. It was also brought to our attention how broad the substrate specificity of the laccases is and that they are also capable of rendering other substances less toxic, like ibuprofen or carbamazepine. Furthermore, Prof. Dr. Susanne Lackner (head of the department of sewage management at the TU Darmstadt) gave us recommendations on the use of biofilm carriers regarding their material and maintenance, plus offering us to send us samples. A bacterial strain of B. subtilis was offered to us as well by courtesy of Prof. Dr. Jörg Stülke. For a complete review of his input, click here. To read more about the input Prof. Dr. Lackner gave us, click here.

Not only did our experts draw attention to other substances we could focus on, but did also confirm some of our approaches, such as the knockout of both sinR and σ^F that regulates the sporulation of B. subtilis. The knockout of both of those genes would eventually make our biofilm more resilient, but would not spare the need of a kill switch. In addition, the abundance of the fusion protein TasA would guarantee an adequate display of our laccases in the biofilm matrix, as it was confirmed by PhD. Yunrong Chai from the Northeastern University in Boston.

Another highlight during our expert interviews was undeniably our conversation with Prof. Dr. Ralf Möller from the Space Microbiology group at the German Aerospace Center (DLR) in Cologne. He inspired us to broaden our horizon by considering a possible implementation of our biofilm in space. Not only did he confirm our kill switch to be a suitable biocontainment measure but did also draw our attention to the fact that an overexpression of TasA could be utilized for the biomining of rare earth elements in space. This turned out particularly surprising, as it could be applied for asteroid mining in the future. Prof. Dr. Möller also pointed out how promising of an employment our biofilm would be for the wastewater purification in a space station and how it could replace currently existing methods. Thanks to him, we have been encouraged to envision potential applications in space travel. For a more detailed review, click here.

We have managed to reach lots of experts from different fields and departments in order to optimise our project idea and bring it closer to realization and an implementation. Hence, we are immensely grateful to each and every one who has helped and guided us towards the final concept as it is.

Best Model

As for many other iGEM teams, due to the SARS-CoV-2 pandemic, it was not possible for us to meet physically. In this context, we focused on in silico approaches aiming to improve our biofilm.
Despite the limitations we were eager to achieve the best project we could possibly create. Therefore, we put a lot of effort in learning new skills in the field of bioinformatics and realized multiple bioinformatic solutions adapted to our project idea: Structural approaches were utilized to further study our enzymes’ characteristics, differential equations were used to observe our quorum sensing kill switch and a new model was developed calculating biofilm properties based on the forces acting on individual cells. With the implementation and analysis of these models the largest modeling team in TU Darmstadt’s iGEM history was able to accomplish convincing results that contributed significantly to our project. We are confident that our models can serve future iGEM teams as a framework, especially if their individual project is within the scope of biofilm engineering.

We managed to develop a software to track and visualize biofilm growth in collaboration with Hannover’s iGEM team. The base model was implemented in Python by Team Hannover and considers multiple parameters essential for biofilm growth. We incorporated growth rate, split length and movement speed of bacteria into our time dependent model. This way we are able to output plots of the position and movement of the bacteria as well as the total strength of the biofilm, which is of special interest for our project. To ensure accuracy of the model, growth parameters would be necessary that can be measured in the lab. Unfortunately, this year we were not able to do these measurements due to the current Covid-19 pandemic and used literature values for B. Subtilis instead that need to be adjusted to fit our application. The simulation can easily be adjusted to meet the requirements of future iGEM teams which focus on projects including biofilms, for example by adjusting growth rates to the utilized organism. We proved the functionality of this software and presented the results on this year's project Wiki.

Secondly, we used MATLAB to model our quorum sensing kill switch mechanism. The model utilizes ordinary differential equations (ODE) to make predictions on its functionality. The kill switch includes multiple messenger proteins and molecules of which we are able to track the development of concentration over time. This way we are able to predict its functionality and reliability which is crucial for kill switches. Unfortunately, the model depends on parameters that we would need to measure in the lab, so additional values are necessary to adjust the model to its application purpose. However, ODE based implementation allowed to derive relations between the kill switch instances and the interaction between the corresponding messenger proteins that helped understanding the mechanism of the used kill switch in more detail.

In the area of biophysics and structure prediction we determined a possible 3D structure of one of our degradation enzymes, EreB, using the RosettaCM application. Here, the EreB sequence was aligned to an enzyme involved in the succinoglycan biosynthesis, which possesses high sequence similarity to EreB in its active site. We further used the software package GROMACS to validate the stability of the predicted structure by performing a molecular dynamics simulation (MD). MD calculates the forces working on every atom of a previously defined system with a force field time dependently. Explicit water molecules are added to simulate the protein’s behavior in aqueous environments. We wanted to determine whether our enzyme immobilization strategy of fusing the enzyme to the matrix protein TasA from B. subtilis leads to functional enzymes. Therefore, we used RosettaCM to predict structures of the fusion proteins and performed a MD simulation to validate stability and correct protein folding. This way, we showed that the protein domains hold structural similarity to their unfused template proteins (TasA + enzyme). Thus, it can be assumed that the individual domains of the fusion proteins retain their original function and the fusions can be employed pharmaceutical degradation.

We also used Rosetta to study the binding affinity of the transforming enzymes to their target substrates by small molecule ligand docking. We therefore created conformational libraries of the small molecules and calculated their binding affinity in different orientations and conformations. We used these results to compare different types of laccases. The kinetic values of oxidation are positively influenced by smaller distances of the ligand to the T1 copper responsible for electron transfer. This way we were able to deeply understand the mechanism of our enzymes and their versatile specificity to multiple phenolic substrates. The commonly used laccase for application in wastewater treatment and transformation of pollutants derives from the funghi Trametes versicolor. Since this fungal laccase was never expressed in prokaryotic cells, e.g. because of its glycosylation, we were looking for an alternative appliable in our B. subtilis biofilm. Small molecule ligand docking helped us to compare the T. versicolor laccase to bacterial laccases from E. coli or even native in B. subtilis and to validate them as alternatives to the fungal laccase.

By focusing on modeling approaches to our project we were able to adapt to the current COVID-19 pandemic and present bioinformatic approaches and data that refined our project. Additionally, our approaches can serve as useful templates for future iGEMers. With this in mind, we hope to support people new to the field of bioinformatics with guides on complex console applications like Rosetta, that can be complex at first sight but are an amazing, versatile tool in biophysics and can therefore be transferred to nearly every iGEM project. Further, our frameworks on both biofilm and kill switch modeling provide platforms which are adjustable and expandable for further use. This way we hope to pass on our gained experience with bioinformatic approaches and their impact on iGEM projects to future iGEM teams.

Medals

Competition Deliverables: We registered for the Virtual Giant Jamboree and are looking forward to the event! Therefore, we created our Wiki, Poster, Presentation Video, Project Promotion Video and filled in the Judging Form.

Attributions: Please visit our attributions pages to see who supported us this year.

Project Description: Click here for our project description.

Contribution:We contributed a variety of things to the iGEM community this year. Click here to see.

Ultimately, we won a gold medal. To see all judging results of our team, click here.