Team:Aachen/Human Practices
Human Practices
Communicating the benefits M.A.R.S. provides for the world
Our Human Practices’ function can be instrumental in creating a culture of sustainability and environmental stewardship. Only through close work with different people of different levels of scientific knowledge,
we can enlighten the world’s problems and discuss their solutions.
This is necessary for implementing the rapid development of our project. Here, numerous examples demonstrate how a focus on each piece of advice has helped us shape M.A.R.S as it exists today.
Our activities in the course of Human Practices:
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Our activities in the course of Human Practices:
- Meetings with experts
- Prof. Dr. Dörte Rother and Dr. Torsten Sehl
- Prof. Dr. Jochen Büchs
- Dr. Ilia Platzman
- Dr. Felix Jakob
- Sir John E. Walker
- Meeting with Costenoble
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Meetings with experts
Prof. Dr. Dörte Rother and Dr. Torsten Sehl (FZ Jülich)
While researching for our project and looking for other experts in the field of synthetic biology, who could give us valuable input for our project progression, we came into contact with Prof. Dr. Dörte Rother and Dr. Torsten Sehl from the Biocatalysis Group of the FZ Jülich. With their expertise in synthetic enzyme catalysis we tried to figure out how to engineer our already existing idea of an ATP based regeneration system to the needs of a modern industrial application.
The first meeting happened in March 2020 and during the progress of our project we kept in close contact with the Team of the FZ Jülich. We apprised them on our project progression while collecting important hints on how to tailor our project in various aspects. For our project, we needed to know how our system could outcompete other already existing cofactor regeneration systems. Additionally, it was important for us to learn whether the sole ATP regeneration has already potential in an industrial field, or if there is a more proficient application in already existing in vitro systems.In vitrosystems for product synthesis are highly complex and therefore knowing what to bear in mind while designing something that meets the needs of such a system is crucial. This cooperation led to the chance for us working there on an enzyme reaction, where an application of a new innovative cofactor regeneration system with the outlook of our chassis getting tested in a real environment. We want to not only prove that it has the ability to regenerate ATP but furthermore show that it is capable of powering an enzymatic reaction. Providing a reliable ATP recycling system that even meets industrial needs has a huge potential. Cost reduction through the reusability of a cofactor regenerating system is a key aspect not only for the production of pharmaceuticals. Every enzymatic process that requires ATP could potentially benefit from such a system.
Find out how we integrated Prof. Rother's and Dr. Sehl's feedback into our project here.
The first meeting happened in March 2020 and during the progress of our project we kept in close contact with the Team of the FZ Jülich. We apprised them on our project progression while collecting important hints on how to tailor our project in various aspects. For our project, we needed to know how our system could outcompete other already existing cofactor regeneration systems. Additionally, it was important for us to learn whether the sole ATP regeneration has already potential in an industrial field, or if there is a more proficient application in already existing in vitro systems.In vitrosystems for product synthesis are highly complex and therefore knowing what to bear in mind while designing something that meets the needs of such a system is crucial. This cooperation led to the chance for us working there on an enzyme reaction, where an application of a new innovative cofactor regeneration system with the outlook of our chassis getting tested in a real environment. We want to not only prove that it has the ability to regenerate ATP but furthermore show that it is capable of powering an enzymatic reaction. Providing a reliable ATP recycling system that even meets industrial needs has a huge potential. Cost reduction through the reusability of a cofactor regenerating system is a key aspect not only for the production of pharmaceuticals. Every enzymatic process that requires ATP could potentially benefit from such a system.
Find out how we integrated Prof. Rother's and Dr. Sehl's feedback into our project here.
Prof. Dr. Jochen Büchs (Process Engineering RWTH Aachen University)
We scheduled a Zoom-Meeting with Prof. Dr. Jochen Büchs from the “Aachener Verfahrenstechnik”, in which we presented our project idea M.A.R.S. to get his advice on our bioreactor design. Since we try to enable the various ATP-dependent processes in the biotechnological industry to be implemented at a bigger scale, the design of our reactor has special significance. Our reactor must be economically accessible and, most importantly, safe and reliable.
Professor Büchs is one of the leading scientists in bioreactor design, specializing in shake flasks systems and bioreactors. He took the time to review our basic concept and provide a vast amount of input and fresh ideas for our system. We faced two major challenges considering our bioreactor design. First, we were not sure how to generate sufficient mixing in our reactor without exerting too much hydrodynamical stress on our chassis. On top of that, we needed a very specific reactor geometry to be able to incorporate magnets into the design, so that they were close enough to reach all magnetic particles inside and also retractable at will to initiate the magnetic mechanism at different stages of recycling. Professor Büchs helped us a lot with both our major challenges and also provided more expertise in fine details and industrial applications.
Especially the approach of using magnetic particles was evaluated as a profoundly new and interesting niche for industrial application.
Find out how we integrated his feedback into our project here.
Professor Büchs is one of the leading scientists in bioreactor design, specializing in shake flasks systems and bioreactors. He took the time to review our basic concept and provide a vast amount of input and fresh ideas for our system. We faced two major challenges considering our bioreactor design. First, we were not sure how to generate sufficient mixing in our reactor without exerting too much hydrodynamical stress on our chassis. On top of that, we needed a very specific reactor geometry to be able to incorporate magnets into the design, so that they were close enough to reach all magnetic particles inside and also retractable at will to initiate the magnetic mechanism at different stages of recycling. Professor Büchs helped us a lot with both our major challenges and also provided more expertise in fine details and industrial applications.
Especially the approach of using magnetic particles was evaluated as a profoundly new and interesting niche for industrial application.
Find out how we integrated his feedback into our project here.
Dr. Ilia Platzman (Max-Planck-Institut)
Trying to finally assemble our cell-like ATP-factories, we got in contact with Dr. Ilia Platzman. Someone who is profoundly skilled in working on bottom-up approaches of liposomes with cell mimicking functions.
We presented him with our project idea as well as the progress we made so far. Moreover, we wanted to troubleshoot our current procedures and evaluate with him whether our current experiment schedule was
created reasonably. Through this meeting, we aimed to improve our understanding of protein integration techniques and which lipids support the integration of our chosen proteins. Additionally, he
presented an easier and more reproducible method for the generation of giant unilamellar liposomes, which are easier to detect with a fluorescence microscope. Furthermore, we were very thankful that Dr.
Platzman was available for further questions via e-mail and scheduled another zoom meeting for that purpose.
Find out how we integrated his feedback into our project here.
Find out how we integrated his feedback into our project here.
Dr. Felix Jakob (DWI Aachen)
Our project had reached a point where we knew what its purpose is and how it could excel other ATP regeneration approaches. Through our previous expert meetings, it was clear that the recycling feature of our system would be the crucial part of what makes our project stand out. Sustainability is a key aspect of today's research and we want to live up to that. How can we combine magnetic particles with our ATP factories?
We came into contact with Dr. Felix Jakob and Christian Simons, who are experienced with anchor peptides. These short peptides are able to bind on various surfaces and therefore find application in several forms of surface modifications. We needed to discuss whether it is possible to establish a connection between different surfaces, and if so, which anchor peptides should be tested for that purpose. Furthermore, we talked about other ideas we had to establish the ability that would make our system magnetically retainable. After presenting our system and current progression, we talked about the possible advantages of various anchor peptides. Reflecting on which molecular interactions could be beneficial for a strong bond between our ATP factory and magnetic particles is crucial for the success of our project. Find out how we integrated his feedback into our project here.
We came into contact with Dr. Felix Jakob and Christian Simons, who are experienced with anchor peptides. These short peptides are able to bind on various surfaces and therefore find application in several forms of surface modifications. We needed to discuss whether it is possible to establish a connection between different surfaces, and if so, which anchor peptides should be tested for that purpose. Furthermore, we talked about other ideas we had to establish the ability that would make our system magnetically retainable. After presenting our system and current progression, we talked about the possible advantages of various anchor peptides. Reflecting on which molecular interactions could be beneficial for a strong bond between our ATP factory and magnetic particles is crucial for the success of our project. Find out how we integrated his feedback into our project here.
Sir John E. Walker
We always wondered how do people get a Nobel Prize? What kind of mind do they have? What is their secret to success?
We got our answers. And those answers came from the Nobel laureate himself, Sir John E. Walker. He received his Nobel Prize in chemistry (1997) for his ground-breaking work about the ATP Synthase. Because of his vast knowledge on this topic and since our project is closely related to his research field, we organized an online meeting with him. In the meeting, he was able to provide information about ATP synthase and, most valuably, the function and utilization of an inhibitor protein (IF1). This protein is crucial for projects such as M.A.R.S., where the inhibition of ATP hydrolysis plays a key role in keeping the system running.
Some random events in his life brought him to one of humanity's significant achievements, namely the Nobel Prize. He met Professor Frederick Sanger at a workshop at the University of Cambridge and subsequently joined him at the Laboratory of Molecular Biology of the Medical Research Council. Later he was asked to found MRC Mitochondrial Biology Unit in Cambridge where he continues his research on the ATP synthase. We appreciate his interest in communicating with us and the constructive discussion about our project.
Finally, we are heavily inspired by this meeting and honestly believe in a positive impact for young scientists to discuss with people who achieved enormous scientific results.
We got our answers. And those answers came from the Nobel laureate himself, Sir John E. Walker. He received his Nobel Prize in chemistry (1997) for his ground-breaking work about the ATP Synthase. Because of his vast knowledge on this topic and since our project is closely related to his research field, we organized an online meeting with him. In the meeting, he was able to provide information about ATP synthase and, most valuably, the function and utilization of an inhibitor protein (IF1). This protein is crucial for projects such as M.A.R.S., where the inhibition of ATP hydrolysis plays a key role in keeping the system running.
Some random events in his life brought him to one of humanity's significant achievements, namely the Nobel Prize. He met Professor Frederick Sanger at a workshop at the University of Cambridge and subsequently joined him at the Laboratory of Molecular Biology of the Medical Research Council. Later he was asked to found MRC Mitochondrial Biology Unit in Cambridge where he continues his research on the ATP synthase. We appreciate his interest in communicating with us and the constructive discussion about our project.
Finally, we are heavily inspired by this meeting and honestly believe in a positive impact for young scientists to discuss with people who achieved enormous scientific results.
Costenoble
Meeting with Costenoble
For the production of the liposomes, according to the paper of Göpfrich et al. (2019) [1], we ordered the oil “Krytox™” as a surfactant in the oily phase. The marketing department of the
manufacturing and sales company Costenoble then contacted us to find out more about our use of their product in a biotechnological context. At the personal meeting, we presented our
project M.A.R.S. with a focus on the formation of liposomes.
We then answered numerous questions from Costenoble regarding the relevance of liposome formation and production for biotechnology
and synthetic biology. Finally, we received an overview of the company’s history, as well as its products and their application, which resulted in further interesting considerations
regarding their use in a biotechnological context. They were so interested in this new application field that they wrote an article about our project and how their product can be used.Costenoble is an international distributor and producer of chemical-technical products and special chemicals such as lubricants, coatings, pigments, and adhesives.
Integrated Human Practices
Transforming advices and disscussions into results
Without the exchange and discussions with experts about our project it, wouldn´t be possible to continue in an optimized way. It was essential to get an insight into different research fields to improve the interdisciplinarity
of our system and our project as a whole. The interviews helped us to reflect on the problems we faced during our work on our project.
People and groups we got in contact with in the course of Integrated Human Practices:
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People and groups we got in contact with in the course of Integrated Human Practices:
- Prof. Dr. Dörte Rother and Dr. Torsten Sehl
- Prof. Dr. Jochen Büchs
- Dr. Ilia Platzman
- Dr. Felix Jakob
- Other iGEM Teams via the iGEM Journal by iGEM MSP-Maastricht
- Students from Costa Rica
Go to Human Practices.
Prof. Dr. Dörte Rother and Dr. Torsten Sehl (FZ Jülich)
Through the constructive input of Prof. Dr. Rother and Dr. Torsten Sehl, we could receive a better understanding of how to power enzymatic reactions and what to consider while working with such in vitro systems. During the first meeting, we quickly noticed that for an industrial application it is significantly more interesting to implement our system in a process in which continuously cofactor regeneration is needed instead of using our system to purely produce ATP. As a consequence, we adapted our title to the term “Magnetic ATP Recycling System”. Reusing the replenished ADP over and over in a reaction system instead of adding a specific amount provides flexibility and saves resources.
The term “recycling” became even more prominent during our meetings, since we came to the conclusion that reusability might be an aspect that could uplift our ATP-Regeneration System from other methods to synthesis ATP. Consequently, we cconcluded that if we engineer the ability to be magnetically retainable into M.A.R.S, a bioreactor with magnetic elements could provide that desired reusability. The vision to power an in vitro enzyme reaction, extracting the synthesized products while holding our ATP-factories back in the reaction vessel to convert new substrates into the wanted product, was determined due to this cooperation with the Jülich Research Centre. Furthermore, we realized how abundant the use of ATP is for enzyme reactions. Hundreds of pharmaceutical products or fine chemicals require ATP for their enzymatic production. Seeing some of the enzymes, such as carboxylate reductases or carboligases in action, made us realize the urgency of ATP-regeneration in today´s even more.
The term “recycling” became even more prominent during our meetings, since we came to the conclusion that reusability might be an aspect that could uplift our ATP-Regeneration System from other methods to synthesis ATP. Consequently, we cconcluded that if we engineer the ability to be magnetically retainable into M.A.R.S, a bioreactor with magnetic elements could provide that desired reusability. The vision to power an in vitro enzyme reaction, extracting the synthesized products while holding our ATP-factories back in the reaction vessel to convert new substrates into the wanted product, was determined due to this cooperation with the Jülich Research Centre. Furthermore, we realized how abundant the use of ATP is for enzyme reactions. Hundreds of pharmaceutical products or fine chemicals require ATP for their enzymatic production. Seeing some of the enzymes, such as carboxylate reductases or carboligases in action, made us realize the urgency of ATP-regeneration in today´s even more.
Prof. Dr. Jochen Büchs (Process Engineering RWTH Aachen University)
Thanks to the detailed advice Professor Büchs provided for the concept of our bioreactor, we were able to rethink our working process and get a different perspective. Our ideal bioreactor would be a continuous system, which can be connected to any process to recycle ATP effectively. For proof of concept for our system, the continuous flow poses a lot of challenges, especially because we first need a demonstration of our chassis in smaller quantities, to make experiments and try different system set-ups. We early on had the vision to make the production of our M.A.R.S. prototype reactor as easy as possible, to enable our system to have the wanted accessibility and easy handling. We came up with the idea to 3D print some of the structures and materials we wanted to incorporate. After the meeting with Professor Büchs, we rethought the layout of our prototype, relying on a batch reaction system, which can be used repeatedly by quickly altering the reaction medium rather than having it flow continuously. Professor Büchs gave us the idea to split up the continuous flow into several smaller batch reactions, to achieve the best results. To get the best combination of mixing and low hydromechanical stress, we opted for a shake flask version of our system on a self-printed base, which provides the power input to our system and also incorporates our magnetic mechanism, which can be turned on and off at will, by being moved under the reactor base or being retracted from underneath it. All design details are shown on our “Hardware” page. This layout enables us to feed medium onto our system in the shake flasks and pumping the recycled ATP-rich medium out at the top, while the magnets keep our chassis in the reactor. Applying the insights and opinions Professor Büchs gave us, we were assured that our system can have a big impact on the industrial level and, furthermore, we were able to steer our project into a much more thought out and reliable direction of design, to ensure safety and quality in its application.
Dr. Ilia Platzman (Max-Planck-Institut)
Dr. Platzman noticeably helped us in refining our experiment procedures. First of all, we tried to find a solution to quantify our liposome
creation more effectively. Therefore, a method that could provide visible liposomes in higher amounts would improve the chance for a successful ATP synthesis. During our meeting, Dr. Platzman taught
us a very efficient shaking method which acts complementary to our currently used film rehydration method. Another big challenge is protein integration. The concept of implementing proteins into a membrane
artificially is nowhere near trivial, therefore we were very fortunate to get an expert opinion on our current procedures. Verifying that our approach is going in the right direction, fine-tuning the procedures
with the practical knowledge of Dr. Platzman leads us on a promising path for the final two months of laboratory work.
Dr. Felix Jakob (DWI Aachen)
The meeting with Dr. Felix Jakob and Christian Simons allowed us to finalize our approach of establishing a way of equipping our ATP factories with the ability to be magnetically retainable. Through our various brainstorming meetings, we came up with many different ideas. Many of them needed to be discarded again since they had too many drawbacks. Creating a special membrane to intercalate magnetic nanoparticles inside the hydrophobic part would result in a membrane, which is too thick to fit the needs of the desired membrane proteins. Integrating magnetic particles in our membrane could as well result in the destruction of the membrane when the magnetic force is applied. Talking to someone who is really experienced in the field of surface functionalization was highly beneficial for us and greatly appreciated. We knew that we had to externally link our system to magnetic particles and therefore could benefit from the properties of anchor peptides. During this meeting we learned that especially the charge and amphiphilic properties play important roles while deciding on an anchor. Using Cecropin A as an anchor was a very interesting suggestion since we were unsure on how tight our current anchor candidates would bind on a membrane like surface. We discussed that through its amphiphilicity it might achieve good binding results because it would interact with the hydrophobic part of the membrane and therefore act as an intercalating anchor. It became clear that we have to decide carefully about the binding domains, too. A lesser recycling yield is unwanted, and therefore wouldn´t be constructive.
Article for the IGEM Journal 2020
We were part of iGEM MSP-Maastricht’s Proceedings Journal. A journal project in which teams from all over the iGEM community could write and submit articles or introductory papers about their projects, informing each other about their ideas,
current results, and further plans. We had a great experience writing a short scientific paper about our current laboratory results and methods. Not only did we showcase our project to the other iGEM teams, but we also gave and received
feedback in a structured peer review process. Reviewing the other teams' articles gave us insight into their projects and the common scientific workflow. The feedback we received for the presentation of our project helped us make our final
goal more precise, and in general, improve our academic writing skills. The edited journal is available here.
Meeting with students from Costa Rica
To spread the idea of iGEM and our project into the world, we organized an online meeting with interested students of the ‘Universidad de Costa Rica’. Around 40 students of the pharmacy career track attended the meeting.
We had the chance to present our project and the idea of iGEM to a different audience. After the presentation, we had a long discussion with the students. Receiving feedback from an audience, which comes from a different
field of research, gave us the opportunity to see our project in a new light. Through their specific questions, which came especially from the medical background, we had the opportunity to explain how our M.A.R.S. can
help to improve the production of pharmaceutical precursors. We benefitted from their deep understanding of the importance of ATP in their field of study. Furthermore, they confirmed the importance of our system and
that not only in theory but also in reality our system is needed more than ever before.Apart from feeling it in our project ourselves, we experienced the importance of spreading the iGEM Spirit to others. Taking action in real fields of application sparked a lot of enthusiasm. At end of the meeting, we received a lot of questions concerning the procedure of becoming an iGEM member.
References
[1] Göpfrich, K., Haller, B., Staufer, O., Dreher, Y., Mersdorf, U., Platzman, I., Spatz, J. P. (2019). One-Pot Assembly of Complex Giant Unilamellar Vesicle-Based Synthetic Cells. ACS Synth. Biol. 2019, 8, 937−947.