Team:Tuebingen/Human Practices
(Integrated) Human Practices
Science is more than just labwork.
Project Conceptualization
After an exciting project planning meeting at the end of February, we meet with several Professors and experts to evaluate our ideas and shape our project.
Four project ideas emerged:
Two more ecological concerned projects – one about using Cyanobacteria to regain nitrogen from liquid manure to reduce nitrogen pollution in soil and water, while using the fixated nitrogen again as fertilizer. The second dealing with heavy metal accumulating algae for water remediation.
One project with a practical application in biotechnological processes: Building up an RNA thermometer library for yeast to control and monitor culturing and expression in bioreactors. The last one concerning antimicrobial peptides to fight multi drug resistant pathogens.
With Prof. Schäffer we discussed the possibilities and applications of RNA thermometers. He reminded us to recap what kind of infrastructure we might need, like special devices and experts. He assumed he might have the suitable tools for working with RNA thermometers and explained to us which kind of tools we generally could use to examine RNA molecules. He pointed out several bottlenecks and difficulties (like needed high sensitivity), so we could shape the first idea to bypass these. One key concern he mentioned was the short time span we have to realize our project in the laboratory, and that we therefore, should focus on only a few targets. Concerning antimicrobial peptides Prof. Schaffer reminded us that the right expression system is crucial, especially when it comes to antimicrobial agents, to make sure, that the product will not kill the producer. That is why he also suggested to use artificial systems and modeling to test our ideas.
Prof. Jansen advices us to consider the application of our RNA thermometers and to proof if our system would actually work in eukaryotes. This advice was helpful for us, since most of us worked mainly with prokaryotes before. So, we then tried to consider more the difference between eukaryotic and prokaryotic systems and the advantages of eukaryotes as expression systems.
Prof. Forchhammer also gave us advice on the experimental setup and could provide us with interesting knowledge about cyanobacterial cultivation. With this information we could plan further which devices each of our ideas might need. A quite important issue he brought up was the future application of our project since we aim to provide an improvement for our society on the one hand. On the other hand, the application designates safety and legal issues. That is why we reconsidered in which form we could use genetically modified cyanobacteria or algae to remediate soil or wastewater without contaminating our environment. Therefore, we thought about special filter or immobilization systems.
Prof. Groß gave us a great insight into the broad spectra of antimicrobial peptides. This helped us to think more focused on special mode of actions or peptide classes. He also mentioned to us the differences in possible applications due to the different properties of the AMP classes. Hence, we started to think about possible applications of antimicrobial compounds besides the use in a clinical application such as treatment of pathogen-containing waste (water). He also reminded us to consider safety and legal rules about handling antibiotics. An interesting topic he brought up was the bio-degradability of our possible products. This was an important issue to us since we always should think in a long term and also have to weight in possible side effects. Since even new antibiotic actions might become quickly irrelevant when bacteria evolve resistance, we thought - inspired by Prof. Groß - about the combination of mode of actions and possibilities to improve already known AMPs. Another important point he highlighted was the relevance of appropriate analytic methods to analyses our products. He encouraged us moreover to try something new, like screening for not yet characterized AMPs.
A lot of the information he gave us proved to be extremely helpful to us when thinking about the implementation of our project, primarily in regard of the possible future application and safety issues.
Through Prof. Groß we also came in contact to Prof Craig. His research shaped our project in major ways towards working with of cyclotides. His publications offered us a great source of information.
Prof. Ziemert as well reminded us of the fact, that AMPs cover a broad spectrum with numerous different properties. She could provide us with a lot of advice and knowledge about bioinformatics, especially the use of BLAST and Hidden Markov Models which laid the foundation stones for the work of our Drylab team . She also inspired us to look for plant-based AMPs, because they might be more suitable for expression in plants. Prof. Ziemert encouraged us to look for something new, as well. Furthermore, she agreed to take part in our podcast and share some of her broad knowledge with our listeners as well, which you can read more about under the section AMPodcast .
From Prof. Tielbörger we received quite inspiring feedback regarding our project ideas. She reminded us that it is not quite efficient to always search for a “technological” way to stop major threats like climate crisis or health crisis, but that first people should consider their lifestyle. And that we rather should combat the cause and not only treat the symptoms.
This is why we, after considering our technical possibilities and the expertise we have around in Tuebingen, wanted to focus more on a project where synthetic biology makes a difference. Beside this we all were keen on trying something new and extend our lab-knowledge, so we liked the idea to work with plants. After further research and studying the work of Prof. Craig we decided to work on cyclotides and plants as expression system.
Another significant aspect of her advice to us, namely that a change of attitude of the public is necessary to fight global crises, deeply influenced the conceptualization of our Human Practices and Education work during the course of our project. We decided to make the raising of awareness about antimicrobial resistance (AMR) one of our main values. This included in particular to explain about the risks of overconsumption and misuse of antibiotics as well as the problems that stem from it. Our podcast episodes with Prof. Ziemert and Prof. Brötz-Oesterhelt are a good illustration of this attempt. Another example is the radio interview we participated in and our social media campaign, on which you can find more information in detail on our communication page.
instrument of science communication with the focus on informing about antimicrobial resistance.
During the time when we concretely planned what to do in the laboratory, we regularly consulted Dr. Maldener from the Forchhammer working group, where we kindly were allowed to use the student laboratory. She held the safety instruction for our laboratory space and we discussed with her different safety issues regarding our project. This and the safety form reminded us to look into possible risks of cyclotides. When we discovered that some already characterized cyclotides have a potential risk to human health we re-thought our project. After further research our project evolved into something new, but yet with the same intention to facilitate the expression of new possible drugs. This new approach still fits perfectly into our design criteria: safety and an application which really gives a benefit to our society. If you are interested in the details of the re-shaping of our project, follow the link to our engineering page , where we provide more background information on that particular topic.
In many ways the meetings with experts helped us a lot to focus on limiting steps and to evaluate from a scientific and technical but additionally from a societal and ethical point of view which project idea might fit best. We are happy that plenty of our meetings with experts and mentors helped us a lot to move our project further.
AMPodcast
One of our main Human Practices projects was our very own podcast! The AMPodcast went online on every major podcast streaming site, for example Spotify , ApplePodcast or PocketCasts
In every episode we got to interview different people from diverse fields and backgrounds and gained insight into many aspects of scientific and industrial research as well as into science communication, education and ethics. All this new information impacted us a lot - as a team as well as our project during different stages of our research.
Podcast Episodes
Ep. 01 | Our project for the iGEM competition, anti-microbial peptides, and cyclotides
Listen to the very first episode of the AMPodcast!
In this episode, we will talk about our project for this year's iGEM competition. Meet 4 of our motivated team members and learn more about cyclotides, a special class of extraordinarily stable proteins, antimicrobial peptides (AMPs), a class of proteins with antibacterial effects, and how they could be useful to combat the ever-growing crisis of antibiotic resistance.
Our very first podcast episode on the 1st of July was a very important experience because we had to try and concisely explain all our project progress and concepts we had made so far. That was a challenge in itself and a first try at science communication (which proved to be handy later on as we had to explain and pitch our project to potential sponsors as well as to the experimenta Heilbronn, an organization we had collaborated on in another HP project later in the year). In the Podcast we started out by talking about our experience with iGEM and our personal motivation. Especially being included in the project conceptualization process and the challenge of innovation played a big role for many members of our team. But also, an interest in recursive work (and really, the need for working in such a way) was there from the start. Reflection on how and why you were doing an experiment or which way you were doing it had already started before the episode thanks to internal discussions in the team, but the interview really put it into perspective for us again that we needed to stay open for any need to change that became apparent to us.
During the episode, we reflected on our methods and the implications of our project in general. For example, it made a huge difference for our work that we were trying to help with a worldwide and societal problem and not just a purely “scientific” one. We knew for a start that synthetic biology could play a role in the solution, but of course would not exactly be a panacea. It was important to know our role – and that we are working on a short-term approach, but an approach that is important none the less. So, from this starting point of tackling the problem of antibiotic resistance (one of the biggest threats to global health and cause of many deaths worldwide), the project slowly began to evolve. Very soon we faced the problem of hemolytic activity in our cyclotides and had to re-evaluate what we were doing. We did not know how safe it was to work with those peptides and had great safety concerns in the cloning mechanism, and after debating and reflecting on what values and needs we had as a group as well as people that wanted to do their best to work in a socially responsible manner. Also, because there was no real possibility that something with hemolytic or cytotoxic activity would ever be applied or used as antibiotics, we thought the potential to actually help with the problem we were concerned with was slim. A change of some sort would be needed to enable our project to be helpful in some way. After employing the help of the biological safety officers at the university, we decided on a different type of cyclotides so that we could continue our research with a sound mind and good consciousness.
We learnt early on that reflecting on your impact and actual chances of success is a major part in project design. To talk about that in the episode has helped to reevaluate what we had done so far and motivated us to keep up this practice in a long run since we noticed again how important it is to be conscious and aware of what you are doing and what it implies. Of course, that means for society in the big picture, but on a personal level as well and that you need to stay true to your own moral principles. What also became clear during our conversation was that there are still problems remaining with the project that have to be worked on (or at least should be looked at more closely in future research if one would like to build upon our project). For example, we noticed that AMPs – like antibiotics – are not really specify-able on certain bacteria which would be technically desirable in a compound, however. The question remains if that even is possible with AMPs, but to even ask questions concerning our limits proved to be very valuable. Even if you cannot solve everything at once, we learnt that small steps are valuable. They are the steppingstone for further ideas after all. That we were open to think about our limitations and what we would not be able to do, allowed us to stay open during the whole project process and not “over-sell” our idea for something that it isn’t. This fact became very important later when we needed to find concepts for science education and communication on our social media and our panel discussion that stayed honest and true to the scientific values we hold.
Ep. 02 | Dr. Üner Kolukisaoglu on Plant Bioscience, Ethics in Biotechnology and Science Communication
In this episode, we are speaking to Dr. Üner Kolukisaoglu, who is a researcher at the Center for Plant Molecular Biology in Tuebingen and a lecturer at the University of Tuebingen.
Topics include his research in Plant Biology, Ethics in Biotechnology including European Legislation, and Science Communication regarding Biotechnology.
As always, thank you for listening. :)
On the 5th of July, we invited Dr. Üner Kolukisaoglu, a specialist for plant molecular biology, to our podcast. Since we were also working with plants, it was of course incredibly helpful to talk with someone who had expertise in the research field. Not only because he could potentially help us for the “technical aspects”, but because he was able to share with us his opinions and experience regarding the reflections on environmental issues and working on projects that affect the future greatly.
For example, if you had direct impact on a chloroplast, you could also have direct impact on plant growth. That is something that could have tremendous impact: the enhancement of photosynthesis, an interesting prospect to solve energy problems, being one of them or another option would be the possibility for new specific herbicides, so specific in fast that they could be prevented from harming animal life at all. The latter is an important issue at the moment since glyphosate needs a replacement because it has been banned under EU law, but you cannot farm big scale agricultural land without any herbicides at all since that would be detrimental to the output of the field. However, thanks to the interview, we learnt that not every prospect which seems helpful stays so in the long run. Which is why reflecting upon possible consequences is (or at least should be) of high priority. Interestingly enough, Dr. Kolukisaoglu was one of the main implementors of an ethics course for natural science students at our university, so we were able to get a great look into this as well! He told us how important it is to always stay truthful and not lie to yourself about advantages and disadvantages. Science is never “black and white”, so you should not picture it as such either – that would not be an ethically sound practice, even if it sometimes could be tempting to portray everything as a wonderous ailment to society. If you are not careful in your positions and think thoroughly about what you are actually impacting, you may find yourself on a side of the spectrum where you would have never wanted to see yourself.
The advice he gave to us as future researchers was that we need to follow ethical guidelines to conduct good (not only in the sense of morally!) research. Those do not have to be carefully selected from a pool of philosophies, sometimes it could be rather simple: First of all, what you need to ask yourselves always and at all times is: Does my work harm someone? Of course, the goal of research should always be to find out something novel and you cannot prevent in every case that your product could be used in a harmful way (an examples he gave was Oppenheimer and the Manhattan project), however if you would answer the questions with yes at the start, you should think more than twice about if you really want to pursue the project. Secondly, you should never do something solely out of personal motives, such as monetary gain or for the sake of fame – there are certain lines that should never be crossed. Of course, those boundaries wary over time, but steps like broad intrusions into life (like CrispCas on stem cells to prevent illnesses later in life) should never be taken lightly.
All this information was so valuable early on – we have never had this deep of an involvement in the designing process of a project, so of course we needed some pointers on how to do it – not only scientifically correctly, but also ethically sound. We tried to remember his words on multiple steps of the project and we are sure that partly because of him, we were able to not cross any of (our or the scientific community’s) moral boundaries. What he also explained to us which later on became one driving factor of another HP project in general was science communication. Between public backlash and emotionalization, many discussions have left the realm of science and are pushed into fake conflicts by the media. Good science communication should try to avoid that at all costs, information needs to be brought to them appropriately, people should be allowed to discuss safely things that may seem “scary” or that they do not understand yet without the polarization of scientific facts that is seen in the media oftentimes. As a science communicator you need to give people transparent guidance on the flood of facts that rises higher every day, and it’s very important to keep in mind that that is what you need to explain to the public – real facts and real arguments instead of politically exploited non-arguments. What Dr. Kolukisaoglu said there to us became very important later on because we needed to keep many of those things (especially the polarization of fronts!) in mind while we were planning and designing our panel discussion as to not fall into the many pitfalls of science communication on a broader scale. More on how we integrated this advice can be read in the section about the discussion on this page.
Ep. 03 | Prof. Nadine Ziemert on bioinformatics-assisted discovery of new medical compounds
In this episode, we talk to Prof. Nadine Ziemert, who is a researcher at the University of Tuebingen.
Her field is the bioinformatics-focused search for new biomedical compounds, especially through the identification of secondary metabolite gene clusters, which encode for the synthesis of different bioactive compounds such as antibiotics. We also talk about potentially interesting organisms, that could be important sources for these novel compounds.
As always thank you for listening! :)
On the 19th of July, we got to talk to Prof. Dr. Nadine Ziemert about applied nature product genome mining - it was very valuable to get some insight into how one could use bioinformatics and computer science to find new antibiotics. Of course, as we all know, antibiotics are a very important achievement in medicine as they drastically reduced deaths by illnesses like cholera or tuberculosis. However, as there are more and more bacteria developing resistances (the WHO even declared this as one of the ten global health threats), the need for new ideas and new compounds is great. That we knew already – after all, we decided to pursue this issue in our very own project as well, but Dr. Ziemert’s approach was new to us: she draws upon the fact that antibiotics actually are produced by many bacteria as secondary metabolites (also called “natural products”) and looks into the genome of bacteria, like for example actinomycetes, to decode their DNA and look into which antibiotics they could produce and if they were new or already known ones. This is possible because nowadays is through research of natural products experts known how the biosynthesis of antibiotics in bacteria works. During the interview, we talked a lot about what the computational work includes that she does and about how her research impacts the scientific and non-scientific world. Especially interesting is her approach to finding new antibiotics: many bacteria encode a lot of natural products (even if not all of those are antibiotic), but one big project is to find out which gene clusters actually encode for novel antibiotics which novel mode of actions (MoA). The MoA describes what kind of cellular process is disturbed in the target cell (which for antibiotics would be the pathogen). Bacterial resistances are mostly built against MoAs, hence, antibiotics with the same MoA are disarmed by the same antibiotic resistance. Therefore, the discovery of antibiotics with a novel MoA is more desireable since resistances against them have not spread yet and they still have clinical use. This is why one of the goals in the solution of the antibiotics crisis is the development of automatic methods on how to predict the MoA of novel antibiotics. We learnt from Dr. Ziemert that this seems to be a “blackbox” as of now, but it is one possibility to think about when researching new antibacterial compounds.
In addition to that, her work and knowledge have impacted us greatly since (in an additional meeting) she explained to us how to set up Hidden Markov Models, which we then used to find new cyclotides in plant genomes - an idea we surely would not have employed if we had not talked to her and learnt about her research process. Thanks to her, we developed the idea that novel antimicrobial peptides (AMPs) could be grafted into our cyclotide construct as well to make them more stable. All this knowledge taken together would impact our project to an even greater degree if we went on with it in further research since we would need to think about if or how AMPs grafted into the cyclotide might influence the MoA of the AMP. Hence, we could edit the tools Prof. Ziemert’s group already uses to predict MoAs. Such tools are very helpful to make the stabilization process more predictable. What we also realized through talking to her – which we could not implement anymore, but definitely would need to think about in a business endeavor – was that a real challenge for AMPs would be that one needed to test the possible digestion as well as the stability in the blood. That would be two very important factors to make them usable in a clinical setting that we had not thought of like this before talking to her. Because of these factors we would perhaps need to re-conceptualize some parts of our project and we are very grateful for gaining this knowledge.
Not only this was very helpful to us, however. She also gave us an interesting perspective into the world of industry since she told us that many companies use the models and databases she and her team develop, and how they are used industrially. This was good to know as this information is very valuable if you want to “scale up” your project. Even if it at this stage it was not our goal to bring our concepts into the industry or build a startup company, information on if our approach would even be feasible “out of the lab” is very important because if we hypothetically were to go into establish ourselves as a business, we of course would need to work in a suitable and practical way. One thing it inspired us to do now (since the other ideas were just thought experiments) was to, firstly, invite Prof. Dr. Heike Brötz-Oesterhelt for an interview in our podcast because we recognized that we needed more information from the industrial stakeholder’s site (and she has worked in the industry as well as in the academic field). And secondly, we got in contact with the company Nomad Bioscience GmbH in Halle, Germany, to gain even more direct insight into the workings of the industry and their opinion on our project idea (which you can read about on this page as well).
The last thing that we talked about was how important it is to recognize that even though we should continue researching novel antibacterial compounds and natural products, it cannot be the main solution (or at least not the only one). Science is supplemental to helping us win the fight against antimicrobial resistances, but we also need to approach the problem from a societal angle. This is why educating about the problems that arise from the overconsumption of antibiotics and the extensive use of antibiotics in agriculture is so important – only if we change our behavior in general, antimicrobial resistance (AMR) will become less of a problem for humans and animals alike. Projects like antibiotic stewardship are one example for this endeavor. We think this is especially important and very much needed which is why we also started educating on the problems for society that AMR holds on our Social Media channels and other of our education projects as well as in some podcast episodes. It is a topic very dear to our heart and we tried to make it very clear that we have recognized it and wanted to communicate the need for change in society – and that only this will be a long-term sustainable solution for the AMR crisis.
Ep. 04 | Jun.-Prof. Dr. Andreas Dräger on systems biology and fighting antimicrobial-resistant pathogens
This week we are talking to Jun.-Prof. Dr. Andreas Dräger and how he is developing computational models for fighting antimicrobial-resistant pathogens and other diseases. We learn about his current work, what systems biology actually is, and what we should look out for in the future. If you want to find out more, check out his YouTube channel at: https://www.youtube.com/c/systemsbiology
Thank you for listening!
On July 30th we had the pleasure of talking to Andreas Dräger, who is assistant professor for Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens at the University of Tuebingen. His working group develops and uses computer models to investigate two major topics, on the one hand the optimization of biotechnological processes and on the other hand the origin and course of diseases at the molecular level. We were interested in talking to him about the future of drug development, in particular of antibiotics and to learn about a slightly different bioinformatical approach to that topic after talking to Prof. Ziemert about genome mining as one possible option in the last episode. His focus as a systems biologist is to gain an understanding of how organisms work in their entirety with the help of bioinformatical tools.
He explained to us that this understanding of metabolic networks can be extremely helpful in tackling infectious diseases which are threatening us as humans. Right now, as we all are terribly aware of, the focus lies on viruses but multi-resistant bacteria are on the rise worldwide and the goal should be to be as well prepared as possible. Unfortunately, not many novel antibiotics have been developed in the recent past.
Systems biology can really be of help there as it can be used to discover the weaknesses of bacteria and therefore be a meaningful tool for the discovery of potential targets, where subsequently other researchers can come in place and figure out how to hit these targets. Prof. Dräger furthermore elucidated how this work fits into the overall drug development process. Firstly, they produce lists of potential targets, however to only have any kind of target is not enough, it needs to be a meaningful one as well. Discouragingly, not every theoretical target can be accessed by a drug as the drug needs to travel all the way through the body to the reach the target. Along this way there can already be an effect on the drug, whereby it us unable to ever reach its target cell. Therefore, the checking of targets from different angels is necessary e.g., accessibility and possible side effects need to be determined. All these steps make the process extremely time-consuming and that’s why Prof. Dräger's research group provides ranked, ordered lists of the targets which can then be evaluated by researchers working on the concrete development and production of drugs for the most promising ones in reality. For example, he told us, that when you can re-use a drug that is already in the pre-clinical phase, the development span gets much shorter as possible side effects of the drug are already studied. This procedure is called drug repurposing.
All these detailed information about the process of drug development he provided us with lay the groundwork for the concepts we developed for the possible further implementation of our project. Specifically, the mentioned administration route and the unclarity about the bioavailability of our grafted antimicrobial peptides (AMPs) was an issue that got us thinking about possible other applications besides the clinical use, even though this would still be our primary goal if we were to pursue our project further.
Additionally, we were inspired by what Prof. Dräger told us on the importance of interdisciplinary work when we asked him what he thinks the future might bring and what his personal goals and dreams for his scientific work are. He underlined that, “we can all learn from each other” and that the ability to combine techniques from different research areas is highly likely to make processes easier and faster, such as in his case machine learning might help to make quicker progress in the building of models.
Interestingly, the main focus of his work are nasal infections in general, for instance with Staphylococcus aureus . He made clear that our nose is the natural first spot to look at when thinking about pathogens as it is the interface between our body and the outside world, which results in a constant exchange with the environment. His big dream is to be able to study the entire interactome in the human nose and build computer models for every nasal inhabitant that has already been discovered. Consequently, after linking them together you could simulate their interactions to figure out helpful bacteria which could be used instead of drugs in the future. Similar to probiotics in yoghurt these “good” bacteria could then be administered via nasal sprays, for example.
Lastly, the interview inspired us to talk to industry leaders to further understand how our research could eventually be integrated into the drug development pipeline. This led us to our field trip to Nomad Biosciences .
Ep. 05 | Prof. Potthast on bioethics and the limits of synthetic biology
This is part 1 of our interview with Prof. Potthast, who is a bioethicist at the IZEW, the ethics institute at the University of Tuebingen. We are talking about the general difference between ethics and morality, and the boundaries of bioethics. This includes how to schedule a scientific project to be ethically viable, and the limits of synthetic biology.
As always, thank you for listening!
Ep. 06 | Prof. Potthast on research ethics, the ethical dimension of projects, and science communication
In this part 2, we continue our interview with Prof. Potthast from the University of Tuebingen. We talk about research ethics in general, what to consider when designing a project with regards to the ethical dimension, and about science communication, for example, during the COVID pandemic.
As always, thank you for listening!
We highly enjoyed talking to Prof. Dr. Thomas Potthast on August 31st. After studying biology and philosophy in Freiburg, Germany, he received his PhD in Tuebingen and worked for the Max-Planck-Institute for the History of Science in Berlin for his post-doc. Now he is full professor for Ethics, Philosophy and History of the Life Sciences as well as the co-director of the International Center for Ethics in the Sciences and Humanities. Among other things Dr. Potthast is researching bio- and environmental ethics as well as sustainable development in selected areas of practice, one of them being agriculture. We were excited to discuss ethical issues and the implications our project might have on society.
In the interview, which we split into two episodes, we discussed topics in research ethics, project design and science communication. The podcast started off by a general definition of the term ‘ethics’. Ethics is the philosophical examination of ‘morals’ which is based on personal judgement. The foundations of the ethics center in Tuebingen actually lie in the same concern we are discussing: the implications of herbicide or antibiotic resistance. We learned that it is important to work interdisciplinary to fully understand such implications in science and technology. This is especially encouraging for projects like the iGEM competition. Since our team like many others is quite interdisciplinary, this might be very beneficial to recognize and deal with ethical concerns arising from synthetic biology projects. As an example of his own work, Prof. Potthast mentioned livestock management in African countries and how a transformation to a more sustainable management could be achieved. The approach he and his coworkers follow could be transferred to synthetic biology projects like ours as well: social science research, interviews with stakeholders and many interactions with involved players in the concerned field are necessary to get to know different opinions and interests on a topic. This change of perspective is very important. Consequently, one of the main outcomes of such an ethical assessment is setting up “points to consider” and illustrating different scenarios, not determining the right opinion on a topic. Thereafter, we tried to implement a small version of such an interdisciplinary assessment into our project by organizing a panel discussion . In doing so we collected opinions on molecular pharming from the standpoints of research, industry, politics and the public audience.
The interview then moved on to responsibilities as a scientist. Prof. Potthast illustrated the importance and the responsibility of scientists to distinguish between their personal opinion and their expertise as a scientist. He also warned us not to exaggerate as scientists. These statements made us think of our point of view as synthetic biologists. Even though we are excited of the possibilities of synthetic biology and our project, it is again important to take a step back and consider limitations and challenges as well. We tried to do this when rethinking the possibilities of AMPs and started considering their drawbacks and difficulties when working with them, like the hemolytic activity of many antimicrobials (for further information, visit our project description page ). Furthermore, though it is important in science and technology to promote yourself and your ideas, this poses the danger of raising hopes and wrong expectations. For instance, we experienced this in our radio interview , when we were cited incorrectly afterwards. These experiences made us evaluate our project more critically.
The podcast was also essential for our understanding of good and ethically advisable research. Even though no judgements or opinions were voiced, the questions passed on to us by Prof. Potthast lead to internal discussions and influenced the planning of the panel discussion. The main questions he brought up were “What is the goal of a project?” and “Is this goal desirable?”. This made us pause and think about our own project. Our main reasoning for the importance of developing AMPs was the issue of antimicrobial resistance (AMR). However, we came to realize that AMPs are actually not addressing the cause of this problem, but fighting the symptoms. AMR is caused by the mis- and overuse of antimicrobials, a societal problem that can’t be solved by synthetic biology. For us, the takeaway of this thought process was that synthetic biology projects like ours shouldn’t be advertised as a single and most promising solution to a real-life problem, but more as one of many approaches to tackle a bigger issue. Also, he mentioned that it is important as a scientist to communicate not only the advantages, but also the limits of technology like synthetic biology. We tried to implement this viewpoint in our public appearance and this wiki. Another point brought up by Prof. Potthast is to ask whether the end justifies the means. Concerning our iGEM project, we came to the conclusion that our project is ethically reasonable in this concern. In our opinion, if properly assessed and conducted, the method of producing AMPs in plants itself does not pose grave risks which could not be justified by the potential of AMPs in medicine. In contrast, we think that molecular pharming bears many advantages compared to chemical synthesis of pharmaceuticals, for instance a lower carbon footprint and relatively native post-translational modifications of the protein. This question was also raised in our panel discussion , which helped us to obtain a more nuanced opinion.
Another main take-away for us was that two-way communication at eye level is very important in science communication. We strive to realize this with our own podcast, by making it accessible for everyone. Finally, we also talked about genetic engineering in agriculture. Prof. Potthast mentioned that at this stage he also stated his own opinion and put his arguments up to discussion. In general, he seconded the strict European regulations of genetically engineered plants. Furthermore, he emphasized the potentials of synthetic biology in closed systems, not in the open field like in agriculture. Together with the panel discussion, where we brought up the question of farming plants in a greenhouse versus in the open field, his statements encouraged us in pursuing our project. This is because molecular pharming is considered best to be conducted in green houses, since their controlled environment is essential for the production of pharmaceuticals.
In summary, this interview gave us space to reflect on our own projects goals and implementation and motivated us for the planning of the panel discussion to further improve science communication and reflection in the field.
Ep. 07 | iGEM Team CCU Taiwan on AMPs in their project, overcoming problems, and their experience in the competition
In this episode, we talked to a fellow iGEM team, the iGEM team from CCU Taiwan. They are also utilizing AMPs in their project, however in a completely different way, so you will learn a lot about a different approach to fight the worldwide problem of antibiotic resistance. Hear about what their project and aims were, which issues they were concerned with the most, and how they overcame the problems they encountered. This episode is also a remarkable example of the internationality of iGEM generally as we shared with each other our experience in the competition so far.
As always, thanks for listening to AMPodcast!
On the 6th of September, we got together with the iGEM Team from CCU Taiwan. Since they are also utilizing AMPs in their project (even though in a completely different way), we thought it could be very beneficial to talk to them in our podcast. We find it very important to think and talk about different approaches to similar problems as well as similar approaches to different problems, because broadening your horizons and what to think about in any given case can only ever benefit science in general and – of course – our project more specifically.
The podcast has always been a great opportunity to talk to a whole range of people and learn from them and our interview with CCU Taiwan proved to be no different. We talked about what their project and aims were, which issues they were concerned with the most and how they overcame the problems they encountered.
Their approach to working with AMPs differed from ours quite a bit, even though we are working on solving similar issues. For example, we learnt that they were using AMPs in combination with so called CPPs (cell penetrating peptides) as they were designing a product to help fight the large problem of multi-resistant germs, whereas we designed an expression system. Even though we did different things, it was very telling to hear that sometimes you have to face the same hurdles (for example, the instability of AMPs and how to work around that). Of course, we also talked about their approach to Human Practices and their interaction with stakeholders. This gave us some more inspiration for our own projects and whose perspective we could further benefit from. For example, since CCU Taiwan talked about their stakeholder analysis and interviews as well as about their picture book project, we got more interested in informing ourselves about practices in the medical field. Our project lays an important basis that a lot of research that revolves around fighting AMR could potentially benefit from and because of that we felt that we needed to get this more practical perspective. This is also one of the reasons why we decided to invite Prof. Dr. Heike Brötz-Oesterhelt to our podcast as we thought that she especially could give us more insight into this perspective and into the medical field that would certainly be very beneficial to us and our project.
All in all, it helped us a lot to talk to CCU Taiwan and to recall that there is no “one” perfect solution. Afterwards, we thought again about why we conceptualized our idea and project the way we did. Maybe it is obvious, as many things seem to be in hindsight, but how you work with a concept and what shapes your ideas is rooted deeply in the way you think about a problem and your approach to a solution is interconnected with what exactly you are even trying to do. You cannot fit a square shape into a round hole, so to say. Instead, you need to smoothen out the edges and create something that fits. It was rather interesting to see how drastically your options and work changes just because the goal is the slightest bit different.
Ep. 08 | Interview with Prof. Dr. Heike Brötz-Oesterhelt
Not yet published, coming soon! :)
We also got the chance, on the 11th of October, to talk to Prof. Dr. Heike Brötz-Oesterhelt who holds a full professorship for Microbiology at the University of Tuebingen. She is also head of the department of microbial bioactive compounds, managing director of the interfaculty institute of microbiology and infection medicine and co-speaker of the excellence cluster “controlling microbes to fight infections” (CMFI).
Inspired by our interview with Prof. Dr. Ziemert we reached out to her because we became aware of the fact that she has been working in antibacterial drug discovery in the academic field as well as in the pharmaceutical industry for more than 20 years. As our project clearly addresses the problem of antimicrobial resistance, we were really excited to talk to her about these topics.
We were very interested in the different ways research is conducted in the industry setting, especially in contrast to the academic one. She explained that scientific work in the industry surrounding is always driven by the goal to find a new target or even better a new drug, whereas in the academia it is mostly about curiosity and the novelty of your findings. This underlying discrepancy is also a reasonable explanation to why most so called ‘big pharma’ companies gave up on the research on novel antibiotics even though we are in great need for them. Prof. Brötz-Oesterhelt once again highlighted the severity of the worldwide antibiotic resistance crisis. However, she also pointed out how time-consuming and costly the drug development process is and gave a number of reasons on how she has come to the conclusion that we are in need of a different funding system for the discovery of new antibiotics. For one thing, we will have to be much more cautious with the usage of newly approved antibiotics owing to the fact that not many of them are being developed right now and therefore the ones that might actually work against multi-resistant pathogens have to be declared a last resort option. That implies low prescription rates and thus low income for the pharmaceutical company. On the other hand, as already mentioned, the whole process to get to a new antimicrobial active compound is very costly and time-consuming because of the long research and development phase in the beginning as well as the clinical studies that are necessary prior to approval by the regulatory offices.
Her proposal is that the whole process should be funded by public grants and that research in academia and industry should be more closely linked to reach the common goal. To hear this had quite an impact on us as young scientists as well as on the concepts we had in mind for the further implementation of our project. For instance, we realized that a next possible development step of our project would not have to necessarily mean to transfer it into an industrial setting but that it could also be developed further in the university surrounding.
Another topic close to our heart was that we wanted to hear about her experiences and thoughts on the compatibility of being a scientist with a full professorship and having a family at the same time. We, particularly the female members of our team, were truly impressed how she manages these two fulltime “jobs”. Consequently, we asked for her advice for women in science in general and she encouraged us to believe in ourselves and in what we are capable of as well as our knowledge and to reach for arising opportunities. In her experience the chances for women in the research environment have drastically changed for the better since her days as a young researcher and today universities offer for instance something called “dual career-couples", that gives families in which both partners are working in research the possibility to work at the same university. Thanks to this both partners may find more compatible work schedules for example. Her input on this subject was incredibly useful and motivating for us.
German Meetup
On May the 14th the iGEM teams Bonn and Kaiserslautern invited us to the German Meetup. At this point our project had already taken shape and we were ready to really get started. Meeting other teams at this point gave us even more motivation. In the first part of the Meetup, we could join four different breakout rooms depending on our interests. One had a scientific focus on the biotechnological production of healthy sugar substitutes, in a second room one could discuss the ethical issues in biotechnology in general and in animal experiments, another one revolved around collaborations and the last one was meant for sharing tips and tricks on sponsoring.
In this room the teams exchanged ideas and advice regarding finding suitable sponsors. Beside tips on how to gain the attention of sponsors - which was valuable for our finance team and helped us through the whole iGEM cycle to ensure a good financial and material support - it also reminded us to keep close contact with our university officials. That proved to be very important for us later on as well, since every university in Germany has different rule sets and procedures for such things.
To be in close contact with the administrators of our university bank account allowed us to keep track of our expenses and helped to plan further spending and acquisition of sponsors.
Also, experienced iGEMers advised us to look for local sponsors, not only to find easier support, but to make sure we address local problems with care, aided by this outside know-how. It proved to be very important to listen and learn - and later on this early input pushed us to ask for the expertise at our local university hospital as well as at the Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI).
An experience we greatly enjoyed, was the brainstorming with the other teams about possible collaborations and social media projects. It inspired us to realize our podcast idea and take part in the postcard project by Team Düsseldorf .
In general, the Meetup helped us to estimate the current state of our topic and to focus on upcoming issues. We greatly value the exchange with the other German teams and hope we could make a contribution to inspire the others as well.
Field Trip to Nomad Biosciences
We tried to get to know more about future applications, the implementation and upscaling of peptide-based drugs produced in plants. Thus, we looked out for companies working on this subject and quickly became interested in two biotechnological companies: Nomad Bioscience GmbH ( https://www.nomadbioscience.com/ ) and ICON Genetics ( https://www.icongenetics.com/ ). We were kindly invited to visit their research site in Halle (Saale) in Germany and got to know the theoretical background of their approach and its practical implementation.
Both Nomad Bioscience GmbH and ICON Genetics were founded by Dr. Yuri Gleba and they are conducting applied research on the production of proteins in plants. ICON Genetics thereby focuses on the production of monoclonal antibodies in plants 1 , while Nomad Bioscience works with diverse protein species. Amongst others, they have successfully produced bacteriocins in Nicotiana species 2 . Bacteriocins are bacterial AMPs, and the classes of bacteriocins Nomad works with are potent and selective antimicrobials against gram-negative pathogens. They are mainly working with the tobacco species Nicotiana benthamiana (N. benthamiana) and Nicotiana tabacum (N. tabacum) . Nomad therefore developed and optimized their expression platform magnICON®. This allows fast and scalable expression of various proteins in plants and involves the following features, summarized in the figure below:
Furthermore, Nomad screens expression levels of the recombinant proteins from 3 to 11 days post infiltration before moving on to upscaling the production. This is to determine the optimal harvest timepoint for maximum protein yield and should definitely be done when the quantity of the recombinantly produced protein matters, as was the case for our project. We also learned a great deal of practical tips that we were able to implement in our lab work. For instance, syringe-infiltration of whole plant leaves is much more efficient when scratching the leaf beforehand which we successfully tried after returning to our own lab. We were also taught that some recombinant proteins may be toxic to the plant, but that this would be visible by plant tissue necrosis at an early stage. Since we didn’t observe necrosis of our infiltrated plants, we were able to exclude this reason as a possible source of error in our expression schedule. When (co-)expressing fluorescent reporter genes, researches at Nomad also assess the success and extent of the agroinfiltration by illuminating whole tobacco plants with UV-light and checking for the extent of fluorescence. After our trip, we also tried this with our plants, but could only observe the chlorophyll autofluorescence. This gave us yet another hint that the expression of our recombinant proteins might be quite low.
During our visit, we also got the opportunity to ask specific questions regarding our project and got a lot of input on aspects concerning lab work and project design. Concerning the expression of small peptides in plants, Nomad was not successful in the past. This indicates that the size of our peptides is one of the difficulties in our approach. Furthermore, we used 2in1 and 3in1 binary vectors for plant transfection, which are vectors for co-expression of two or three genes, respectively. However, experience at Nomad shows that co-infiltration of multiple agrobacteria harboring different vectors with a single gene each works better than using a single vector with multiple genes. Further troubleshooting of our expression platform could involve testing different promoters and terminators, switching the orientation of our genes in the expression vector or testing different silencer agrobacteria strains than the p19 strain we used.
The by-far most helpful advice we received was that, at the point of our visit, we had not focused on the right steps in our screening system. In the beginning, we tried to prove the success of our expression, extraction and purification approaches at the same time by testing the antibacterial activity of our purified samples. However, since we didn’t detect any antibacterial activity at this stage, we were unable to conduct proper troubleshooting: Information on which step in our schedule went wrong was missing. Therefore, the guidance we got in Halle helped us to change our point of view . We started assessing our extraction method, tested different extraction buffers, included more controls and expanded our analytical methods to multiple western blots and MALDI-TOF mass spectrometry. In the end, this change in our approach was fundamental to the main results we got.
Except from the knowledge that we implemented in our own project, we also learned a great deal about how our approach may develop beyond iGEM . Nomad currently runs field experiments in Spain, where it is legal for N. tabacum expressing recombinant proteins to be grown in larger quantities. There are three main alterations in this approach compared to the small-scale screening system that we have worked on. First of all, the tobacco species N. tabacum generates more biomass and therefore more protein compared to our N. benthamiana . Secondly, the plants cultivated are not transiently, but stably transfected and are therefore transgenic plants. This also has the benefit of yielding more protein, and it also allows more control of the protein expression since the transgenic plant line can be screened beforehand on the location of transgene insertion in the plant genome and so on. Concerning the safety of using transgenic plants, Nomad conducted research and found that agrobacteria carrying the transgenes quickly disappear within several days and therefore no longer pose a risk for horizontal gene transfer of the transgene. And thirdly, the protein expression in these transgenic plants is not constitutive but induced by ethanol. Benefits are a temporal control over protein expression and therefore the ability to express recombinant protein in larger amounts, which might be deleterious to the plant if constitutively expressed. We also got to know which types of quality control would be necessary to put in place when producing antimicrobials for medical use. For instance, the presence of toxins like nicotine, endotoxins and herbicides would have to be assessed before getting a product with herbal origin into the clinic.
In conclusion, our excursion to Nomad Bioscience GmbH and ICON Genetics in Halle has had a great impact on our project. We successfully integrated the gained knowledge into our project and were also able to develop a mindset for the future of molecular pharming in plants. Apart from these scientific benefits, the trip had a cultural dimension as well. We visited the cities of Leipzig and Halle, which are sites influenced by the works of famous musicians like Bach and Händel, respectively. Finally, we got to do a lot of teambuilding through joint activities like pub tours in the evening.
References
1 Giritch, A., Marillonnet, S., Engler, C., van Eldik, G., Botterman, J., Klimyuk, V., & Gleba, Y. (2006). Rapid high-yield expression of full-size IgG antibodies in plants coinfected with noncompeting viral vectors. Proceedings of the National Academy of Sciences, 103(40), 14701–14706. https://doi.org/10.1073/pnas.0606631103
2 Schneider, T., Hahn-Löbmann, S., Stephan, A., Schulz, S., Giritch, A., Naumann, M., Kleinschmidt, M., Tusé, D., & Gleba, Y. (2018). Plant-made Salmonella bacteriocins salmocins for control of Salmonella pathovars. Scientific Reports, 8(1), 4078. https://doi.org/10.1038/s41598-018-22465-9
3 Marillonnet, S., Thoeringer, C., Kandzia, R., Klimyuk, V., & Gleba, Y. (2005). Systemic Agrobacterium tumefaciens-mediated transfection of viral replicons for efficient transient expression in plants. Nature Biotechnology, 23(6), 718–723. https://doi.org/10.1038/nbt1094
Panel Discussion
As already mentioned in the section about our podcast , as time went by in the iGEM competition the idea to host a panel discussion matured within us. Especially the podcast episodes with Dr. Kolukisaoglu and Prof. Dr. Potthast taught us about the importance of clear and comprehensible science communication and education. Hence, in the planning of the discussion we tried to implement this knowledge, we had already gained to make it a great learning opportunity for us and our project as well as for our audience.
One the one hand, we wanted to find a way to raise awareness about antibiotic resistance and inform about the possibilities that protein expression in plants harbors. And on the other hand, we had the goal to get into contact with experienced scientists as well as future young researchers at the same time.
Together with our collaboration partner, the science center experimenta in Heilbronn (Germany), we organized the panel discussion for students between the age of 16 to 18. As the topic we chose in-planta pharming and its opportunities and limits since this gave us the possibility to discuss both scientific questions, but also the associated legal and ethical as well as societal issues.
We invited three guests from various backgrounds to take part in the discussion to be able to represent a broad picture on the topic. Dr. Martha Mertens is an expert for genetic engineering from the BUND Germany and therefore highly involved in the ethical and societal implications of in-planta pharming. Representing the plant biotechnology industry was Dr. Peter Welters, CEO of phytowelt Green Technologies GmbH. His company is (among other fields) active in the pharmaceutical sector. Last but not least, Prof. Dr. Stefan Schillberg, head of the molecular biotechnology department at the Fraunhofer IME, presented a more fundamentally scientific point of view. Furthermore, two members of our team were also panelists to contribute our perspective as junior researchers.
To ensure a fluent conversation during the course of the discussion we prepared some guiding questions, which made sure that the different aspects we wanted to reflect on were covered.
One side that we were particularly interested in was the one of the legal guidelines and restrictions that are connected with heterologous expression of proteins, for instance pharmaceutical active compounds, in plants. The current regulations of the European Union, which are applicable for Germany as well, are quite restrictive in regard to genetically modified organisms in general and thus we argued about what these laws actually mean for the plant biotechnology industry. Of special importance to us was to find out what the students as the next generation of researchers in our audience thought, which conditions would have to be fulfilled to make the production of drugs in plants feasible.
As another major point, we exchanged our views about what possible safety concerns the public might generally have when being confronted with the topic of growing genetically modified plants in the field. Prof. Schillberg was able to eradicate those concerns as he explained that molecular pharming is highly unlikely to be performed outside of greenhouses since the protection of the product is crucial when you plan on using it in a clinical application. This is the case due to the strict regulations of drug approval and as a consequence contamination from the environment would let the product fail. Being news to us too, this information led us to re-think a possible implementation of our project, especially in regard of the upscaling and the safety aspect. Thus far, we had envisioned a step from the greenhouse into the open field as a logical consequence from our work and so, this answer alone already will have an enormous impact on our project if we think about possibly pursuing it further.
Taken together the exchange of opinions and ideas with the other participants of the panel discussion, be it accomplished scientists or students, was incredibly helpful for us. This event broadened our horizon and notably the mature views of the students have impressed us deeply.
About Us
We are the iGEM Team Tuebingen, a group of motivated students who are working on creating a fast screening platform for stabilized peptides. We are aiming to provide a system that gives everyone the ability to stabilize peptides such as antimicrobial peptides to create better medical agents.
