Human practices
Human Practices form the bridge between scientific innovation and real-world application. They ensure that research is not only technically sound but also ethically grounded, socially relevant, and implementable in real life. Especially in projects with a potential for real-world impact, Human Practices play a crucial role in every project, so the team can align their work with the needs of society, environment, but also retain feasibility for the industry. By reflecting on the implications of their project and integrating feedback from various experts from all industries, teams are able to refine their design, anticipate challenges, and ensure that their solution contributes to a more sustainable and responsible future.
Human Practices guided our project by connecting our research to real-world perspectives and expertise. By engaging with experts from academia and industry, we gained feedback on sensor implementation, chemostat design, and bioprocess optimisation. These insights helped us refine our experiments, address practical limitations, and ensure our project is both responsible and relevant to the world. In this section, we summarise our key expert meetings, what we learned, how we reflected on it, and the remaining questions. We demonstrate how Human Practices shaped and improved our project throughout the year.
Academia
24.07.2025 Dr. Milan Zupunski
Why did we meet him?
We consulted Dr. Milan Zupunski, an expert in fluorescence measurement techniques and a postdoctoral researcher at the HHU Düsseldorf, to gain input on how to design and optimise a low-budget fluorescence camera. We aimed to ensure that our setup would produce reliable and accurate results while remaining cost-efficient and accessible.
What did we talk about/learn?
Dr. Zupunski pointed out several key factors that we needed to consider. He explained that the maturation time of fluorescent proteins could influence measurements and that our initial light setup, using only one LED placed behind the cuvette, might cause uneven excitation. We discussed better fluorophore combinations, potential autofluorescence issues that may arise once plasmids are introduced, and possible ways to avoid using filters or dichroic mirrors. Importantly, Dr. Zupunski confirmed that a photospectrometer could work for our application, but he emphasised the need to verify whether our LEDs excite the cuvette evenly.
Figure 1: The team with Dr. Zupunski
Reflection
Reflection
Following his advice, we made significant modifications to our setup. We introduced two LEDs positioned at 90° to the detector and separated by a wall, allowing for more even excitation. We also added another fluorophore combination and adjusted the order of fluorophores to better account for maturation speed. Zupunski encouraged us to contact him again and offered to test our sensor with a portable spectrometer, which could provide valuable validation.
Open questions
Despite these improvements, open questions remain: Will our system perform reliably without a dichroic mirror or filter? Will cross-talk or autofluorescence compromise our measurements? And ultimately, will the redesigned setup function as intended? Answering these questions would include a comparison of signal quality with and without optical filters, via spectrometer, a single-fluorophore control experiment and measuring autofluorescence baselines.
27.08.2025 Professor Wolf Frommer
Why did we meet him
We reached out to Professor Wolf Frommer, a leading scientist in the field of ratiometric biosensors and group leader at HHU Düsseldorf, Stanford University and Nagoya University, to gain valuable insights into how to implement and test the effectiveness of our own biosensor system. His expertise made him an ideal advisor for addressing key challenges related to specificity, sensor performance, and cellular context.
What did we talk about/learn?
Since our biosensor design relies on allosteric transcription factors (aTFs), Professor Frommer, being an expert in ratiometric biosensor design and cellular signalling processes, helped us frame the critical research questions that we needed to address to validate and optimise our biosensor:
- Specificity of the aTF: He emphasised the importance of systematically validating that only the target analyte interacts with the sensor, and not structurally similar precursors. Structure docking studies and activity relationship modelling could support this.
- Concentration-dependent output: He recommended titration studies to establish accurate affinity constants (Kd values) and map the functional concentration range of the biosensor.
- Characterisation of the aTF: Professor Frommer encouraged us to examine binding kinetics, DNA-binding specificity, transcriptional dynamics, Hill coefficients, and dynamic range under various conditions.
- Protein turnover and cellular impact: He advised measuring synthesis and degradation rates of the aTF to understand how protein turnover influences sensor performance, while also analysing the metabolic effects on the host cell.
- Analyte export: Finally, he emphasised the importance of evaluating export mechanisms to prevent intracellular accumulation by measuring transport efficiency and kinetics.
Reflection
Reflection
This discussion provided us with a clear roadmap for systematically testing our biosensors. Professor Frommer's input highlighted the importance of combining experimental assays with computational modelling to better understand and predict sensor behaviour. Due to time constraints, we were unable to implement his advice further. Next steps would have included a Ligand Binding Assay, Molecular Docking studies, Titration Multi-Point Dose-Response Curves, Hill Coefficient and Kinetic response measurements, signal-to-noise ratio, and ratiometric validation.
03.09.2025 Professor Nick Wierckx & Felicia Zlati
Why did we meet them?
We reached out to Professor Nick Wierckx and Felicia Zlati, who both work extensively with chemostats in the context of developing microbial catalysts for the bio-based production of chemicals. Professor Wierckx is the group leader for Microbial Catalysis at the Research Centre Jülich, and Ms Zlati is a PhD student there. Since their research involves fermentation technology and continuous cultivation, they were well-positioned to advise us on the practical implementation of our own chemostat system. Our discussion focused on potential limitations of the hardware design and strategies to overcome them.
What did we talk about/learn?
Professor Wierckx and Ms Zlati shared valuable advice on two key aspects of chemostat operation:
Sterilisation: They explained that sterilisation can be performed in place using both chemicals and temperature. For example, by increasing the pH to 10 with a base and raising the temperature to 60 °C, most microbes and fungi can be effectively eliminated. They also highlighted that contamination risk is naturally reduced due to the constant gas outflow, which creates positive pressure and prevents microorganisms from being drawn in. We implemented this in the sterilization protocol Stirring: Professor Wierckx recommended maintaining a constant air inflow and redesigning the rotor to prevent the formation of anaerobic zones, which could severely impact microbial productivity. Together, we discussed using a smaller, pitch-bladed rotor to improve mixing and ensure a more homogeneous environment within the chemostat.
Reflection
Reflection
The meeting with Professor Wierckx and Ms Zlati provided us with concrete strategies to strengthen our chemostat design. As a direct outcome, we established an improved stirrer design and developed a detailed sterilisation schedule, both of which increased the reliability and robustness of our setup.
Open questions
This discussion led us to consider the practical scalability of our chemostat adjustments. To what extent can our sterilisation protocol be standardised for different organisms? And how can we further optimise rotor design to balance mixing efficiency with energy consumption? To answer these questions we would for example need tests with representative microbial species (Gram-positive, Gram-negative, yeast) under different pH, temperature, and other variables, or dye-mixing tests and oxygen mapping to measure mixing efficiency and homogeneity and the comparison between different rotor geometries.
04.09.2025 Professor Wolfgang Wiechert
Why did we meet him?
Professor Wiechert is an expert in systems biology and bioprocess engineering at RWTH Aachen and department head at Research Centre Jülich. We met him to gain insights into how to model and control induction in continuous bioreactor systems. Since our project involves optimising induction strategies in a chemostat environment, we wanted to better understand how process engineers think about productivity, regulation, and experimental design, and whether machine learning could play a role.
What did we learn?
Professor Wiechert recommends focusing on a mechanistic induction model with a clear target variable. Continuous induction is more realistic than on/off induction, as it reduces heterogeneity between cells. He advised refraining from machine learning methods, as chemostats do not produce the amount of usable/reliable data that is needed for successful training of an algorithm. We should aim to solve an optimisation problem, balancing production and growth.
Figure 2: The team with Prof. Dr. Wiechert
Reflection
Reflection
Following the discussions, we considered our model design and decided to include the proposed optimisation problem in the model. Further, we decided against machine learning methods, because for the optimisation of inducer timing and dosage it is, based on his experience, not feasible to get enough, reliable data. This is mostly due to technical difficulties and a problem all researchers in this field face.
08.09.2025 Dr. Ana Del Arco
Why did we meet her?
We reached out to Dr. Ana Del Arco, from the University of Jaén, who works in evolutionary biology, water ecology, and ecotoxicology, to discuss the practical aspects of building and using DIY chemostats, as our project relied on continuous cultivation systems. We aimed to understand both the opportunities and limitations of such setups, as well as how to address technical challenges such as sterilisation and sensor integration.
What did we talk about/learn?
Dr. Del Arco shared her experience with setting up chemostats and gave us valuable advice on sterilisation and lab handling. Since our sensors could not be autoclaved, she suggested alternatives such as chemical sterilisation, working in a clean bench, or adapting our system to avoid contamination risks.
We also discussed the accessibility of DIY chemostats. Dr. Del Arco explained that, while they are inexpensive and protocols are openly available, building them requires time, coding skills, and careful handling to prevent contamination. In many cases, commercial chemostats are preferred because they can be reused and are less labour-intensive. She pointed out limitations such as the small cultivation volume, but also reassured us that materials can be sourced cheaply and easily (e.g., simple glass bottles with custom lids for sensors).
Reflection
Reflection
Talking to Dr. Del Arco helped us to realistically assess the strengths and weaknesses of DIY chemostats. While they are a cost-effective option that could make continuous cultivation more accessible to small labs, we realised that the time commitment and contamination risk might limit their usefulness for broader adoption. For our own project, we decided to carefully consider which parts of the system truly benefit from a DIY approach and which components are better bought commercially. We also considered her recommendations while compiling our detailed manual for assembling a DIY chemostat by including pictures and ready-to-use software interface for operation of the chemostat to maximise the value provided to the community.
Open questions
This meeting left us reflecting on how to strike a balance between cost efficiency and reliability in our hardware choices. Could the design of DIY chemostats be further simplified to reduce the risk of contamination and setup time? And how can we make such tools more attractive to a broader scientific community, beyond those with strong coding or engineering backgrounds? Interviews and surveys with experts as well as with topic newcomers in forums and discussions to see the interests and demand could provide feedback to answer these questions.
Industry
01.07.2025 Dr.Tobias Klement
Why did we meet them?
At an early stage of our project, we had the opportunity to interview Dr.Tobias Klement, Deputy Cluster Manager and Deputy Managing Director of the CLIB Cluster (Cluster Industrial Biotechnology), a significant network of relevant actors and stakeholders in the European industrial biotechnology sector. The purpose of this conversation was to find out whether our project could provide potential to solve real-world problems in the future implementation of sustainable practices in the industrial bioproduction industry.
What did we talk about/learn?
Perspectives on Continuous Bioproduction
After introducing our project, Dr. Klement shared his views on continuous bioproduction, which lies at the core of our work. He expressed strong confidence that continuous processes will play a central role in the future of industrial biotechnology. According to him, the field is already a rapidly growing market, and companies worldwide are increasingly shifting toward continuous production methods due to their efficiency and scalability.
Strategic Advice: Market Focus
A key recommendation Dr. Klement gave us was to carefully consider which kinds of products we aim to target with our system. From an economic perspective, he suggested focusing on the large-scale production of cost-efficient bulk chemicals rather than expensive, niche compounds such as pharmaceuticals. While pharmaceutical products are highly valuable, they often come with strict regulatory barriers and smaller markets. In contrast, bulk chemicals represent a field where the economic benefit and scalability of a new bioproduction platform could have a much greater impact.
Communication and Positioning of the Project
In terms of how to present and communicate our project, Dr.Klement advised us to emphasise the academic and economic aspects of our work rather than focusing primarily on the ecological benefits. He argued that the market potential and technological innovation are likely to resonate more strongly with industrial stakeholders and academic peers.
Future Potentials and Challenges
Looking further ahead, Dr. Klement highlighted several exciting possibilities for systems like ours: Because our approach is based on a closed bioproduction system, he speculated that it might one day enable biotechnology to be carried out with less highly trained personnel or in less strictly sterile environments. This could make bioproduction more accessible and less resource-intensive. On the other hand, he also pointed out an important challenge: the disposal of genetically modified organisms (GMOs). Since strict regulations govern the handling and disposal of GMOs, this could represent a costly bottleneck for future implementation.
Inspiration for Further Project Development
One particularly valuable piece of advice was to consider the needs of potential customers and the scientific community that might build upon our findings in the future. This recommendation directly inspired us to contact other experts in this matter, such as Phytowelt Green Technologies GmbH, with the goal of understanding how our project could benefit researchers and innovators beyond our own team.
Reflection
Reflection
The interview with Dr. Tobias Klement provided us with crucial insights at a very early stage of our project. His feedback helped us to:
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Recognise the growing importance of continuous bioproduction.
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Understand the greater economic potential of focusing on bulk chemicals.
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Adjust our communication strategy towards academic and economic value
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Identify challenges such as GMO disposal early on. As of now, we disposed GMOs according to university regulations. Future considerations could be a kill-switch or auxotrophic strains, when working with more hazardous constructs.
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Develop outreach tools to assess community needs.
Overall, Dr. Klement's perspective broadened our understanding of the industrial and economic context of our project and encouraged us to think about its long-term positioning within the biotechnology landscape. Dr.Klement represented one of our key meetings, with the most impact for the following project development. It helped refine our vision of how our project can be implemented in the future.
01./03.09.2025 Phytowelt GreenTechnologies GmbH (Dr.Peter Welters)
Why did we meet him?
We met with Phytowelt Green Technologies, a biotechnology company specialising in sustainable bioproduction of aroma compounds such as raspberry flavour and vanillin. Dr. Peter Welters represented Phytowelt. Our aim was to present our project, receive professional feedback, and explore possible applications within an industrial context.
What did we talk about/learn?
Phytowelt currently relies on a traditional optimisation strategy using promoter databases. In this approach, multiple promoter versions are cloned and tested to fine-tune production levels. Our project offers a different perspective: instead of relying on extensive cloning, it aims to use variable inducer concentrations to optimise relative expression levels and achieve a stable production stream. This method provides greater flexibility while saving time and resources in the optimisation process.
Dr. Welters showed strong interest in two aspects of our work. They recognised the potential of our biosensor technology to monitor and control bioprocess parameters. Additionally, they were intrigued by our chemostat system, which allows continuous culture maintenance and precise regulation of production conditions.
Reflection
Reflection
The discussion with Dr. Welters confirmed the industrial relevance of our project. Especially because Phytowelt uses the same vanillin pathway but no continuous culture system, their interest in our biosensors and chemostats demonstrated that our concepts address real challenges in bioprocessing. We realised that presenting alternative methods to established practices could highlight the innovative potential of our system and open doors for collaboration with industry, an aspect we integrated into our storytelling.
Open questions
This meeting raised the question of how our system could be integrated into existing industrial workflows. What would be required to adapt our biosensors and chemostats to large-scale operations, and how could we ensure reliability under industrial conditions? We are eager to stay in contact with Phytowelt and other companies, to test for those questions.
Technician
28.05.2025 Tanja Noch (we met her over the course of two months, roughly every two weeks)
Why did we meet her?
We met with Ms Tanja Noch because she is the glassblower at our university and highly skilled/experienced in manufacturing custom hardware designs for diverse applications. As we developed the concept for our chemostat, we sought glassware that perfectly fit our overall setup. To achieve this, we wanted to have it custom-made by Ms Noch. Due to her expertise in the industrial design of glassware used in various fields, we asked her numerous questions regarding the design of our chemostat. Especially questions concerning the technical limitations were relevant during this phase.
What did we talk about/learn?
In general, we learned more about equipment and chemical production, and we heard a first-hand account about how glassware for laboratories is produced. More specifically, we were able to further adapt our design through new knowledge about industrial/technical design and implementation. One of the design adaptations was the use of a clamp mechanism to secure the lid to the vessel. We also learned that the lid can only hold a certain number of openings and that the side input of our probes is only feasible at a certain angle due to technical limitations.
Reflection
Reflection
In conclusion, the discussions with Ms Noch helped us refine and adjust our design of the chemostat based on technical limitations. The various adaptations included changes in the layout of the lid, the size of the vessel and probe placement. Without her input, we would not have been able to optimise our chemostat in the way we did.
Figure 4: Glassblower-Workshop at HHU
Integrated Human Practices
Through the Expert Meetings, we have refined our project in both conceptual and technical aspects. For the biosensor design, we focused on allosteric transcription factors (aTFs) as versatile elements, because experts in synthetic biology and protein engineering helped us shape our strategy to validate and calibrate them with standardised reporter systems. Furthermore, in future directions to characterise our sensors, experiments could measure the fluorescence with an inducer gradient to determine the dynamic range, EC50 or sensitivity of each sensor, or test the system for robustness under different growth conditions. The EC50 is the concentration of a drug or chemical, that gives half-maximal response. It is used to quantify the potence and measure the active ingredient strength. To ensure reliability in complex metabolic environments, experiments could analyse whether sensors exclusively respond to their intended ligands or also to structurally similar molecules. For the hardware, advice from researchers with practical experience in bioreactors improved our chemostat design, for example, the choice of glassware, tubing materials to reactor geometry, sterile handling, and modularity. Even small aspects, like the position of LEDs for accurate fluorescence measurements, could be optimised. These improvements ensured that our system remained scientifically rigorous while approaching a stage where both researchers and industry can use our idea.
After integrating all this feedback, we reflected on the real-world relevance of our project, particularly in the context of sustainable bioproduction. Expert discussions revealed several potential paths for implementation. One option would be to use our system to produce and market specific chemicals, but we recognised that competing with low-cost commodity production is not our strongest niche. While bulk chemicals offer a large potential and demand, our system's unique advantages make it more suitable for complex, high-value compounds. For bulk chemicals, cost-efficiency in well-optimised processes is important, while our biosensor-based regulation system has the advantage of precisely balancing multiple enzymes and promoters in metabolic pathways. Through this, a level of fine-tuning expression can be unlocked that accesses yields otherwise inaccessible. A second, more realistic strategy would be to position ourselves as a service provider, similar to companies like Phytowelt, helping partners optimise production pathways. Alternatively, our modular plasmid–sensor system could be licensed directly to industry, providing a flexible toolkit for fine-tuning expression in complex metabolic pathways. Importantly, experts emphasised that our approach is particularly powerful for bulk chemicals.
At this stage, some open questions remain. For example, the robustness of our sensors in industrial conditions and the scalability of our chemostat setup require validation with experimental data. To address these, we plan systematic lab validation: quantifying sensor performance, benchmarking reactor stability, and testing modular plasmids across different metabolic pathways. These experiments will help us determine which of the proposed business models—chemical production, service provision, or licensing—is most feasible. By closing this loop between expert advice, experimental validation, and real-world needs, our project moves from a proof-of-concept idea toward a concrete vision for impact in sustainable bioproduction.
Conclusion
Our Human Practices activities enabled us to continuously align our project with real-world needs, expert knowledge, and practical constraints. Through discussions with scientists and industry professionals, we critically assessed ideas and adapted our project to be more practical, reliable, and impactful. By integrating the advice, we improved our chemostat design, optimised our sensor setup, and identified clear strategies to progress at different stages of our project. These interactions highlighted both the potential and limitations of our approaches, guided critical design decisions, and revealed new questions for future work.
Overall, Human Practices played a crucial role in closing the feedback loop of our project, ensuring that our scientific innovations are not only technically sound but also feasible, applicable, and responsible. This iterative process strengthened our understanding of the broader context of synthetic biology and prepared us to implement solutions that are both effective and socially conscious.