Our Contributions to the iGEM Community
Explore how the Hannover iGEM 2024 team has advanced synthetic biology through our innovative contributions. From novel genetic parts to open-source tools, learn about the impact we've made this year.
Explore how the Hannover iGEM 2024 team has advanced synthetic biology through our innovative contributions. From novel genetic parts to open-source tools, learn about the impact we've made this year.
Our project contributed profoundly to synthetic biology by different aspects and approaches. Firstly, we developed 22 genetic parts. These parts include bacterial genes, which have been codon-optimized for the use in eukaryotic cells, active promoters and fusion peptide sequences of transcription factors and fluorescence proteins for detecting antibiotics and heavy metals. We also developed a comprehensive computer-simulated model that predicts the spread of multi-resistant bacteria under varying conditions, which is accessible via an inlay in or wiki. Furthermore, we have developed a versatile 3D-printed Petri dish holder for our Whispering Gallery Mode (WGM) resonator setup in our Spectroscopy Analysis, and provide the freely available STL file for printing and implementation into lab setups by any iGEM team. These contributions will support future iGEM teams and researchers in advancing biosensor technology and environmental health.
We have registered a total of 22 new parts that can be used by other iGEM teams in the future. These include two reporter genes we used, as well as three codon-optimized genes for expression in human cells that encode the β-lactam antibiotic-detecting enzyme and three transcription-activating enzymes. In addition to these basic parts, the corresponding composite parts were registered in which the gene was combined with a respective constitutive promoter and/ or reporter gene to track localization in the cell. For metal detection, we submitted a gene encoding heavy metal detecting enzyme and its combination with a reporter gene as a composite part. In addition, we have developed four promoters, of which two are highly active, for both detection pathways to ensure efficient signal transduction.
The gene pknB encodes a serine-threonine protein kinase originating from Staphylococcus aureus. This gene has been optimised in terms of codon usage to ensure efficient expression in HEK293T cells. Furthermore, the gene was combined with EGFP to verify the localization of PknB in the cell.
graR codes for a transcription activator in Staphylococcus aureus, whose DNA-binding activity increases through phosphorylation.Text To ensure optimal translation in our system, the gene sequence was codon optimised for the use in HEK293T cells and combined with mRuby2 to verify localization.
The ccpA gene encodes a catabolite control protein, a crucial regulator in Staphylococcus aureus. For our project, we adapted the gene sequence by optimizing codon usage to improve its translation in HEK293T cells and combined it with mRuby2 to detect the protein (trans-)localization.
As a human transcription factor, the Cyclic AMP-dependent transcription factor 2 (ATF2) plays a crucial role in DNA binding to regulate gene expression. We have introduced this gene in combination with mRuby2 into HEK293T cells to exploit its regulatory functions and monitor its localization in the cell.
The antibiotic promoter comprises three repeats of the Activator Protein 1 (AP1) sequence and three repeats of the cAMP Response Element (CRE) sequence. The binding of the transcription factor ATF2 to these elements enhances the expression of the miRFP reporter gene, which is used to detect the presence of β-lactams.
The mtf1 gene encodes a transcription factor that responds to heavy metal exposure.Text In order to utilize its function, we introduced this gene into HEK293T cells and combined it with mRuby2 for spatial analysis.
mRuby2 is a bright red fluorescent protein used to monitor protein localization and expression in mammalian cells.
miRFP670 is a monomeric near-infrared (NIR) fluorescent protein that enables efficient detection in human cells.
In our two cell-based sensor systems, we had the opportunity to utilize two parts already included in the registry and expand their area of application.
Firstly, the reporter gene EGFP (BBa_K3338006) was used in all four metal-sensitive promoters as well as in the CMV-EGFP-PknB cassette. Thus, it could be shown for this part that the fluorescent protein can be used for multiple upstream positioned promoters and also fulfils its purpose in another cell line (HEK293T) without any problems.
Secondly, the pEGFP-C2 plasmid (BBa_K3338020) was the backbone used for all basic parts to enable the transfection experiments. Our series of cloning and transfection experiments extends our knowledge of the plasmid's range of applications. its small size makes it a flexible backbone plasmid for partial integration into our longer composite parts. In addition, our experiments demonstrate another cell line that can be easily transfected with the pEGFP-C2 backbone.
We have developed a comprehensive model that integrates the effects of both heavy metals and antibiotics on the spread of multi-resistant bacterial strains, such as E. coli. This model combines two sub-models — one focused on antibiotics and the other on heavy metals contamination — into a working unified system. By simulating real-world conditions, the model predicts how various environmental factors, such as metal concentrations, antibiotic influx, and their interactions, influence bacterial resistance development. It highlights both individual and combined resistance mechanisms, providing detailed insights into how each contaminant promotes the persistence of multi-resistant bacterial strains.
The model is built on a solid foundation of differential equations and advanced algorithms, making it adaptable to various use cases. It distinguishes between different origins of resistance, allowing researchers to break down the specific roles of heavy metals versus antibiotics in driving resistance. This is particularly useful for identifying which environmental conditions pose the highest risk of resistance spread.
Beyond predicting resistance patterns, the model incorporates key biological processes such as horizontal gene transfer, mutation rates, and bacterial growth dynamics under different stressors. These additional features enhance the model's predictive accuracy and relevance, making it a powerful tool for exploring complex bacterial population dynamics.
Future iGEM teams can easily adapt our model to suit their specific needs by adjusting environmental parameters like metal or antibiotic types, concentrations, and exposure durations. For example, teams working on aquatic environments or wastewater treatment could simulate how different contaminant levels impact bacterial resistance in those ecosystems. The model's flexibility means that it can be used not only for bacterial species like E. coli, but also for other organisms and environments where resistance is a concern.
Additionally, our model can serve as a baseline for testing novel biosensing systems, bioremediation strategies, or synthetic biology interventions aimed at reducing antibiotic or heavy metal contamination. Teams can extend its functionality by incorporating additional parameters, such as environmental pH, temperature, or the presence of co-contaminants.
Our code and a detailed guide are available in our Gitlab to assist new teams in applying and modifying our model for their research. We also encourage other teams to contribute improvements or modifications, fostering collaboration within the iGEM community. The model’s user-friendly documentation ensures that it is accessible to both beginner and advanced teams, promoting wider adoption and further development.
This model not only offers practical applications but also supports broader goals related to combating antimicrobial resistance, aligning with the United Nations' Sustainable Development Goals (SDGs), particularly SDG 3 (Good Health and Well-being) and SDG 6 (Clean Water and Sanitation). By providing a tool to better understand and mitigate the spread of resistance, our model helps to address critical global health challenges (see our SDG-page).
As part of Hydro Guardian project, we have developed a versatile 3D-printed Petri dish holder, designed to enhance the precision and adaptability of laboratory setups. Originally created to support the optical experiments involved in our Whispering Gallery Mode (WGM) resonator setup (see our Spectroscopy Analysis page), this component offers a wide range of applications that can benefit other iGEM teams and the broader research community.
The Petri dish holder was designed using Autodesk Inventor to meet the specific requirements of the WGM resonator experiments, which require the precise positioning of Petri dishes for accurate optical measurements. These measurements support our wet lab work by providing key insights into optical properties and interactions at the microscopic level. The holder ensures that our samples remain in the optimal position, allowing for accurate, reproducible results in both our physics and biological experiments. This cross-disciplinary approach highlights the integration of physics and synthetic biology, showing how innovative tools can facilitate complex measurements that directly inform and improve wet lab processes.
The holder is securely fastened to any standard laboratory post, thereby enabling researchers to adjust the dish to the exact angles required for experimental setups. It is suitable for a variety of applications, including optics-based physics experiments, imaging, and biological assays that require angled plating, where it provides stability and reproducibility in any laboratory setting.
Understanding the value of sharing resources within the iGEM community, we have made the STL file for this part open-source and freely available. By doing so, we are actively offering a tangible resource to support future research and experimentation of iGEM teams by providing a practical tool that can be easily incorporated into their own projects, enhancing the precision and flexibility
of their experiments.
The holder may be downloaded, printed, and implemented in laboratory setups by any iGEM team or non-iGEM researchers. The design is compatible with the majority of standard 3D printers, thereby offering an accessible and cost-effective solution for teams across the globe.
The Petri dish holder serves not only as a tool for our project but also as an exemplar of the collaborative spirit that characterizes iGEM. Furthermore, we aim to connect with other iGEM teams at the 2024 Grand Jamboree to discuss the potential for this holder to enhance their experimental designs, particularly for teams engaged in precision measurements, microscopy, or culture growth experiments. Following the 2024 Grand Jamboree in Paris, an updated version of the Petri dish holder will be uploaded, if necessary, in order to address the feedback of other iGEM teams in the 2.0 version. It is our intention to contribute to the broader collaborative ecosystem that drives innovation in synthetic biology by fostering inter-team collaborations.
Although the holder was developed for our specific physics setup, it can be used in a wide variety of experimental contexts. This flexibility renders it an optimal instrument for a multitude of applications, including:
