In carrying out our work, we have not only focused on the project itself, we have been thinking about how we can inspire future iGEM teams through the project and how we can devise viable solutions to the world's common problems. Through our tireless efforts, we have made some outstanding contributions to the line components and modeling work, which can provide references and ideas for the work of future iGEMers. Our products also have the potential to be developed into bioluminescent sustainable products that can provide templates for solving other problems.
We built several BioBricks that cover various aspects of our entire program and make up our Light Emitting Module and Safety Module.
Our basic parts
| Name | Type | Description |
|---|---|---|
| BBa_K5210000 | Promoter | PumuDC |
| BBa_K5210001 | Coding | LuxA |
| BBa_K5210002 | Coding | LuxB |
| BBa_K5210003 | Coding | LuxC |
| BBa_K5210004 | Coding | LuxD |
| BBa_K5210005 | Coding | LuxE |
| BBa_K5210006 | Coding | LuxF |
| BBa_K5210007 | Coding | LuxG |
| BBa_K5210008 | Coding | SOD |
| BBa_K5210009 | Coding | Catalase |
| BBa_K5210010 | Coding | GVP |
| BBa_K5210011 | Coding | RecO |
| BBa_K5210012 | Coding | RecF |
| BBa_K5210013 | Coding | ScrR |
| BBa_K5210014 | Promoter | Pompc |
| BBa_K5210015 | Promoter | PMrka |
Our composite parts
| Name | Type | Description |
|---|---|---|
| BBa_K5210016 | Composite | PMrka-Cl-Plam-LuxAB |
| BBa_K5210017 | Composite | Pompc-LuxCDEFG |
| BBa_K5210018 | Composite | PsacB-SOD-catalase |
| BBa_K5210019 | Composite | ProU-ScrR-Pscr-lacl-Plac-MazF |
| BBa_K5210020 | Composite | pBAD-MazF |
| BBa_K5210021 | Composite | pRM-Cl857-pR-MazF |
In order to match the application scenarios and needs of our products, we mainly use the following sensing components:
①Osmotic pressure sensing component: we sense changes in external osmotic pressure through the EnvZ/OmpR two-component system, and EnvZ sensing high osmotic pressure is able to phosphorylate OmpR and activate the promoter PompC to start transcription[1].PompC components can be seen in BBa_K5210014.
②Circadian components: for the purpose of circadian rhythm, we mainly consider the photoreceptor components. We first used PumuDC, the promoter that can be activated by UV-C from sunlight. However, we found that in the natural environment, UV-C is almost completely absorbed by the atmosphere[2]. We then decided to replace it with the optogenetic tool PMrka, which senses far-red light, a sensor whose usefulness has been well documented.
③Sucrose sensing component: PSacB itself has the ability to transcribe without inducers and the intensity is enhanced 100-fold after sucrose induction. The presence of sucrose in the sucrose manipulator containing ScrR and Pscr inhibits the deterrent effect of ScrR on Pscr and functions as a sucrose sensor, which we verified by molecular docking.The PSacB component can be seen in BBa_K4043004.
The light emitting module was built on the basis of sensing components that sense osmotic pressure and circadian rhythms. LuxCDEAB fulfilled the basic requirements for luminescence, while the addition of LuxFG enhanced the luminescence effect.
The safety module was mainly built based on the sensing components that feel sucrose.
①Passive anti-leakage: In the algal-bacterial coexistence system, the sodium-demanding Vibrio vulnificus is able to feel the sucrose secreted by Polysaccharomyces cerevisiae to express SOD and catalase in order to achieve the effect of cold resistance. After the leakage, the coexistence system was destroyed, the sucrose concentration around the bacteria decreased, the transcription of PSacB was greatly inhibited, and the accumulation of ROS led to the death of the bacteria to achieve the purpose of leakage prevention.
②Active anti-leakage: after the addition of the sucrose manipulator, the absence of sucrose after bacterial leakage causes ScrR to deter Pscr from transcribing lacI, and the decrease in Plac deterrence after the decrease in lacI expression, and the expression of the toxic protein MazF kills the bacteria.
③Treatment after product recovery: We initially designed a temperature-controlled suicide system and a drug-controlled suicide system to regulate the expression of the toxin protein MazF by controlling the temperature or by adding arabinose, which is an ideal inducer in seawater environments.
For the contributions, we completed the experimental characterization of the parts BBa_K5210011, BBa_K5210012, BBa_K5210014, BBa_K5210000, and BBa_K5210018, simulated the functionality of BBa_K5210013, and added the data and documentation to the corresponding BioBricks. All of this may be useful to other teams.
Through organic integration with sensing components, our luminescence module and safety module performed well. We further refined the details of bioluminescence using engineered bacteria, and the data recorded will be of great value to other teams. We explored how engineered bacteria used in marine environments can survive and function properly while preventing it from polluting the marine environment, which is an important reference for the application of synthetic biology in the ocean. In addition, the application of synthetic biology in space is still in its infancy, and the safety module we designed can increase the survivability of engineered bacteria in space, which is of great significance to Space village.
In addition, we added information to the existing widget BBa_K4594004 created by Shanghaitech-China, clearly documenting our experimental design and data on the widget homepage in the registry.
This year, in order to promote the application of LuminAid in reality, the NMU-China team not only analyzed the current application prospects of life-saving materials from a macro perspective, but also simulated the molecular and even genetic level regulation from a microscopic point of view, and optimized the design of genetic circuits. Meanwhile, the luminescence potential of the whole set of protein engineering was verified through experiments.
In order to analyze the high-risk time periods and high-risk locations of maritime and air accidents, and to provide greater protection for air transport and public safety, the model utilizes authoritative data sources such as the International Maritime Organization (IMO) and combines techniques such as big data analysis, density analysis, and time-series analysis, to provide a comprehensive analysis of the global safety situation of shipping and air transport in recent years, especially after the New Crown Epidemic.
Firstly, through the analysis of the time series characteristics of accidents by ARIMA model, the model is able to predict the frequency and trend of accidents in the coming period of time, which provides a scientific basis for formulating response strategies in advance.
Secondly, the choice of using the random forest regression algorithm to predict geographic coordinates further refines the granularity of risk assessment. In addition to the time and geographic dimensions, the model also refers to relevant literature and considers a variety of risk factors such as nighttime visibility, operational errors, and decision-making errors.
In our interviews with shipping and air transportation industry personnel, we learned that there is a lack of current risk prediction models that balance simplicity and high reliability. Our attempt demonstrates the broad prospect of big data, machine learning and other technologies in the field of safety, which can help relevant departments and enterprises to identify risks and formulate preventive measures in advance, so as to improve the overall safety management level. Meanwhile, the data we have collected involves many countries and regions, and by integrating the characteristics of different regions, we have promoted international cooperation and exchanges in the field of shipping and air transportation safety. This will help to form a more complete global safety regulatory system and jointly address cross-border challenges and problems.
The universe is vast and mankind has never stopped exploring it. With the upgrading of science and technology, the space industry has ushered in a vigorous development, and interplanetary exploration has gradually become a reality. Therefore, we hope that the Bio-Beacon Rescue Locator is no longer limited to life-saving activities on earth, but can go to the space and have a broader application space.
We consulted with professionals in the aerospace field and determined to establish a multi-dimensional evaluation index system that includes light conditions, atmospheric composition, temperature, gravity and supply conditions, etc., and quantitatively analyzed it using the Rank and Ratio Comprehensive Evaluation (RSR) method, which provides a standardized method for evaluating the adaptability of space equipment on different planets. This method is not only applicable to BRL, but can also be extended to the environmental adaptability assessment of other space equipment or technologies, providing a certain basis for the preparation and planning of future space exploration missions. By combining knowledge from multiple disciplines, including biology, astronomy, geology, meteorology, physics, and engineering, we demonstrate the important role of interdisciplinary research in solving complex spaceflight problems.
The evaluation results of our model reveal the limitations of current technologies (e.g., the luxAB system) in harsh environments such as high gravity, low light, and extreme temperatures. In the future, researchers can develop more efficient and stable bioluminescent systems or other types of rescue localization technologies for these extreme environments to meet the needs of space exploration and other extreme environments.
As synthetic biology continues to delve deeper, the design of genetic circuits is progressively evolving towards multi-modularity and multi-functionality. Beyond traditional physicochemical factors causing cellular damage, numerous studies have revealed that biological factors can mediate various signaling pathways, ultimately leading to cytotoxicity. Complex circuit designs encompass more genes and proteins, introducing greater uncertainty regarding the survival state of the host cell.
A review of prior research indicates that while some scholars have noted the potential toxicity of genetic circuit systems on host cells and proposed optimization strategies for specific engineered bacteria, there is a lack of systematic studies estimating toxicity. Current optimization strategies are relatively limited. To design safer and more efficient genetic circuits, further exploration in related fields is necessary.
Capitalizing on this opportunity, we have developed a genetic circuit and, by comprehensively considering the two key indicators of cell growth rate and survival rate, combined with expert consultation, employed the Analytic Hierarchy Process (AHP) to determine the weights of each indicator. This has assisted us in comprehensively quantifying the toxicity level of the host bacteria.
Furthermore, the application of this model aids iGEM teams in designing and optimizing genetic circuits with a greater focus on the health status of the host cell, balancing both quality and quantity. By comparing differences between experimental and control groups of host bacteria, potentially toxic genetic elements can be promptly identified and adjusted, thereby enhancing the genetic stability and predictability of the system.
Understanding how different modules, genes, and proteins interact and influence the survival state of host cells in genetic circuit design remains a pressing challenge. We hope that our simplified toxicity assessment model provides a universal analytical approach, enhancing awareness of safety aspects in circuit design.
We have designed a range of products such as bioluminescent lifejackets, parachutes, and spacesuits utilizing a hybrid system of algae and bacteria. Unlike the original chemical-based luminescence, our algal autotrophic system is self-supporting, which means that our products have sustainable luminescent properties. In addition, under different application scenarios, we have chosen different materials - electrostatic spinning, bacterial filter membrane and other carriers to load the algal system.
In addition, the closed-loop life system constructed by our algal-bacterial system has a wide range of applications, and future iGEM teams can refer to this design to modify chassis microorganisms to work continuously without an external energy supply - hopefully, this unique idea will inspire future teams to conceptualize in the field of synthetic biology!
To view more detailed information about the product design, please go to the product page.