This year we won Gold medal.
Criteria
Bronze
| Competition Deliverables | Wiki, Project Promotion Video, Team Presentation, Judging Form |
| Attributions | From our wiki page, you can see that our team is both united and efficient 1. Students from all departments perform their duties responsibly and enthusiastically. Members of the Wetlab are responsible for experiments and providing data; IT students are responsible for modeling and web page production; members of the Secretariat are responsible for the minutes of the meeting and writing the copy; HP students are responsible for activity design, communication and cooperation. 2. A meeting is held at the beginning of each month, and heads of all departments report the results and jointly formulate future plans. 3. People without tasks in the team take the initiative to participate in other activities to reduce pressure. |
| Project Description | In the wake of the continual release of vast amounts of carbon dioxide (and other acidic substances) into the environment, the water on Earth, particularly seawater, is gradually faced with acidification. Water acidification is generally characterized by the increase in concentration of H+, causing serious ecological hazards, including the dissolution of the exoskeleton of coral and shellfish and low fertility of many marine lives. Fortunately, in the literature, we found a solution, the Xenorhodopsin, an inward H+ pump expressed on the plasma membrane of some archaea. In our project, a genetically engineered E. coli, the AcidOceanus, is planned to be constructed and applied to absorb H+ in the surrounding water under the condition of lighting. Integrating the Xenorhodopsin gene, AcidOceanus expresses Xenorhodopsin on its plasma membrane and then constantly transports H+ into intracellular space. Furthermore, as an approach to recycling H+, we are about to coordinate with some companies to design a device where engineered E. coli releases the H+ in dark conditions. Our project is devoted to providing a feasible direction for water acidification in a small range of areas, and at the same time instructing the public, especially teens, to be aware of its harm to marine life and the urgency to resolve it. |
| Contribution | The light-driven inward proton pump XeR(BBa_K4357000) is derived from xenorhodopsin in Nanosalina spp. It is a seven-transmembrane alpha-helix protein that functions with its cofactor called retinal(chromophore). When there is a light source applied to the protein, the conformational change of the retinal will induce inward proton pumping of bacteria and generate an electrochemical proton gradient across the membrane. In most of the previous studies, scholars are researching action potentials that react on neural cells; this kind of mechanism only occurs within milli-seconds. In our studies, instead of performing a short term light induction experiment, we performed a long term protein functional assay for the XeR protein, which will become useful data for the iGEMers for years to come. The Pasr promoter is a pH-sensitive promoter that can trigger transcription under an acidic environment, and it was the key factor that regulated our proton pump’s expression level. Pasr promoter is a pH-sensitive promoter that can trigger transcription under an acidic environment, and it was the key factor that regulated our proton pump’s expression level. |
Silver
| Engineering Success | We aim to use an inward proton pump XeR (Xenorhodopsin) to tackle water acidification, and an acid trigger promoter–Pasr–was applied in our system to control the expression of XeR protein in our E. coli bacteria to only function in acidic water. So, we primarily designed 3 plasmids. Pasr-XeR-mCherry-pSB1C3 uses a pH-controlled promoter to regulate the H+ pump synthesis. J23100-XeR-mCherry-pSB1C3 is the control group for verifying the basic function of the H+ pump. J23100-mCherry-pSB1C3 is the control group used for the intensity of mCherry signaling. |
| New Parts | BBa_K4357006, BBa_K4357001, BBa_K4357004 |
| Collaboration | We collaborated with various iGEM teams. First, we exchanged plasmid with Jiangnan University and Puiching Macau and implemented them into our own model and system. We also participated in several alliances such as the Freshwater Bioremediation Alliances for exchange of ideas and collaboration in some projects like sharing experimental work mutually. The HydroAqua iGEM League 2022 that we co-organised with the PuiChing Macau team allowed us to come up with sustainable solutions with partner teams to apply our project ideas to Hydroponic farming. Through liaising and communicating through social media, we have created a comic book, colourless pages, videos and iGEM map collaborative projects with iGEM MetaThess Team, iGEM eTc Chihuahua, USAFA and iGEM NTHU respectively. All these events connected with different iGEM teams around the world through collaboration. |
| Human Practices | From the start of the project, we have approached different parties for feedback on our project. We engaged with our supervisors, managers from the wastewater treatment plant and other iGEM teams for opinions. Since leakage and safety of modified E.coli are the major concern for the project, we plan to add a structure to the final designed device to prevent engineered bacteria from leaking, so as to prevent engineered bacteria from entering the environment. If the device works well, we can eliminate water acidification (such as in ponds) in a small range. |
| Proposed Implementation | Since the aim of our project is to regulate the acidity of freshwater and oceanwater, our project could be implemented into sustainable hydroponics systems and water treatment processes. In order to achieve this, we would collaborate with some companies to design a device where engineered bacteria can do their work but cannot exit. We would first repeat the experiment again in samples we collected from a local water body. If it’s of good effect and there is no leakage of our engineered E.coli to the water environment, we will apply this device in trials and generate various reports and data to prove the safety, cost and potential outcome of our system. Once the related department from the government reviews our system and agrees to the implementation plan of our project, we will apply our project in a local hydroponic farming system, and then monitor and review it to evaluate its effectiveness. We will also engage the stakeholders and provide questionnaires to obtain feedback when implementing the systems. |
Gold
| Integrated Human Practices | Our human practice work is extensive, integrated, and close-looped. In the previous state, we designed our project name and related background information. We performed abundant research not only through the academic literature online but also through real-life surveys of the wastewater treatment plants and via inquiries with experts. In the metaphase, we Our human practice work is extensive, integrated, and close-looped. In the previous state, we designed our project name and related background information. We performed abundant research not only through the academic literature online but also through real-life surveys of the wastewater treatment plants and via inquiries with experts. In the metaphase, we performed outreach to other teams and corporations. All these outreach activities provided us opportunities to better communicate and immensely improved our projects. In the later period, we had many educational events for the public, especially interfacing with middle and primary school students to stimulate their interest in synthetic biology. |
| Improvement of an Existing Part | BBa_K1231000 -> BBa_K4357004 |
| Project Modeling | Paying attention to the intermediates in the steady photo-induced current, we simplify the XeR photocycle and build a model of photo-induced current due to the H+ transport via XeR. Based on the simplified fast transition and rate transition process, this model is designed to show the real-time variation of the concentration of hydrogen, XeR and excited XeR in the medium, allowing us to calculate the efficiency of our system. The model works well for the simulation and shows a successful pH increase from 5.5 to 7. It assisted in directing us to modify the rates with regulated XeR proteins, which then became in line with the parameters of the model. The model also allows us to confirm that our assumptions and designation are feasible before further efforts. However, due to our strong assumptions, we cannot use the model to precisely predict our entire system. |
| Proof of Concept | For the XeR function, we processed a long term pH measurement to record the properties of the E. coli with different plasmids in LB medium at pH 5.5 and 7. In general, with long term incubation, all the groups, increased the pH to around 8.5 regardless the initial pH value. For the Pasr-XeR constructs, they are unable to change the pH value at the beginning of the experiment. Regarding the modelling part, based on the simplified fast transition and rate transition process in the steady photo-induced current, this model is designed to show the real-time variation of the concentration of hydrogen, XeR and excited XeR in the medium, allowing us to calculate the efficiency of our system and prove the success of our ocean deacidification system. |
| Partnership | We have had close partnerships with Jiangnan-China, Puiching_Macau, and Freshwater Bioremediation Alliance throughout the year. With Jiangnan-China and Puiching_Macau, we not only have deep discussions among our projects but also exchange our plasmids with them. We were impressed by each other’s projects and this improved our projects accordingly. We also set up a league and hosted a conference with Puiching_Macau. With FBA, we held a series of events with them throughout the year, such as online classes. |
| Education and Communication | For education, we have actively participated in a series of educational events on our campus for promoting our projects and attracting people to synthetic biology and the importance of ocean deacidification. We also held online classes for middle school students in mainland China’s remote mountain area for impressing them with interesting biology knowledge and related information concerning our projects. In addition, we contacted a local primary school to allow us to have an introductory lecture on our project for their students and will hold a competition for students coloring our coloring brochure. For science communication, we have held many meetups with other teams to communicate our projects. We also have close collaborations with other teams. We also communicated with the local government by visiting the wastewater treatment plant. For outreach materials, we exchanged our lab work materials with some teams for a few times and created works related to synthetic biology with other teams. |