Our project's contributions encompass enriching libraries, improving technologies, advancing antibody engineering, promoting access to synthetic biology, and fostering knowledge exchange within the iGEM community.

We enrich the iGEM parts library by introducing tRNA-like structures (TLSs) into RNA molecules, enhancing their transport capabilities and enabling the expression of target proteins in non-transformed plant cells. Additionally, our project focuses on improving large plasmid transformation efficiency using electrotransformed E. coli, providing a useful protocol for other teams. We also contribute to the field of antibody engineering by generating models for antibody sequences and measuring the nanobody binding effect. Moreover, we promote access to synthetic biology through our educational programs, reaching diverse communities and addressing issues of inequality. Our low-cost fluorescence microscope design and pressing punching module further facilitate accessibility to essential laboratory equipment.

We sincerely hope that our year's work will inspire and help many more iGEMers and synthetic biologists. At the same time, we hope that the impact of our program can be extended to a wider audience, so that experts outside of our field can be involved in solving agricultural problems.

The incorporation of tRNA-like structures (TLSs) into RNA molecules has significant potential in synthetic biology and agriculture. By adding TLS modules, RNA molecules can acquire transport capabilities, allowing them to efficiently move through plant vascular bundles. This enables the expression of target proteins in non-transformed plant cells and provides a novel avenue for genetic modification and trait enhancement in crops. The ability of TLSs to enhance translation and facilitate RNA-protein interactions also opens up possibilities for regulating RNA replication and other biological processes. Moreover, the introduction of TLS into the iGEM parts library enriches the available toolkit for genetic engineering. This technology offers opportunities for improving plant biotechnology and furthering our understanding of RNA biology, particularly in the context of engineering modifications in plants, which serves as a challenging chassis for such advancements.

For more details, please see our Part page.

Figure 1: Secondary structure prediction of natural tRNA sequence and artificially modified tRNA sequence.

In this year's igem project, we often constructed large plasmids of around 10,000 base pairs (e.g. pGreen-TMV-GFP, etc.). At the beginning of the experiment, we used the original chemical transformation method, but the ratio of positive clones obtained was low. Therefore, we prepared our own E. coli STABLE competent cells suitable for electro-transformation and tried out a protocol with higher transformation efficiency, which can be used as a reference for other teams in the iGEM community.

For more details, please see our Protocol page.

Figure 2: Component cells preparation (DH5α/Fast-T1/STABLE/GV3101(pSoup-P19) competent cell)

Traditional antibodies are more complex in structure and have many difficulties in cloning construction and expression. In this year's iGEM project, we used an antibody derived from alpaca's peripheral blood with a naturally missing light chain, which greatly reduced its size and made it more suitable for engineering and transformation. Meanwhile, by measuring the immunization effect of the plant, we can also confirm that the nanobodies have a good performance in terms of binding benefit to antigen, which can be considered as a direction for antibody engineering in the future.

Figure 3: Measuring result for our nanobody binding effect

We aspired to construct a generative model for antibody sequences, guided by the structural and sequential attributes of antigens.

By replacing ID sequences of nanobodies with computationally generated sequences exhibiting strong antigen affinity, the project offers a more efficient and cost-effective alternative to the time-consuming and expensive immunoscreening process. This capability not only expands the scope of the project to more diseases but also reduces the resources required, allowing for faster and more affordable development of targeted therapeutic interventions. This advancement can have broader applications in the field of synthetic biology, providing a valuable tool for the engineering of nanobodies for various diseases and potentially accelerating progress in the development of novel treatments.

Figure 4: User interface of our software

The model part makes its contributions to the field of agricultural synthetic biology by addressing the global challenge of crop disease. By modeling the processes of virus infection, vaccine transport and delivery, efficacy time, and antigen-antibody matching, the project offers insights and feasibility demonstrations for biological phenomena in biopesticide.

In the modeling part, the large eddy simulation (LES) method considering field effect is established, and the plant virus spread infection model is derived by combining finite element method (FEM) simulation and pattern dynamics (PD). The physical morphology and entropic elasticity of RNA in plant vascular tubes are established based on the Wiener process and transpiration tension together with Ito-Langevin equation and Poiseuille flow. Combined with the method of deep learning to solve the stochastic differential equation, the "central dogma" of saRNA is established. Finally, the lattice model was used to calculate the binding efficiency of antigens and antibodies, which provided assistance for the explanation of the mechanism of the experiment.

For more details, please see our Model page.

Figure 5: Workflow of models for agricultural synthetic biology

We usually observe fluorescence using a dedicated fluorescence microscope. But because of the high price, not every laboratory can have a fluorescence microscope. To address this problem, we provide a simple, low-cost design scheme for a fluorescence microscope, so that other laboratories that need to observe fluorescence but lack equipment can refer to imitation to make a simple device. In addition, because the traditional blade perforator needs to be cut repeatedly when used, the operation is inconvenient, and the device is scattered and inconvenient to store, we added a pressing punching module to the hardware device, which can achieve punching through simple pressing. And the module is located in the device for easy loading immediately after cutting the blade.

For more details, please see our Hardware page.

Figure 6 & 7: Low-cost fluorescence microscope(left) with pressing punching module(right)

One of the main contributions our project makes to synthetic biology is raising awareness about important global issues such as hunger and inequality, as well as other ethical problems of scientific development. By highlighting the steps and actors involved in food production and emphasizing the significance of agriculture and related industries, the project sheds light on the importance of these fields and contributes to their recognition and appreciation.

Additionally, our project aims to break down barriers that prevent people from accessing cutting-edge knowledge in synthetic biology and other fields. By consulting experts in education and incorporating their advice, as well as providing engaging and unforgettable educational programs, the project strives to make synthetic biology more accessible and inclusive.

The educational program implemented by our project reaches a wide range of communities, including primary schools, high schools, and both urban and rural areas. Attention is given to addressing economic and gender inequality, and tailored educational activities are designed to suit specific audiences. This approach ensures that different segments of society have access to information about food safety and synthetic biology.

By engaging with society through educational activities, our project creates a two-way exchange of knowledge and ideas. Feedback collected from participants is used to improve the educational approach and program design, fostering continuous improvement and responsiveness to societal needs.

In summary, our project contributes to synthetic biology by raising awareness about global issues, making synthetic biology more accessible, and providing educational programs that reach diverse communities, ultimately fostering greater understanding and appreciation of agricultural and biotechnological fields.

For more details, please see our Human Practice page.

Figure 8: Empowering Communities through Education: Breaking Barriers to Synthetic Biology and Addressing Global Issues