--November

--Week 1

General:

Project kickoff for Human Practices (HP). The team reviewed global disease reports, biomanufacturing policies, and company annual reports to understand the societal and industrial needs for high-value plant natural products.

Specific Content:

The team studied major infectious and non-infectious diseases and their treatment methods. Key insights: plant natural products are crucial for treatment but face high costs, long cycles, and low accessibility. Policies from different regions supporting biomanufacturing were reviewed to align the project with regional industry priorities. Initial discussions emphasized the need for enzyme engineering tools to overcome heterologous synthesis bottlenecks.

--Week 2

General:

Focused on industry insights and protein design tool needs through corporate annual report surveys.

Specific Content:

Analyzed reports from multiple biotechnology and pharmaceutical companies. Identified strong demand for enzyme engineering and pathway optimization. The team decided to focus on plant enzyme design and synthetic biology solutions, aiming to create tools that align with industrial pain points and accelerate product development.

--Week 3

General:

Initiated expert consultation and academic interviews to refine technical objectives.

Specific Content:

Discussed current biomanufacturing challenges, enzyme modification needs, and strategies for pharmaceutical natural products and pigments. Insights guided the project to target key enzymes in pathways such as paclitaxel and lycopene biosynthesis.

--Week 4

General:

Expanded academic consultation to include cell factory and synthetic biology experts.

Specific Content:

Learned that missing or low-activity enzymes are the main barriers in heterologous synthesis. Emphasis on balancing research value with industrial application to maximize societal impact.

--December

--Week 1

General:

Conducted market and industry-oriented consultations with agricultural and biomanufacturing enterprises.

Specific Content:

Gained practical industry insights on consumer group analysis, market trends, and competition landscape. Team recognized the importance of developing tools with practical application value and high industrial adoption potential.

--Week 2

General:

Analyzed literature and existing protein design platforms to identify limitations.

Specific Content:

Compared PROSS, FuncLib, and ProteinMPNN. Found that current platforms are limited in integration with experiments, complexity, and coverage of active sites. This motivated the development of a tool specifically addressing heterologous plant enzyme stability and activity.

--Week 3

General:

Protein design technical consultations with academic experts.

Specific Content:

Discussed strategies for enzyme modification, pathway analysis, co-evolutionary analysis, function-oriented design, multi-dimensional iteration, backbone optimization, and mutation-combination prediction. Insights informed REvoDesign development, emphasizing stability, activity, and industrial applicability.

--Week 4

General:

Continued refinement of tool design and workflow optimization.

Specific Content:

Integrated semi-rational modification workflows with co-evolutionary analysis and rational protein design. Focused on minimal experimental burden, synergistic stability and activity improvement, and alleviation of epistasis effects. Developed a visualization module to support expert review.

--January

--Week 1

General:

Development of the first version of REvoDesign tool.

Specific Content:

Completed initial integration of semi-rational modification workflows, co-evolutionary analysis, and rational protein design modules.

--Week 2

General:

Field research in hospitals to understand clinical needs of high-value plant products.

Specific Content:

Collected information on limitations in patient access to plant-derived drugs due to high prices and production cycles. Insights highlighted the societal importance of improving heterologous synthesis of natural products via REvoDesign.

--Week 3

General:

Human health and microbiome considerations.

Specific Content:

Considered variability in drug metabolism and precision medicine applications. Learned to incorporate public health awareness alongside technological development.

--Week 4

General:

Industrial feasibility evaluation.

Specific Content:

Analyzed production, supply chain, and regulatory challenges in pharmaceutical manufacturing. Adjusted REvoDesign goals to align with industrial adoption, R&D cycle reduction, and regulatory standards.

--February

--Week 1

General:

Selection and research on high-value plant products for case studies.

Specific Content:

Identified potential plant targets with high-value active compounds. Heterologous synthesis proposed as a solution to resource scarcity.

--Week 2

General:

Investigation of key enzyme pathways for industrial production.

Specific Content:

Observed that precursors are limited, growth cycles are long, and yields are unstable. Identified key rate-limiting enzymes. REvoDesign set to optimize these enzymes for industrial production efficiency.

--Week 3

General:

Academic consultations for integration with drug discovery.

Specific Content:

Evaluated structure-based approaches and fragmentation methods. REvoDesign identified as a complementary tool for enzyme modification and large-scale production.

--Week 4

General:

Traditional medicinal product synthesis analysis.

Specific Content:

Analyzed bottlenecks in enzyme activity and multi-gene expression. Confirmed REvoDesign’s potential for industrial enzyme modification and pathway optimization.

--March

--Week 1

General:

Pilot case studies for REvoDesign.

Specific Content:

Selected lycopene and paclitaxel pathways as demonstration cases. Focused on increasing catalytic efficiency and reducing byproducts. Initial computational designs completed; planning wet-lab validation.

--Week 2

General:

Expert evaluation and tool refinement.

Specific Content:

Collected feedback from protein design and industry experts. Adjusted REvoDesign features to improve interpretability, usability, and industrial applicability.

--Week 3

General:

Social dissemination and public engagement.

Specific Content:

Shared knowledge on heterologous synthesis, plant natural products, and synthetic biology. Engaged public via webinars and social media to increase awareness of accessibility, cost reduction, and sustainable production.

--Week 4

General:

Industrial partnership exploration.

Specific Content:

Negotiated strategic cooperation with industry partners. Applied REvoDesign to industrial lycopene production case. Plan to monitor performance, collect data, and further optimize workflow for real-world application.

--April

--Week 1

General:

Tool validation and data analysis

Specific Content:

Analyzed REvoDesign outputs for target enzymes. Evaluated improvements in stability and catalytic efficiency. Data informed iterative updates to the tool and documentation for industry adoption.

--Week 2

General:

Expert review and workshop.

Specific Content:

Held workshops with scholars and industry experts. Discussed case study results, tool interface improvements, and future applications. Collected feedback for enhanced workflow and broader applicability.

--Week 3

General:

Finalization of REvoDesign tool features.

Specific Content:

Incorporated all feedback, refined visualization, mutation prediction modules, and DBTL workflow. Ensured modular outputs and industrial usability.

--Week 4

General:

Project wrap-up and reporting.

Specific Content:

Prepared comprehensive report documenting Human Practices, industry insights, tool development, and case studies. Ensured alignment with sustainable development goals and iGEM competition requirements.

- May

--Week 1

General:

After the conclusion of the school competition selection, students from different departments joined the YNNU-China team, and everyone is full of energy and enthusiasm! So far, we have successfully identified the members in charge of the wet lab section.

We held our first team meeting, where all members introduced themselves and got to know each other. We also elected our student team leader and deputy team leader. In addition, we had a preliminary discussion with our PI regarding the project direction, aiming to accelerate the development and utilization of the REvoDesign tool. Meanwhile, our WiKi team is also learning the basic knowledge of Web development and familiarizing themselves with frameworks to prepare for the subsequent website construction phase.

--Week 2

General:

A brief introduction was provided to the background of the IGEM (International Genetically Engineered Machine) competition project: "using the REvoDesign tool to engineer natural enzymes, enabling the heterologous efficient synthesis of natural products". Discussions were also held on experimental details such as candidate cases and the combination of genes to be used in synthetic pathways.

Task assignments were made for all participants, who were specifically divided into the Dry Team and the Wet Team.

Wet Team: Conduct wet experiments, and record and organize wet experiment data; this data will be used for the production and distribution of PPTs, animations, and other materials.

Dry Team responsibilities: Undertake software development; create promotional PPTs, design the team logo, produce animations (with assistance from professionals required in the later stage), and handle post-production subtitle dubbing; organize team recruitment presentations and carry out Human Practices (HP) work, while being responsible for the team's subsequent communication with potential new members; collate project-related materials ("Stories") and provide textual materials for subsequent PPTs, animations, etc.; design and coordinate the procurement of team uniforms and team flags; coordinate personnel and book meetings; take meeting minutes, track project progress, and record updates in real time; create promotional handout cards.

--Week 3

General:

Discussion on Phased Work and Arrangements for Subsequent Tasks

Specific Content:

We held an online meeting with students majoring in media who are interested in joining the team, introduced the iGEM project, clarified the tasks to be undertaken, and we will follow up on the recruitment of new members subsequently.

The team discussed the team logo design, developed the initial version of the logo, and discussed its color scheme, implied meaning, and other aspects during the meeting. A consensus was reached within the day, and this logo will be used for the production of team uniforms and flags.

Discuss the work arrangements for promotional presentations, including the following specific items:

1. Web design (personnel to be determined);

2. Promotional posters (to be produced after the materials are finalized);

3. Promotion Venues and Methods: The initially proposed venues include companies, hospitals, government agencies, and schools, while the initially proposed methods cover roadshows, presentations, and more. During the meeting, in-depth discussions were held on how to conduct promotion efficiently and accurately, with a focus on two key aspects: how to fully introduce the story background (to demonstrate its theoretical feasibility, social value, and potential future value) and how to achieve targeted delivery of promotional content. All team members expressed their respective opinions; among them, the person in charge of this section took Chenguang Biotechnology Co., Ltd. as an example, explaining how to align corporate pain points with the project's highlights, and planned to conduct a presentation and promotion at this company in the subsequent phase.

--Week 4

General:

Main Content: The team summarized the work of the previous phase and made arrangements for subsequent tasks. The Principal Investigator (PI) attended the meeting online and provided guiding suggestions. New team members also participated in the online meeting.

Specific Content:On the part of the Dry Team, its members reviewed the work of the previous phase and assigned personnel for various tasks in the next phase, including the following details:

1. Public media platforms: These include Bilibili, Xiaohongshu (Little Red Book), WeChat Official Account, etc. It was initially planned to start with the WeChat Official Account—members of the Dry Team will take turns to provide articles on a weekly basis, and Gao Yu will be in charge of publishing and management. During this period, the PI suggested that for international competitions, the team should also pay attention to the operation and content release of foreign social media platforms, while ensuring the breadth of the audience and focusing on popular science content.

2. Animation design: Two students from the Academy of Fine Arts of Yunnan Normal University, introduced by a team member, will be responsible for the production and are required to submit the first draft before June 1st.

3. Poster design: Team members will optimize and revise the first draft, and finalize the final version before May 15th.

4. PPT production and external promotion: The person in charge of this work proposed a series of practical options for promotion venues, including primary schools, Yunnan Normal University Provincial Academy of Sciences, Kunming University of Chinese Medicine, Chenguang Biotechnology Co., Ltd., Henan Muyuan Laboratory, Zhengzhou Municipal Health Commission, etc. This work will be launched immediately after the completion of PPT and poster production, aiming to expand the team's influence and recruit new team members at the same time.

5. Website design: Design of the WiKi website, including the webpage framework and specific content.

On the part of the Wet Team, they reported the current difficulties and problems. Team members stated that the Wet Team is facing a tight schedule, heavy tasks, large workload of experiments, and a significant shortage of personnel. After discussion at the meeting, members of the Dry Team will assist in wet experiments: Wet Team members will create an experiment schedule and inform Dry Team members in advance when assistance is needed to complete the experiments.

During the meeting, the PIs delivered guiding opinions online and informed the team that they would invite other teachers to assist in the project implementation later. These teachers will provide support in areas such as experience in participating in iGEM, social application value of REvoDesign, and guidance on enzyme engineering.

- June

--Week 1

General:

Main Content of the Meeting: Reviewed the experimental ideas of the Wet Team and refined the work arrangements for the Dry Team

Specific Content: The team analyzed the requirements for various iGEM awards and discussed whether objective conditions (such as time) could meet the rigid requirements, including the DBTL cycle. Subsequently, the PI (Principal Investigator) explained the wet experiment section from the perspectives of experimental ideas and overall planning. He pointed out that currently, plant enzymes exhibit poor stability and low activity in microbial hosts, which is a major bottleneck in the production of high-value natural products in synthetic biology. To address this, we have developed a rational evolution-guided enzyme reconstruction (REvoDesign) workflow to guide the rapid evolution of enzymes with target functions and adaptability in microorganisms. The PI emphasized that this iGEM project will only focus on the key enzymes (involved in lycopene and taxadien-5α-ol (T5OH) production) modified by REvoDesign, and the Wet Team's experiments only need to proceed to verifying that the product yield shows a significant difference compared with that before modification. Additionally, the PI suggested that the team create a mind map based on the Wet Team's experimental ideas—this will not only facilitate the implementation of subsequent experiments but also help the team gain a clearer understanding of the tasks to be completed and their objectives.

Afterwards, the team further subdivided the work for the Dry Team. Due to the relatively heavy workload of Human Practices (HP) presentations, personnel allocation for other iGEM projects was temporarily reduced. Meanwhile, the team coordinated with members from the School of Media and Communication regarding video and poster production. A work discussion was held with four students from the School of Media and Communication, during which the storyboards for the video were further discussed and the person in charge of subsequent poster work was clarified. Additionally, these four students decided to join the iGEM team and will participate in project-related work as official team members subsequently.

--Week 2

General:

All-team Meeting: Discussed team task division and next-step plans. We outlined the specific technical roadmap for the Wet Team. Our WiKi team also continued to delve deeper into web-related knowledge. During this busy week, everyone on the team worked tirelessly toward the same goal, hardly having any personal rest time.

The addition of new members in areas such as graphic design, video production, and costume design has made our team officially complete! After the regular meeting on Tuesday, we took a group photo in front of the main building of the college. This week, our project design finally began to take shape. The team dedicated to enzyme engineering is planning to use REvoDesign to address the issue of heterologous synthesis of plant natural products. Meanwhile, work has begun on constructing a fusion expression system in yeast cells. We also discussed the feasibility of various technologies such as multi-gene integration. Our WiKi members are currently collecting materials, and our HP (Human Practices) team member presented their overall plan—and we are confident that we will definitely succeed!

--Week 3

General:

Main Content of the Meeting: The PI (Principal Investigator) led the team to review the relevant requirements and tasks on the iGEM official website, and made specific arrangements for them.

Specific Items:

1.White List Check: Conduct checks on items including materials used in experiments to ensure all materials are included in the iGEM White List (approved materials list).

2.Completion of the Preliminary Safety Form: Submit the preliminary filled content to the PI for review and verification before Sunday, followed by the official submission of the form.

3.Personnel Work Adjustments: Some team members will shift their main work from the Dry Team to the Wet Team to assist in completing wet experiments. In addition, with the assistance of teachers and after communication, a new student from the School of Information Science and Technology will join the team, taking charge of the WiKi webpage design.

4.Verification of Experimental Materials: The team will check all expression vector sequences to be used by the team to ensure the experiment proceeds without any errors. Additionally, all chassis strains used have been reported in academic literature. The Wet Team will continue to focus on vector construction and natural product expression. First, we will transform unmodified genes (such as T5αH and CarRP) into yeast cells and conduct PCR identification to confirm whether they have been successfully transformed.

Students in charge of costume design have started designing team uniforms for the team.

--Week 4

General:

Main Content of the Meeting: Divided the work of the Dry Team, conducted in-depth discussions on the details of video storyboards, and all participants reached a consensus.

Work Allocation for Communication PPTs: The PPT tasks were divided into modules. The team focused on collecting materials for the "Problem Statement" and "Current Situation Introduction" sections, and providing content for presentation—this is to facilitate subsequent discussions and experience sharing with gold award winners.

Specific Content:

1. Team members learned from previous award-winning teams and proposed additional tasks to be implemented, including the development of a business plan, modeling, and the design of questionnaires.

2. The team conducted in-depth analysis and discussion on the content of the video storyboards, reached a consensus, and confirmed the final version. For the specific storyboard content, please refer to the following link: https://static.igem.wiki/teams/5915/notebook/notebook.pdf.

- July

--Week 1

General:

Dry Team Key Content:

1. Arranged the date for the exchange meeting with Nanjing Normal University (NNU) and the specific matters to be prepared.

2. Made arrangements for the coordination work for the WiKi video.

3. Discussed the specific implementation strategies for social media operations.

4. Divided the work for promotional presentations.

Specific Details:

Confirmed that the exchange meeting with Nanjing Normal University (a two-time iGEM gold award winner) will be held this Saturday. The team split the PPT preparation work into tasks and assigned them to specific team members.

Social media operations were divided into three segments, corresponding to three platforms: Xiaohongshu (Little Red Book), WeChat Official Account, and Bilibili Video Platform. In addition to promoting and distributing WeChat Official Account articles across all three platforms, Xiaohongshu and Bilibili will update video or graphic content regularly. This work is tentatively assigned to members from the media team, and a detailed plan will be formulated later.

The work for promotional presentations was subdivided into two parts: pre-preparation and the presentation itself. Pre-preparation includes preparing team flags, team uniforms, leaflets, posters, and other materials.

--Week 2

General:

iGEM Peer Exchange Meeting

Exchanging Teams: Nanjing Normal University (NNU) – Yunnan Normal University (YNNU)

Participants: All members of YNNU iGEM Team, representatives of NNU iGEM Team, etc.

Main Meeting Content

Nanjing Normal University and Yunnan Normal University took turns to share their iGEM teams' work and progress. The PIs (Principal Investigators) of our team and NNU's PI put forward guiding suggestions, and suggestions for improvement on the current project progress were also proposed during the meeting.

Specific Meeting Content

Nanjing Normal University reported on its project related to folate metabolism. Based on their presentation, we gained a deeper understanding of the specific requirements for iGEM projects and made corresponding adjustments. As NNU has participated in the iGEM competition many times and won gold awards on multiple occasions, it has a profound understanding of the competition and rich experience. Based on their report, we made the following adjustments:

1. For the Human Practices (HP) section, we need to intensify efforts and accelerate the dual advancement of promotional presentations and research surveys.

2. Accelerate project progress: provide timely feedback when problems arise, establish additional collaboration mechanisms and a "responsibility assignment" mechanism (ensuring each task is assigned to a specific person), to promote project progress more efficiently.

3. Combine the core of the project with traditional culture: promote the green production of traditional Chinese medicines using synthetic biology, elaborate on the project's contributions of synthetic biology to society at a deeper level, and embody the entrepreneurial spirit.

--Week 3

General:

Meeting Content: Reviewed the exchange meeting with Nanjing Normal University held last Saturday. Based on the improvement suggestions proposed earlier, a task tracker was created: tasks were broken down among each individual, and deadlines were clearly marked. The team communicated with the art team to redesign the posters, and planned to have a further discussion with the art team tomorrow evening to provide a detailed description of the project background, so as to facilitate the drawing of video storyboards.

The meeting focused on discussing the content of the WiKi and video. Team members made new arrangements for work schedules; all members participated in the discussion and clarified the specific details of tasks as well as their completion dates. The WiKi tasks were mainly divided into two sections: the text section and the webpage design section. These two sections were assigned to different team members respectively, and the work content under each section was further broken down. After discussion, it was decided that the art team would submit the first draft of the video in early August, and the revised final version would be submitted in late August. Meanwhile, the meeting also discussed the phased team work summary meeting to be attended by the PI, and summarized the work that has been completed so far and the tasks planned to be finished in the future.

After modifying the CarRP protein, the Wet Team successfully turned the final product into lycopene, with almost no β-carotene produced. This case demonstrates the feasibility of modifying enzymes using the REvoDesign tool. In subsequent experiments, the team will also continue to explore the optimal conditions for its fermentation production, aiming to achieve the goal of efficient heterologous synthesis of lycopene.

--Week 4

General:

Human Practices and Wet Team Progress

In terms of Human Practices (HP), the team organized a science outreach activity titled "Sowing the Seeds of Science, Illuminating the Light of the Future" at Jinning Primary School. The activity included sessions such as educational lectures, DIY iGEM logo painting, knowledge quizzes, and rolling lucky draws. The children were highly enthusiastic, and everyone developed a great interest in synthetic biology and iGEM!

As always, the Wet Team remained busy in the laboratory—both protein modification and product extraction experiments have entered a critical stage.

After modification using the REvoDesign tool, the CarRP protein successfully enabled the synthesis of lycopene, which confirmed the tool's reliability. This marks a major success for the enzyme modification project!

However, the success of a single case is not sufficient to convince more people of the REvoDesign tool's effectiveness. Therefore, our team will start working on protein modification for the second case next week, and we believe that the team's full collaboration will help overcome these challenges.

- August

--Week 1

General:

As we enter August, the experiments are entering the final stage.

The Wet Team made significant progress this week—after adjusting the experimental conditions, they successfully obtained recombinant plasmids based on the modified T5αH gene. Following this method, we will construct the remaining mutants in one batch and introduce the constructed plasmids into Saccharomyces cerevisiae (baker’s yeast).

The team conducted an objective analysis of the experimental data from the lycopene case, discussed the performance of product data under different modification conditions, and is now working to find the optimal solution.

The HP Team attended the CCiC (China Conference for iGEMers) meeting, conducted in-depth exchanges with Chinese teams participating in the iGEM competition, and held profound discussions after listening to each other’s presentations.

--Week 2

General:

This week, the experiments achieved another significant breakthrough. Members of the Wet Team successfully expressed and purified taxadien-5α-ol (T5OH)—the catalytic product of T5αH—in yeast. They also continued to adjust enzyme modification sites and test more optimization schemes.

After multiple experiments, the team finally identified some enzyme modification sites and successfully completed the double-site mutations that enable the efficient synthesis of taxadien-5α-ol (T5OH). This marks another important milestone in the successful enzyme modification using the REvoDesign tool.

The WiKi team made solid progress by improving the basic framework of the website. When we showcase it later, it will definitely be impressive.

Additionally, this week we held a collaborative exchange meeting with students from Sichuan University (SCU). We learned about their innovative design concepts and strategies, which led to an exciting exchange of ideas and insights, leaving valuable practical experience for both teams.

--Week 3

General:

Our experimental progress is going more smoothly day by day! The Wet Team is approaching the final stage of data collection, and all experiments are advancing steadily—this makes us more and more confident in the stability of the experimental data.

What is exciting is that after conducting instrumental detection and analyzing the calculated data of the product, we found that the T5OH yield of multiple groups of mutants has significantly increased compared with that of the unmodified protein.

The Modeling Team continues to test various mutants—this is a complex process, but progress is steady.

Although the pace in the laboratory is busy, the preparation work for the WiKi is still proceeding in parallel, with continuous efforts to enhance the website's functions.

--Week 4

General:

The Laboratory Team (consistent with the "Wet Team" in previous contexts, referring to the team responsible for experimental operations) continued to adjust the conditions for lycopene fermentation experiments. Repeated experiments require patience, but each attempt seems to boost everyone's confidence even more.

The team had a relatively smooth week with revisions and discussions on HP (Human Practices) and WiKi. Notably, the team has started drafting some basic documents in the WiKi, marking steady progress in the team's tasks.

- September

--Week 1

General:

In September, the team focused its efforts on the writing and organizing of WiKi documents. Members of the Wet Team fully compiled and carefully reviewed their experimental results, and now everyone is focused on systematically integrating these results and data into the WiKi. Additionally, the team has begun drafting documents for its models to ensure that the integration of experiments and theory is well reflected in the WiKi. The entire team is working together to integrate the data in the WiKi, ensuring that our team's achievements are clearly and accurately presented.

--Week 2

General:

This week, the WiKi writing process has entered a critical stage. Most of the experimental content from the team responsible for enzyme modification using REvoDesign has been incorporated into the WiKi, and the documentation from the Modeling Team has also begun to take shape. The team is now focused on refining the language and logical structure to ensure that the content is not only scientifically rigorous but also easily understandable. The team is working hard to integrate the various modules in the WiKi, and overall, progress is going smoothly.

--Week 3

General:

The WiKi document is nearly complete. All experimental data, model results, and relevant discussions have been fully integrated into the document. We have conducted multiple rounds of discussions with the PI (Principal Investigator) to ensure the content is both comprehensive and scientifically accurate. We have conducted multiple careful reviews of the results obtained from enzyme modification using REvoDesign, to ensure there are no omissions or misrepresentations. The Modeling Team has also completed their model documentation, successfully linking the theoretical and experimental aspects of the project. The team has now entered the final stage of adjusting the format and layout.

--Week 4

General:

The final version of the WiKi document has been completed! All content from each experimental module has been fully integrated, and the theoretical content developed by the Modeling Team is rigorous and detailed. The team has done an excellent job with the document formatting and proofreading in the WiKi, making the overall presentation of the project highly professional and polished.

Thank you all for your hard work—we have finally showcased our team's efforts in a clear and impressive manner, highlighting all the work we put in to achieve our goals.