May
Wet Lab
1. Read many papers to understand the significance of ancestral sequences and machine learning.
2. We visited the laboratory to learn basic laboratory operations and how to properly dispose of laboratory waste.
Human Practice
1. We held our first IGEM presentation, through which we had a clearer plan and identified common goals to work towards.
2. In order to better understand the biological explanation of PET plastics, we went to the School of Environment of Nanjing Normal University and interviewed Professor Fengxiao Zhu.
3. In order to improve mutual understanding and communication among team members, we held our first team building activity.
4. We participated in the IGEM Alliance Nanjing Regional Meeting organised by Nanjing University and the on-campus publicity.
June
Wet Lab
1. Learn how to reconstruct ancestral sequences and use machine learning algorithms to predict the potential variants.
2. We extracted the ASR1-PETase plasmid, and ASR1-PETase variants were constructed using a two-step PCR method for DNA amplification. The recombinant plasmids above were transformed into Escherichia coli BL21 (DE3) for protein expression.
3. Learn to perform MD simulations using GROMACS 2022 simulation package with the GROMOS96 (54a7) force field.
Human Practice
1. In order to further promote the green concept of iGEM team and get more practical inspiration, our team participated in Biological Carnival.
2. We went to the Nanjing Quality Supervision Institute to visit, study and interview.
3. We went to Nanjing Refinery Primary School, Nanjing Huashu Village community, and Jurong City Children's Palace to introduce our team, synthetic biology and basic knowledge about plastics to the children in a simple and easily comprehensible manner. For young and middle-aged groups, we carried out science popularization activities in Xianlin Lake community. For the elderly, we went to Suojin Four Village community to introduce our project and plastic-related knowledge to the elderly.
July
Wet Lab
1. We constructed a PETase phylogenetic tree and reconstructed ancestral sequences for evolutionary nodes. Experimentally, the ancestral sequences of PETase constructed into pET-22b(+) vector by Gibson assembly technique and verified the activity by protein expression.
2. For the promising ASR1-PETase, we used the ESM-1v model to design variants and compare it with other machine learning algorithms .
3. We verified the hydrolytic activity of ASR1-PETase variants using BHET as the substrate and processed experimental data using Graphpad Prism software.
4. Learn to perform MD simulations using GROMACS 2022 simulation package with the GROMOS96 (54a7) force field.
Human Practice
1. Our team embarked on a campus initiative to collect PET plastic bottles, subsequently employing the creative ingenuity of our members to metamorphose these bottles into an array of exquisite artworks.
2. We carried out a debate on the topic of “Whether bioenzyme degradation of plastics is a feasible way to solve plastic pollution”.
3. We organized the environmental protection and sustainable development summit and invited eight teams.
4. In order to further explore more efficient ways of environmental protection and deeper exploration in the field of synthetic biology, our team came to Nanjing Vazyme Bioiech Co., Lid. for a visit and study.
5. We visited Zhejiang Kingsun Eco-Pack Co., Ltd.
6. To get a detailed understanding of the waste disposal process, we came to Suzhou Everbright Environmental Protection Energy Co., Ltd.
7. We visited Zhihe Biotechnology Co.,Ltd.
August
Wet Lab
1. We modified the phylogenetic tree and processed experimental data using Graphpad Prism software.
2. Plotting machine learning schematics and visualization of substitution using PYMOL.
3. We verified the hydrolytic activity of ASR1-PETase variants upon PET film, and also constructed a two-enzyme system to degrade PET into the homogeneous TPA. Moreover, we regenerate the virgin PET using TPA as a substrate to achieve the closed-loop recycling of PET.
4. MD was performed on the wild type PETase and variants at different temperatures to figure out the driving force behind the increased degradation capacity at high temperature.
Human Practice
1. We participated in the Bioremediation themed academic forum organized by ZJUT-CHINA. At the meeting, we presented our work and focused on experimental design and human practice collaboration.
2. We participated in the 14th National Symposium on Enzyme Engineering, learned about the most cutting-edge achievements in the field of enzyme engineering.
September
Wet Lab
1. Collating experimental data and accomplish all the script.
2. Analyzing the MD results and processed the data using Graphpad Prism software.
Human Practice
After the experiments, our team, together with Zhejiang University of Technology, released a questionnaire on plastic degradation, and we found that there is still a need to educate the public about PET biodegradation.
October
Human Practice
To promote synthetic biology widely, our team participated in the biological podcast project and chose the theme of "Science Popularization of Biological knowledge".
