Team:UESTC-China/Achievement

description

This year we met all following requirements of medal standards, and we worked a lot for these iGEM awards:

- Best New Application Project

- Best Education & Public Engagement

- Best Integrated Human Practices

- Best Hardware

- Best Model

- Best Supporting Entrepreneurship

- Best Presentation

In this section, we clearly show each entry up to the standards.

Bronze

1.Competition Deliverables

We have made Team Wiki, and prepared a wonderful presentation vedio. We have accomplished and submitted the Judging Form and Safety Form on time.

2.Attributions

We have created a page on the team wiki with clear attribution of each aspect of the project. Click herefor more details about our Attributions.

3.Project Description

We recorded what inspired us at the beginning, why we chose this project, and also how we achieved our goals. Click herefor more details about our Project Inspiration and Description.

4.Contribution

（1）Part Contribution：

This year we chose Pichia pastoris as a chassis organism to express our deinking enzymes and cellulosome components, and in order to have better expression in Pichia pastoris, we have done codon optimization on the sequences we used this year (BBa_K2155004, BBa_K2155007, BBa_K2155005 and BBa_K1830009) in the previous iGEM part library. In addition, we found that the sequence of one part (BBa_K3819012) of the iGEM16_NWPU team had a lot of terminators after importing into Snapgene, so we corrected it as well. And as the chassis organism we chose this year is Pichia pastoris, so we also have done codon optimization for yeast expression. Click here for more details.

（2）Yeast Handbook：

This year is the first time that Pichia pastoris has been used as a chassis organism in our school, and also the first time to use the eukaryote as a chassis organism. Since only a few members in the school’s existing laboratories have used yeast as a chassis organism, the guidance available is limited. Therefore, we tried to form a complete protocol by researching public information on the Internet and combining useful comments from some forums. However, there still exist many problems, such as low colony PCR efficiency, serious contamination of bacteria, low screening efficiency, and many false positives.

The good news is that we have produced a product of intellectual contributions! Yeast handbook was edited by UESTC-China and UM_Mucau, and seven teams participated. Without exception, when every team first started using yeast, they were once or more misled by protocols that were lack of implementation, unsystematic, incomplete, and even incorrect. Suffering from groping experience all the time, We found it difficult to obtain substantive project results. So we have summarized several teams’ experience from selection of strains, selection of plasmids, to design of plasmids, experimental protocols that have been revised many times, and some experimental problems we encountered and solutions. We have completed this handbook at the end of the competition, hoping to record iGEMer's personal experience with yeast so that the teams using yeast will avoid some detours in the future. Click herefor more details.

（3）Team Handbook：

This year we made a lot of effort in producing a work guide/ team manual that includes every aspect of an iGEM team, such as funds management, laboratory material management, laboratory safety manual, etc.You can see more details in the Contribution page.

（4）3D printer：

In the process of making hardware, in order to make our hardware more stable, we used 3D printing technology to make the bottom tube. They are placed under the guide rail to enhance the stability of the entire track system. If you want to learn more, you can click here.

Silver

1.Engineering Success

To realize in-situ regeneration of office waste paper, we apply biomethods on this field. At the same time, we are also facing numerous problems. After several surveying-imagining-designing-building-learning and redesign loops, we established DEINKER, a whole, integral, enviromental-friendly, safe and humanized system!

For gene, we successfully tranfected plasmids we designed into chassis and expressed our target proteins. During this, endonuclease EGL7, xylanase XynB and Lipase showed their enzymes' activity just as we have expected.

For biodeink system, we use commercial enzymes to help us create a brand new measurement, validate and provide information for our redesign. During this, we removed laccase from our design, set the concentration ratio of enzymes to reach the best deinking effect.

For measurement, we designed a scientific identification indicator after multiple iterations, for the absence of a universal measurement of non-pulping deinking efficiency. At the same time, we also solved two main problems: the force balance and what features we can accouts after several attempts.

For hardware, during the improving process of hardware, we have completed three iterations of hardware by the engineering design cycle, tackling problems including the large volume, the insufficient stability, the unsatisfactory drying effects and deinking effects, and the destruction of the integrity of the paper. By the way, the fourth generation is still under working..
Click herefor more details.

2.Collaboration

We are very surprised to find that we have collaborated with more than twenty 2021 iGEM teams. We hosted Southwestern iGEM Exchange Conference with Sichuan University, Xian Jiaotong University and Beijing University of Chemical Technology. And we took part in the online meet-up hosted by SZU-China. At this meet-up, we met many teams who used yeast as their expression vector, similar to ours. So we established Yeast Alliance, which provides a platform for these teams to communicate and cooperate with each other, and more than ten teams followed us. It was the best part of our collaboration. And then we hosted two meet-ups as founders of Yeast Alliance. The first one was a mini meet-up to discuss how to fill in safety form. And the other was Yeast Meet-up for teams to share protocols and problems. We communicated with CPU-China and then determined our partnership. Besides, we took part in a national outreach publicity campaign named ICII organized by CPU-China. Because Beijing 101ID also focused on paper, they interviewed us to know more about our project. We sent our cultural products to 14 iGEM teams in the name of Pen and Ink Grocery Store, which was inspired by the famous Japanese novelist Keigo Higashino's novel "The Unworrying Grocery Store" . And the response was enthusiastic. Click herefor more details about our Collaboration.

3.Human Practices

We have thought carefully and creatively about whether our work is responsible and good for the world. We have documented our team WIKI on how we have investigated these issues and engaged with our relevant communities, why we chose this approach and what we have learned. At the same time, our surveys followed scientifically valid methods which fulfilled iGEM's criteria. Click herefor more details about our Human Practice.

4.Proposed Implementation

First of all, we use synthetic biology technology to successfully realize gene pathways. After extensive reference, we have determined the technical route of our project according to the actual needs. Secondly, under the existing conditions, we have proved the possibility of project implementation in theory through modeling and algorithms. We have also made a preliminary risk analysis of entrepreneurship and formulated a series of response plans. Finally, we are making continuous progress on the road to practice and entrepreneurship. We hope that our project can finally realize its value. Click herefor more details.

Gold

1.Integrated Human Practices

Recycling office waste paper in situ is a comprehensive project involving many fields such as society, humanities, science, environmental protection and resource reuse. Therefore, we designed comprehensive human practice activities from 1. practical issues, 2. science and technology, 3. market industry and 4. policy and law, and strive to carry out work and influence in a broader human field.

A stepped questionnaire was conducted to help us better understand the problems and the consumer's needs. Then we visited producing and recycling sources of office waste paper and propagated our ideas. Also, Yeast Alliance's establishment and our communication with academic frontier researchers in China's paper industry helped the Deinker's design a lot. Writing a business plan and engaging in innovation competitions gave us confidence and suggestions, so we could iterate this project again and again. Click here to learn more details.

2.Improve an Existing Part

We have constructed a BBa_K3819066 part as the improvement of BBa_K2155004, and a BBa_K3819012 part as the improvement of BBa_K2155012. Click hereto see more details of our improved parts.

3.Project Modeling

In synthetic biology experiments, we genetically modify several enzymes that we add linker and Dockerin domains. We build mathematical models for protein structure prediction and molecular docking, which helps us intuitively and quantitatively solve the two problems: whether the enzyme activity can be changed after fusion and the scaffoldin structure has steric hindrance after connecting multiple proteins. Among them, we improved prediction models of existing protein structure to make specific predictions for the proteins we used. This contributes to guide experiments in synthetic biology. Click herefor more details.

It's easy to tell how many words and pictures are on a piece of paper, but it's hard when it comes to ink. Therefore, aiming at the hardware system design, we built a model to accurately identify ink and assist hardware tracking deinking. This model greatly improves the scalability and generalization of hardware functions. The model faces the possible future of various types of paper with autonomous learning ability, freeing hardware from the shackles of human experience. Click herefor more details.

4.Proof of Concept

We have proved the feasibility of paper Deinking by biological method in situ and put the concept of the Deinker machine into practise.

For experiment, we have succesfully proved that endoglucanase EGL7 ,xylanase XynB and lipase Lipase have satisfactory enzyme activity in our lab, Click herefor more details about our Collaboration.

And in De-inking Efficiency Validation, single-enzyme experiment tells us the most important biological enzymes in deinking for example cellulase and xylanase have significant effects in deinking, while laccase's behavior is not as well as we expected. Click herefor more details.

For modeling, it supports our experiments by offering theoretical basics, which include four aspects:
1.Proposing an ink residue count method to judge ink's amount;
2.Establishing a model of "Computer Vision Completed Ink Recognition" to recognize ink dots;
3.Constructing the spatial structure of proteins we design and carrying out molecular docking to prove our parts function;
4.Building a Deinkers Location Decision-making model to decide Deinker's deployment.
Click here for more details.

For Hardware, we have successfully produced our hardware which can complete paper deinking in situ after three iterations by 3D printing technology, embedded development technology, electronic design technology, automation technology and synthetic biology technology. To be specific, this machine can remove the surface fiber from paper after enzymes' reaction and specific physical means. In terms of environmental protection and machine's volume, our equipment is a better than other solutions on the market. In addition, we decide to improve several aspects such as system stability, volume and power consumption, and add new functions such as point-to-point deinking, intelligent control, Internet of Things, etc. We believe these improvements can make our equipment truly enter people's lives. Click herefor more details.

For Human Practices, we tried our best to understand the key problem: what is in-situ regerneration of office paper means, and launched tailored work in four aspects: 1. pratical problems, 2. science and technology, 3. market industry and 4. policy and law. After months of hard work, we have a better understanding of what Deinker should focus on, and we iterated our design again and again. Also, we have made a lot of friends and spread our effect to the wider world.Click here to learn more details.

5.Partnership

Among all the happiness, friendship is the most important. We are fortunate to have CPU-China as our partner while preparing for the competition. Not only do we have a long and continuous interaction in the experiment, but also we have a lot of social communication. We have shared protocols, helped each other to design experiments, found experts to solve problems together and sent parts to each other. We will cherish this friendship for a long time. Click herefor more details about our Partnership.

6.Education & Communication

To determine the type of materials we produce, we research in communities, offices and recycling stations, which helps us to know the status of paper using and recycling. Then we did requirement survey in all walks of life to find our target user and their willingness to use our product. In order to improve our project design, we communicate with a number of experts in related fields and obtain a lot of valuable suggestions for reference. To get more people to accept our projects and concepts in the future, we have designed a series of educational activities to publicize our project knowledge. Click here for more details about our Education & Communication.

7.Excellence in Another Area

We are not reconciled to make the idea of recycling office waste in situ be some files locked in a filing cabinet. Through entrepreneurship, we set the goal of our project to make office waste paper recycled in situ, and make the conception of efficient and environmentally friendly office experience be recognized and accepted by more people. It can be a quite meaningful and interesting work. To complete the business, we first conducted a stepped research. Through these hierarchical research activities, we contacted a wide range of interested parties, learned about the current facts and their needs and introduced our ideas to them. We even received high praise from government officials, and further carried out an interview with them. The business plan is a guide to the actual implementation of a project. We wrote a business plan, participated in a number of entrepreneurial competitions, received a wide range of market suggestions and even received several large bonuses. We also communicated with experts from commercial and academic circles. While receiving marketization and productization suggestions, we also received many affirmations for our project. Click herefor more details about our Excellence in Another Area.

Special Prizes

1.Best Education

This year, UESTC-China are ready to do something different. We first designed a series of activities related to waste paper recycling. It arouses a great response on campus and successfully spreaded our project concept. Then we partnered with Beijing 101ID to bring the history of paper to remote areas. Now let's come to the most surprising activity: "Science not Silence"! We believe that science is not composed of cold numbers or rigid formulas, but could be presented more colorfully. Just do it! Click herefor more details about our Education.

2.Best Integrated Human Practices

Human-centered project is the one that really benefits human-beings. There is no doubt that we have a good grasp of this key point. The train of thought while promoting integrated human practices of our project is very logical. We divide our integrated human practice into four parts, along the lines of what a complete project needs to achieve. They are: 1.practical problems, 2.science and technology, 3.market industries and 4.policies and laws. Understanding the practical problems can help us recognize it in the world directly. Science and technology are tools to improve the world. The market industry is the environment in which projects sprout and grow. Policies and laws are the framework of the operation of society. All of the activities that we design with these ideas in mind make our projects more complete. Click herefor more details about our Human Practices.

3.Best Hardware

Our goal is to design and build a hardware device that can automatically apply enzyme solution or bacteria solution to solid materials. After three iterations of updates, we have obtained a hardware device in our project that can automatically complete the application of deinking enzyme solution on paper and realize the entire process of deinking. We have realized the combination of our hardware with enzyme solution in our project. The result shows that it can meet our requirements. Our device is actually a platform. Through the replacement of this module, it can realize the automatic task that any enzyme solution or bacteria solution can apply to the solid matter. We are firmly convinced that other teams can use our platform for their projects. To help other teams quickly build their own devices, we have made most of our hardware models available for download.

Our hardware also demonstrates the commercialisation potential of our project to really bring synthetic biology into people's lives and realize the concept of in-situ deinking. To achieve this, we are continuously designing a new generation of device that is closer to the commercial version so as to bring our ideas of synthetic biology into people's lives and make problems closer to the reality. Click herefor more details about our Hardware.

4.Best Model

Unlike most other teams who conduct modeling primarily in synthetic biology, we combine modeling with experiment, human practices and hardware in order to give our project a higher degree of unity and integrity. We improved the protein structure prediction model according to the characteristics of our project, then designed a high precision and autonomy ink recognition model for deinking processes. At last we provide a solution for location decision-making to deinkers in the city. Each part is improved under the guidance of modeling. At the same time, we try to use simple and plain language to describe our model, so that anyone who does not understand mathematical modeling can understand what our model has done. Click herefor more details about our Model.

5. Best Supporting Entrepreneurship

We are not reconciled to make the idea of recycling office waste in situ be some files locked in a filing cabinet. Through entrepreneurship, we set the goal of our project to make office waste paper recycled in situ, and make the conception of efficient and environmentally friendly office experience be recognized and accepted by more people. It can be a quite meaningful and interesting work. To complete the business, we first conducted a stepped research. Through these hierarchical research activities, we contacted a wide range of interested parties, learned about the current facts and their needs and introduced our ideas to them. We even received high praise from government officials, and further carried out an interview with them. The business plan is a guide to the actual implementation of a project. We wrote a business plan, participated in a number of entrepreneurial competitions, received a wide range of market suggestions and even received several large bonuses. We also communicated with experts from commercial and academic circles. While receiving marketization and productization suggestions, we also received many affirmations for our project. Click herefor more details about our Entrepreneurship.

Track Awards

Best New Application Projects

Deinker is a brand new application, where exactly is it new? From our aspect:

It is a new concept: office waste paper regeneration in situ is a valuable renewable resource, which can be used in paper factories for paper making. Using waste paper as the raw material of paper making can greatly reduce resource wasting and environmental pollution. However, according to our research, office waste paper is difficult to enter the paper circulation, for the reason that office waste paper recycling situation is not optimistic. Considering the recycling characteristics of office waste paper and the needs of office people, we put forward the concept of office waste paper regeneration in situ, which can advocate the simultaneous recovery, treatment and reuse of waste paper directly.

It is a new equipment: is a machine that combines biological technology, electronic design, automation equipment design, mathematical modeling, and other technology. It can realize the safe, low-cost and efficient paper deinking and regeneration process in office.

It has new biological technology: is the first time that cellulosome system is introduced in the deinking field.

Click here for more details about our Proof of concept.

Final Result

In this year's competition, our team won the gold medal and was nominated for Best New Application Project and Best Supporting Partnership Project.

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