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As an interdisciplinary branch of biology and engineering, synthetic biology has been widely used in many different areas and is relative to everyone. However, because of the enlarging gap between the public and synthetic biology, which is mainly caused by the public’s misconception and lack of knowledge on the subject, we find it hard to popularize, let alone getting more people involved in it. In this context, we think that iGEM presents to us a great opportunity to try our best to fill the gap and set up a bridge between the public and synthetic biology. To make our human practice work better targeted, we divided the audience into three groups: children, students, and general public. For children, we want to help them to realize the captivation of science and stimulate their interest in biology. For students, we focused on encouraging them to explore and participate in some real work in the field of synthetic biology. For the general public, we considered more about eliminating their misconceptions as well as inspiring them what can be achieved through synthetic biology to make the world a better place. So, to them, we mainly talked about the basic knowledge and concepts of synthetic biology research, and showed them some of the achievements across the years.
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The final product of our system is an in vivo library of the target sequence carrying different versions of mutations. Researchers can then continue to implement the selection process directly using this library, enabling the continuous evolution of our target towards its desired function. Moreover, as bacterial cells can express multiple genes in a polycistronic transcript, our system has the ability to evolve a series of genes at the same time, which opens up possible application in whole metabolic pathway evolution. The nature of our target sequence can be either protein or RNA, allowing for mutation library construction of a broader range. Our system also has the advantage of using parts orthogonal to native bacterial systems, thus could be applicated in various prokaryotic hosts.
 
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At the beginning of our project, we found that we had no clue about how to start our Human Practice work. That’s how we realized that the conduct of previous teams is a valuable source of inspiration. Although the track they chose may be different, the goal of Human Practice has always been to reach out to more people and make a difference with your project. Thus, we compiled two guidebooks, one on Education and Public engagement, and one on Integrated Human Practice. We shared our guidebook with other teams and asked for their suggestions. In doing so, we hope to offer guidance to future teams on how to carry out Human Practice.
 
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Here we present you our two Guidebooks. For Education and Public Engagement, we mainly focused on how to inspire public interest in synthetic biology targeting different groups of people.
 
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What can we do to get children involved in biology? To answer this question, we chose to work with Shanghai Jiuqian volunteer club, a voluntary association in our university devoting to providing long-term education support for migrant children. They showed a great interest in promoting biology. We cooperated with them in purpose of guiding children to excavate the fun of biology through motivating their creation and imagination.
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Through application of our system, researchers would be able to evolve enzymes towards higher efficiency, higher precision and novel functionality, or to evolve metabolic pathways towards more balanced function, less toxic to host cell and higher total yield, or to evolve different functional RNAs. In addition, the mutagenesis system could be applied in different prokaryotic hosts.
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<div class="col">Environmental resistance</div>
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<b>Workshop for migrant kids with volunteers from Shanghai Jiuqian volunteer club</b><br />
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On October 6th, members from our team and their association held a public class for children aged nine to fifteen together. To start with, we asked how they think of biology. We found that most of them understand biology as macro-level creatures like animal and plants. Then we introduced to them the basic knowledge of DNA structure and function, and showed them a DNA model which can be taken apart and reassembled. Afterwards, we invited them to build their own DNA model. One of the kids expressed to us that how amazing it is that such a small and simple molecule can play such an important role in maintaining and shaping our lives. We then gave a brief introduction of synthetic biology and held a discussion about what can be achieved by it. To our surprise, the perspectives they have about synthetic biology are so different and innovative that we were also inspired by them. One of them compared synthetic biology to a 3D printer which can create whatever you want by precise design and programming. They also proposed that synthetic biology can be very useful in medical field.
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Enzyme function greatly relies on stable and fitting environment. A small change in environmental factor such as temperature, pH, osmotic pressure or metal ion concentration could greatly affect the activity of a certain enzyme. The native environment is often moderate and cannot meet researchers’ divergent needs. Researchers have been applying directed evolution methods in generating enzymes which could function under their desired conditions, for example, heat-resisting enzymes. Employing our system could easily and efficiently create a mutation library that can be used for further selection.  
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Our team and Jiuqian association both felt that the workshop is a mutually beneficial activity, and decided to establish a long-term collaboration between us.  
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Nature provides us with proteins exhibiting an almost endless diversity of functions. But we often find them acting less to satisfactory in heterologous systems or when our need exceeds the output of the native system. To meet our needs, we could associate the mutagenesis output with selection pressure such as antibiotic resistance, and only those who performs best will be able to survive. After gradient increase of selection pressure, the protein construct with highest efficiency can be easily selected out.
 
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It is always easier for people to get involved and learn new things when are playing and enjoying themselves. When considering what can be done to stimulate students’ interest in synthetic biology and make it a fun thing to learn, we thought of board game. When we first set our sights on board games, we were impressed by its slogan: Everything is a board game. Numerous areas can be combined with board games including but not limited to education, careers and life. We regard it a perfect medium to introduce our system design and popularize synthetic biology among students.  
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Off-targeting and crosstalk are not uncommon even in heterologous systems, let alone the complex intertwined relationship of proteins within the native system. To minimize or even eliminate crosstalk, researchers could employ our system to generate diverse mutations, and add selection pressure to obtain the desired result.
 
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To design a board game which can both be fun and educational, we held a brainstorm and came up with three prototypes. The first one is called Gene Expression War. Every player in this board game is an “E. coli”. Each E. coli will try its best to fully accomplish the travel of genome, and during this process it will utilize the function cards to express various proteins and gain the product cards to help itself to accelerate its journey or block other E. coli. The rules may seem easy to understand, but the overall design lack of scientific rigor and entertainment. We abandoned it after many unsuccessful revisions.
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In our effort to create orthogonal systems, expanding our genetic code, producing proteins with non-canonical amino acids, or generating novel compounds, researchers are in need of enzymes which does not exist in nature. Similar methods have already been used in generating orthogonal aminoacyl-tRNA synthetases, orthogonal ribosomes, and novel compounds such as organosilicons.  
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Our second prototype is based on co-culture and expression competition. By randomly drawing cards, players will be able to put different parts on a basic plasmid vector, including improved promoters, origin and various functional genes. Under the limitation of culture medium and the bacteria burden, players will compete with each other. The one who can produce most proteins and energy is the winner. However, this version is so complicated that we are still working on it and we truly hope to finish it in the future.
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Our system is our sword penetrating the wall of natural world, through which we could not only take a glimpse, but also take a tentative step out and embrace the vastness of unknown. The existing world has its limitations, but out imagination does not, through in-lab evolution, we’re turning imagination into reality.  
 
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And here is our final prototype called Bio Mahjong Cards. It is succinct and quite easy to understand, based on a traditional board game in China: Mahjong. The goal of Mahjong is to collect special melds with different tiles, which is much like using different parts to construct a biological system. For detailed introduction, please visit our Boardgame Page.
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On June 1st, we delivered a lecture to high school students from Jiading No. 2 Middle School. As they are students of high school who already have some basic knowledge in different subjects such as mathematics, chemistry and biology, we believed that we should center our lecture around that synthetic biology is a new interdisciplinary area, and that it involves applying engineering principles to biology. Thus, not only students majoring in biology, but also others who are interested in relevant subjects such as engineering, are welcomed to participate in iGEM. Even if you’re from a less academic background, you could take part in it by conducting the work of human practices. By introducing iGEM to them, we hope to get them involved in next year’s competition.  
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Bacteria is a rapidly developing factory for biological and chemical synthesis. It is common for researchers to transfer multiple enzymes or even whole metabolic pathways at one time into the engineered bacteria. However, heterologous expression is often met with problems regarding metabolic pathway interference and differed expression profile in nonnative host. Our system could mutate a sequence of a relatively long length (~10 kb) due to the outstanding processivity of our reverse transcriptase. Since our target sequence can be transcribed as a whole into RNA and go through the cycles of mutagenesis, no matter this sequence encodes protein or functions as regulatory component, our system has the potential of evolving full metabolic pathway together.
 
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In the lecture, we introduced synthetic biology from the basic concepts to its forefront applications, hoping to present an overview of synthetic biology to our audience. We also shared with them some basic experimental skills and our experience in laboratory. We believed that this could both be of great help in bringing them closer to synthetic biology and revealing how it is actually like to work in a laboratory.
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As for students from high schools who showed great enthusiasm in biology, we joined them in a Biology Summer Camp and held a seminar of synthetic biology on July 19th. Hosting over 300 students from 30 different high schools around China, the summer camp was a perfect approach for us to get access to students from wider areas. During the camp, we shared our experience of working on synthetic biology and iGEM with them. In order to give them a concrete idea of synthetic biology and our project, our team members shared their first-hand experiences in lab research and iGEM participation. After that, we gave a short presentation of our project, hoping to inspire them to come up with their own innovative ideas. Moreover, we had a more thorough conversation with students who showed specific interest in synthetic biology after the presentation. To our surprise, they brought up some creative ideas and new interpretations of our project.
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The nature of target sequence can vary. Apart from proteins, functional RNA can also be our target of mutagenesis. Cellular RNA has varied functions, including miRNA and riboswitch, both which are commonly used in synthetic biology. The RNA sequence could be inserted in the place of target sequence and be transcribed, then go through mutagenesis cycles of reverse transcription and recombination, which would output a mutation library of the RNA target. By utilizing our system, a mutation library of miRNA and riboswitch could be easily generated and be tested in later experiments.
 
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We also held a workshop with students from BIOS (Biology Intensive Orientation Summer) summer course. BIOS is a course for students with high interest in biological research and aims to cultivate their lab skills.We believed that the students have already possessed the capability of starting their own work in synthetic biology. What they need is just an idea and some inspiration. On July 30th, our team hosted a workshop with students from BIOS to introduce iGEM and our project to them. We also invited them to join in next year's iGEM competition. In the workshop, we delivered a presentation to introduce of the summary and experimental details of our project, through which we hope to excite the formation of new ideas.  
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In our Integrated Human Practice, we interviewed Prof. Chen Ling, who expressed great interest in our system and conveyed to us that our system could be used in library construction for AAV’s capsid protein. The constructed library could be later used to generate gene delivery vehicles of enhanced function.
 
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On August 16th, we invited Prof. Hal Alper to deliver a lecture about his recent research. (We also had a brainstorm session with Prof. Alper, details can be found in our <a href="https://2019.igem.org/Team:Fudan-TSI/Integrated_Human_Practice">Integrated HP</a>.) Dozens of undergraduates from our university attended this lecture, hoping to learn more about synthetic biology as well as system biology. During the session, Prof. Alper talked about his work on bioengineering and directed evolution, which is very inspiring to us.
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Prof. Alper also held a Fireside with other biology-majored students. Fireside session is a tradition of Fudan University, during which the invited professor would share his research experience and answer students’ questions regarding life choice and research.
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We found through careful examination that this failure is due to problems with our plasmid construct, so we moved the RT to another tested plasmid, and through SDS-PAGE, verified its successful expression (Fig. 4).
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Before trying to popularize biology to general public, we carried out a questionnaire survey in order to have a preliminary understanding of the average level of biological knowledge among the general public. In the questionnaire, we first designed questions to collect some basic information of our respondents for further analysis. Then a few questions like ‘Have you ever heard of gene?’ were asked to evaluate the respondents’ level of basic biological knowledge. In the end, we asked some questions about synthetic biology and iGEM. Even though we know that the misconception between public and biological research has existed for a long time, the result showed that their current understanding of biology is even below our expectation. Over 97.85% respondents have heard of gene but most of them learned it from hot topics like GMF (genetically modified food). Only 50.77% are aware of synthetic biology. This indicates that there is still a long way to go for the promotion of synthetic biology and elimination of misunderstandings. The development of biology requires the understanding and acceptance of the public as the fertile soil for its growth, we hope that through our effort, we could contribute to this process.
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To start with, we designed a pamphlet of synthetic biology. Our first edition was distributed to student of different majors in our school. We collected their feedback to improve our pamphlet before we distributed to the general public to make it more attractive and easier to understand. Considering that our target audiences lack specialized knowledge, we tried to avoid using professional terms, and made our statement as concise and clear as possible. In order to promote understanding, we also added some examples about how synthetic biology enhanced our daily life in various aspects including food, medicine and fuel. We believed that by reading this pamphlet, people could learn some basic knowledge about synthetic biology in a short time. And we hope this could encourage the public to think further about biology and to get more involved in it.
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In parallel with popularizing synthetic biology, we also dedicated our effort to shortening the distance between the public and the scientific researchers. The most direct way is to reveal the daily work of the researchers to the public. PCR (Polymerase Chain Reaction) is a basic molecular biology technique and is widely used in biology laboratories. Thus, we chose the demonstration of PCR as a window to show the public how the daily work in laboratory is like. Collaborating with students majoring in journalism, we took two vlogs, one records the main steps of PCR while another is about BioArt and uploaded them to the internet platforms such as Bilibili. By 21st October, our video had been viewed more than 370 times. We hope that through the propagation of simple experiment procedures, the public would be amazed to see that such elaborate demonstrations and such important theories all originate from adding up such ‘simple’ experiments.  
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In our system, we utilized parts that are orthogonal to native prokaryotic systems. The reverse transcriptase is of mammalian origin, and the priming tRNA sequence is orthogonal to that of prokaryotes or could be modified to align the target directly as the user wishes. Cre recombinase is originated from bacteriophage P1 and already widely applied in prokaryotic engineering. Our system has the ability of functioning in different bacteria and could enable directed evolution in different host species in parallel. This ability to build and test the target within the same system greatly increases the efficiency of desired part selection.
 
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Revision as of 23:37, 21 October 2019

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Team:Fudan-TSI/Public Engagement

The final product of our system is an in vivo library of the target sequence carrying different versions of mutations. Researchers can then continue to implement the selection process directly using this library, enabling the continuous evolution of our target towards its desired function. Moreover, as bacterial cells can express multiple genes in a polycistronic transcript, our system has the ability to evolve a series of genes at the same time, which opens up possible application in whole metabolic pathway evolution. The nature of our target sequence can be either protein or RNA, allowing for mutation library construction of a broader range. Our system also has the advantage of using parts orthogonal to native bacterial systems, thus could be applicated in various prokaryotic hosts.
Through application of our system, researchers would be able to evolve enzymes towards higher efficiency, higher precision and novel functionality, or to evolve metabolic pathways towards more balanced function, less toxic to host cell and higher total yield, or to evolve different functional RNAs. In addition, the mutagenesis system could be applied in different prokaryotic hosts.
Environmental resistance
Enzyme function greatly relies on stable and fitting environment. A small change in environmental factor such as temperature, pH, osmotic pressure or metal ion concentration could greatly affect the activity of a certain enzyme. The native environment is often moderate and cannot meet researchers’ divergent needs. Researchers have been applying directed evolution methods in generating enzymes which could function under their desired conditions, for example, heat-resisting enzymes. Employing our system could easily and efficiently create a mutation library that can be used for further selection.
Higher efficiency
Nature provides us with proteins exhibiting an almost endless diversity of functions. But we often find them acting less to satisfactory in heterologous systems or when our need exceeds the output of the native system. To meet our needs, we could associate the mutagenesis output with selection pressure such as antibiotic resistance, and only those who performs best will be able to survive. After gradient increase of selection pressure, the protein construct with highest efficiency can be easily selected out.
Higher precision
Off-targeting and crosstalk are not uncommon even in heterologous systems, let alone the complex intertwined relationship of proteins within the native system. To minimize or even eliminate crosstalk, researchers could employ our system to generate diverse mutations, and add selection pressure to obtain the desired result.
Novel function
In our effort to create orthogonal systems, expanding our genetic code, producing proteins with non-canonical amino acids, or generating novel compounds, researchers are in need of enzymes which does not exist in nature. Similar methods have already been used in generating orthogonal aminoacyl-tRNA synthetases, orthogonal ribosomes, and novel compounds such as organosilicons.
Our system is our sword penetrating the wall of natural world, through which we could not only take a glimpse, but also take a tentative step out and embrace the vastness of unknown. The existing world has its limitations, but out imagination does not, through in-lab evolution, we’re turning imagination into reality.
Metabolic pathway
Bacteria is a rapidly developing factory for biological and chemical synthesis. It is common for researchers to transfer multiple enzymes or even whole metabolic pathways at one time into the engineered bacteria. However, heterologous expression is often met with problems regarding metabolic pathway interference and differed expression profile in nonnative host. Our system could mutate a sequence of a relatively long length (~10 kb) due to the outstanding processivity of our reverse transcriptase. Since our target sequence can be transcribed as a whole into RNA and go through the cycles of mutagenesis, no matter this sequence encodes protein or functions as regulatory component, our system has the potential of evolving full metabolic pathway together.
RNA
The nature of target sequence can vary. Apart from proteins, functional RNA can also be our target of mutagenesis. Cellular RNA has varied functions, including miRNA and riboswitch, both which are commonly used in synthetic biology. The RNA sequence could be inserted in the place of target sequence and be transcribed, then go through mutagenesis cycles of reverse transcription and recombination, which would output a mutation library of the RNA target. By utilizing our system, a mutation library of miRNA and riboswitch could be easily generated and be tested in later experiments.
Adenovirus associated virus (AAV) library
In our Integrated Human Practice, we interviewed Prof. Chen Ling, who expressed great interest in our system and conveyed to us that our system could be used in library construction for AAV’s capsid protein. The constructed library could be later used to generate gene delivery vehicles of enhanced function.
Multi-host directed evolution
In our system, we utilized parts that are orthogonal to native prokaryotic systems. The reverse transcriptase is of mammalian origin, and the priming tRNA sequence is orthogonal to that of prokaryotes or could be modified to align the target directly as the user wishes. Cre recombinase is originated from bacteriophage P1 and already widely applied in prokaryotic engineering. Our system has the ability of functioning in different bacteria and could enable directed evolution in different host species in parallel. This ability to build and test the target within the same system greatly increases the efficiency of desired part selection.