General Description

What is life?

This is an esoteric topic, and in iGEM competitions we often try to solve some topics related to life by means of synthetic biology, we tend to focus on the more microscopic areas of life, but the subject of life is with everyone throughout their lives, when we try to convey to the public some of our understanding of life and synthetic biology, the first thing we need to do is to understand "What is life?" in more people's eyes.

In this year's topic, we tried to develop EcN as a platform that can be regulated using erythritol, a sweetener commonly found in nature and also added to a variety of foods, and such an interesting topic gave us inspiration for another part of the topic about education - sugar.

Therefore, when we decided on this year's topic, the theme of education was also determined, and we started a series of educational activities with the key words "life" and "sugar" as the core.

However, we are concerned that in today's society, both students and many professionals are facing more stress in their lives than in the past. Insomnia, anxiety, and other negative words are often associated with our lives, so in this section of education, we hope to convey the value of "life is sweet" to the society, hoping that people can face the tasks of life with ease, and even in the face of stress, and they can choose the appropriate way to cope with difficulties, so that they can lead their lives in a more relaxed way. Setting this concept as the core, we hope to have a two-way dialogue with society through a variety of formats, in order to convey the knowledge related to life science and synthetic biology to more people.

6000+

Participator

700h+

Total Duration

20+

Form

Activities

We hope to involve more people in our education by organizing a variety of activities, and the context and opportunity of the activities are our main focus. We hope that more people can enjoy the festival and culture while participating in our activities and learning about synthetic biology related to our topic this year.

Communication with schools

1. Inspiration

In our group, basically all the second to third year college students, during the summer experiment in the lab, had asked the question, "Do you remember your own view of life as a child?" Surprisingly, we had a discussion that lasted a long time. People talked about their experiences learning to ride a bicycle as a child, the first time they went to the zoo and were so happy that they were overwhelmed, the first time they did a chemistry experiment and were amazed at the results, and many, many precious moments ......

Such an unintentional discussion gave us a good inspiration for our educational activities. As we grow up, we are constantly exploring new knowledge, and at the same time, our perceptions of life are constantly changing. An idea immediately came to us that we wanted to talk to children of different ages, to ask them what life is like in their eyes, and to explain something that is relevant to their age and to the social context in which we live.

2. Innovation

We hope to plant a seed of scientific research in the hearts of children of all ages through the educational activities on campus. During this period, we actively communicated with experts in the field to understand the general character traits of children of all ages and what interests them at that age, and these suggestions were very important in guiding our design. Combining the suggestions from pedagogical related fields and our own ideas, we designed nearly ten different types of souvenirs. For kindergarten children, we designed simpler puzzles and some beautiful keychains, taking into account the safety of the material, we blunted all the edges when making the keychains and used a safer acrylic material. For the elementary school students, we designed a slightly more difficult puzzle, as well as some very practical sticky notes for study. When we headed to high school, we chose USB flash drives for high school students. Since high school generally faces greater study pressure, we also made mugs with the panda logo, hoping they would study hard while also paying attention to their physical health and developing a sound physique.

3. Solid content, rich format and meaningful feedback

We also made a lot of plans for the content of the lecture, and discussed with many school teachers to determine the specific content of the lecture. For example, for kindergarteners, they are generally very good at interacting with each other, and at the same time, they are not very receptive to written information, so when we conduct educational activities with kindergarteners, we adopt more of a game format, hoping to reap the effect of fun and education. Therefore, we hope to design a prize exchange program to stimulate their desire to win and to interact better in the classroom. ...... All in all, we focus on the age of the educated group when conducting educational activities on campus and do our best to achieve better educational results. In the next section, we will also present further details of the educational content for each age group, and we will upload some pictures of the communication process to share the joy with you, and, thanks to the excellent progress we have made on social media this year, we have also made videos of the narratives and activities, with English subtitles, in the hope that all those who visit our pages will be able to access some useful resources, and it is our wish to pass on some useful knowledge on a wider scale.

3.1 Kindergarten

For the kindergarten children, we planned four games, hoping that through the interactive format, children can have a preliminary understanding of some basic concepts related to life and realize that the conception of life is a magical and interesting thing.

First of all, there is a leaf matching competition.Each child was given a leaf, and the teacher would introduce the name and main characteristics of the leaf. The children had to remember the name and characteristics of the leaf , and they need to match with a friend who had the same leaf and repeat the name and characteristics of the leaf they had. This activity was designed to help kindergarteners learn teamwork after learning the teacher's introduction to leaves, as well as forming an initial understanding of the plants represented by leaves.

The next activity was animal sketching, where each child was given a piece of white paper with four circles and a marker. The children were required to add each circle into a complete cartoon pattern through the teacher's demonstration. The purpose of this activity is for the children to form an initial understanding of animals represented by frogs and snails by using their imagination to make a complete animal cartoon image out of a circle.

Then comes Healthy Eating Monopoly, where the teacher first divides the children into two groups, A and B. Two groups will decide who will roll the dice first by finger-guessing game, and then every student advances on the map by the number of steps according to the number each student dices. After advancing to the designated position, they need to complete the corresponding tasks according to the map instructions. The activity was designed by referring to the popularization of science from a professor of the nutrition department of West China Hospital of Sichuan University and Monopoly basic play rules, and we designed a Monopoly line (25 frames) for children to practice on it personally, to understand some common dietary tips, and then form the correct perceptual cognition of diet.

Finally, there was a protein translation challenge, where each child held four types of letter cards, A/T/C/G, and paired them with two other children to form a group, arranged them in a certain order to form a string of three letters, checked the amino acids corresponding to the string against the amino acid translation table, and finally speak out the names of the corresponding amino acids loudly, and the teacher would give everyone a small card as a reward after confirmation. This activity is difficult for kindergarteners, but we hope that in the process of participating in this activity, kindergarteners will develop a basic rational understanding of biology.

Feedback:

We recorded these activities as fun demonstration videos with our elaborate animations and posted them on our social media platforms, so that more kindergarteners could participate in our educational activities through these fun science fiction, during which we received a lot of feedback from parents of kindergarteners. Initially, we were worried whether the kindergarteners could complete the task of matching amino acids according to base order, which seemed very challenging to them, but to our surprise, the children were very interested in this activity and the matching results were very accurate. When we asked the children if they understood the reason why we need to wear masks in public places in the past few years, basically every child could answer that it was due to the COVID-19 pandemic outbreak, and when we asked them if they knew that the New Coronavirus itself is a virus, a few children could even tell the difference and similarity between the virus and other microorganisms. This feedback was very surprising and also pointed the way to improve our educational content.

3.2Primary School

In order to create a healthy diet for elementary school students and to clarify the dangers of eating too many sweets, such as dental caries, obesity, diabetes, and the effects on growth and development, we conducted lectures on "The Dangers of Eating Too Many Sweets" in many elementary schools.

Our presentation started with the story of Chenchen's addiction to sugar and ended with the question of why eating sugar is addictive. We explained the problem from two aspects, one is the lack of self-control and the other is the brain's dependence on sugar.

Next, we described the various dangers of excessive consumption of sweets. The first harm is to cause tooth decay. Dental caries is a kind of oral disease in which the tooth tissue is decayed and gradually destroyed and disintegrated to form cavities. The caries of tooth tissue occurs under the interaction of three factors, such as microorganism, food and host, and the main process is that Streptococcus pyogenes, certain Lactobacillus and Radiation Bacteria encounter sugar in the oral cavity, so that the sugar ferments and produces acid, and the acid will slowly corrode the teeth. To help students understand acid production by fermentation, examples such as fermentation with lactobacilli to turn milk into yogurt and rice going rancid when left at room temperature for a long time in summer are given.

The second danger is that it leads to obesity. Excess sugar is converted into fat in the body, and the accumulation of fat leads to obesity. We introduced the concepts of sugar and fat, expanded the definition of sugar to include carbohydrates, and distinguished between sugar with a sweet taste and sugar without a sweet taste, using the example that chewing a steamed bun will give you a sweet taste. Then, the relationship between sugars and fats in the body for energy supply is described. Simply put, the body prefers sugar as "fuel", first breaking it down into glucose, and then "burning" the glucose to provide energy. The excess glucose is then transported to the liver and muscles where it is converted into a compound called glycogen. Since the body has a limited amount of glycogen to store, excess glycogen is converted into fat, and only after the body's glycogen reserves are depleted does the body begin to use fat as its primary fuel. The purpose of describing this biochemical process is to show students that losing weight is not an easy task.

The third hazard is the impact on growth and development. It is first clarified that the hunger sensation is regulated by blood sugar and is a sensation in the nerve center, not a feeling that the stomach is empty. Then tell the students that eating sweets before meals will make the blood sugar rise, leading to a reduction or disappearance of hunger, which in turn will reduce the amount of food eaten, and eat less and unbalanced nutrition is prone to poor growth and development. The last hazard is diabetes. We briefly describe the process of insulin secretion and regulation. Insulin is a hormone secreted by the pancreas in the human body. Normally after eating, our blood sugar will rise. When everyone's blood sugar rises, the pancreas receives the signal and secretes insulin. Insulin promotes the uptake and utilization of glucose and the conversion of glucose into glycogen, thus coming to lower blood sugar. Then, we told the students that diabetes is caused by the problem of insulin regulation and mentioned the typical symptoms of diabetes: three more and one less.

After talking about the dangers of eating too many sweets, we came to the next topic - healthy eating. Considering the advanced food industry nowadays, we will focus on finding relatively healthy foods from a wide range of products. Therefore, students will be taught to read the "ingredient list" and "nutrition facts" first. The key to the ingredient list is that the higher the ranking, the greater the amount added. By doing this we can see if there are any ingredients in the front of the list that are not suitable to eat more. In addition, we have to look at the ingredients and try to choose a clean ingredient list; to reduce the intake of synthetic sugar substitutes, such as aspartame, sucralose, acesulfame, etc.; and to refuse the intake of trans fatty acids. The first column shows the names of the main nutrients, protein, fat, carbohydrate, sodium and energy; the second column shows the amount of each nutrient per 100g (ml) of food; the third column shows the percentage of nutrients per 100g (ml) of food to the body's daily nutrient requirement.

In order to consolidate what the students have just learned, we conducted an interactive quiz by first showing a picture of a food and asking the students to raise their hands to answer whether the food is healthy or not and give reasons, and after the students finished answering, we showed the ingredient list or nutrient list of the food and gave reasons for its health or not. Among them, sports drinks like Pulse, many dairy drinks such as yogurt drinks, lactobacillus drinks, ketchup, barbecue sauce and dried meat and dried fruit were included as unhealthy foods because of their high sugar content. Processed cereals are also classified as unhealthy because of the destruction of dietary fiber and high sugar content. In contrast, milk, yogurt with simple ingredients, fresh fruit, meat with few processing procedures and plain cereal are classified as healthy foods. To prevent students from unknowingly consuming too much sugar, we offer three suggestions: the first suggestion is to eat more natural foods; the second suggestion is to try to buy and cook your own food; and the third suggestion is to look carefully at the ingredient list when buying packaged foods and try to choose products with fewer types of added sugars.

Feedback:

We went to many elementary schools in Chengdu and talked to the local children. The elementary students were always very enthusiastic about the interaction in the classroom. The most surprising result was that most of the children asked us about "weight loss" and they were very interested in the healthy diet we talked about in the class. He said he was often stressed about his weight and had thought about dieting to lose weight, but his mom and dad didn't approve of it, and deliberately not eating led to a poor performance at school, and he also talked about how he was often teased by his classmates because of his size, and he hoped we could give him some useful advice.

We first explained to him the definition of beauty, that we didn't want him to feel inferior because of his weight at such a young age, and that he should be confident in himself, and that health is the most important asset, and we also analyzed with him the problems of his current eating habits and recommended to him a diet that is low in calories but can meet the energy needs of a fast growing teenager.

We were so inspired by this incident that, on the one hand, when we went to elementary school to educate them about healthy eating, we also included some relatively emotional content. We hope that the students will not feel inferior because of their body shape, but will pay more attention to their health and not affect their growth and development at this age just for the sake of losing weight, and this incident also provided inspiration for our software design.

3.3High School

In the high school section, our educational content contains two topics. One topic is the popularization of the classification and design of vaccines in the context of the global pneumonia epidemic, and the other topic is the popularization of machine learning, using AlphaFold2 as an example.

Vaccine popularization.

In the context of the epidemic, we wanted to build on our knowledge of high school biology and popularise vaccines to high school students in order to deepen their understanding of vaccines. We presented a lecture titled "What do you know about vaccines" to the students by talking about four aspects, namely, the previous synopsis, vaccine classification, mRNA vaccines and vaccine applications.

We started our talk by asking what a vaccine is, which led to the definition of a vaccine and the topic of the talk. We then began the first part of the class by taking the students through what they had already learned about immunology in high school and expanding on some of their knowledge. We started by taking the students through the critical concept of antigen, pointing out that an antigen is a substance that activates and induces an immune response in the body (immunogenicity) and binds specifically to the products of the immune response in vitro and in vivo (immunoreactivity). To help students gain a better macroscopic understanding of the background knowledge of immunity, we made a tree diagram and showed the classification of immunity acquisition, pointing out that immunity includes both natural and artificial immunity, giving examples of the acquisition of antibodies by the organism as a result of infection with pathogens or maternal transmission as natural immunity, vaccines as artificial active immunity and antitoxins as artificial passive immunity. We also introduce two crucial immune mechanisms in the organism, humoral and cellular immunity. Humoral immunity is the process by which antigens and helper T cells present cytokines to stimulate undifferentiated B cells, which differentiate into plasma cells and memory cells, producing antibodies that bind to the antigen and render it inactive and toxic. T-cells attack the corresponding target cells invaded by the antigen. From the visual presentation, we also explained that the two immune mechanisms are interrelated and coordinated and are two essential mechanisms for the protection of the body.

After this background on vaccines, we moved on to the next part of the lecture, namely the classification of vaccines. We introduced the definitions and applications as well as the advantages and disadvantages of the following five types of vaccines: live attenuated, inactivated, subunit, recombinant vector, and nucleic acid vaccines. Live attenuated vaccines are vaccines made from live, attenuated or non-virulent pathogenic microorganisms, which are traditionally prepared by repeatedly passing the pathogen through a culture medium or animal cells so that it loses or significantly reduces its virulence but retains immunogenicity. BCG vaccine is a typical live attenuated vaccine. We point out that live attenuated vaccines have a good and long-lasting immune effect, and in addition to inducing humoral immunity in the body, they also produce cellular immunity and local immunity to mucous membranes through the natural route of infection; however, their shortcoming is that there is a risk of reversion to a mutation in the body, and special attention is paid to the fact that immunodeficient persons and pregnant women should generally not receive live vaccines. Inactivated vaccines are also known as dead vaccines and are made by inactivating a pathogen by physical and chemical means after it has been artificially cultured in large numbers.

We pointed out that most of the new vaccines that students are now commonly vaccinated with are inactivated vaccines. We also mentioned that the advantage of inactivated vaccines is that they mainly induce the production of specific antibodies, but the disadvantage is that they often require multiple doses in order to maintain serum antibody levels and sometimes cause severe local and systemic reactions to the injection, whereas subunit vaccines are vaccines made by removing components of the pathogen that are not relevant to the stimulation of protective immunity, leaving the active immunogenic component intact. The advantages of subunit vaccines are that they do not contain live pathogens or viral nucleic acids, they are safe and effective, and they are inexpensive. A vaccine. The most widely used vaccine is the poxvirus vaccine, for example, and we briefly introduced the students to its research in the treatment of hepatitis A and B, measles, herpes simplex, tumors, etc. Finally, we introduced the type of vaccine that will be the focus of this lecture - the nucleic acid vaccine, which is a recombinant vaccine constructed from the gene encoding the effective immunogen of a pathogen and a bacterial plasmid. A recombinant vaccine is constructed from a gene encoding an effective immunogen of a pathogen and a bacterial plasmid. Introduced into the body by injection, the vaccine transfects host cells with an antigen that induces an effective protective immune response, thereby inducing adaptive immunity.

After the second part of the presentation, we move on to the core of the lecture - an introduction to mRNA vaccines, which is presented in three parts: the central rule, the nature of mRNA, and the cell-free system. Firstly, we showed a diagram of the central rule to take students back to their knowledge of junior biology; then, we introduced the structure of mRNA and the nature of mRNA by adding caps to mRNA. Based on the diagram, we show that in vitro transcribed mRNA mimics the structure of endogenous mRNA, which is composed of the necessary components: the cap structure (Cap), the 5'UTR region, the open reading frame (ORF) encoding the antigenic protein, the 3'UTR region, and the Poly(A) tail structure. Further deepening, we provide a straightforward interpretation of enzymatic capping in the mRNA capping reaction. The first step of enzymatic capping, i.e., the γ-phosphate at the 5' end of the original mRNA transcript is removed by RNA triphosphatase to form an mRNA containing two phosphate groups at the 5' end, and the second step, i.e., guanylyltransferase, adds the GMP from the GTP donor is added to the β-phosphate at the 5' end of the mRNA to form a 5'-5' triphosphate-linked unmethylated cap structure, and the third step, methyltransferase, use SAM as a methyl donor to methylate the unmethylated guanine base at position N7 at the 5' end of the mRNA. We have also mentioned the nature of mRNA leading to its half-life and the ability of the body to degrade exogenous mRNA. At the end of the presentation on the nature of mRNA, we briefly showed the students a flow chart of a cell-free system.

After explaining the structure of mRNA to the students, we introduce the mRNA vaccine in three steps. Firstly, we briefly explained the principle of action of mRNA vaccines using the new crown vaccine that we all inject nowadays as an example; then, we introduced the idea of designing mRNA vaccines. The three commonly used vectors for mRNA are LNP, nanopolymer, and peptide; finally, we introduced the production process of mRNA. The process mainly includes six steps: 1. sequence design: design and optimize the sequence of the antigen according to the sequence of the pathogen genome and insert it into the plasmid DNA 2. in vitro transcription: transcribe the plasmid DNA in vitro by phage RNA polymerase mRNA. 3: Purification: mRNA is purified using high-performance liquid chromatography (HPLC) to remove contaminants and other reactants. 4: Nanoprecipitation: purified mRNA is mixed with lipids in a microfluidic mixer to form lipid nanoparticles (LNP), which are rapidly mixed to instantly encapsulate the mRNA and precipitate as self-assembled nanoparticles. 5: Screening: the nanoparticle solution is dialysis or filtration, thereby removing the non-aqueous solvent and any unencapsulated mRNA; 6. Making a vaccine: the filtered mRNA vaccine solution is stored in sterile vials.

Finally, we move on to the fourth part of the lecture: the use of mRNA vaccines. We again used the example of the control of the new coronavirus, specifically the antigens of the new coronavirus, and how several R&D companies have designed antibodies based on the antigens. We explained to the students that, similar to other coronaviruses, the spike protein (Spike, S) of SARS-CoV-2 is abundantly distributed on the surface of the viral capsid and mediates the entry of the virus into the cell, playing a significant role in the early stages of viral infection and is currently the primary immunogen in the development of a new coronavirus vaccine. During viral infection, the S protein is cleaved into S1 and S2 subunits. In contrast, the S1 subunit consists of a signal peptide, an N-terminal structural domain, an RBD receptor binding domain, a c-terminal structural domain 1 and a c-terminal structural domain 2, which interact with the cellular angiotensin-converting enzyme 2 receptor mainly through the RBD; in addition, we briefly introduce the S2 subunit, which mainly consists of a fusion peptide, two heptapeptides, a central helix region, a linker domain, a transmembrane domain, and cytoplasmic tail, which are responsible for mediating the fusion of the virus with the host cell membrane. We then cite two main design ideas for targeting S proteins in the development of mRNA vaccines for new coronaviruses, which are the 2P mutagenesis strategy and the S1/S2 cleavage site strategy. For example, BioNTech, together with Pfizer and Modena, has adopted the 2P mutation strategy. In this strategy, the two amino acids (K986P and V987P) at the top of the central helix position of the S2 subunit are replaced by proline, effectively improving the stability of the S protein conformation prior to fusion. After introducing the use of mRNA vaccines in the prevention and treatment of new crowns, we also introduced the use of mRNA vaccines in oncology, such as the TriMixDC-MEL vaccine, a dendritic cell-based mRNA tumor vaccine made by electrotransfection of a fusion mRNA encoding a full-length melanoma-associated antigen (MAA) with a molecule encoding an HLA class II molecule (DC-LAMP) into DCs This allows DCs to deliver the full-length peptide of MAA while overcoming the HLA limitations of previous peptide vaccines.

We also mentioned that the mRNA vaccine could also be used against bacterial and parasitic infections. Scientists have developed mRNA vaccines against different antigens and are still in the process of establishing immune models in mice, looking at the potential for future mRNA vaccine development and application.

Machine Learning Science

To educate secondary school students about cutting-edge scientific advances at the intersection of computing and biology, we used AlphaFold2 as an example of scientific activity.

We started with an introduction to machine learning. In this section, we used a real-life example as an introduction. This example is how machine learning is helping doctors to diagnose prostate cancer accurately. Prostate cancer is the second most common cancer among men worldwide, causing more than 350,000 deaths yearly. The key to reducing mortality is to develop more accurate diagnostics. The existing diagnostic system requires doctors to examine sections of a patient's prostate tissue to make a diagnosis, but often misses and misdiagnoses. By learning from many existing slides, the computer can diagnose images that have never been seen before, a process known as machine learning. We then define machine learning precisely: machine learning is the science of developing algorithms and statistical models that computer systems use to perform tasks without explicit instructions, relying on established patterns and reasoning.

We then introduce the differences between several commonly related concepts: artificial intelligence, machine learning and deep learning.

Artificial intelligence attempts to make a computer intelligent to mimic human cognitive functions. AI is a broad concept that includes computer vision, natural language processing, etc.

Machine learning is a subset of AI. It is primarily the statistical part of AI and can be likened to how humans learn knowledge. It tells a computer to learn how to solve a problem from thousands of examples and then use that experience to solve the same problem in a new situation.

Deep learning is a subset of machine learning, which is based on artificial neural networks. The learning process is profound because the structure of an artificial neural network consists of multiple input, output, and hidden layers. Each layer contains units that convert input data into information for the next layer to be used for a specific prediction task. Thanks to this structure, machines can learn through their own data processing.

That is an introduction to machine learning. Moving on to the section on protein structure, billions of tiny molecular machines are hard at work inside every cell in every human body. They enable eyes to detect light and read the 'instructions' in your DNA, making you uniquely human. These delicate, complex machines are proteins. They underpin not only the biological processes in your body but every biological process in every living thing. They are the building blocks of life.

There are over 200 million known proteins, and more are being discovered yearly. Each one has a unique three-dimensional shape that determines how it works and what it does. However, figuring out the exact structure of a protein remains an expensive and often time-consuming process. Until now, scientists have known the exact three-dimensional structure of only a tiny fraction of proteins. Finding ways to speed up this process could not only help us solve diseases and find new drugs more quickly but perhaps also unlock the mysteries of how life itself works.

If you could unravel a protein, you would see that it is like a string of beads made up of sequences of different chemicals called amino acids. These sequences are assembled according to the genetic instructions of the organism's DNA. the forces of attraction and repulsion between the 20 different types of amino acids cause the string of beads to fold spontaneously, forming the complex helix, folding, and cornering of the protein's three-dimensional structure.

The structure of proteins can be divided into four levels:

• Protein primary structure: the linear sequence of amino acids that make up a protein's polypeptide chain.
• Protein secondary structure: a stable structure that relies on hydrogen bonds between C=O and N-H groups, mainly including alpha helices and beta folding.
• Protein tertiary structure: the three-dimensional structure of a protein molecule formed by the arrangement of multiple secondary structure elements in three-dimensional space.
• Protein quaternary structure: used to describe a functional protein complex molecule formed by the interaction of different polypeptide chains (subunits).

For decades, scientists have been trying to find a way to determine a reliable protein structure by its amino acid sequence alone. This great scientific challenge is known as the protein folding problem. AlphaFold2 is the answer to such a problem that has existed for 50 years.

Before introducing the Alphafold, let us introduce some of its predecessors.

First is the earliest and best-known laboratory method: X-ray diffraction.The principle of X-ray diffraction When a beam of monochromatic X-rays is incident on a crystal, since the crystal is composed of cells with regularly arranged atoms, and the distance between these regularly arranged atoms is of the same order of magnitude as the wavelength of the incident X-rays, the X-rays scattered by the different atoms interfere with each other and produce strong X-ray diffraction in certain specific directions, and the orientation and intensity of the diffraction lines distributed in space are closely related to the crystal structure. This is the basic principle of X-ray diffraction.

The second is the cryo-electron microscopy technique, which has become very popular recently. To see the structure at the molecular level clearly, an optical microscope is not sufficient, and an electron microscope, i.e., an electron beam instead of light, must be used for imaging. Theoretically, the higher the electron dose, the better the imaging quality. However, biological molecules are too fragile to withstand the high dose of electrons. If we compare biomolecules to ants, the damage caused by a high dose of electrons to a biomolecule is equivalent to the power of an atomic bomb exploding on an ant. The way to protect the sample from these extreme conditions is to freeze it. By rapid freezing, the sample is vitrified and glassy so that ice crystals do not form, and the glassy state holds the protein without destroying it. Once it is held in place, a series of 2D images are taken that can be combined to reconstruct a 3D image, which can then be reconstructed in 3D by computer algorithms.

In addition to laboratory methods, there are many other modeling approaches, most notably homology modeling, which refers to the use of a protein with a known structure that is homologous to an unknown structural protein as a template, and the use of bioinformatics methods to predict its 3D spatial structure from primary sequences using computer simulations and calculations.

Homology modeling is based on two principles. Firstly, the structure of a protein is uniquely determined by its amino acid sequence, and knowing its primary sequence theoretically gives access to its secondary and tertiary structure. Secondly, the tertiary structure of a protein is more stable or conserved in evolution. If the amino acid sequences of two proteins are 50% identical, then approximately 90% of the a-carbon atoms deviate by no more than 3 Å. This is a guarantee of the success of homology modeling methods in structure prediction. Homology modeling usually requires more than 30% sequence identity between the template protein and the target protein. We then show the power of AF2's performance based on the first figure in the AlphFold paper and briefly describe its internal architecture, which we disassemble into three parts, feature extraction, encoder, and decoder. Finally, we introduce AF2 and the infinite possibilities that lie within the protein universe based on it.

Feedback:

When we designed the content to educate high school students, we took into account that they already had an excellent foundation in biology, so after identifying the two topics of vaccines and machine learning, we added some introduction to the basics of synthetic biology, and students fed back that it was a bit difficult to understand this part of the content fully, so after each presentation, we made adjustments to the presentation format and the content of the presentation After each lecture, we have adjusted the format and content of the lectures in order to present some abstract concepts more simply. It is also worth noting that many high school students talked to us after class about choosing a university major, and many did not have a specific understanding of life sciences and synthetic biology.

Social platform

Our team has always had an excellent Inheriting culture. When new members first entered our team, they often needed help and guidance of senior students in literature reading and experiments. For example, in the experiments involved in iGEM, some experimental steps are very common and universal. Every member of the team was faced with the dilemma of learning from scratch when they just joined the team. Traditional teaching and learning also had certain disadvantages, such as new members could not memorize all the operating steps at once, if there was no one to ask for help immediately, serious problems would occur.

Take it as a chance, In this year, we created a social account of the club in Bilibili, trying to play a better educational effect through the form of video. First of all, we used this platform to solve the problem we initially proposed. We recorded the complete process of molecular cloning experiment, and made the animation of experimental principles before each video. By combining principle animation with experimental procedures, our video became a fantastic teaching tool. During the summer experiment, the phenomenon of how to do a specific step in the experiment process often occurred. Due to the conduct of this work, students could promptly open our account and browse related videos when they were not sure about the experiment steps, which greatly improved the efficiency of the experiment and was praised by all the members.

In this process, surprisingly, we found that our videos did more than just help our team, after a month, each video in our series had more than 1,000 views. In the comment section, many viewers pointed out that they benefited a lot from these videos, which were of great help to the experimental work. At the same time, some of the viewers sent us private messages to discuss some points that were worth improving during the experiment, such as the placement of items in the ultra-clean table and the specific time setting of PCR, etc., which is also a good feedback for our experiment.

An even greater idea was born. In routine group meeting every Sunday, we will share some interesting subject of iGEM in the past years, as well as some latest articles related to synthetic biology. In the past, only members of our team participated in these activities, while after creating the account of Bilibili, we also live streaming at the same time during each group meeting, so the online viewers can discuss with us through the bullet screen. After the group meeting, we will also upload the video recording to our account. People who did not come to watch the live broadcast can also gain something by watching the video replay. Gradually, the content of our live has become more and more diverse, as explaining some of the less common experimental principles or discussing the related acting design, we will also turn on the live streaming. Through the live-broadcasting platform, more and more people participate in our discussions and get useful support from our live.

In addition, we conducted relevant special lectures for students of different age groups, the content of this part is described in detail in the previous section. We not only got in touch with many schools offline, walking into many campuses and conducting educational activities and exchanges with a lot of primary and secondary school students, but also shooting corresponding online educational videos and posted them on our social platforms. Even in places where we can't go offline, many students have watched our records and learned the relevant knowledge. It is especially worth mentioning the activities we have with the kindergarten children, these activities have achieved good effects when carried out offline, but they are different from the educational activities designed for primary and secondary school students. We prefer to have some games with kindergarten children rather than just one-sided knowledge explanation, however, how to shoot games into videos posed a great challenge to us.

We watched many preschool education videos, learned related skills of video recording and production, and finally completed a series of videos on the section of kindergarten game. What’s more, we also asked the parents of the children who in this age group for their suggestions, repeatedly adjusted the content of the videos, and finally formed the final work. The series of videos were immediately acclaimed after being released, many parents have commented in the comments section that children can watch the video and "move" at the same time to get effective exercise, Instead of just watching the screen for a long time. It’s great for kindergartners to both learn the basic knowledge of life and get effective exercise while watching the video.

Video producing is a very challenging business, the recording, editing and dubbing of the video all need a lot of attention, during which the most impressive thing is the dubbing process. In the molecular cloning experiment series, we chose a steady voice for the dubbing at first, but when the first version of the video was released, our team members all reflected that the experiment itself was a thing that could be successful or failed, so we hoped to have a more relaxed atmosphere when doing the experiment, therefore, we adjusted the voice of the video dubbing, turning it into a cute girl voice, while adding cheerful background music in some positions of the video. Sure enough, when this version of the video was sent to everyone, all the members of our team thought it was very good, and the boring experimental process became more dynamic. As soon as our video was released, many viewers in the comments section pointed out that the voice acting was excellent, which encouraged us greatly.

Communication with hospitals

Hospital publicity

This year we have used Erythritol as a carbon source for the probiotics. This sugar substitute stabilizes blood glucose metabolism and plays a vital role in preventing oral diseases.

Erythritol not only inhibits the growth of cariogenic bacteria and prevents caries but also reduces the ability of bacteria to metabolize acid and raises the mouth's pH, thus reducing the erosion of enamel by acidic substances. The amount of sugar intake and the frequency of consumption play a vital role in the development of caries, and sucrose is the most cariogenic of all sugar. So in many cases, Erythritol is a suitable replacement for sugar substitutes when we want to taste sweetness while reducing the risk of dental caries.

Erythritol has many applications in the oral cavity and is often added to food and beverages. When taking Erythritol orally, the effect on oral hygiene can be maximized, so the impact of caries prevention is quite remarkable. In collaboration with the Prevention Department of West China Stomatology Hospital of Sichuan University, we have produced a leaflet on using Erythritol in the oral cavity. We have come to the department to educate the public on the benefits of Erythritol to remove the psychological barrier between sugar substitutes and the general public.

Our science folders cover the four main areas of whole body health, caries-causing properties, sweetness, and safety.

Whole-body health

Compared to sugar, sugar substitute products effectively aid in maintaining reduced energy intake and body weight and can reduce the risk of type II diabetes and cardiovascular disease. Sugar substitutes do not cause changes in blood glucose or insulin levels when ingested. For diabetic patients, it can also lower glycated hemoglobin levels, facilitating long-term blood glucose control. In addition, they promote the maintenance of a nutritionally balanced diet by satisfying sweet cravings and assisting in possession of calorie intake for diabetic patients.

Cariogenicity

Regarding cariogenicity, sugar substitutes play an even more important role in caries prevention.

Both the amount of sugar consumed and the frequency of sugar intake are crucial to causing tooth decay. Sugar in the diet can quickly spread into plaque and be fermented into lactic acid, eroding tooth enamel, leading to tooth demineralization and, eventually, cavity formation.

The sucrose we typically consume facilitates the colonization of oral microorganisms and increases plaque stickiness, allowing it to adhere to the teeth in large quantities. This property makes sucrose a facilitating role in the development of dental caries. As a result, sucrose is more cariogenic than other sugars.

Xylitol is a non-fermentable, pleasant-tasting, non-cariogenic polyol. It is similar to sucrose in sweetness, which has a cooling effect on the mouth and is mainly used in chewing gum. Regular use of xylitol-containing chewing gum decreases the amount of plaque and increases saliva flow. Xylitol affects the ability of cariogenic bacteria to adhere to hydroxyapatite and inhibits the formation of plaque and biofilm. What's more, xylitol also has a direct inhibitory effect on cariogenic bacteria.

Other sugar substitutes, such as Erythritol, are not fermented or are challenging to ferment in plaque, and it's hard for them to be metabolized and produce acid, thus weakening the ability of various bacteria to acid-etch enamel. Meanwhile, Erythritol can promote the ability to remineralize demineralized enamel and inhibit the growth of cariogenic bacteria in the mouth, playing a critical anti-caries function.

The anti-caries effects of sugar substitute products include.

• Inhibition of matrix formation in dental plaque
• Reduces the number of Streptococcus mutans in the whole saliva and plaque
• Increases buffering capacity and pH of dental plaque
• Interference with enamel demineralization and increased enamel remineralization

Sweetness

Regarding sweetness, sugar substitute products are often used as sweeteners and have a refreshing taste. Sweeteners are divided into carbohydrate sweeteners and non-carbohydrate sweeteners.

• Carbohydrate sweeteners include sugar alcohols such as Erythritol, sorbitol, and xylitol.
• Non-carbohydrate sweeteners include plant-derived stevioside, kiwi sweet proteins, and monellin, which are usually much more precious than sucrose and can be added to foods in small amounts to adjust the taste.

Security

Blood pressure, blood glucose, or lipids: Sugar substitutes do not cause adverse effects on overall health and metabolism when used per the FDA's daily intake. In a study of children using aspartame and placebo, no differences in blood pressure, blood glucose, or blood lipids were observed between the two groups. In another study, no group differences were found in blood pressure, waist circumference, or blood lipids between the two groups of adolescents using sugar and sugar substitute products.

Mutagenicity: Erythritol, one of the widely used sugar substitutes, has been shown in short-term genotoxicity tests to be non-mutagenic to bacterial cells and does not cause chromosomal damage in mammalian cells in vitro or in vivo. Sugar substitutes are also used as a substitute for sucrose in most of the best-selling sugar-free products, such as the range of products launched by Genki Forest and Coca-Cola, which shows that sugar substitutes have been proven in the food sector and are already being produced industrially and used on a large scale in everyday life.

In addition, stevia is classified as Generally Recognised as Safe (GRAS). A study has shown that stevia extract has a better inhibitory effect on Streptococcus pyogenes than chlorhexidine, suggesting that it has many applications in the dental field.

Laboratory experience

In order to allow the public to observe the preventive effect of erythritol on caries and the inhibitory effect of erythritol on acid-producing bacteria in the oral cavity more visually, we selected several simple Caries activity tests to allow the public to experience this effect.

The cariogenicity is constituted by the cariogenic bacteria and the ability to metabolize acid production, and the test to detect the risk factors of caries occurrence is called the Caries activity test, including the Cariostat test, Dentocult SM test and Dentocult LB test. Bacteria in plaque biofilm have a low ability to use erythritol to metabolize and produce acid, and some cariogenic bacteria cannot even use it as a substrate to produce lactic acid. 1 In addition, erythritol has an inhibitory effect on the growth of cariogenic bacteria and the formation of plaque. 2 In addition, erythritol has an inhibitory effect on the growth of cariogenic bacteria and the formation of dental plaque.

For the effect of erythritol on caries-causing bacteria, we set up a control group (without any sugar intake), a sucrose group and an erythritol group, which were verified with the Dentocult SM test and the Dentocult LB test.

Dentocult SM test

Experimental purpose: To determine the caries activity based on the number of Streptococcus mutant colony-forming units (CFU/mL) per milliliter in saliva.

Reagent kit: 5mL culture tubes with screw caps containing light saliva selection solution, standard plastic attachment plates, bacillus peptide paper sheets and paraffin wax.

Assay method: The subjects were first made to ingest erythritol orally and chew a paraffin pill for 1 minute. After 10 minutes, hold the attachment plate and turn it over on the back of the tongue and apply it 10 times. Immediately place the plate in the culture test tube, screw the screw cap at 37°C. After 48 hours of incubation, and observe the density of Streptococcus mutants (blue colonies) on the attachment plate. In contrast, the control group did not receive any sugar.

Result Judgment.

• Class 0 and 1: colony density <10^5
• Grade 2: Colony density <10^5~10^6
• Grade 3: Colony density >10^6

Dentocult LB test

Objective: To mainly observe the number of Lactobacillus in saliva.

Reagent kit: solid medium plate with Lactobacillus selection, culture tube with screw cap.

Assay method: The subjects chewed a paraffin pill for 1 minute after consuming erythritol, collected saliva in a container, then poured the saliva evenly on the surface of the medium on the culture plate, suspended the excess saliva, placed it in the culture tube, 35°C, 4 days incubation, and observed the density of Lactobacillus colonies attached to the culture plate. Meanwhile, the control group and sucrose administration group were set up.

Result Judgment.

• Grade 1: colony density ≈ 10^3<10^5
• Class 2: Colony density ≈ 10^4<10^5~10^6
• Level 3: Colony density ≈ 10^5
• Class 4: Colony density ≈ 10^6

Grade 2 or above is high caries activity

For the ability of erythritol to be metabolized by bacteria for acid production, a control group (without any sugar intake), a sucrose group and an erythritol group can be set up and verified by measuring Stephan curves as well as Cariostat experiments.

Stephan curve

Purpose: To measure the ability of ingested sugars and carbohydrates to be metabolized by bacteria in the oral cavity for acid production.

Apparatus: glass electrode with fine tip, recorder.

Detection method: The pH change of dental plaque after the intake of sugar or carbohydrates is continuously measured by a glass electrode, and the pH change curve is recorded.

Judgment of the results:
Before the intake of sugar, the pH within the dental plaque is steadily maintained at about 6-7, depending on the number of cariogenic bacteria in the mouth. And after sugar intake, plaque metabolizes sugar to produce acids, mainly lactic acid and acetic acid, resulting in a decrease in pH within the plaque matrix. When the pH value is lower than the critical value of 5.5, the enamel turns from mineralization to demineralization tendency, and the calcium ions free out, causing the hard tissues of the teeth to be less resistant to acid, resulting in the development of caries, and the duration of lower than the critical pH value also greatly affects the degree of caries-causing. Cariogenic bacteria easily use sucrose to produce acid, so the pH value will drop rapidly to below the critical value in a few minutes after eating and can reach as low as 3.9, causing tooth demineralization. Sugar substitutes such as erythritol are more difficult to be used by cariogenic bacteria to produce acid than sucrose, and even have an inhibitory effect on cariogenic bacteria, so their minimum pH may be higher than the critical pH and less cariogenic.

Cariostat test

Objective: To detect the acid-producing ability of acid-producing bacteria within the plaque on the tooth surface.

Reagent kit: liquid culture tubes containing bromocresol violet and bromocresol green, standard swabs.

Detection method: Apply the swab to one side of the buccal surface plaque 4-5 times under three situations of edible erythritol, sucrose and no sugar intake, respectively, place the swab in the culture tube, 37°C, 48 hours incubation, observe the color change of the culture solution.

The results were judged:
the acid-producing capacity was blue-purple, green, yellow-green and yellow in descending order, with scores of 0, 0.5, 1.0, 1.5, 2.0, 2.5 and 3.0, respectively.

• A score of 0 and 0.5 is a low risk of caries
• A score of 1.0 and 1.5 is a moderate risk of caries
• A score of 2.0, 2.5 and 3.0 is considered a high caries risk.

Artistic expressions about life

In our educational activities related to life and synthetic biology, we realized a problem that synthetic biology is a field in the life sciences, which itself is not universally understood, and that the concepts related to synthetic biology are abstract and difficult to understand for people without basic knowledge, and we urgently need to find some more enjoyable forms to link synthetic biology and life science related knowledge together so that more people can participate in our education.

When we think of Sichuan and Chengdu, we think of Sichuan opera face changing, shadow puppets, mahjong, Shu embroidery, and tea culture ...... Sichuan province is an important part of Chinese culture, with thousands of years of history. Here in this region was born a rich and diverse art and culture, with the great geographical discovery and the process of globalization, exchanges and fusions have also taken place between ancient Shu civilization and other civilizations. Sichuan University is also home to the School of Art, the largest school of art at the University, where students of different majors express themselves in the art they have studied.

Art can cross languages and borders, and is a very good way to communicate and spread knowledge. So we took a camera and a light board and went into the art school of Sichuan University and into the streets of Chengdu, and talked to many people about the artistic expression of life, and asked them how to integrate synthetic biology and artistic expression to achieve better communication effects.

We made videos of these interviews and posted them on relevant social media platforms, and, not surprisingly, compared to our previous videos on molecular cloning experiments and live streaming of literature-sharing sessions on the frontiers of synthetic biology, the diversity of people watching these videos was much richer, and we actively discussed with these viewers, who said that these interviews were more accessible because they talked about understanding life from an artistic perspective. And because they include many artistic elements, it is a very popular format.

During the interviews, we learned about the artistic expression of life and understood the concept of life from a more diversified perspective. In addition, the exchange with people from different art fields inspired us to think of more ways to convey some synthetic biological concepts through art. More importantly, just as our concept: life is sweet, through the interview, we also realized that in the current society with so much pressure, art often has a soothing effect on the mind, so when we use art to convey the concept of synthetic biology, we can also convey some ideas that hope people can face life more easily. This is certainly a sublimation of our educational activities.

In the following video, we will show one of the interviews with several students from the School of Arts of Sichuan University, who, because of their love for popular music, have overcome many obstacles to give us wonderful performances on campus, which is undoubtedly a good remedy for the stressful university routine. In the interview, we discussed the expression form of this abstract conceptual art about life, and they talked about the life cycle of art and the commonalities between art and traditional bioscience concerns. We also talked about one of the more poignant issues of the day, which is the perception of the future of synthetic biology, which is undoubtedly the result of thousands of failures and sometimes the difficult situation of "no rainbow after the storm ."Therefore, when university students choose synthetic biology as their future research direction, they will have some additional concerns, which seems to be contradictory to our "life is sweet" and in the interview, they also talked about the so-called life is sweet, which is also a process of from bitter to sweet, which is consistent with the experimental process related to life sciences. Of course, not all efforts can eventually yield the sweetness of life, but we become stronger and make advances. So how can this be considered all bitter?

Reference

1. Kawanabe, J., Hirasawa, M., Takeuchi, T., Oda, T. & Ikeda, T. Noncariogenicity of erythritol as a substrate. Caries Res. 26, 358–362 (1992).

2. de Cock, P. Erythritol Functional Roles in Oral-Systemic Health. Adv. Dent. Res. 29, 104–109 (2018).