Team:ZJU-China/humanpractice.htm

This year, ZJU-China brainstormed so many fascinating ideas about human practice. Actually, thinking about creative human practices becomes the most effective way to bring joy and laughter to our discussions as well as our lab life. In fact, though all the brilliant ideas from our HP creative idea workshop, we discover the true inner beauty of iGEM, which is, being ethical, being versatile, and being creative.

This year, ZJU-China aims to be different. So, don’t hesitate to join our journey with a view of fantastic iGEM human practices.

This year, ZJU-China made full use of our Synthetic Biology Club. We recruited XXX members throughout the campus. They are coming from different majors. We have members from mathematics, computer science, biotechnology, agriculture, food science, clinical medicine, bioinformatics, Polymer materials science and engineering, Plant protection, Geographic Information Systems, Optical Engineering, Accounting, Business, Electrical Engineering and Automation, Energy and Environmental Engineering, Tea Science, Chemistry. And half of them participate in our annual experiencing iGEM activity, namely, ZJU Jamboree.

This year, ZJU-China did a few lectures to widespread the value of iGEM, participated in some scientific activities to display our projects and gain funding ourselves, put special highlight on our high school friends, provided opportunities to others who are interested in experience a real iGEM lab life.

(red bold words have hyperlinks, and the links content are shown as following)

Synthetic Biology Club

Synthetic Biology Club (SBC) is academic student societies based on International Genetics Engineering Machine (iGEM) Competition. SBC is aimed to promote synthetic biology and attract more students fond of synthetic biology in campus.

Last year was SBC’s first year, with the outstanding performance from ZJU-China 2011, SBC attract huge attention in campus. In order to make full use of SBC and provide more opportunities for ZJU students to have a basic understanding of iGEM as well as synthetic biology, we held several lectures for not only the club members but also students from different colleges. Then, we ran the process of on-line and at-site club recruiting together with the individual registration for ZJU Jamboree. Undergraduates and Graduates from different colleges express their will in participating, which is out of our expectation. We recruited for about XX members this year, and 60 of them registered for ZJU Jamboree for the coming winter holiday. SBC also attract attention outside the campus, our SBC Renren Homepage (Facebook in China) has 178 followers throughout the country right now, and the number is keeping going up.

SBC provided firm support to iGEM ZJU-China, and gave birth to the brand-new iGEM ZJU-China 2012. Thanks for all the activities held by Synthetic Biology Club, iGEM and synthetic biology have attracted increasing attention in our campus.

References:

[1] SBC Renren Homepage: http://page.renren.com/601409290

[2] iGEM ZJU-China Renren Homepage: http://page.renren.com/601236243

[3] Official Website of ZJU-China: http://www.cls.zju.edu.cn/binfo/sbc/

ZJU Jamboree

ZJU Jamboree is top big event in ZJU-China Human Practice for this year. There were 60 members of SBC registered for ZJU Jamboree. We divided the ZJU Jamboree for 3 sections: introduction sessions, winter brainstorming, and final presentations.

During sessions, SBC members (three of the ex-participant of ZJU-China 2011, Luyi Tian) delivered lectures. Then the participants were divided into 20 groups randomly with 3 in each, and were assigned randomly with projects from previous iGEM projects in order to familiarize them with the content of a mature iGEM project. Each of group has a mentor (senior SBC members, who are also team members of ZJU-iGEM 2011). Then each team was required to give a presentation of the assigned previous projects and had a discussion with their mentors.

Winter brainstorming is most exciting part of ZJU Jamboree, from which our participants could truly grasp the joy of finding their specific interests in synthetic biology. In winter vacation, our participants were asked to form groups freely and to design one or more detailed projects. There will be requirements about their paper-based Mid-report, which was due on Jan 30, 2012; their Final-report was due before the jamboree. And they did a fantastic job in bringing out brilliant ideas; remarkably, some of them (Wenhao Ling and Heng Yao) even visited the local high school as a human practice part of their winter projects.

In the beginning of February, our ZJU Jamboree started (on Feb 11-12, 2012)! Each group gave a presentation to all other club members to introduce their project plan, and most importantly their original ideas. We are all greatly inspired by their presentations, and so proud of our members. ZJU Jamboree also gave birth to the original thought of HP Creative Workshop (We received so many interesting ideas of human practice). Some of the club members remarked that it's one of the best academic experiences they ever had in college.

Group "Lignin Cinderella"

Project Abstract: Synthetic biology holds great promise regarding the production of important compounds, and the degradation of harmful ones. In this grogram, we harness the power of synthetic biology to meet the world’s needs for fuel and environment. We try to express the gene coding lignin prtoxidase (Lip), found in the white rot fungus Phanerochaete Chrysosporium, into genetically modified crop cells and degrade lignin after mechanically breaking up the structure of crop cell. And to control the expression, we design a molecular logical switch through the amplification of cascade reaction, combining the start controlling condition of expression of lignin peroxidase (Lip) or its promotor into the metabolic regulation of crop growth-related genes. So that controlling the accumulation of Lip in cell will reach peak when crop is in a specific period, such as harvest. In this way, we can also insert into another lignin degrading enzyme, such as Glox, Mnp and Lac. If we make it, it will become a new way in degrading lignin and cut the cost in paper pulp industry and biofinery. And it is also a novel way to bring and control heterologous gene in eukaryotic

Promotor Library:

Group Member: Wenhao Lin, Xinyi Guo, Heng Yao, Kexin Nie, Jiajun Lv.

Highlight in this group:

"Lignin Cinderella" is probably one of the best in this Jamboree due to their fully developed project; they grasp the crucial idea of synthetic biology and brainstorm a project in detail. By going through their final report, we can see they did a good background study, and provide detailed methods in both experiment itself and plasmid designing. It’s innovative and fully developed. Apart from their experiment design, the project also has modeling part and even a website. We enjoy their idea of using Cinderella as well as the logo animation. What’s more, they even go to local high school to introduce iGEM and synthetic biology as their human practice part, which is really impressive.

Group "Algae Digester"

Project Abstract: In this project, we tackle the issue of biofuels, which is a hot spot in synthesis biology nowadays. Based on some recent researches, we plan to enable the engineered E.coli to digest algae and turn the polysaccharide to fuel substitutes or precursors suitable for gasoline, diesel, and jet engines. We also tried to make efforts in dry lab, which can contribute to our project at a systematic level.

Group Member: Qian Mei, Tianqi Chen, Xiao Xu, Zhile Ren.

Highlight in this group:

Their systematic way of organizing their final report and presentation leave a good impression on us.

Group "Methane Alarm"

Project Abstract: We aim to design a methane alarm for coal mine by methanotrophs, which consists of four parts: decomposition, sensor, signal tuner and output. Decomposition part takes in methane and conducts catalytic decomposition of methane to CO2 or assimilates methane as its own organic compounds. This function is the naturally exist in methanotrophs. Sensor senses the concentration of methane and produces activator A. As for signal tuner part, we plan to find a substance B which is sensitive to the concentration of activator A. Activator A and substance B combines to control the activity of substance C. Substance C acts as the switch of promoter--when the concentration of methane has been exceeded the alarm threshold, promoter will turn on. Output part will give the alarm by producing pigment of red lycopene when promoter is open. We plan to put methanotrophs on the miner lamp. When the bacteria produce pigment, the light through bacteria will turn out to be red.

Group Member: Yan yan, Huachun Liu, Yue Zhang, Mengqi Hu.

Group "Tanbio"

Project Abstract: Tanbio is a bacterial system which can switch between different states by light. The system consists of a synthetic sensor of light and a switch which can control the express of anti-melanin gene. Thus, when exposed under the light, the bacterial system will produce melanin, while it will not without light. Tanbio can function as a biological film, such that the projection of a pattern of light on to the bacteria produces a high-definition, two-dimensional chemical image. It can also be applied to make light-tight materials which can adapt to the intensity of light automatically.

Tan means ‘brown’ or make skin brown by receiving illumination of the sun. We name the system ‘Tanbio’, because the bacteria turn brown under the light, just like people who get a good sun - tan on the beach.

Group Member: Jiahui Zhang, Zhewei Wang, Yanjing Liu, Jiayi Chen

Group "Magnetosome"

Project Abstract: The mean point of our project is to utilize the magnetism of the magnetic bacteria to construct targeted medicine that can cure cancer. The magnetic bacteria can produce a membrane structure, magnetosome. Our work is to modify the magnetosome to carry with drug molecule. To detect them, we also fuse the yellow fluorescing protein to the membrane of magnetosome. Use additional magnetic field to fix the location of the drug molecule just in the cancer cell area in the human body. When the magnetosome and cancer cell combine, the drug molecule in the magnetosome will be released because we also fuse an antibody to the membrane protein of magnetosome. This antibody can cause the endocytosis, so the magnetosome as well as drug molecule are swallowed by the cancer cell.

Group Member: Niu Fang, Kaifeng Bo

Group "Pribnow box"

Project Abstract: We want to explore the influence of the change of the consensus sequence in prokaryotes. The sequence is TATAAT.

1. Point mutations in the Pribnow box: a transversion (G-->T) in the first base for one mutant or a transition (G-->A) in the fifth base of the -10 consensus sequence.

2. Length of the Pribnow box: insert a copy of consensus sequence in the upstream or downstream of the Pribnow box, but before the starting point.

3. Location of the Pribnow box: put the Pribnow box in other place in the range of promoter.

After the promoters of all mutants, we insert gene of RFP. So the function of device is characterized by the amount of RFP expressed. The amount of RFP expressed is reflected by the light emitted when RFP acts on the appropriate substrate.

Group Member: Tiantian Zhou, Xiao Liu, Jiansi Gao, Hongyi You

Group "Methane synthesizer"

Project Abstract: Our project aims to study the mechanisms and genetic nature of anaerobic archaea methanogens using small molecules such as CO2 and hydrogen to synthetizing methane. Transform its genetic code to make it a stronger ability to adapt to the environment and to be regulated, and increase their metabolism and reproductive efficiency to improve the efficiency of methane production. Building blocks to make it into sleep under aerobic conditions and make it back to active and produce much methane under high concentration of CO2

Group Member: Qianliang Pan, Bohan Zhou.

Lectures

This year is the third year of ZJU-China in iGEM, we make efforts to spread the basic principles of synthetic biology and introduce iGEM to more and more people. Presentation is always a classic way. This year, we seek opportunities among class presentations, visiting high school, high school summer camp, and SBC activities.

12.10.2011: Intruduction to iGEM

12.17.2011: The function of programming in iGEM

12.25.2011: Plans for next year & Instructions on winter projects

Links: http://zjuchina.tk/igem2012.html

01. ?.2012: Wenhao Lin, Heng Yao, iGEM at high school intruduction about project Auxin in 2011, Hangzhou No.2 High School

05.29.2012: Huachun Liu, Adventure in Synthetic Biology and iGEM, discussion section in Biological Science.

07. ?.2012: Huachun Liu, Adventure in Synthetic Biology and iGEM, Qiushi Summer Camp

Scientific Activities

We always find it accomplished and exciting to participate in scientific activities. This year ZJU-China seized the opportunities to present our idea to more fellow students, teachers and even scientists.

iGEM ZJU-China took part in the first technological innovation buffet meeting held by College of Life Science (CLS). It was in grass hall on May 25th, 2012. Professor Jianzhong Shao of cells and developmental biology institute, professor Xiaohang Yang of Genetics Institute, professor Ming Chen and Xin Chen of Plant scientific research institute, professor Xin Chen of ko-institut and Professor Yongquan Li of biochemistry institute were invited to be members of the jury. Sixteen research projects of postgraduates, undergraduates and iGEM group, involving in both microcosmic and macroscopic aspect, participated in the buffet meeting. Participants introduced their own works and answered questions raised by the jury. The buffet meeting lasted two hours. The atmosphere combined academic and lighthearted as well owing to the tasty food and drinks prepared. The buffet meeting reinforced the academic communication and innovation of among the students from CLS, which undoubtedly promoted the progress of CLS students’ Academic researches. The awards were decided based on the grades from the jury and vote result at the scene, and we are so glad to win the first place.

News links: www.cls.zju.edu.cn/cn/news.php?action=show&id=5779

Our projects also apply for National University Students Innovation Training Program and both two of them have already been authorized. We exhibited our research plan on June 8, 2012, and answered the questions within all students research groups from different colleges and departments.

News links: ugrs.zju.edu.cn/redir.php?catalog_id=711156&object_id=751961

High School

Hangzhou No.2 High School

Our High school visit back start from winter project: Group "Lignin Cinderella" went to the local high school, Hangzhou No.2 High School, delivered a presentation to the school’s biology interesting group. "Hangzhou No.2 High School has always enjoyed a high reputation in Zhejiang", in the group’s description, they mentioned that "and we’d been honored to take this as a start to introduce iGEM to all the excellent high schools in Hangzhou". Their discussion about synthetic biology triggered the interest of some high school students there, and we received emails from them. After that, two of them even pay a visit to our lab in summer, and participate our activity, "experience a real iGEM lab life".

Qiushi Science Summer Camp

ZJU was the host for the Qiushi Science Summer Camp, where high school senior students came from around the country to study. As the host, ZJU gave us a chance to do a presentation about iGEM and our project. Some high school students who participate in our discussion were also gaven a brochure we made as a gift, which about iGEM ZJU-China and our previous year projects.

After presentation, some high school student showed interest to our lab and took a visit there. Our lab instructor profesor Ming Ding, together with our members, introduced the facilities and our experients in detail. All of our visitors took the iGEM bookmarks and badages of last year’s biofilm.

Experience a Real iGEM Lab Life

Want to be a scientist and experience a real iGEM lab life? ZJU-China also provides you that opportunity! After the visiting of Hangzhou No.2 High School, we received emails from a high school student, Xin-he Shan, who expressed an interest in participating. He and his classmate, Wen-zhou Chen, visited our lab in summer. And we gave them short lab training about safety on July 12, 2012. And they start to apply what they learn in class to real lab practice.

One of our experiencer Xiaoting Lu, who majored in animal science, joined the 3rd Animal Science and Life Science Hangzhou Summer Camp. This summer camp intended to promote the undergraduates’ understanding of cutting-edge science focusing on animal and Life aspect, which attracted lots of outstanding undergrads to apply from all over the nation since its first year, and it lasted for 5 days (from July 7,2012 to July 12, 2012). There was a section for the campers to exchange their academic experience, and our college experiencer Xiaoting choose her experience as a intern in our lab and synthetic adventure as the content of presentation.

News Link: http://www.cas.zju.edu.cn/dky2008/cn/news.php?action=show&id=4393

This year, ZJU-China had tremendous interesting ideas about human practice and actually did research about it. With the spirit of share and fun, here comes our HP creative idea workshop, aiming to provide brilliant and workable thoughts about iGEM human practice for future teams, and trying to develop insights of a real effective human practice. Needless to say, we even try some ideas of our workshop. Well, it went well!

Let’s take a look at what we tried this year! ZJU-China held a special event called "Scaffold in your eyes" in campus, and attracted a lot of attention. ZJU-China created a cute love story to illustrate our main idea of project, then we made an animation of this story, "a love story between Syn & Bio", in which we even create our own song. It is so interesting and so fun, definitely worth seeing! Additionally, ZJU-China thought ethical thinking is also crucial, and apart from the safety sheet we undergraduate researchers have to think about, we left the question directly to our freshmen in their first English Speech Contest.

HP creative idea workshop

Actually, the idea of doing such a workshop comes from ZJU Jamboree. We saw so many inspired human practices in our Jamboree, which will make iGEM really fun. ZJU-China is eager to share all these to other iGEMers from all over the world, and present the thoughts of our SBC members to the world.

Some of them made pokers which have previous iGEM programs’ abstracts on each card, some even create a brand-new Card Game.

Let’s take a look at one of our SBC member, Yue Zhang’s idea.

Card game: Methane Killer

In the game cards are divided into four categories: methane cards, gene cards, bacteria cards, instructions cards and life cards.

Methane cards: cause a damage for the rival.

Gene cards: include alarm gene 1, 2, 3 and methane eating gene, which can build alarming factory and methane swallowing factory with bacteria cards according to certain rules.

Alarming gene 1+2+3 + bacteria cards= methane alarming factory: makes the attack of your rival invalid after you show the alarm starting card.

methane eating gene+ bacteria cards= methane swallowing factory: make the methane card put down by your rival into your hand after you show the swallow starting card.

instructions cards: the alarming starting card, swallowing starting card

Alarm frozen cards, swallow frozen cards: make the rival's alarming factories and swallowing factory invalid in a cycle.

Alarm thaw cards, swallow thaw cards: make the rival 's alarm frozen cards, swallow frozen cards invalid in a cycle

Life cards: every card has five red dots;you will lose a dots if you get an effective attack.

At the beginning of the game, each player will get a piece of life card and 2 pieces of methane cards.Each player take two cards from the Pile (including four categories), confront with the rival according to the function of the cards.the one who lose the five red dots first is the failer.

HP creative idea workshop still has a lot to do afterwards; we are going to conduct a real research to serious think about humanity and science, which will be described in detail in our future work.

"Scaffold in your eyes"

RNA Scaffold is flexible in designing, which makes it perfectly applicable in many biological pathways and acts different roles in biological systems in vivo. And designing is the most important and highlighted part of our project, we want to share the "design and re-design" concept in synthetic biology with the public. According to that, we came up with "Scaffold in your eyes". There’s a famous movie at that time in China, "You Are the Apple of My Eye". Both the Chinese and English name of this activity borrowed part of that movie, which successfully catch public’s attention. We design our scaffolds follow certain principles, one of them is that we still use the PP7 & MS2 binding site. We post the activity on our university’s BBS, and hang up posters on each dormitory hall. Then we set site in the center of campus, provided color pen and paper with the shape of PP7 & MS2 binding site, asked them to draw whatever they like based on that, and introduced our idea of designing after that. Each of our participants received a chance in a small lottery afterwards, together with a synbio bookmark we made ourselves. Lots of people passed, stopped to take up the pen, and listened to our mini-presentations. We received more than 100 drawings. Besides, there’re foreign students and even a seven year old girl draw in this activity.

"A love story between Syn & Bio"

Members of 2012 iGEM ZJU-China are versatile in many aspects. We decided to create an animation to illustrate our project in a more recreational way! Then, producing a music video bumped into our mind. ZJU-iGEM changed the lyrics of the song "I'm Yours" (sing by Jazon Mraz), draw the entire animation and finish the song all by ourselves during lab time. All of us felt so proud of it, and can’t wait to share with you.

It is a love story of Syn and Bio, they’re both genes in the same chromosome of a same E.coli. They are destined to transcribe and translated into enzymes, and they fall in love with each other when they’re still gene. As it was told, they’re going to play an important role, catalyzing in the same biological pathway, however, it’s still extremely hard to meet each other because the E.coli is so big! And of course, the efficiency of the pathway is very low because they’re separated. The young lovely couple S&B were in a broken heart, they’re just like Romeo and Juliet, Rose and Jack, Liang shanbo and Zhu Yingtai, Xu Xian and Bai Niangzi. However, ZJU-China believes in true love and won’t let this tragedy happen! We are going to send a RNA scaffold, it’s like a messenger with radar, help to find both enzymes and bind them in one scaffold. Thanks to ZJU-China, S and B could stay with each other happily ever after, catalyzing, catalyzing, catalyzing..

English Speech Contest

Critical thoughts in human practice are placed weight. ZJU-China this year collaborated with one specific English enhancing club of our university, Power of Voice (POV). We participate in their free developed speech section, and bring about three general questions concern about ethics in synthetic biology.

1 As a famous adage goes, scientific technique is a two-edged sword. What’s your opinion about transgene?

2 Synthetic Biology is to design and re-design a new biological system. Do you agree that human can create new creature in the future?

3 Do you think new technology like transgene will raise biosafety issues?

And among all the participants, there’s one student to get the first topic.

Dr. Yuhua Hu from Edinburgh University visiting our team

Dr. Yuhua Hu, the technologies manager of school of biology sciences, the university of Edinburgh, visited our team on August first. We briefly introduced our team and project to her. And she described the project and recent progress of Edinburgh team. Then we talked about the collaboration between two teams, and hoped to build a strong connection in the long run. We are all looking forward to the future collaboration of iGEM teams and students associations between Zhejiang University and Edinburgh University!

Peking team visiting our team

Seven team members of Peking team, Hongyu Xiong, Wenyuan Zhou, Sibai Sun, Hong Zhang, Wenming Xing, Tian Lu and Zidong Zhang visited us on July 27th. Before they came, we thought to work together on a project of Human Practice, addressing lectures related to iGEM and synthetic biology to high school students in Zhejiang Science and Technology Museum. This was a good project and also a rare chance, after all, Hangzhou was nearly 1600 kilometers away from Beijing. Peking team provided event planning and contacted with the person in charge of museum, our team designed and printed the post and tried to contacted with teachers of several high schools in Hangzhou. But due to summer holidays, it was difficult to call together highschool students. At last, we had to give up this project. It was really a pity. Anyway, our team communicated with Peking team happily. We exchanged the project and recent progress with each other, and had a wonderful dinner together! Though we can't collaborate on Human Practice this year, this visit no doubt strengthened the friendship between Peking team and ZJU team!

Terrific trip to UIUC

One of our team members, Xinyi Guo, reached out to the UIUC team and coincidentally discovered that both of our teams focus on RNA scaffold this year. The fact that we are all interested in developing RNA scaffolds as a full comprehensive project made us excited, and we had a deep talk about both our projects and specifically exchange ideas in scaffold characterizations.

Research about Human Practice

We are going to enrich the content of HP creative idea workshop by conducting a research focusing on the effectiveness and creativeness of human practice. By doing this, we’re trying to figure out the relation between humanity and science. People used to think science is a pretty serious stuff with lots of data and critical analysis (But it is only one aspect of being a scientist). Actually iGEM Human Practice provide us a good opportunity to combine a great number of other fields to science, and create amazing new things to introduce science concept to the society. And it is such an amazement that during the past few years, iGEMers from all over the world contribute their effort to explore this perspective. We find it extremely interesting to do research on this topic. We hope to summarize the previous iGEM project human practices, seek other successful cases which add different elements to science projects, and conclude the true inner beauty of Human practice and project outreach. By doing this, we intend to provide a whole picture of science and humanity in iGEM, and wish to inspire other iGEM team in some sense.

Ethic thinking and love project

From the experience of English speech contest, we find it necessary to create a chance for undergraduates to really think about new technology in biology as well as ethics in biosafety. And we’re thinking of organizing an English essay competition concerning about biosafety. It will certainly inspire our young biologists or even the general public, and provide a good chance for them to get to know about synthetic biology instead of receiving other’s opinions passively.

Collaborations with UIUC

Since our projects has a certain similarity, ZJU-China focusing on the improvement of the discrete RNA scaffold by adding riboswitch in order to make our own scaffold, while UIUC pay more attention on finding a new pathway by changing the scaffold’s RNA binding sites. We find it possible to discuss and collaborate with each other. We can help in modeling and they share experience in doing protein experiment with us. And ZJU-China also wants to explore more about biosafety in outreach with UIUC team.

Collaborations with Edinburgh University

Dr. Yuhua Hu from Edinburgh did a detailed interview about teamwork in iGEM project with almost every member in our 2012 iGEM ZJU-China team. We are very glad to share our stories with Dr.Yuhua Hu and participate in her research. There’s going to be another two interviews with all of our members around November.