Team:SJTU-BioX-Shanghai/HP/Gold Integrated
IntegratedThis year, the SJTU-BioX-Shanghai iGEM team created an original analysis method and an approach to present HP's work. We can apply this method in the process of understanding, planning and showing HP work. We named it the “subject analysis method”.
In the integrated HP part, our goal is to integrate our work into our project, which must involve two subjects, "we" and "the people involved in our HP work" (in our theory, named "they"), we think:
- When we design HP work, we should be from the two main point of view, analysis of what we need, they can get what, so that more appropriate to carry out our work to achieve better results.
- To sum up our HP work from the two main point of view, from a different point of view the results of things, there is no effect, the parties have what the harvest.
- To show our HP work should be from the two main way to show, so that readers can experience the feelings of both sides, while a better understanding of our integrated HP work.
We will be a demonstration, use this method to analyze our integrated HP work, perhaps read, you can clearly understand our overall thinking, feel the beauty of this method!
We believe that looking at our HP work from two perspectives can demonstrate more clearly what is integrated HP. Additionally, this approach can provide reference and ideas for other iGEM teams. In the understanding, planning, display your iGEM integration HP, you can try this method, maybe there will be unexpected discovery!
This method is mainly composed of the following aspects:
For the "WE" part, the main use of "we want to ... ..." "We understand ... ..." and other statements organization, mainly on your project development process encountered problems and your ideas , Your measures, and your solution.
For the "they" part, the main "they are provided ..." "They need ..." "They tell us ...", mainly about their help to us and They need us any help.
Note: We recommend organizing “THEY” part in tips, instead of using the form of story, because others mental activity of THEY is not known, and for “WE” part, we understand our own ideas and our behaviors, so “WE”part is recommended to use the form of story.
Let's take a look at our analysis below! Click on the bottom of the "WE" or "they", you can see two different analysis page.
Finding reporter
When we were designing this year's project, we visited Professor Lee Ronggui, Dean of the College of Life Sciences, Qingdao University. He introduced us to a research work conducted by him in 2006 - the accumulated lycopene E.coli engineering bacteria and its culture conditions. In his study, he analyzed the genes circuits of the zeaxanthin-p-diglucoside synthesis pathway, and efficiently synthesized lycopene by cloning three genes crtE, crtB, crtl related to lycopene synthesis in Erwinia uredovora into pET-15b to construct expressing vector pET-15bEIB. He showed us the circuit. He also told us that in this circuit, genes can be combined and sorted to express different pigments, so that bacteria can produce different colors.
Communication with Prof. Lee inspired us that we can make use of these genes as reporter genes. We can even make use of the circuit to do a detection system. The system has the advantage of:
- Color is visible, and can be seen by naked eyes
- The system can simultaneously report a variety of factors
After reviewing relevant literature and information, we identified the core idea of the project - making a visible multi-factor detection system. The initial concept of the system was largely inspired by Prof. Lee's project.
In order to learn more about the feasibility of our project, we asked the professor about the possibility of the circuit as a reporter system. He told us that the circuit had low expression efficiency, low spectral range, minor difference between colors and leakage expression and other shortcomings. Due to the disadvantages of the pigment, we tried to explore other visible indicators. Professor Lee to provided us with the idea of chromoprotein. We searched the relevant information online and found that chomoprotein has higher expression efficiency, wider spectral range compared to pigment. It has remarkable advantages. In the end, we decided to use choromoprotein instead of pigment.
Overcoming the problems of principle
Because we use color to report multi-factor system, so our design of the project involves the principle of color mixing and superposition. Meanwhile, we hope to enrich our system by using fluorescent protein and chromoprotein. However, the mechanism of emitted light and pigment light is different. If we want to apply color mixing, we have to explore the mechanism of light and color mixing. So we visited Professor Shiyong Liu from SJTU Department of Physics and Astronomy. We asked him about trichromatic principle of pigment and fluorescence. We had a deeper understanding of color mixing which provided much help for our later game design.
Carrying the system
As for the detection system we use in our project, we initially decided to test the heavy metal ions in the water, so we interviewed the staff responsible for the Ningbo River management.
They said that the current standard of heavy metal detection is the national standard. If the government does not set standards, they will adopt the industry standard CJ / T51-2004. Most of the detection methods rely on laboratories, such as atomic absorption spectroscopy, chemical reagents, and the like. Meanwhile, the managerial staff said that going to the factory to get samples and sending the samples to the laboratory for testing is a step that cannot be omitted. With the intention to simplify the detection steps, we come up with an idea that we can use the cheap, visual and portable engineering bacteria to do a portable heavy metal detector. And to ensure portability and safety, we need a carrier to carry our engineering bacteria.
Bacteria choosing and wet laboratory experiments
The bacteria we choose, should provide our users with a variety of color systems, as well as meeting the need for multi-factor detection. After discussing much about various kinds of bacteria with the previous SJTU iGEM team members, we finally chose the commonly used E. coli. Because it is known for its compatibility and thoroughness of research, so it is a good engineering bacteria. At the same time, when doing laboratory experiments, we also consulted previous SJTU iGEM team members the problems we encountered.
Finding loaders
We decided to use a microfluidic chip to carry the initial report system. We got in touch with SJTU Micro Nano Research Institute Professor Xiang Chen. Their laboratory has been doing research related to microfluidic chips. He suggested us that we can combine our report system with chip. We can further combine the chip with mobile devices to extend its function. So we start to try chips.
Meanwhile, Professor Chen’s team was recently doing research on the condition controlling in microfluidic chips. They needed cells that can be induced to exhibit colors. So we provided them cells that can be induced by ITPG (isopropyl thiogalactoside) to emit green fluorescence. We helped them progress their research.
However, after the experiment, we found that the chip is not suitable because the color is difficult to distinguish. We began to consider other possible carriers.
At this point, Professor Chen suggested that we could try test papers or microdroplet. We have analyzed the feasibility of the two possible loaders and carried out relevant experiment. We gave up the idea of microdroplet after communicating with a senior in the lab who reminded us some details we had missed. Ultimately, we used the idea of filter paper which presents good results. (For more details in Loader)
The design of detection system
Our detection system mainly consists of two parts: the box and the smartphone App. The Micro-Nano Science and Technology Institute provided us with great help in these two aspects. Firstly, in the aspect of app software development, the micro-nano laboratory provided us with the Java language OpenCv jar package, which offer us some reference to pick color and help us improve our palette game 2048. Secondly, in the aspect of box making, our model is made in Micro-Nano Science and Technology Institute. After the box was finished, they checked our box and offered us some suggestions such as changing some of the parameters, making the box more responsive to the demand and so on.
Business Plan
We have studied how our equipment can fit into society under the current market environment by writing a business plan. If we want to bring our equipment to the market, we need to evaluate the product in detail.
In order to promote our product, and modify it to better meet the social needs, we wrote a business plan. In which we discussed in detail the product development background, market analysis and risk analysis. While doing market research, the conclusions also guided us to improve our products to make it more competitive in the market. We also thought about the meaning of our products to the community, and did some change to our product design.
Biosecurity
In order to ensure our biosafety, we communicated with Professor Shi Jianxin, and briefly introduced the project to him.
We first discussed the way to deal with used bacteria. Because our product is a portable device, so it can not be put under high pressure or high temperature, so we first would like to have bacteria burnt for safety our bacteria. We considered it reasonable because people can reach fire or other forms of combustion. But after the talking with Professor Shi, we realized that this method will have some problems. For instance, it will cause pollution of gas emissions. What’s more the test paper is difficult to ignite, etc. We then asked what was the most common method to sterilize, he mentioned fungicides. Our team members came up with the idea of using disinfectant (its main ingredient is sodium hypochlorite) people can reach in their daily life. It is later confirmed by Prof. Shi that having an overnight treatment with higher concentration of NaClO can successfully inactivate bacteria. Thus safety can be ensured.
Of course, biosecurity also involves many aspects, Professor Shi also made a variety of recommendations for us, the details can be seen biosafety interface.
Professor Ronggui Lee, Department of Molecular Biology, College of Life Science and Technology, Qingdao University
He offered us:
- His study of the pigment
- The shortcomings of the pigment as a reporter
- The strain he used (schistosomiasis)
- The forefront applications of pigment protein
Professor Shiyong Liu, Department of Physics and Astronomy, Shanghai Jiaotong University
He offered us:
- The mechanism of color superposition
- The mechanism of fluorescence and pigment
- Theory analysis of possible results to mix light-emitting protein and chromoprotein
Mrs. Lu and Mr. Chen
They offered us:
- Detection standards of heavy metal ions
- The current water quality detecting process
Micro Nano Research Institute, Shanghai Jiaotong University
They provided us with:
- Technical guidance on microfluidic chip
- The idea of other carriers
- The toolkit of the app
- Advice and adjustment on parameters of the box
they need:
Cells that can be induced to exhibit colors for their research
Shanghai Jiaotong University Professor Shi Jianxin
He offers us:
- Specific explanation to biosafety
- Biosecurity in our experiments
- Advice on the product safety management
