Team:TokyoTech/Specialists
Discuss with Prof.Kondo
As we proceed with this Turing Pattern project, we have seek advices from Professor Shigeru Kondo of Graduate School of Frontier Biosciences in Osaka University, who is a leading expert in Turing Pattern research.
First of all, we received the following comments regarding the Turing Pattern experiment system we aim to complete and the David Karig system we are using this time.
âI don't think there is an example of creating a beautiful Turing pattern using the so-called Turing reaction-diffusion system. Even in the case of Karig's system from his publication, the spot is very small and not a typical pattern.If the spot is small (= the peak width is narrow but very high), the pattern tends to be fixed and dependent on the initial conditions, and the wave nature (always reproducible) cannot be obtained. I don't think it will return to the initial state even if it breaks. â
From this, it was found that the establishment of the experimental system, which is our goal, is highly sought after in the Turing Pattern research and holds high academic significance. However, on the other hand, the signal substance (AHL) of the original system for this project was found to have a slow diffusion rate, so that there was a defect in the so-called Turing Pattern system.
Therefore, we came out with an idea that the diffusion rate of the AHL can be accelerated by using a liquid medium instead of a solid medium. However, in that case, there will be a problem that E. coli will to be able to move freely across the medium. In order to solve this problem, we considered a system that separate the petri dish into many segments while using liquid medium as shown in the image, which is also referred by Prof. Yamamura and Mr. Yasuda. In the future, by creating an array with one E. coli in each segment, we hope to establish the conditions for the pattern to be formed easier by increasing the diffusion rate of the substance and broadening the peak while fixing the location of E. coli.
Second, we received opinions on the idea of manipulating environmental conditions that we are trying to incorporate into the experimental system as new elements. The feedback was slightly negative regarding temperature conditions. The opinion of the professor is as follows:
âTemperature is a difficult parameter to manipulate. The temperature changes spontaneously due to metabolism in each individual cells. Furthermore, as you use the cells, you don't know what perturbation the change in temperature will gives to the system. In a system that includes gene expression, transcription and translation, it will involve numerous enzyme reactions, so it cannot be predicted.Most organisms are living in an environment where the temperature rises and falls, so I think that they have a system that guarantees that. 20 degree and 30 degree zebrafish are exactly the same. Of course, the width of the striped pattern too. â
For this reason, the temperature condition is considered to be slightly less realistic in terms of system clarity, as well as duplication of natural systems. So we would like to explore other conditions in the future.
Third, by making Turing Pattern in a visible manner and creating more patterns, we hoped to spread the attractiveness of Turing Pattern through our Human Practice events. We have thought about creating BioArt and exploring the 3D possibilities using liquid medium. We were told by Professor Kondo that fingerprint authentication are also a powerful candidate as an application of the Turing Pattern reaction-diffusion equation.
âDid you know that the reaction-diffusion equation is used for fingerprint authentication?It is used to create the original fingerprint pattern from an incompletely entered fingerprint pattern.I have also been told that it can be used as a method for automatic generating fabric patterns. â
Based on this knowledge, we looked for a model that can restore fingerprints using reaction-diffusion equations with higher accuracy, and duplicate this into a liquid medium array, thus connecting the experimental part and the simulation part of this project. This is because there is a similarity between the system of this array and the modeling process by the current reaction diffusion equation. In the modeling process, the pattern is determined by dividing the system into blocks and calculating the degree of antagonistic promotion / suppression for each block. Therefore, this can be considered as dividing the system like an array and allowing only movement of materials.
In addition, regarding the application to fabrics, we have thought about the possibility to create clothes which the patterns can change depending on light and temperature by weaving the fabric with hollow fibers and flowing in solution containing microorganisms inside. With this, we may be able to make clothes that change their patterns depending on the season.
Discuss with Prof.Mikami
Our team conducts some educational activities for human practices every year and at the initial stage of our project, but I could not come up with new activities and approaches which should be adopted to enhance the value of human practices in the whole project design. Thanks to the introduction from our PI, Prof. Tagawa, we had an active discussion with Prof. Koichi Mikami of the Faculty of Science and Technology, Keio University. From his point of view as an expert on ELSI (Ethical, Legal and Social Issues) blew off our mindset and gave us hints to rethink about the previous activities.
Prof. Mikami also came to iGEM Japan Summer Meetup, where we organized, and he gave advices to other teams. We would like to be a âhubâ of human practices among Japanese iGEM teams continuously, and hopefully, among Asian iGEM teams in the near future to gain more international viewpoints.
Discuss with Prof.Yamamura & Dr.Yasuda
Meeting with our instructor, Professor Yamamura and advisor, Dr. Yasuda was a good opportunity to gain an insight into iGEM projectâs hardware and modeling.
First, in modeling, we learned that by translating the mathematical formula predicted by Alan Turing into "digital", the calculation process can be simplified. In this method, the diffusion of inhibitor and activator is considered to start at a fixed compartment.
Then, we came up with a plan to use petri dishes which are divided into compartments in our experiment to connect Wet with this digital Turing pattern processing. We believe that by culturing E. coli in petri dishes divided into compartments in liquid culture could immobilise E. coli, and improve the diffusion rate of substances and the ability of Turing pattern formation compared to solid culture.
Furthermore, the technique of dividing E. coli into compartments shares similarities with the modeling method used in this project.
Click here for more information on modeling
