Team:Shanghaitech/Hardware
Hardware
Introduction
To lower the barrier of synthetic biology to the public, we aimed to develop an integrated hardware platform that allows building a complex bio-product free of lab work and with minimal requirement of experience in synthetic biology for the designers. This platform comprises of an interface to a cloud server, a special tube to culture bacteria, and a liquid-handling robot to transfer liquid. Upon receiving the command, the gene circuits to produce a bio-product through a cloud server, bacteria representing the blocks in gene circuits will be inoculated into our special tube. The tube can separate signal molecule-containing supernatant from bacteria cell mass. The supernatant is transferred as desired to another tube through our robot, thus connecting two blocks in the circuits. With delicate gene circuits, a bio-product is produced. Therefore, the designers produce a bio-product without visiting bio-labs. We have built a low cost prototype hardware platform and showed it functioned properly.
Here is a brief introduction of our hardware design. With our proper design and manufacture, we can make our prototype hardware within 1 day and with less than $180, which is very cost effective.
A. Interface with a cloud server.
As shown in the demo video, we have successfully built the prototype hardware platform and verified that this platform could be controlled remotely through our software interface. It will work autonomously after receiving proper commands via internets or a cloud server. ($120)
B. Special tube to culture bacteria.
Design
Manufacture
Our magic blocks are bacteria cultures with desired information processing ability. To connect bacteria with clear logic rules, bacteria need them to communicate with each other according to gene circuits designed by the designers. We used quorum sensing system to communicate one bacteria population with another. The secreted signal chemicals need to be transferred between bacteria to induce further signal production. However, the transfer of bacteria cells should be avoided so as to reduce the interference between different bacteria populations. Therefore, we need to design a special culture tube (Fig.B) so that the culture supernatant can be easily sucked away and cells will stay in the original tubes. As shown below, to make our special tube, we glued two tubes together separated by a 0.22um membrane so that the bacteria will stay in the larger tube outside and signal chemicals can diffuse into the smaller tube inside. The supernatant inside of the smaller tube can be transferred out by our liquid handling robot as needed.
Fig.B The design of the special bacteria culture tube. Only supernatant that contains signal molecules can be transferred out to initiate further responses.
Specific steps:
Step1: Cut a 15 ml centrifuge tube at the position of 0.6 ml. 5s pre-heating to soft the tube is recommended.
Step2: Apply a layer of glue evenly to the exposed cross section of cut and then glue a piece of 0.22 um membrane to it. Apply additional layer of glue to strengthen the attachment between the membrane and the cross section.
Step3: In the lid center of a 50 ml centrifuge tube, make a hole so that the 15 ml tube can pass by. And then fix the 15 ml tube inside of the 50 ml tube with glue as showing in the left. Now the bacteria can be culture in the 50 ml tube and the signal containing supernatant can be removed from the 15 ml tube.
C. Liquid-handling robot
- Get an X-Y-Z 3 axes programmable platform
- Assemble a syringe pump
- Mount the syringe pump to the 3D printer
- Program the 3D printer and the syringe
Design
Considering the cost and manufacture difficulties, we decided to DIY a liquid handling robot by reconfiguration of a 3D printer together with a syringe pump. The ready-made interface port in the printer allows automatic and remote control. We therefore can program the 3D printer rig to move the syringe pump to suck and transfer liquid from the special tube we designed above.
Manufacture
We bought an anycubic-i3 3D printer for reconfiguration from Taobao:
(https://item.taobao.com/item.htm?id=530445909316)
DIY Components
Assembled Rig
To assemble a syringe pump, we bought a screw rod ($1.5) to mount an extruder’s stepping motor with its coupler (https://item.taobao.com/item.htm?id=16191694967) 5mm transfer to 8mm $3.2.
screw rod
coupler
stepping motor
Assembled syringe pump
Attach the syringe’s pushrod with the nut of screw rod. Link the syringe to the plastic tubing on the mobile platform.
Any serial assistant software outputting G-code commands can control the 3D printer and the syringe pump. We used the pronterface (http://www.pronterface.com/) with baud rate 250000 to control both. Now the assembled platform with the 3D printer and the syringe pump is in action. The 3D printer rig can move the suction tip to desired tubes specified by gene circuits. Then the pump can suck the supernatant via the suction tip and transfer liquid to another tube to initiate further signaling.
The pronterface window
