In the Open Lab activity, we realized the urban-rural gap is not just a term in the textbook, but a real situation. To support rural teachers without an assistant, we designed a gel preparation machine to allow teachers to prepare the experimental equipment in advance. Since an electronic autopipette is unaffordable in rural schools, we designed an agar faucet to assist in and standardize agar plate production.
Initially, we tested our ideas and generated a prototype of an agar faucet with a 3D printer. The first prototype had an agar bottle cap, which was abandoned because it was not air-tight or user friendly. Therefore, we rebuilt the design and generated a prototype agar faucet using PLA material and a 3D printer. This PLA-based agar faucet works well, is convenient, and allows standardization. Next, we turned to improving this agar faucet using aluminum, to allow for sterilization. Finally, according to feedback from the users, we decided to evolve the agar faucet into an agar revolver in the future.
To save rural teachers from the time-consuming preparation needed to do experimental work in synthetic biology in their classes, and thus encourage them to do such lab work, we designed a gel preparation machine with remote control. The design of the gel preparation machine follows the sequence of gel preparation, from mixing agarose powder with TAE buffer, heating, shaking, solidifying, to demoding. We further designed a remote control so teachers would not have to be in the lab to use it.
With the agar faucet and gel preparation machine, we hope to contribute resources and ideas to this society to help reduce the urban-rural gap.
The tilt-shaped agar cap was composed of a cap with a metric thread, and a tub-shaped container with a bevel to pour agar.
The tilt shape helps the agar liquid flowing out smoothly for convenience.
The metric thread could fit the common serum bottle, which is a general container in a biology lab.
This could help us to pour a quantitative amount of agar from bevel.
The pressure-control makes it easy to control the amount of liquid agar flowing into the tub.
Agar bottle cap
Test result of the agar bottle cap
The agar bottle cap design had lots of problems in testing. For example, the tilt-shaped body was not ergonomic. The angle of tilt and rigid sharp made it hard to handle and to pour the agar smoothly. What's worse, the pressure-control button did not work, because the metric thread was not air-tight. The thread could not perfectly fit the opening of the serum bottle, even though we adjusted the thread and printed an o-ring. Therefore, we decided to stop developing this idea, and move to a different design.
Remove the tilt shape
Test o-ring
Adjust thread
What if we skipped the idea of a container with a fixed volume and let the gel flow steadily? Then the quantification could be achieved by controlling the flowing time. Along with this idea, we decided to focus our design on easy operation. Inspired by a batter dispenser, which can be operated with one hand, we built a second version, Agar faucet.
The agar faucet is composed of a handle, a funnel-shaped channel, and a flow blocker based on leverage.
This lets the user more easily hold the faucet with a container on it.
The funnel shape helps to control the flow rate.
Helps users to control the gel using leverage.
Quantification results
To examine whether the agar faucet assists the standardization of agar plates, we respectively weighted 13 agar plates poured by agar faucet or by hand. The box plot of the quantization result indicated that the weight of agar plates made by agar faucett is more precise, as compared to manual ones. Therefore, we moved to deal with other questions: the sterilization requirement and the speed of operation.
The accuracy between two methods
Sterilization requirement for the agar faucet
In practice, the agar faucet would need to be sterilized in an autoclave, which is impossible with the PLA material. Therefore, we changed the material from PLA to Aluminum.
The original design of the flow blocker had a curved, aesthetically pleasing surface, which is practical for 3D printing, but not processing a metal workpiece. After discussing with Professor Wu, we adjusted the blueprint of the agar faucet, and separated the agar faucet into four pieces to produce.
Before
After
Components of the aluminum agar faucet
The parts of the flow blocker are processed by sawing and the pillar drilling machine. After processing, the components will be welded together.
We first turned the outer diameter to the proper size by lathe, and then drilled and bored the internal diameter to fit the diameter of the funnel. Finally, we adjusted the blueprint of the agar faucet, and separated the agar faucet into four pieces to produce.
The largest and smallest outer diameters of the funnel shape, the funnel and the channel, respectively, are turned by lathe. The taper of the funnel is turned by swiveling the turning tool, and the inner diameter of the funnel is bored with a pillar drilling machine. Finally the bevel of the channel is cut by a milling machine.
We turned the outer diameter to the proper size using a lathe, and cut the curved surface to fit the outside diameter of the thread with a milling machine.
Components of aluminum agar faucet
After discussing with Dr. Lee from the precision molding research center, we came up with a new idea – Agar revolver. The agar revolver will be composed of the following three parts:
This part includes a metric thread to fit the common serum bottle.
The chambers will look like the cylinder of a revolver.The agar will be loaded into chambers one by one.
The wheel will turn the chambers one by one to the exit barrel.
Agar revolver
Agarose gel electrophoresis is a routine in experiment to examine the size of DNA fragments. The electrophoresis experiment is simple, but the agarose gels should be prepared freshly for the best resolution. To save time and manpower when making agarose gel, we designed an automatic machine to make agarose gels remotely.
The machine is comprised of five parts, following the gel preparation steps:
"Preparation of solution" quantifies the amount of TAE and agarose, while "heating" and "blending" heat and mix the TAE with agarose and deliver it to the mold. The "demolding" part demolds the gel after solidification. The "cutting" part slices the gel into ideal sizes and stores the sliced gels in TAE buffer.
Archimedes screw
An Archimedes screw is used for transferring materials from lower to higher places through turning. By setting the number of turns of the screw, the amount of materials transferred can be determined.
To quantify TAE and agarose, we included Archimedes screws in our design. The design of the Archimedes screw for the TAE buffer is conventional, while the design for the agarose powder is quite different. The screw for the agarose powder has an outer screw with an inverse spiral to increase the flow of powder and avoid jamming.
The Archimedes screws will be powered by gear motors, which are installed on the demolding platform. The adjustable speed of the gear motors enables us to operate the Archimedes screws at a certain speed to measure the amount of TAE buffer and agarose.
Storage box
The storage boxes for the solute and the solvent are designed to cooperate with the Archimedes screws. The walls of the storage box are tilted to fit the angle of the screw and to collect the TAE buffer even when the level is low. The U-type trench in the wall is designed to connect the water outlet of the screw and to collect the TAE buffer non-directionally, because rapid screw movement could splash the transferred materials.
Front elevation (TAE box)
Corss section of front elevation (TAE box)
End elevation (TAE box)
The route of TAE (TAE box)
Agarose box
TAE screw animation
Agarose screw animation
Enameled copper wire and heating box
We applied enameled copper wire as the heat source. The electric current going through the enameled copper wire will be transformed into heat. To provide the heat uniformly, the enameled copper wires are twined around the heating box. The heating box is made of aluminum, due to its light weight and high thermal conductivity. The light weight of the box can reduce the load to the blending device, while high thermal conductivity can not only increase the dissolution rate but also dissipate heat quickly when cooling to solidify the gel.
Shaking pedestal
Agitation is necessary for the uniform mixing of heated TAE buffer and agarose powder. Therefore, we made a shaking pedestal under the heating box with a servo motor. The servo motor horizontally moves the pedestal through an attached cylinder. The motion trail will be a roughly 60 degrees circular arc, presenting a regular oscillation.
Upper mold
The upper mold is vertically controlled by a stepper motor linear actuator. The upper mold moves down after the shaking pedestal uniformly mixes the dissolved agarose, and the agarose gel will be solidified on the bottom plate of the upper mold. After the agarose gel is fully solidified, the upper mold can move upward to demold the gel from the lower mold.
Upper mold
Lower mold
The lower mold is actually the same as the heating and blending part, but adding a comb for the wells in the agarose gel. The comb is made of aluminum by a milling machine to limit weight and increase temperature resistance. The intervals between each well are 2 mm, the length of each well is about 1.5 mm, the width is about 4.5 mm and the height is about 8 mm. The upper mold will go through the comb to manufacture wells on the gel.
Lower mold
Gel pusher
After the gel is solidified, the upper mold will move vertically to a fixed height. At that time, the upper mold, the gel pusher, and the cutting tunnel will be horizontal coplanar. The final demolding step is executed by the gel pusher. The pusher uses a motor to drive the gear and the gear rack to implement forward motion to demold the gel from the upper mold.
Gel pusher
The cutting tunnel
A tunnel loaded with blades is designed in front of the demolding platform. There are equidistant grooves on the tunnel to load blades, which allows users to choose the size of the gel. When the gel is demolded by the gel pusher, the blades loaded in the grooves will cut it into ideal pieces. Gel pieces then slide into the gel storage box.
Gel storage box
After manufacture of the gel is complete, the gels have to be stored in the TAE buffer. Therefore, a box filled with TAE is made for this purpose. There are three boards in the storing box. One is a dust cover, another is a platform to stack the gel , and a third perpendicular board connects these two as a handle.
Gel storage box
To accomplish remote control, we use Raspberry Pi as the embedded system in our machine. Control of all components is coded in C programming language to command each GPIO pin.
We coded a program which can switch the signal between 0 and 1 and change the ratio of two signals. As a PWM signal, the turning direction of the motor can be controlled. This is coordinated with the mechanism design to attain the desired blending effect.
Through controlling the ratio of 1 and 0 signals, we can create a unique sound for warning or finish.
To illustrate the information needed by the user, we control the signal from the CLK pin and two DIO pins.
We need to apply 24 volts to drive the gear motor and heating coil but the Raspberry Pi can only supply 3 volts. To solve this problem, we use a relay to control another power supply.
Raspberry Pi cannot achieve concurrent and countercurrent signals of 5 volt, but this is what we need to control the clockwise and counterclockwise rotation of the motor. Thus, we apply a motor controller module to help us to control the direction of rotation of the motor.
This is a relatively special motor. It cannot be controlled simply by transmitting electric current. Instead, it needs four pins to output the signal sequentially so that the motor can function. Therefore, we also use the motor controller module to change the output and input signal of different pins.
We use C programming language calling the wget command from linux to receive messages from the server every five seconds and return its current state. For multiple threads, we can receive commands while controlling the signal from each pin.
We use a website to build a user interface available to users. By using php programming language manipulating mysql database, user commands and status messages from Raspberry Pi can be stored and exchanged.
User interface
For users, we can operate the data on the server through a specific website, indirectly controlling the operation of the Raspberry Pi. We can also check the current operating state of the Raspberry Pi on the website.
In order to quickly test the feasibility of our concept and build complex shapes, we utilized 3D printing technology to build our prototype, because it is relatively simple and straightforward compared to traditional machining. Before printing it, we had to first build a model with a Computer-Aided-Design (CAD) diagram. Based on a course in the mechanical engineering department we chose CREO, a convenient software for engineering drawing used worldwide. After that, we needed to turn the file into mechanical code (.gcode ). Then, our 3D printer Ultimaker Cura 4.0 could read our blueprint and start to print.
3D printer
In order to allow our product to withstand moist heat sterilization, a widely used method in the laboratory, we made a model, completing most of the process in our factory classroom.
Cutting metal sheets, metal rods and acrylic boards.
Turning and drilling the metal rod.
Cutting metal sheets and conducting face milling and side milling operations.
Cutting the acrylic board.
Drilling out metal workpieces and acrylic boards
We could not even imagine how much time and money we would need to spend if we did not have access to those tools. Processing in the factory not only saved us lots of time but also taught us a lot!
Agar faucet
Agarose straw ( 
TAE straw ( 
The cutting tunnel