Device Prototype

Our team decided that in order to ensure that this system is physically feasible that we would aim to produce a working physical prototype. In this process it was imperative that the end-user was considered and that the materials used made our system economically feasible and compatible with the biological system. Through collaboration with the transformers, detectors and our human practices sub-teams we were able to manufacture a working prototype as the first stage of development.

Process

(Edit)***Integrate creation paragraph below into this section*** Our device is portable and user friendly and manufactured specifically with informed design considerations for the developing world. A drop of blood from a patient first needs to go through sample preparation to extract target DNA out of the sample. A sample with extracted DNA then flows into the Polymerase Chain Reaction (PCR) chamber where target DNA is amplified via isothermal PCR. Reaction takes a couple of hours to complete and the sample is manually pushed out of the PCR chamber into separate chambers with B. subtilis. In each of the chambers, B. subtilis is engineered to detect a specific disease allowing for multidiagnosis.

Economic feasability - Two-Tiered Model

Economic feasibility is of the utmost importance when dealing with diagnostics in the developing world and therefore our team chose to tackle this issue using a two-tiered development phase. An inexpensive model would utilize the basics of the colourmetric system in which a simple colour change would indicate presence of the specified disease. This signal is easily visible and readable and requires very little technology other than a chamber for Polymerase Chain Reaction (PCR) to occurs and consequential separation of the sample into separate detection wells. Additionally in order to ensure that there is development potential should this modular system expand to other industries a completely digitized device was also explored. The colourmetric signal of the reporter is picked up by a colour sensor that detects the reflected light of this signal, converts it into a voltage and is output to an LCD screen. This exercises the potential of being able to send results of a test directly to a patient's file with bluetooth use.

Cost Analysis

Manufacturing

The goal of producing a physical prototype brought different perspectives of the best way to produce such a device. Through expert consultation it was determined that microfluidics would increase the price greatly and would not be ideal for our device, however using polytetrafluoroethylene tubing would alleviate this issue and prevent cells from adhering to the inner walls of the device. Both options of 3D printing and machine manufacturing were explored, however it was determined that manufacturing the device would allow us to have direct control of the use of polytetrafluoroethylene for both the chambers and the transport tubing. In collaboration with a mechanical engineering student William Gill from the Schulich School of Engineering Machine Shop - a design was created and analyzed and produced from the desired materials.

Fluid Flow Analysis and Angle Optimization

In our initial design, most of the fluid would flow into the outside chambers from the PCR chamber. In order to make sure the fluid flows equally into the three chambers, fluid flow analysis was performed. On optimal angle for the tubings was found to be 20 degrees.

Figure 1: Fluid flow analysis for different angles between the tubings and the fluid flow in the PCR chamber

The design on the device was then changed to have chambers located symmetrically and radially oriented around the chamber. This allows the end user to alter the number of chambers if necessary which consequentially decreases the tubing distance and the resulting cost. The fluid flow analysis on the new design with three chambers was also performed to ensure that with this changed design the fluid is still flowing equally into the chambers. Additionally it was very important to ensure that when adding more chambers, considerations are made for the amount of fluid available in the PCR chamber. This should not be an issue for our developed prototypes and their designs, however if the need arose to have a very large amount of detection chambers, this would be a very important fact to consider.

Figure 2: Fluid flow analysis for the new design with three chambers around the PCR chamber

Colour Sensor

For digitalized version of our device, we are using ColorPal Parallax colour and light sensor to detect colour change in bacteria culture in each of the three chambers. Parallax sensor uses its’ LED lights to shine red, green, and blue at the sample. Then the sensor measures the reflected light and outputs the voltage proportional to all the light that it sees. The Arduino Code then converts the sensor values to red, green, and blue components and outputs it to the screen (or LCD display). Since our prototype has three different chambers with bacteria, the initial plan with the ColorPal Parallax colour and light sensor was to measure the colour in all three chambers at once. In order to achieve that, we would need to have three different colours for the chambers. In theory, we expected to see noticeable change in red, green, and blue components when just one of the colours was present versus two different colours present at a time (co-infection). Figure 1 shows the set up that we used to test the colour sensor with three chambers. However, the results were inconsistent. We had little control over the system and the sensitivity of the sensor goes down in this set up. For example, if one of the stripes got contaminated with RFP, we would not be able to tell using the colour sensor.

Figure 3: Colour sensor testing set up: three stripes within 1 cm range imitating the three chambers. Four test squares clockwise: 3 blank; 1 red and 2 blank; 1 red, 1 blue, and 1 blank; 1 blue and 2 blank.

After initial testing, we decided to measure each chamber individually. The sensor was much more effective when detecting one colour at a time, even if the sample was rather faint and less distinguishable. Initially, the code for the colour sensor was referenced the from Parallax website, but was thoroughly modified to suit our specific purposes. The sensor needs to output five consistent measurements before the colour is outputted. Once the colour is changed, the sensor detects new measurements and outputs the new colour after 5 consistent measurements.

Figure 3: 3D model of the initial design (left); 3D model of the first manufactured device (right)

Design Optimization and New Design

Our first design was analyzed and optimized to make the prototype cheaper, more compact, and allow for the addition of extra chambers. The main change to the design is the location of B. subtilis chambers. The three chambers are now aligned radially and symmetrically (120° angle between the chambers) around the PCR chamber. First of all, this allows us to use shorter pieces of tubing for transport of the sample reducing the cost of the device and making it more compact. Secondly, this design allows us to easily add more and adjust the number of chambers if needed. Analysis proved that as long as the chambers are symmetrical and radial around the PCR chamber, the fluid would flow equally into each chamber. This means when the design is altered for a specific purpose or disease set, fluid flow analysis would not be necessary as the flow would be guaranteed to be equal. The volume of the B. subtilis chambers was reduced so the size of the chambers was also reduced making the device even more compact. The device can now fit on a circular aluminum pad with a diameter of 4 inches. Alternative materials were explored as opposed to the steel plate from the first design. This was for the purpose of showcasing our device over the course of several months, however cheaper alternatives were explored for implementation of our final device.

Figure 4: 3D model of the new design with three chambers located radially around the PCR chamber to ensure equal fluid flow to each chamber (120° between the chambers)