Before beginning the design for our device or any part of it, the team went through the engineering design process, revisiting a few steps multiple times. Before going into each of the processes, a timeline was developed for summer work. Team was expected to adhere to this timeline to ensure a enough time for each step.
Figure 1. Engineering Timeline
The engineering process started with research, during which all the members of the engineering team divided into groups of two, to learn more about our core topic: “Food Safety”. One group dealt with potential target groups, one with patents in this field, one with current devices for food safety and another with current detection devices (more details). This research gave the team an overall understanding of what the current market and current academia had to offer to different groups of users and their needs. It was during this process that the team agreed to work on a device that was specific for travellers. As we continued working on this track, we got opportunities to interview people from different backgrounds and different specialisations (more details). The input we received from these experts directed our project towards customisable devices, later in the timeline.
From the analysis phase, the team moved into ideation together. We explored numerous methods of ideation and went through the process with the biologists present as well, to make sure that the idea was feasible in terms of biology and engineering (more details). The previously pitch of the use of a microfluidic device was confirmed, while a sample collector idea became more specific and concrete through this process.
Figure 2. Board of possible ideas / inspirations for the device
After the ideas were evaluated and the team settled on the sample collector and microfluidic chip, the team worked separately on proving the working principles for these two devices.
Designing the microfluidic chip involved meeting the regulations and requirements given by different parts of the project. Through our ideation process, we wanted a relatively cheap chip that could be easily used by end-users, which meant that the chip needed to be filled with the sample with a simple motion while avoiding contamination during the process. It also had to be portable and the results needed to be visible relatively easily. There were also specific requirements to ensure that LAMP/RPA reactions occurs properly. The reaction wells needed to have a 25um volume at least and the chip also needed to be able to withstand and transfer heat well. Engineering requirements from other parts of the Pathogene device was also present. The chip had to fit well on the heater and needed to be easily visible within the device. For the purpose of fitting well on a square heater, being easily visible, and making sure that each sample would arrive at the reaction well at the same time, the chip had a radial design. The circular chip had a circular inlet in the middle. The reactions wells were around the edges of the chip connected to the inlet by small channels.
Figure 3. Microfluidic Chip Design Evolution
To reduce the cost of production we used a laser cutter to cut the chip. The first material we chose to prototype was clear acrylic as it was a relatively good heat conductor, cheap, and readily available. However, prototyping with clear acrylic proved to be problematic. One of the main issues was that it needed pressure for the liquid to properly flow into the wells as acrylic is hydrophobic. Although we could have added a device that would be able to apply pressure to the chip, for the sake of reducing the cost and the steps involved in using the device, we decided to use a hydrophilic material. The hydrophilic material that was then used was the 3M diagnostic hydrophilic film. Different prototypes were created using the film and double-sided tape. The conventional channel width for microfluidic chip is less than 200μm due to capillary action. However, as the chip we made was made with hydrophilic film, for the sample liquid to flow well, it was more important to increase the area that liquid comes to contact with the film to ensure good flow. Through prototyping, we found out that 600um was the best width that would make sure that the sample flows well in the chip but does not flow back into the inlet.
Integrating the chip with actual LAMP/RPA reaction brought more challenges. We had to make sure that the reagents in the chip will not evaporate during the reaction. Making sure that there are no bubbles in the chip so that all the appropriate volume can be filled was another challenge. To make sure that the bubbles are eliminated, holes on the film were created where bubbles typically form to make sure they can safely escape from the chip without causing cross-contamination or backflow. The holes are on the most outer part of the reaction wells. Evaporation was also prevented by adding oil on top of the chip. As oil is less dense than the sample and the reagents, but has a higher boiling point, the oil remained on top without mixing and prevented evaporation.
Figure 4. Excerpt from Microfluidic Chip Technical Drawing (Available in Lab Notebook)
The sample collection and preparation method used by the previous iGEM NYUAD Team involves the use of a sterile medical swab to brush the sample, swirling it inside a pre prepared solution inside a Pasteur Pipette and loading the sample using a pipette. This method requires training, careful usage, many separate pieces and both hands. Our design for the sample collector device is portable, sturdy, requires minimal training and has a mostly one handed use. Furthermore, it is cheap to produce. We achieved this design by first identifying the working principles of a pen-like design and tested them using small scale rapid prototyping and and 3D printing for more complicated structures.
Figure 5. Identification of sample collector working principle
The main working principles for which the sample collector needed testing were effective collection / release of sample, safe storage of TE buffer solution, and prevention of cross contamination. These principles were tested at their most basic level and refined with each successive test. Some examples are illustrated below. Full documentation may be found in the Sample Collector Engineering Lab Notebook.
Figure 6. Testing effective collection (using a swab) and release (passing water pressure through the swab) of a sample. Working principle was effective.
Figure 7. Test the safe storage and effective release of the TE buffer using a film sealed plastic chamber released by a plunger. Showed film kept TE buffer sterile before use.
Figure 8. Testing TE buffer chamber cross contamination from a contaminated used cotton swab. Small blue dots inside the chamber show cross contamination. This indicated we needed a single-use device.
After confirming the working principles and reiterating the design process several times, all the working principles of the sample collector were integrated into a general design. All versions of the sample collector will follow this general design.
The final sample collection design works by brushing the sterile cotton swab against the desired sample. The design contains a sterile watertight chamber for TE buffer solution sealed with a thin watertight film for safe transportation and use. The funnel maintains the film in place through pressure with the use of three screws. Once sample collection occurs, TE buffer is released through the press of a plunger, which the funnel guides into the cotton swab with the sample, washing it out in the process. The lid directs the liquid flow into the microfluidic chip inlet, making the integration and transition between sample collection and sample preparation seamless.
The sample collector is currently manufactured with 3D printed PLA with the exception of the sterile cotton tip swab and the plunger retrieved from standard 10 ml medical syringes. It uses two O-rings (at the base of the sample collector and funnel) to ensure water tightness. The design is easily scalable and optimizable for other applications.
After the working principles were verified and the first prototypes were made, these two parts were tested together in integration. Main aims of these tests were to make sure that the user did not have to touch the sample and to ensure that this process was simple and intuitive. The video below illustrates the working of these two parts together.
In the bigger picture- these two parts replace numerous steps involved it the same reaction was to be run in a lab setting. The sample creator replaces the cotton swab, test tube with buffer and pipette while the microfluidic chip replaces the numerous test tubes and the need for a mechanism to separate the collected sample for different tests.