NEW YORK (GenomeWeb) – In low-resource settings with poor infrastructure, setting up and staffing remote lab sites during an infectious disease outbreak is a huge challenge.
Researchers have long sought ways to deliver molecular diagnostic testing capabilities to far-flung areas. Now, scientists at Texas A&M University have developed an inexpensive way to perform rapid molecular testing using quadcopter drones and a rapid PCR-based system.
The technique, published in Analytical Chemistry last month, relies on a thermal cycling method that is unlike typical spatial or temporal thermal cycling, in which either the sample moves between heat sources or the sample is stationary and the heat source fluctuates between melting and annealing temperatures.
Convective flow thermal cycling is actually isothermal, in so far as there is only a single temperature applied to the sample tube. The heat source is set against one face of a small reaction column, such that the opposite face is cooled by convection.
With just the right height and width, a convective flow pattern will become established within the column. Nucleic acids melt at the bottom of the column, but as they become hotter and less dense they rise to the top, passing through lower temperature zones and elongating along the way. They then cool, becoming more dense, annealing, and sinking back to the bottom to melt again.
Thus, the method is spatial PCR in that the sample is traveling between heat sources. It is also isothermal — with respect to the instrument, not the PCR reaction — in the sense that only a single temperature is applied, and this enables very low electrical power consumption.
Lead investigator Victor Ugaz, a chemical engineer at TAMU, said he had been working for over 10 years on the convective flow method, beginning as a post-doc at the University of Michigan.
"It's like a mini lava lamp," Ugaz said. "You heat reagents from below, and if you do it correctly you can generate a flow pattern by imposing a temperature gradient."
But unlike its conceptual cousin, which perhaps evokes a more meditative and tranquil mindset, convective flow PCR is based on some hardcore physics and is quite rapid, with 35-second equivalent cycle times, demonstrating 20-minute in-flight replication of Staphylococcus aureus and λ-phage DNA targets. It is also quite small, with reaction volumes of about 20 microliters.
A previous iteration of the system published in the Journal of Visualized Experiments showed the relationship between the aspect ratio of the column and the circulatory flow. The previous method, however, used two hot plates, while the current method uses only one. The system has also now been upgraded so that the shape of the PCR column allows the same system to run reactions with different melting and annealing temperatures and is optimized by adopting a chaotic flow pattern.
The convective method was initially described in a 2002 Science paper. "Since then, it's been like a curiosity; we hadn't found the right niche," Ugaz said. However, the current incarnation has proven to be remarkably rugged.
Case in point: it can run on a flying quadcopter drone.
The work was inspired in part by a graduate student, who showed Ugaz a video illustrating the portability of a 3D printer by having it print something while flying on a drone.
"That gave us an idea. ... We should be able to attach [our system] as a payload and do the reaction during flight," Ugaz said.
But ultimately the drone project was taken on by a team of undergrads participating in an engineering challenge at TAMU. Ugaz mentored the team, with the challenge of creating a prototype commercial product from ongoing research.
The team then made the first prototype of the device, winning second place in the "AggiE-Challenge" for the project. All 14 members are authors on the Analytical Chemistry study.
The PCR is performed with heat from two resistors, requiring a 5-volt USB power source. It can also be run with a battery, or using solar or hand crank power. And, although the quadcopter drone can cost around $500, the PCR system costs only about $50 to make. It is also very "simple to produce," and weighs only about 300 grams, or roughly the same as the GoPro cameras that are standard payloads for quadcopter drones.
Additionally, the method uses fluorescent detection with a smartphone camera and an app called PCR to Go, developed by grad student and co-author Aashish Priye.
The app takes a sequence of photos and analyzes intensity of a region of interest to derive fluorescence changes over time. For now, this data has to be corrected, thresholded, and plotted offline to get a real-time curve, but the group is working to build these functions into a future app.
The group also collaborated with Season Wong of TAMU and AI Biosciences. Wong, who has recently developed a low-resource method of PCR using thermoses, collaborated to help apply the device for specific diagnostics tests.
Wong has "been working on a lot of low-cost, diagnostic gadgets," Ugaz said, and also saw that the motors of the quadcopter could be repurposed for centrifuging spin columns. He and a colleague at AI Biosciences 3D-printed attachments that enabled centrifugation at speeds of 10,000 RPM.
"Sample prep is another ongoing need for portable analysis," Ugaz explained, noting other low-power solutions, such as using a salad-spinner or bicycle wheel, are good for separating plasma from whole blood but can't achieve the speeds needed for conventional sample prep spin columns.
"The drone has four motors, so we got the idea we could use the drone itself as a lab instrument to do part of the workflow," Ugaz said. And from a mobile PCR platform with centrifuging capabilities, several scenarios could arise, he said, such as deploying the drone to be used as a lab instrument at a remote site. "Or you could imagine sending more than one, with one used as a centrifuge and another used for transportation," Ugaz said.
Ultimately, the ability to send out easily-modifiable networks of diagnostic modules, rather than laboratorians themselves, could alter public health approaches to outbreaks and infectious disease emergencies.
"You have to kind of change the way you think about deploying things," Ugaz said. "Conventional ways are in a set sequence of events, but maybe there are other ways that could be enabled if you have a low-cost way to deploy many things, in many different ways."
The convection flow thermal cycling method is currently under patent protection, and the lab is seeking additional funding. The group is also interested in collaboration, said Ugaz.
"We're excited about this work because we're hoping it can really help us connect with an industrial partner, or anyone, and that this could get on the radar screen and maybe lead to a practical application," Ugaz said, adding, "I think that's what anybody in science would love to see — their discovery actually translate into a product that can really help people."