Publications

RT-qPCR is the gold standard for testing for COVID-19 infections, but its equipment is too costly for low-resource settings and extraction step can take a significant amount of time and labor. We found that the RT-qPCR assay can be performed directly on patient sample material in VTM without an RNA extraction step, while still producing sensitive test results. We also developed a $300 USD water bath based device that can process up to 96 samples at a time in 12 minutes and validated our work with COVID-19 clinical specimens.

The Omics in Space team developed the μTitan (simulated microgravity tested instrument for automated nucleic acid) system capable of automated, streamlined, nucleic acid extraction that is adapted for use in microgravity. Its performance is equal or greater than similar commercially available, earth-based, automated nucleic acid extraction devices and it produces laboratory results even when deployed in low resource and field settings. The μTitan system was validated using a whole cell microbial reference (WCMR) standard comprised of a suspension of nine bacterial strains, titrated to concentrations that would challenge the performance of the instrument, as well as to determine the detection limits for isolating DNA.

This article outlines converting a 3D printer into a sample preparation instrument using magnetic coupling to implement nucleic acid extraction in an individually-enclosed setting. With this work, it also reviews the design of reagent wells to have optimized fluidic control in microgravity to additionally meet the challenges of molecular diagnostics in space. It references current works on sequencing in space and lastly reviews the potential of microfluidic technologies for molecular diagnostics in space.

We repurposed a 3D printer for use as a cost effective, rapid point-of-care test with medium-throughput capabilities for nucleic acid extraction and detection. We demonstrated our system’s capabilities to perform recombinase polymerase amplification reactions, isothermal amplification and detection of template DNA or RNA using foodborne pathogens and Zika virus.

We developed a low-cost platform that can automate high quality RNA extraction from up to 12 ZIKV-spiked urine samples simultaneously. It can also perform reverse transcription recombinase polymerase amplification reactions (RT-RPA) in under 15 minutes. Existing immuno-based rapid tests often fail to distinguish between Zika and related flaviviruses that are common in affected regions. However, the RT-RPA and RT-PCR assays shown here also do not cross-react with dengue and chikungunya viral RNA, diminishing this issue.

MnZn nanoparticles have composition-tunable magnetic properties. We investigated factors influencing the size and morphology of these nanoparticles during the thermochemical synthesis process. An increase in reaction temperature and time increases size and formation of cubic shapes. The size growth process can be described by an aggregative growth mechanism. While the apparent rate constant decreases with the reaction temperature, the growth factor remains at 1–2, consistent with a low-dimensionality growth mode. The dependence of the overall average particle size on the reaction temperature yields a diffusional activation energy in the order of 10–20 kJ mol−1, a value slightly smaller than those reported for aggregative growth of other types of NPs in solutions.

We modified a 3D printer to conduct magnetic particle-based nucleic acid extraction and shuttle PCR. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation is comparable to gold-standard spin-column-based extraction technology. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%.

Consumer-class quadcopter drones are used as a portable biochemical analysis platform for rapid field deployment of nucleic acid-based diagnostics. This approach exploits the ability to isothermally perform PCR with a single heater. A smartphone camera and integrated image analysis app is used for detection and quantification. Standard sample preparation is enabled by leveraging the drone’s motors as centrifuges via 3D printed snap-on attachments. These advancements make it possible to build a complete DNA/RNA analysis system at a cost of ∼$50 ($US). This capability is demonstrated by successful in-flight replication of Staphylococcus aureus and λ-phage DNA targets in under 20 min.

Here, we added on our previously reported $200 Thermos Thermal Cycler (TTC) set up to enable the detection of viral RNA targets by RT-PCR, thus expanding to identify highly infectious, RNA virus-based diseases in low resource settings. The TTC was successful in demonstrating high-speed and sensitive detection of DNA or RNA targets of sexually transmitted diseases, HIV/AIDS, Ebola hemorrhagic fever, and dengue fever. The TTC’s speed exceeded that of commercial thermal cyclers tested and it can process 8 tubes at a time.

Thermoses were used for a rapid water bath based thermal cycler that does not require active temperature control or continuous power supply during PCR. It can also accept any size or shape of tube. This unit costs $130 to build using commercial off-the-shelf items. The thermoses contain heated water (for denaturation and annealing/extension steps) and a layer of oil on top of the water stabilize temperatures for PCR to take place. Using an Arduino-based microcontroller, we automate the “archaic” method of hand-transferring PCR tubes between water baths. This unit can deliver high speed PCR and can amplify from templates down to at least 20 copies per reaction.