Current multiplexed diagnostics for Zika, dengue, and chikungunya viruses are situated outside the intersection of affordability, high performance, and suitability for use at the point-of-care in resource-limited settings. Consequently, insufficient diagnostic capabilities are a key limitation facing current Zika outbreak management strategies. Here we demonstrate highly sensitive and specific detection of Zika, chikungunya, and dengue viruses by coupling reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with our recently developed quenching of unincorporated amplification signal reporters (QUASR) technique. We conduct reactions in a simple, inexpensive and portable “LAMP box” supplemented with a consumer class smartphone. The entire assembly can be powered by a 5 V USB source such as a USB power bank or solar panel. Our smartphone employs a novel algorithm utilizing chromaticity to analyze fluorescence signals, which improves the discrimination of positive/negative signals by 5-fold when compared to detection with traditional RGB intensity sensors or the naked eye. The ability to detect ZIKV directly from crude human sample matrices (blood, urine, and saliva) demonstrates our device’s utility for widespread clinical deployment. Together, these advances enable our system to host the key components necessary to expand the use of nucleic acid amplification-based detection assays towards point-of-care settings where they are needed most.

We introduce a portable biochemical analysis platform for rapid field deployment of nucleic acid-based diagnostics using consumer-class quadcopter drones. This approach exploits the ability to isothermally perform the polymerase chain reaction (PCR) with a single heater, enabling the system to be operated using standard 5 V USB sources that power mobile devices (via battery, solar, or hand crank action). Time-resolved fluorescence detection and quantification is achieved using a smartphone camera and integrated image analysis app. 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). Our instrument is rugged and versatile, enabling pinpoint deployment of sophisticated diagnostics to distributed field sites. This capability is demonstrated by successful in-flight replication of Staphylococcus aureus and λ-phage DNA targets in under 20 min. The ability to perform rapid in-flight assays with smartphone connectivity eliminates delays between sample collection and analysis so that test results can be delivered in minutes, suggesting new possibilities for drone-based systems to function in broader and more sophisticated roles beyond cargo transport and imaging.

Loop-mediated isothermal amplification (LAMP), coupled with reverse transcription (RT), has become a popular technique for detection of viral RNA due to several desirable characteristics for use in point-of-care or low-resource settings. The large number of primers in LAMP (six per target) leads to an increased likelihood of primer dimer interactions, and the inner primers in particular are prone to formation of stable hairpin structures due to their length (typically 40-45 bases). Although primer dimers and hairpin structures are known features to avoid in nucleic acid amplification techniques, there is little quantitative information in literature regarding the impact of these structures on LAMP or RT-LAMP assays. In this study, we examine the impact of primer dimers and hairpins on previously published primer sets for dengue virus and yellow fever virus. We demonstrate that minor changes to the primers to eliminate amplifiable primer dimers and hairpins improves the performance of the assays when monitored in real time with intercalating dyes, and when monitoring a fluorescent endpoint using the QUASR technique. We also discuss the thermodynamic implications of these minor changes on the overall stability of amplifiable secondary structures, and we present a single thermodynamic parameter that can be correlated to the probability of non-specific amplification associated with LAMP primers.

Smartphones have shown promise as an enabling technology for portable and distributed point-of-care diagnostic tests. The CMOS camera sensor can be used for detecting optical signals, including fluorescence for applications such as isothermal nucleic acid amplification tests. However, such analysis is typically limited mostly to endpoint detection of single targets. Here we present a smartphone-phone based image analysis pipeline that utilizes the CIE xyY (chromaticity-luminance) color space to measure the luminance (in lieu of RGB intensities) of fluorescent signals arising from nucleic acid amplification targets, with a discrimination sensitivity (ratio between the positive to negative signals) which is an order of magnitude more than traditional RGB intensity based analysis. Furthermore, the chromaticity part of the analysis enables reliable multiplexed detection of different targets labeled with spectrally separated fluorophores. We apply this chromaticity-luminance formulation to simultaneously detect Zika and chikungunya viral RNA via endpoint RT-LAMP (Reverse transcription Loop-Mediated isothermal amplification). We also show real time LAMP detection of Neisseria gonorrhoeae samples down to a copy number of 3.5 copies per 10 μL of reaction volume in our smartphone-operated portable LAMP box. Furthermore, the chromaticity-luminance analysis is readily adaptable to other types of multiplexed fluorescence measurements using a smartphone camera.

We report a unique naturally derived activated carbon with optimally incorporated nitrogen functional groups and ultra-microporous structure to enable high CO 2 adsorption capacity. The coprocessing of biomass (Citrus aurantium waste leaves) and microalgae (Spirulina) as the N-doping agent was investigated by probing the parameter space (biomass/microalgae weight ratio, reaction temperature, and reaction time) of hydrothermal carbonization and activation process (via the ZnCl 2 /CO 2 activation) to generate hydrochars and activated carbons, respectively, with tunable nitrogen content and pore sizes. The central composite-based design of the experiment was applied to optimize the parameters of the prehydrothermal carbonization procedure resulting in the fabrication of N-enriched carbonaceous products with the highest possible mass yield and nitrogen content. The resulting hydrochars and activated carbon samples were characterized using elemental analysis, X-ray diffraction, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, field emission scanning electron microscopy, and Brunauer−Emmett−Teller surface area analysis. We observe that while N-doping and the activation process can individually enhance the CO 2 adsorption capacity to some extent, it is the combined effect of the two processes that synergistically work to greatly increase the adsorption capacity of the N-doped activated carbon by an amount which is more than the sum of individual contributions. We analyze the origins of this synergy with both physical and chemical characterization techniques. The resulting naturally derived activated carbon demonstrates one of the highest CO 2 adsorption capacities (8.43 mmol/g) with rapid adsorption kinetics and good selectivity and reusability.

The ability of chaotic advection under microscale confinement to direct chemical processes along accelerated kinetic pathways has been recognized for some time. However, practical applications have been slow to emerge because optimal results are often counterintuitively achieved in flows that appear to possess undesirably high disorder. Here we present a 3D time-resolved analysis of polymerase chain reaction (PCR)-mediated DNA replication across a broad ensemble of geometric states. The resulting parametric map reveals an unexpectedly wide operating regime where reaction rates remain constant over 2 orders of magnitude of the Rayleigh number, encompassing virtually any realistic PCR condition (temperature, volume, gravitational alignment), a level of robustness previously thought unattainable in the convective format.

Porous mineral formations near subsea alkaline hydrothermal vents embed microenvironments that make them potential hot spots for prebiotic biochemistry. But, synthesis of long-chain macromolecules needed to support higher-order functions in living systems (e.g., polypeptides, proteins, and nucleic acids) cannot occur without enrichment of chemical precursors before initiating polymerization, and identifying a suitable mechanism has become a key unanswered question in the origin of life. Here, we apply simulations and in situ experiments to show how 3D chaotic thermal convection-flows that naturally permeate hydrothermal pore networks-supplies a robust mechanism for focused accumulation at discrete targeted surface sites. This interfacial enrichment is synchronized with bulk homogenization of chemical species, yielding two distinct processes that are seemingly opposed yet synergistically combine to accelerate surface reaction kinetics by several orders of magnitude. Our results suggest that chaotic thermal convection may play a previously unappreciated role in mediating surface-catalyzed synthesis in the prebiotic milieu.thermal convection | prebiotic biochemistry | hydrothermal vents | chaos S ubsea hydrothermal microenvironments uniquely embed catalytically active mineral surfaces in the presence of thermal and chemical gradients, establishing disequilibrium pathways essential for emergence of biochemical complexity (1-3). Synthesis of organic monomers, for example, can be supported in these systems via pH conditions that favor hydrogen-dependent redox processes similar to the CO 2 reducing acetyl-CoA biochemical pathway (4). The recent discovery of alkaline vent systems [e.g., Lost City vent, mid-Atlantic ridge (5, 6)] has generated particular excitement because geochemical serpentinization yields surroundings abundant in hydrogen at moderate temperatures (150-200°C) (Fig. 1A). These attributes, combined with the excess hydrogen's ability to exothermically reduce carbon dioxide into methane, have fueled interest in elucidating the role of alkaline vents in orchestrating synthesis of prebiotic chemical precursors critical to the origin of life (4, 7).But, a favorable chemical environment alone is not sufficient to drive macromolecular synthesis owing to the extremely dilute concentrations of precursor compounds in the prebiotic ocean (8-11). Recent studies have explored the combined action of laminar (2D) thermal convection and thermophoresis as a physical enrichment mechanism, albeit in hairline-sized fissures (diameter d ≤ 100 μm) under steep thermal gradients (100-1,000°C/mm) (12-15). In contrast, surprisingly complex 3D flows characterized by chaotic thermal convection (16, 17) emerge over a broader pore size range [millimeters to centimeters, consistent with porosities in young active carbonate chimneys (18)] and under moderate temperature gradients (0.1-10°C/mm) (19,20) (Fig. 1A and SI Appendix). Here we apply simulations and in situ experiments to show how chaotic thermal convection under conditions mimi...

There is a need for innovative educational experiences that unify and reinforce fundamental principles at the interface between the physical, chemical, and life sciences. These experiences empower and excite students by helping them recognize how interdisciplinary knowledge can be applied to develop new products and technologies that benefit society. Microfluidics offers an incredibly versatile tool to address this need. Here we describe our efforts to create innovative hands-on activities that introduce chemical engineering students to molecular biology by challenging them to harness microscale natural convection phenomena to perform DNA replication via the polymerase chain reaction (PCR). Experimentally, we have constructed convective PCR stations incorporating a simple design for loading and mounting cylindrical microfluidic reactors between independently controlled thermal plates. A portable motion analysis microscope enables flow patterns inside the convective reactors to be directly visualized using fluorescent bead tracers. We have also developed a hands-on computational fluid dynamics (CFD) exercise based on modeling microscale thermal convection to identify optimal geometries for DNA replication. A cognitive assessment reveals that these activities strongly impact student learning in a positive way.