Combining avidin with CD63 improves basophil activation test accuracy in classifying peanut allergy.

BACKGROUND: Conventional basophil activation tests (BATs) measure basophil activation by the increased expression of CD63. Previously, fluorophore-labeled avidin, a positively-charged molecule, was found to bind to activated basophils, which tend to expose negatively charged granule constituents during degranulation. This study further compares avidin versus CD63 as basophil activation biomarkers in classifying peanut allergy. METHODS: Seventy subjects with either a peanut allergy (N = 47), a food allergy other than peanut (N = 6), or no food allergy (N = 17) were evaluated. We conducted BATs in response to seven peanut extract (PE) concentrations (0.01-10,000 ng/mL) and four control conditions (no stimulant, anti-IgE, fMLP (N-formylmethionine-leucyl-phenylalanine), and anti-FcεRI). We measured avidin binding and CD63 expression on basophils with flow cytometry. We evaluated logistic regression and XGBoost models for peanut allergy classification and feature identification. RESULTS: Avidin binding was correlated with CD63 expression. Both markers discriminated between subjects with and without a peanut allergy. Although small by percentage, an avidin+ /CD63- cell subset was found in all allergic subjects tested, indicating that the combination of avidin and CD63 could allow a more comprehensive identification of activated basophils. Indeed, we obtained the best classification accuracy (97.8% sensitivity, 96.7% specificity) by combining avidin and CD63 across seven PE doses. Similar accuracy was obtained by combining PE dose of 10,000 ng/mL for avidin and PE doses of 10 and 100 ng/mL for CD63. CONCLUSIONS: Avidin and CD63 are reliable BAT activation markers associated with degranulation. Their combination enhances the identification of activated basophils and improves the classification accuracy of peanut allergy.

Microfluidic Surgery in Single Cells and Multicellular Systems.

Microscale surgery on single cells and small organisms has enabled major advances in fundamental biology and in engineering biological systems. Examples of applications range from wound healing and regeneration studies to the generation of hybridoma to produce monoclonal antibodies. Even today, these surgical operations are often performed manually, but they are labor intensive and lack reproducibility. Microfluidics has emerged as a powerful technology to control and manipulate cells and multicellular systems at the micro- and nanoscale with high precision. Here, we review the physical and chemical mechanisms of microscale surgery and the corresponding design principles, applications, and implementations in microfluidic systems. We consider four types of surgical operations: (1) sectioning, which splits a biological entity into multiple parts, (2) ablation, which destroys part of an entity, (3) biopsy, which extracts materials from within a living cell, and (4) fusion, which joins multiple entities into one. For each type of surgery, we summarize the motivating applications and the microfluidic devices developed. Throughout this review, we highlight existing challenges and opportunities. We hope that this review will inspire scientists and engineers to continue to explore and improve microfluidic surgical methods.

Strategic placement of an obstacle suppresses droplet break up in the hopper flow of a microfluidic soft crystal.

When granular materials, colloidal suspensions, and even animals and crowds exit through a narrow outlet, clogs can form spontaneously when multiple particles or entities attempt to exit simultaneously, thereby obstructing the outlet and ultimately halting the flow. Counterintuitively, the presence of an obstacle upstream of the outlet has been found to suppress clog formation. For soft particles such as emulsion drops, clogging has not been observed in the fast flow limit due to their deformability and vanishing interparticle friction. Instead, they pinch off each other and undergo break up when multiple drops attempt to exit simultaneously. Similar to how an obstacle reduces clogging in a rigid particle system, we hypothesize and demonstrate that an obstacle could suppress break up in the two-dimensional hopper flow of a microfluidic crystal consisting of dense emulsion drops by preventing the simultaneous exit of multiple drops. A regime map plotting the fraction of drops that undergo break up in a channel with different obstacle sizes and locations delineates the geometrical constraints necessary for effective break up suppression. When optimally placed, the obstacle induced an unexpected ordering of the drops, causing them to alternate and exit the outlet one at a time. Droplet break up is suppressed drastically by almost three orders of magnitude compared to when the obstacle is absent. This result can provide a simple, passive strategy to prevent droplet break up and can find use in improving the robustness and integrity of droplet microfluidic biochemical assays as well as in extrusion-based three-dimensional printing of emulsion or foam-based materials.

The living interface between synthetic biology and biomaterial design.

Recent far-reaching advances in synthetic biology have yielded exciting tools for the creation of new materials. Conversely, advances in the fundamental understanding of soft-condensed matter, polymers and biomaterials offer new avenues to extend the reach of synthetic biology. The broad and exciting range of possible applications have substantial implications to address grand challenges in health, biotechnology and sustainability. Despite the potentially transformative impact that lies at the interface of synthetic biology and biomaterials, the two fields have, so far, progressed mostly separately. This Perspective provides a review of recent key advances in these two fields, and a roadmap for collaboration at the interface between the two communities. We highlight the near-term applications of this interface to the development of hierarchically structured biomaterials, from bioinspired building blocks to 'living' materials that sense and respond based on the reciprocal interactions between materials and embedded cells.

Microfluidic guillotine reveals multiple timescales and mechanical modes of wound response in Stentor coeruleus.

BACKGROUND: Wound healing is one of the defining features of life and is seen not only in tissues but also within individual cells. Understanding wound response at the single-cell level is critical for determining fundamental cellular functions needed for cell repair and survival. This understanding could also enable the engineering of single-cell wound repair strategies in emerging synthetic cell research. One approach is to examine and adapt self-repair mechanisms from a living system that already demonstrates robust capacity to heal from large wounds. Towards this end, Stentor coeruleus, a single-celled free-living ciliate protozoan, is a unique model because of its robust wound healing capacity. This capacity allows one to perturb the wounding conditions and measure their effect on the repair process without immediately causing cell death, thereby providing a robust platform for probing the self-repair mechanism. RESULTS: Here we used a microfluidic guillotine and a fluorescence-based assay to probe the timescales of wound repair and of mechanical modes of wound response in Stentor. We found that Stentor requires ~ 100-1000 s to close bisection wounds, depending on the severity of the wound. This corresponds to a healing rate of ~ 8-80 µm2/s, faster than most other single cells reported in the literature. Further, we characterized three distinct mechanical modes of wound response in Stentor: contraction, cytoplasm retrieval, and twisting/pulling. Using chemical perturbations, active cilia were found to be important for only the twisting/pulling mode. Contraction of myonemes, a major contractile fiber in Stentor, was surprisingly not important for the contraction mode and was of low importance for the others. CONCLUSIONS: While events local to the wound site have been the focus of many single-cell wound repair studies, our results suggest that large-scale mechanical behaviors may be of greater importance to single-cell wound repair than previously thought. The work here advances our understanding of the wound response in Stentor and will lay the foundation for further investigations into the underlying components and molecular mechanisms involved.

Microfluidics-Coupled Radioluminescence Microscopy for In Vitro Radiotracer Kinetic Studies.

Integrated bioassay systems that combine microfluidics and radiation detectors can deliver medical radiopharmaceuticals to live cells with precise timing, while minimizing radiation dose and sample volume. However, the spatial resolution of many radiation imaging systems is limited to bulk cell populations. Here, we demonstrate microfluidics-coupled radioluminescence microscopy (µF-RLM), a new integrated system that can image radiotracer uptake in live adherent cells growing inside microincubators with spatial resolution better than 30 µm. Our method enables on-chip radionuclide imaging by incorporating an inorganic scintillator plate (CdWO4) into a microfluidic chip. We apply this approach to investigate the factors that influence the dynamic uptake of [18F]fluorodeoxyglucose (FDG) by cancer cells. In the first experiment, we measured the effect of flow on FDG uptake of cells and found that a continuous flow of the radiotracer led to fourfold higher uptake than static incubation, suggesting that convective replenishment enhances molecular radiotracer transport into cells. In the second set of experiments, we applied pharmacokinetic modeling to show that lactic acidosis inhibits FDG uptake by cancer cells in vitro and that this decrease is primarily due to downregulation of FDG transport into the cells. The other two rate constants, which represent FDG export and FDG metabolism, were relatively unaffected by lactic acidosis. Lactic acidosis is common in solid tumors because of the dysregulated metabolism and inefficient vasculature. In conclusion, µF-RLM is a simple and practical approach for integrating high-resolution radionuclide imaging within standard microfluidics devices, thus potentially opening venues for investigating the efficacy of radiopharmaceuticals in in vitro cancer models.

Microfluidic guillotine for single-cell wound repair studies.

Wound repair is a key feature distinguishing living from nonliving matter. Single cells are increasingly recognized to be capable of healing wounds. The lack of reproducible, high-throughput wounding methods has hindered single-cell wound repair studies. This work describes a microfluidic guillotine for bisecting single Stentor coeruleus cells in a continuous-flow manner. Stentor is used as a model due to its robust repair capacity and the ability to perform gene knockdown in a high-throughput manner. Local cutting dynamics reveals two regimes under which cells are bisected, one at low viscous stress where cells are cut with small membrane ruptures and high viability and one at high viscous stress where cells are cut with extended membrane ruptures and decreased viability. A cutting throughput up to 64 cells per minute-more than 200 times faster than current methods-is achieved. The method allows the generation of more than 100 cells in a synchronized stage of their repair process. This capacity, combined with high-throughput gene knockdown in Stentor, enables time-course mechanistic studies impossible with current wounding methods.

Using machine learning to discover shape descriptors for predicting emulsion stability in a microfluidic channel.

In soft matter consisting of many deformable objects, object shapes often carry important information about local forces and their interactions with the local environment, and can be tightly coupled to the bulk properties and functions. In a concentrated emulsion, for example, the shapes of individual droplets are directly related to the local stress arising from interactions with neighboring drops, which in turn determine their stability and the resulting rheological properties. Shape descriptors used in prior work on single drops and dilute emulsions, where droplet-droplet interactions are largely negligible and the drop shapes are simple, are insufficient to fully capture the broad range of droplet shapes in a concentrated system. This paper describes the application of a machine learning method, specifically a convolutional autoencoder model, that learns to: (1) discover a low-dimensional code (8-dimensional) to describe droplet shapes within a concentrated emulsion, and (2) predict whether the drop will become unstable and undergo break-up. The input consists of images (N = 500 002) of two-dimensional droplet boundaries extracted from movies of a concentrated emulsion flowing through a confined microfluidic channel as a monolayer. The model is able to faithfully reconstruct droplet shapes, as well as to achieve a classification accuracy of 91.7% in the prediction of droplet break-up, compared with ∼60% using conventional scalar descriptors based on droplet elongation. It is observed that 4 out of the 8 dimensions of the code are interpretable, corresponding to drop skewness, elongation, throat size, and surface curvature, respectively. Furthermore, the results show that drop elongation, throat size, and surface curvature are dominant factors in predicting droplet break-up for the flow conditions tested. The method presented is expected to facilitate follow-on work to identify the relationship between drop shapes and the interactions with other drops, and to identify potentially new modes of break-up mechanisms in a concentrated system. Finally, the method developed here should also apply to other soft materials such as foams, gels, and cells and tissues.

Spatiotemporal periodicity of dislocation dynamics in a two-dimensional microfluidic crystal flowing in a tapered channel.

When a many-body system is driven away from equilibrium, order can spontaneously emerge in places where disorder might be expected. Here we report an unexpected order in the flow of a concentrated emulsion in a tapered microfluidic channel. The velocity profiles of individual drops in the emulsion show periodic patterns in both space and time. Such periodic patterns appear surprising from both a fluid and a solid mechanics point of view. In particular, when the emulsion is considered as a soft crystal under extrusion, a disordered scenario might be expected based on the stochastic nature of dislocation dynamics in microscopic crystals. However, an orchestrated sequence of dislocation nucleation and migration is observed to give rise to a highly ordered deformation mode. This discovery suggests that nanocrystals can be made to deform more controllably than previously thought. It can also lead to novel flow control and mixing strategies in droplet microfluidics.

Toward a Droplet-Based Single-Cell Radiometric Assay.

Radiotracers are widely used to track molecular processes, both in vitro and in vivo, with high sensitivity and specificity. However, most radionuclide detection methods have spatial resolution inadequate for single-cell analysis. A few existing methods can extract single-cell information from radioactive decays, but the stochastic nature of the process precludes high-throughput measurement (and sorting) of single cells. In this work, we introduce a new concept for translating radioactive decays occurring stochastically within radiolabeled single-cells into an integrated, long-lasting fluorescence signal. Single cells are encapsulated in radiofluorogenic droplets containing molecular probes sensitive to byproducts of ionizing radiation (primarily reactive oxygen species, or ROS). Different probes were examined in bulk solutions, and dihydrorhodamine 123 (DHRh 123) was selected as the lead candidate due to its sensitivity and reproducibility. Fluorescence intensity of DHRh 123 in bulk increased at a rate of 54% per Gy of X-ray radiation and 15% per MBq/ml of 2-deoxy-2-[18F]-fluoro-d-glucose ([18F]FDG). Fluorescence imaging of microfluidic droplets showed the same linear response, but droplets were less sensitive overall than the bulk ROS sensor (detection limit of 3 Gy per droplet). Finally, droplets encapsulating radiolabeled cancer cells allowed, for the first time, the detection of [18F]FDG radiotracer uptake in single cells through fluorescence activation. With further improvements, we expect this technology to enable quantitative measurement and selective sorting of single cells based on the uptake of radiolabeled small molecules.

Bioinspired self-repairing slippery surfaces with pressure-stable omniphobicity.

Creating a robust synthetic surface that repels various liquids would have broad technological implications for areas ranging from biomedical devices and fuel transport to architecture but has proved extremely challenging. Inspirations from natural nonwetting structures, particularly the leaves of the lotus, have led to the development of liquid-repellent microtextured surfaces that rely on the formation of a stable air-liquid interface. Despite over a decade of intense research, these surfaces are, however, still plagued with problems that restrict their practical applications: limited oleophobicity with high contact angle hysteresis, failure under pressure and upon physical damage, inability to self-heal and high production cost. To address these challenges, here we report a strategy to create self-healing, slippery liquid-infused porous surface(s) (SLIPS) with exceptional liquid- and ice-repellency, pressure stability and enhanced optical transparency. Our approach-inspired by Nepenthes pitcher plants-is conceptually different from the lotus effect, because we use nano/microstructured substrates to lock in place the infused lubricating fluid. We define the requirements for which the lubricant forms a stable, defect-free and inert 'slippery' interface. This surface outperforms its natural counterparts and state-of-the-art synthetic liquid-repellent surfaces in its capability to repel various simple and complex liquids (water, hydrocarbons, crude oil and blood), maintain low contact angle hysteresis (<2.5°), quickly restore liquid-repellency after physical damage (within 0.1-1 s), resist ice adhesion, and function at high pressures (up to about 680 atm). We show that these properties are insensitive to the precise geometry of the underlying substrate, making our approach applicable to various inexpensive, low-surface-energy structured materials (such as porous Teflon membrane). We envision that these slippery surfaces will be useful in fluid handling and transportation, optical sensing, medicine, and as self-cleaning and anti-fouling materials operating in extreme environments.

Prospective identification of parasitic sequences in phage display screens.

Phage display empowered the development of proteins with new function and ligands for clinically relevant targets. In this report, we use next-generation sequencing to analyze phage-displayed libraries and uncover a strong bias induced by amplification preferences of phage in bacteria. This bias favors fast-growing sequences that collectively constitute <0.01% of the available diversity. Specifically, a library of 10(9) random 7-mer peptides (Ph.D.-7) includes a few thousand sequences that grow quickly (the 'parasites'), which are the sequences that are typically identified in phage display screens published to date. A similar collapse was observed in other libraries. Using Illumina and Ion Torrent sequencing and multiple biological replicates of amplification of Ph.D.-7 library, we identified a focused population of 770 'parasites'. In all, 197 sequences from this population have been identified in literature reports that used Ph.D.-7 library. Many of these enriched sequences have confirmed function (e.g. target binding capacity). The bias in the literature, thus, can be viewed as a selection with two different selection pressures: (i) target-binding selection, and (ii) amplification-induced selection. Enrichment of parasitic sequences could be minimized if amplification bias is removed. Here, we demonstrate that emulsion amplification in libraries of ∼ 10(6) diverse clones prevents the biased selection of parasitic clones.

Fluorinated Pickering Emulsions with Nonadsorbing Interfaces for Droplet-based Enzymatic Assays.

This work describes the use of fluorinated Pickering emulsions with nonadsorbing interfaces in droplet-based enzymatic assays. State-of-the-art droplet assays have relied on one type of surfactants consisting of perfluorinated polyether and polyethylene glycol (PFPE-PEG). These surfactants are known to have limitations including the tedious synthesis and interdrop molecular transport which leads to the cross-contamination of droplet contents. Previously we have shown that replacing surfactants with nanoparticles as droplet stabilizers mitigate interdrop transport of small molecules. The nonspecific adsorption of enzymes on nanoparticle surface, however, could cause structural changes in enzymes and consequently the loss of enzymatic activity. To overcome such challenge, we render nanoparticle surface nonadsorbing to enzymes by in situ adsorption of polyethylene glycol (PEG) on particle surfaces. We show that enzyme activities are preserved in droplets stabilized by PEG-adsorbed nanoparticles, and are comparable with those in drops stabilized by PFPE-PEG surfactants. In addition, our nonadsorbing Pickering emulsions successfully prevent interdrop molecular transport, thereby maintaining the accuracy of droplet assays. The particles are also simple and economical to synthesize. The PEG-adsorbed nanoparticles described in this work are thus a competitive alternative to the current surfactant system, and can potentially enable new droplet-based biochemical assays.

Break-up of droplets in a concentrated emulsion flowing through a narrow constriction.

This paper describes the break-up of droplets in a concentrated emulsion during its flow as a 2D monolayer in a microchannel consisting of a narrow constriction. Analysis of the behavior of a large number of drops (N > 4000) shows that the number of break-ups increases with increasing flow rate, entrance angle to the constriction, and size of the drops relative to the width of the constriction. As single drops do not break at the highest flow rate used in the system, break-ups arise primarily from droplet-droplet interactions. Analysis of droplet properties at a high temporal resolution of 10 microseconds makes it possible to relate droplet deformation with droplet break-up probability. Similar to previous studies on single drops, no break-up is observed below a set of critical flow rates and droplet deformations. Unlike previous studies, however, not all drops undergo break-up above the critical values. Instead, the probability of droplet break-up increases with flow rate and the deformation of the drops. The probabilistic nature of the break-up process arises from the stochastic variations in the packing configuration of the drops as they enter the constriction. Local break-up dynamics involves two primary drops. A close look at the interactions between the pair of drops reveals that the competing time scales of droplet rearrangement relative to the relaxation of the opposing drop govern whether break-up occurs or not. Practically, these results can be used to calculate the maximum throughput of the serial interrogation process often employed in droplet microfluidics. For 40 pL-drops, the highest throughput with less than 1% droplet break-up was measured to be approximately 7000 drops per second. In addition, the results presented are useful for understanding the behavior of concentrated emulsions in applications such as mobility control in enhanced oil recovery, and for extrapolating critical parameters such as injection rates to ensure the stability of the fluids going through small pore throats.

SMORES: a simple microfluidic operating room for the examination and surgery of Stentor coeruleus.

Ciliates are powerful unicellular model organisms that have been used to elucidate fundamental biological processes. However, the high motility of ciliates presents a major challenge in studies using live-cell microscopy and microsurgery. While various immobilization methods have been developed, they are physiologically disruptive to the cell and incompatible with microscopy and/or microsurgery. Here, we describe a Simple Microfluidic Operating Room for the Examination and Surgery of Stentor coeruleus (SMORES). SMORES uses Quake valve-based microfluidics to trap, compress, and perform surgery on Stentor as our model ciliate. Compared with previous methods, immobilization by physical compression in SMORES is more effective and uniform. The mean velocity of compressed cells is 24 times less than that of uncompressed cells. The compression is minimally disruptive to the cell and is easily applied or removed using a 3D-printed pressure rig. We demonstrate cell immobilization for up to 2 h without sacrificing cell viability. SMORES is compatible with confocal microscopy and is capable of media exchange for pharmacokinetic studies. Finally, the modular design of SMORES allows laser ablation or mechanical dissection of a cell into many cell fragments at once. These capabilities are expected to enable biological studies previously impossible in ciliates and other motile species.

Physical Forces in Regeneration of Cells and Tissues.

The ability to regenerate after the loss of a part is a hallmark of living systems and occurs at both the tissue and organ scales, but also within individual cells. Regeneration entails many processes that are physical and mechanical in nature, including the closure of wounds, the repositioning of material from one place to another, and the restoration of symmetry following perturbations. However, we currently know far more about the genetics and molecular signaling pathways involved in regeneration, and there is a need to investigate the role of physical forces in the process. Here, we will provide an overview of how physical forces may play a role in wound healing and regeneration, in which we compare and contrast regenerative processes at the tissue and cell scales.

SMORES: A Simple Microfluidic Operating Room for the Examination and Surgery of Stentor coeruleus.

Ciliates are powerful unicellular model organisms that have been used to elucidate fundamental biological processes. However, the high motility of ciliates presents a major challenge in studies using live-cell microscopy and microsurgery. While various immobilization methods have been developed, they are physiologically disruptive to the cell and incompatible with microscopy and/or microsurgery. Here, we describe a Simple Microfluidic Operating Room for the Examination and Surgery of Stentor coeruleus (SMORES). SMORES uses Quake valve-based microfluidics to trap, compress, and perform surgery on Stentor as our model ciliate. Compared with previous methods, immobilization by physical compression in SMORES is more effective and uniform. The mean velocity of compressed cells is 24 times less than that of uncompressed cells. The compression is minimally disruptive to the cell and is easily applied or removed using a 3D-printed pressure rig. We demonstrate cell immobilization for up to 2 hours without sacrificing cell viability. SMORES is compatible with confocal microscopy and is capable of media exchange for pharmacokinetic studies. Finally, the modular design of SMORES allows laser ablation or mechanical dissection of a cell into many cell fragments at once. These capabilities are expected to enable biological studies previously impossible in ciliates and other motile species.

Filter-based assay for Escherichia coli in aqueous samples using bacteriophage-based amplification.

This paper describes a method to detect the presence of bacteria in aqueous samples, based on the capture of bacteria on a syringe filter, and the infection of targeted bacterial species with a bacteriophage (phage). The use of phage as a reagent provides two opportunities for signal amplification: (i) the replication of phage inside a live bacterial host and (ii) the delivery and expression of the complementing gene that turns on enzymatic activity and produces a colored or fluorescent product. Here we demonstrate a phage-based amplification scheme with an M13KE phage that delivers a small peptide motif to an F(+), α-complementing strain of Escherichia coli K12, which expresses the ω-domain of ß-galactosidase (ß-gal). The result of this complementation-an active form of ß-gal-was detected colorimetrically, and the high level of expression of the ω-domain of ß-gal in the model K12 strains allowed us to detect, on average, five colony-forming units (CFUs) of this strain in 1 L of water with an overnight culture-based assay. We also detected 50 CFUs of the model K12 strain in 1 L of water (or 10 mL of orange juice, or 10 mL of skim milk) in less than 4 h with a solution-based assay with visual readout. The solution-based assay does not require specialized equipment or access to a laboratory, and is more rapid than existing tests that are suitable for use at the point of access. This method could potentially be extended to detect many different bacteria with bacteriophages that deliver genes encoding a full-length enzyme that is not natively expressed in the target bacteria.

Single particle detection in CMOS compatible photonic crystal nanobeam cavities.

We report the label-free detection of single particles using photonic crystal nanobeam cavities fabricated in silicon-on-insulator platform, and embedded inside microfluidic channels fabricated in poly-dimethylsiloxane (PDMS). Our system operates in the telecommunication wavelength band, thus leveraging the widely available, robust and tunable telecom laser sources. Using this approach, we demonstrated the detection of polystyrene nanoparticles with dimensions down to 12.5nm in radius. Furthermore, binding events of a single streptavidin molecule have been observed.