Droplet confinement and leakage: Causes, underlying effects, and amelioration strategies

A programmable and automated optical electrowetting-on-dielectric (oEWOD) driven platform for massively parallel and sequential processing of single cell assay operations

Recently, there has been an increasing emphasis on single cell profiling for high-throughput screening workflows in drug discovery and life sciences research. However, the biology underpinning these screens is often complex and is insufficiently addressed by singleplex assay screens. Traditional single cell screening technologies have created powerful sets of 'omic data that allow users to bioinformatically infer biological function, but have as of yet not empowered direct functional analysis at the level of each individual cell. Consequently, screening campaigns often require multiple secondary screens leading to laborious, time-consuming and expensive workflows in which attrition points may not be queried until late in the process. We describe a platform that harnesses droplet microfluidics and optical electrowetting-on-dielectric (oEWOD) to perform highly-controlled sequential and multiplexed single cell assays in massively parallelised workflows to enable complex cell profiling during screening. Soluble reagents or objects, such as cells or assay beads, are encapsulated into droplets of media in fluorous oil and are actively filtered based on size and optical features ensuring only desirable droplets (e.g. single cell droplets) are retained for analysis, thereby overcoming the Poisson probability distribution. Droplets are stored in an array on a temperature-controlled chip and the history of individual droplets is logged from the point of filter until completion of the workflow. On chip, droplets are subject to an automated and flexible suite of operations including the merging of sample droplets and the fluorescent acquisition of assay readouts to enable complex sequential assay workflows. To demonstrate the broad utility of the platform, we present examples of single-cell functional workflows for various applications such as antibody discovery, infectious disease, and cell and gene therapy.

Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments

Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >10⁷-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >10⁷ variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.

Physicochemical Properties Predict Retention of Antibiotics in Water-in-Oil Droplets

Water-in-oil droplet microfluidics promises capacity for high-throughput single-cell antimicrobial susceptibility assays and investigation of drug resistance mechanisms. Every droplet must serve as an isolated environment with a controlled antibiotic concentration in such assays. While technologies for generation, incubation, screening, and sorting droplets mature, predictable retention of active molecules inside droplets remains a major outstanding challenge. Here, we analyzed 36 descriptors of the antibiotic molecules against experimental results on the cross-talk of antibiotics in droplets. We show that partition coefficient and fractional polar surface area are the key physicochemical properties that predict antibiotic retention. We verified the prediction by monitoring growth inhibition by antibiotic-loaded neighboring droplets. Our experiments also demonstrate that transfer of antibiotics between droplets is concentration- and distance-dependent. Our findings immediately apply to designing droplet antibiotic assays and give deeper insight into the retention of small molecules in water-in-oil emulsions.

Investigating the effect of phospholipids on droplet formation and surface property evolution in microfluidic devices for droplet interface bilayer (DIB) formation

Despite growing interest in droplet microfluidic methods for droplet interface bilayer (DIB) formation, there is a dearth of information regarding how phospholipids impact device function. Limited characterization has been carried out for phospholipids, either computationally (in silico) or experimentally (in situ) in polydimethylsiloxane (PDMS) microfluidic devices, despite recent work providing a better understanding of how other surfactants behave in microfluidic systems. Hence, microfluidic device design for DIB applications relies heavily on trial and error, with many assumptions made about the impact of phospholipids on droplet formation and surface properties. Here, we examine the effects of phospholipids on interfacial tension, droplet formation, wetting, and hence device longevity, using DPhPC as the most widely used lipid for DIB formation. We use a customized COMSOL in silico model in comparison with in situ experimental data to establish that the stabilization of droplet formation seen when the lipid is dosed in the aqueous phase (lipid-in) or in the oil phase (lipid-out) is directly dependent on the effects of lipids on the device surface properties, rather than on how fast they coat the droplet. Furthermore, we establish a means to visually characterize surface property evolution in the presence of lipids and explore rates of device failure in the absence of lipid, lipid-out, and lipid-in. This first exploration of the effects of lipids on device function may serve to inform the design of microfluidic devices for DIB formation as well as to troubleshoot causes of device failure during microfluidic DIB experiments.

Materials and methods for droplet microfluidic device fabrication

Since the first reports two decades ago, droplet-based systems have emerged as a compelling tool for microbiological and (bio)chemical science, with droplet flow providing multiple advantages over standard single-phase microfluidics such as removal of Taylor dispersion, enhanced mixing, isolation of droplet contents from surfaces, and the ability to contain and address individual cells or biomolecules. Typically, a droplet microfluidic device is designed to produce droplets with well-defined sizes and compositions that flow through the device without interacting with channel walls. Successful droplet flow is fundamentally dependent on the microfluidic device - not only its geometry but moreover how the channel surfaces interact with the fluids. Here we summarise the materials and fabrication techniques required to make microfluidic devices that deliver controlled uniform droplet flow, looking not just at physical fabrication methods, but moreover how to select and modify surfaces to yield the required surface/fluid interactions. We describe the various materials, surface modification techniques, and channel geometry approaches that can be used, and give examples of the decision process when determining which material or method to use by describing the design process for five different devices with applications ranging from field-deployable chemical analysers to water-in-water droplet creation. Finally we consider how droplet microfluidic device fabrication is changing and will change in the future, and what challenges remain to be addressed in the field.

A large-scale pico-droplet array for viable bacteria digital counting and dynamic tracking based on a thermosetting oil

A simple and rapid method was developed for real-time monitoring and digital counting of bacterial growth, and it can provide dynamic information at high resolution in the process.

The role of temperature in the formation of human-mimetic artificial cell membranes using droplet interface bilayers (DIBs)

Droplet interface bilayers (DIBs) have recently started to be used as human-mimetic artificial cell membranes. DIBs are bilayer sections created at the interface of two aqueous droplets, such that one droplet can be used as a donor compartment and the other as an acceptor compartment for the quantification of molecular transport across the artificial cell membrane. However, synthetic phospholipids are overwhelmingly used to create DIBs instead of naturally derived phospholipids, even though the diverse distribution of phospholipids in the latter is more biomimetic. We present the first systematic study of the role of temperature in DIB formation, which shows that the temperature at which DIBs are formed is a key parameter for the formation of DIBs using naturally derived phospholipids in a microfluidic platform. The phospholipids that are most abundant in mammalian cell membranes (phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), and phosphatidylinositol (PI)) only form DIBs when the temperature is above the phase transition temperature (T_m). Similarly, DIB formation usually only occurs above the highest T_m of a single phospholipid in a bespoke formulation. In addition, we show a new phenomenon wherein the DIB "melts" without disintegrating for bilayers formed predominantly of phospholipids that occupy cylindrical spaces. We also demonstrate differences in DIB formation rates as well as permeability of these biomimetic membranes. Given the difficulties associated with making DIBs using naturally derived phospholipids, we anticipate this work will illuminate the role of phospholipid phase transition in mono- and bilayer formation and lay the foundation for DIBs to be used as human-mimetic artificial cell membranes.

A plug-and-play modular microcapillary platform for the generation of multicompartmental double emulsions using glass or fluorocarbon capillaries

Although multiple emulsions have a wide range of applications in biology, medicine, chemistry and cosmetics, the use of microfluidic devices to generate them remains limited to specialist laboratories. This is because of the expertise required to design and operate these technologies. Here we show a plug-and-play microcapillary platform for the generation of multicompartmental double emulsions which only requires a low cost 3D printer for fabrication and syringe pumps for operation. Our microcapillary platform is modular because we fabricate junction boxes from a flexible resin to hold and align any type of standard glass capillary or piece of tubing for droplet formation without the need for capillary alignment. The flexible resin enables total sealing of the capillaries without the need for gaskets or adhesives, and the ability to use any type of capillary or tubing means that surface treatment is not required. We show how our microcapillary platform is able to generate water-in-oil-in-water, oil-in-water-in-oil, and oil-in-oil-in-water multicompartmental double emulsions with between 1 and 10 inner droplets with high accuracy and reproducibility using standard oils (FC40, mineral oil) and inexpensive surfactants (sodium dodecyl sulfate, SDS or 1H,1H,2H,2H-perfluoro-1-octanol, PFO). Additionally, we show the formation of binary multicompartmental double emulsions, where two types of inner phase droplets can be encapsulated in the multicompartmental emulsions. Our results demonstrate how simple and accessible tools can be employed to generate a powerful modular microcapillary platform. We anticipate that the simplicity of fabrication and operation of this platform, coupled with its ability to make a wide variety of different types of emulsions, will be attractive both to microfluidic laboratories and to those without microfluidic expertise who need an enabling tool for multicompartmental double emulsion formation.

Microfluidic technologies for drug discovery and development: friend or foe?

There is a point in the evolution of every new technology when questions need to be asked regarding its usefulness and impact. Although microfluidic technologies have drastically decreased the scales at which laboratory processes can be performed and have enabled scientific advances that would have otherwise not been possible, it is time to consider whether these technologies are more disruptive than enabling. Here, my aims are to introduce researchers in the broad fields of drug discovery and development to the advantages and disadvantages of microfluidic technologies, to highlight current work showing how microfluidic technologies can be used at different stages in the drug discovery and development process, to discuss how we can transfer academic breakthroughs in the field of microfluidic technologies to industrial environments, and to examine whether microfluidic technologies have the potential to cause a fundamental paradigm shift in the way that drug discovery and development occurs.

Recent advances in the design of microfluidic technologies for the manufacture of drug releasing particles

Drug releasing particles are valued for their ability to deliver therapeutics to targeted locations and for their controllable release patterns. The development of microfluidic technologies, which are designed specifically to manipulate small amounts of fluids, to manufacture particles for drug delivery applications reflects a recent trend due to the advantages they confer in terms of control over particle size and material composition. This review takes a comprehensive look at the different types of microfluidic devices used to fabricate such particles from different types of biomaterials, and at how the on-chip features enable the production of particles with different types of properties. The review concludes by suggesting avenues for future work that will enable these technologies to fulfill their potential and be used in industrial settings for the manufacture of drug releasing particles with unique capabilities.

A bespoke microfluidic pharmacokinetic compartment model for drug absorption using artificial cell membranes

Early prediction of the rate and extent of intestinal absorption is vital for the efficient development of orally administered drugs. Here we show a new type of pharmacokinetic compartment model that shows a threefold improvement in the prediction of molecular absorption in the jejunum than the current state-of-the-art in vitro technique, parallel artificial membrane permeability assays (PAMPA). Our three-stage pharmacokinetic compartment model uses microfluidic droplets and bespoke, biomimetic artificial cells to model the path of a drug proxy from the intestinal space into the blood via an enterocyte. Each droplet models the buffer and salt composition of each pharmacokinetic compartment. The artificial cell membranes are made from the major components of human intestinal cell membranes (l-α-phosphatidylcholine, PC and l-α-phosphatidylethanolamine, PE) and sizes are comparable to human cells (∼0.5 nL). We demonstrate the use of the microfluidic platform to quantify common pharmacokinetic parameters such as half-life, flux and the apparent permeability coefficient (P_app). Our determined P_app more closely resembles that of actual intestinal tissue than PAMPA, which overestimates it by a factor of 20.

Easily fabricated monolithic fluoropolymer chips for sensitive long-term absorbance measurement in droplet microfluidics

Maintaining a hydrophobic channel surface is critical to ensuring long-term stable flow in droplet microfluidics. Monolithic fluoropolymer chips ensure robust and reliable droplet flow as their native fluorous surfaces naturally preferentially wet fluorocarbon oils and do not deteriorate over time. Their fabrication, however, typically requires expensive heated hydraulic presses that make them inaccessible to many laboratories. Here we describe a method for micropatterning and bonding monolithic fluoropolymer flow cells from a commercially available melt-processable fluoropolymer, Dyneon THV 500GZ, that only requires a standard laboratory oven. Using this technique, we demonstrate the formation of complex microstructures, specifically the fabrication of sensitive absorbance flow cells for probing droplets in flow, featuring path lengths up to 10 mm. The native fluorous channel surface means the flow cells can be operated over extended periods, demonstrated by running droplets continuously through a chip for 16 weeks.

We present a widely accessible method for fabricating monolithic fluoropolymer microfluidic chips, which allows droplet absorbance measurement over multi-month periods.

Rapid Production and Recovery of Cell Spheroids by Automated Droplet Microfluidics

The future of the life sciences is linked to automation and microfluidics. As robots start working side by side with scientists, robotic automation of microfluidics in general, and droplet microfluidics in particular, will significantly extend and accelerate the life sciences. Here, we demonstrate the automation of droplet microfluidics using an inexpensive liquid-handling robot to produce human scaffold-free cell spheroids at high throughput. We use pipette actuation and interface the pipetting tip with a droplet-generating microfluidic device. In this device, we produce highly monodisperse droplets with a diameter coefficient of variation (CV) lower than 2%. By encapsulating cells in these droplets, we produce cell spheroids in droplets and recover them to standard labware containers at a throughput of 85,000 spheroids per microfluidic circuit per hour. The viability of the cells in spheroids remains high throughout the process and decreases by >10% (depending on the cell line used) after a 16 h incubation period in nanoliter droplets and automated recovery. Scaffold-free cell spheroids and 3D tissue constructs recapitulate many aspects of functional human tissue more accurately than 2D or single-cell cultures, but assembly methods for spheroids (e.g., hanging drop microplates) have limited throughput. The increased throughput and decreased cost of our method enable spheroid production at the scale needed for lead discovery drug screening, and approach the cost at which these microtissues could be used as building blocks for organ-scale regenerative medicine.

Extraction of electrokinetically separated analytes with on-demand encapsulation

Microchip electrokinetic methods are capable of increasing the sensitivity of molecular assays by enriching and purifying target analytes. However, their use is currently limited to assays that can be performed under a high external electric field, as spatial separation and focusing is lost when the electric field is removed. We present a novel method that uses two-phase encapsulation to overcome this limitation. The method uses passive filling and pinning of an oil phase in hydrophobic channels to encapsulate electrokinetically separated and focused analytes with a brief pressure pulse. The resulting encapsulated sample droplet maintains its concentration over long periods of time without requiring an electric field and can be manipulated for further analysis, either on- or off-chip. We demonstrate the method by encapsulating DNA oligonucleotides in a 240 pL aqueous segment after isotachophoresis (ITP) focusing, and show that the concentration remains at 60% of the initial value for tens of minutes, a 22-fold increase over free diffusion after 20 minutes. Furthermore, we demonstrate manipulation of a single droplet by selectively encapsulating amplicon after ITP purification from a polymerase chain reaction (PCR) mix, and performing parallel off-chip detection reactions using the droplet. We provide geometrical design guidelines for devices implementing the encapsulation method, and show how the method can be scaled to multiple analyte zones.

Simple and Precise Counting of Viable Bacteria by Resazurin-Amplified Picoarray Detection

Simple, fast, and precise counting of viable bacteria is fundamental to a variety of microbiological applications such as food quality monitoring and clinical diagnosis. To this end, agar plating, microscopy, and emerging microfluidic devices for single bacteria detection have provided useful means for counting viable bacteria, but they also have their limitations ranging from complexity, time, and inaccuracy. We present herein our new method RAPiD (Resazurin-Amplified Picoarray Detection) for addressing this important problem. In RAPiD, we employ vacuum-assisted sample loading and oil-driven sample digitization to stochastically confine single bacteria in Picoarray, a microfluidic device with picoliter-sized isolation chambers (picochambers), in <30 s with only a few minutes of hands-on time. We add AlamarBlue, a resazurin-based fluorescent dye for bacterial growth, in our assay to accelerate the detection of "microcolonies" proliferated from single bacteria within picochambers. Detecting fluorescence in picochambers as an amplified surrogate for bacterial cells allows us to count hundreds of microcolonies with a single image taken via wide-field fluorescence microscopy. We have also expanded our method to practically test multiple titrations from a single bacterial sample in parallel. Using this expanded "multi-RAPiD" strategy, we can quantify viable cells in E. coli and S. aureus samples with precision in ∼3 h, illustrating RAPiD as a promising new method for counting viable bacteria for microbiological applications.

Nitrate measurement in droplet flow: gas-mediated crosstalk and correction

In droplet microfluidics, droplets have traditionally been considered discrete self-contained reaction chambers, however recent work has shown that dissolved solutes can transfer into the oil phase and migrate into neighbouring droplets under certain conditions. The majority of reports on such inter-droplet "crosstalk" have focused on surfactant-driven mechanisms, such as transport within micelles. While trialling a droplet-based system for quantifying nitrate in water, we encountered crosstalk driven by a very different mechanism: conversion of the analyte to a gaseous intermediate which subsequently diffused between droplets. Importantly we found that the crosstalk occurred predictably, could be experimentally quantified, and measurements rationally post-corrected. This showed that droplet microfluidic systems susceptible to crosstalk such as this can nonetheless be used for quantitative analysis.

Approach to classify, separate, and enrich objects in groups using ensemble sorting

The sorting of objects into groups is a fundamental operation, critical in the preparation and purification of populations of cells, crystals, beads, or droplets, necessary for research and applications in biology, chemistry, and materials science. Most of the efforts exploring such purification have focused on two areas: the degree of separation and the measurement precision required for effective separation. Conventionally, achieving good separation ultimately requires that the objects are considered one by one (which can be both slow and expensive), and the ability to measure the sorted objects by increasing sensitivity as well as reducing sorting errors. Here we present an approach to sorting that addresses both critical limitations with a scheme that allows us to approach the theoretical limit for the accuracy of sorting decisions. Rather than sorting individual objects, we sort the objects in ensembles, via a set of registers which are then in turn sorted themselves into a second symmetric set of registers in a lossless manner. By repeating this process, we can arrive at high sorting purity with a low set of constraints. We demonstrate both the theory behind this idea and identify the critical parameters (ensemble population and sorting time), and show the utility and robustness of our method with simulations and experimental systems spanning several orders of scale, sorting populations of macroscopic beads and microfluidic droplets. Our method is general in nature and simplifies the sorting process, and thus stands to enhance many different areas of science, such as purification, enrichment of rare objects, and separation of dynamic populations.

Speeding up enzyme discovery and engineering with ultrahigh-throughput methods

Exploring the sequence space of enzyme catalysts is ultimately a numbers game. Ultrahigh-throughput screening methods for rapid analysis of millions of variants are therefore increasingly important for investigating sequence-function relationships, searching large metagenomic libraries for interesting activities, and accelerating enzyme evolution in the laboratory. Recent applications of such technologies are reviewed here, with a particular focus on the practical benefits of droplet-based microfluidics for the directed evolution of natural and artificial enzymes. Broader implementation of such rapid, cost-effective screening technologies is likely to redefine the way enzymes are studied and engineered for academic and industrial purposes.

From single-molecule detection to next-generation sequencing: microfluidic droplets for high-throughput nucleic acid analysis

Droplet-based microfluidic technologies have proved themselves to be of significant utility in the performance of high-throughput chemical and biological experiments. By encapsulating and isolating reagents within femtoliter-nanoliter droplet, millions of (bio) chemical reactions can be processed in a parallel fashion and on ultra-short timescales. Recent applications of such technologies to genetic analysis have suggested significant utility in low-cost, efficient and rapid workflows for DNA amplification, rare mutation detection, antibody screening and next-generation sequencing. To this end, we describe and highlight some of the most interesting recent developments and applications of droplet-based microfluidics in the broad area of nucleic acid analysis. In addition, we also present a cursory description of some of the most essential functional components, which allow the creation of integrated and complex workflows based on flowing streams of droplets.

Droplet confinement and leakage: Causes, underlying effects, and amelioration strategies

The applicability of droplet-based microfluidic systems to many research fields stems from the fact that droplets are generally considered individual and self-contained reaction vessels. This study demonstrates that, more often than not, the integrity of droplets is not complete, and depends on a range of factors including surfactant type and concentration, the micro-channel surface, droplet storage conditions, and the flow rates used to form and process droplets. Herein, a model microfluidic device is used for droplet generation and storage to allow the comparative study of forty-four different oil/surfactant conditions. Assessment of droplet stability under these conditions suggests a diversity of different droplet failure modes. These failure modes have been classified into families depending on the underlying effect, with both numerical and qualitative models being used to describe the causative effect and to provide practical solutions for droplet failure amelioration in microfluidic systems.