1-Million droplet array with wide-field fluorescence imaging for digital PCR

A piezoelectric drop-on-demand generator for accurate samples in capillary electrophoresis

In this work, we propose a piezoelectric droplet generator for injection of well-defined amounts of sample in capillary electrophoresis. We demonstrate stable, precise and drop-on-demand droplet formation for various solutions, with precise control of waveform driving piezoelectric crystal inside the ink-jet head. By tuning the waveform, we can also manipulate the droplet size and delivery frequency. This injector was used in sampling for capillary electrophoresis. As a state-of-the-art application, the analysis of theobromine, caffeine and theophiline using micellar electrokinetic chromatography was developed. The volume of sample (single droplet) analyzed in this experiment was 179 pL (RSD=1.2%, n=10). The detection limits for caffeine, theobromine, and theophiline are 0.02, 0.08 and 0.06 mM L(-1), respectively. Compared with conventional methods, the combination of picoliter droplet dispenser with capillary electrophoresis allows precise and accurate sampling, as well as for reduced sample consumption, which will prove to be an efficient tool in quantitative separation and analysis.

Adding reagent to droplets with controlled rupture of encapsulated double emulsions

We present a method to add reagent to microfluidic droplets by enveloping them as a double emulsions in reagent-filled droplets and then rupturing them with an electric field. When the double emulsions rupture, they release their contents into the enveloping droplets, ensuring mixing with reagent while limiting cross-droplet contamination.

Population transcriptomics with single-cell resolution: a new field made possible by microfluidics: a technology for high throughput transcript counting and data-driven definition of cell types

Tissues contain complex populations of cells. Like countries, which are comprised of mixed populations of people, tissues are not homogeneous. Gene expression studies that analyze entire populations of cells from tissues as a mixture are blind to this diversity. Thus, critical information is lost when studying samples rich in specialized but diverse cells such as tumors, iPS colonies, or brain tissue. High throughput methods are needed to address, model and understand the constitutive and stochastic differences between individual cells. Here, we describe microfluidics technologies that utilize a combination of molecular biology and miniaturized labs on chips to study gene expression at the single cell level. We discuss how the characterization of the transcriptome of each cell in a sample will open a new field in gene expression analysis, population transcriptomics, that will change the academic and biomedical analysis of complex samples by defining them as quantified populations of single cells.

Rapid clinical bacteriology and its future impact

Clinical microbiology has always been a slowly evolving and conservative science. The sub-field of bacteriology has been and still is dominated for over a century by culture-based technologies. The integration of serological and molecular methodologies during the seventies and eighties of the previous century took place relatively slowly and in a cumbersome fashion. When nucleic acid amplification technologies became available in the early nineties, the predicted "revolution" was again slow but in the end a real paradigm shift did take place. Several of the culture-based technologies were successfully replaced by tests aimed at nucleic acid detection. More recently a second revolution occurred. Mass spectrometry was introduced and broadly accepted as a new diagnostic gold standard for microbial species identification. Apparently, the diagnostic landscape is changing, albeit slowly, and the combination of newly identified infectious etiologies and the availability of innovative technologies has now opened new avenues for modernizing clinical microbiology. However, the improvement of microbial antibiotic susceptibility testing is still lagging behind. In this review we aim to sketch the most recent developments in laboratory-based clinical bacteriology and to provide an overview of emerging novel diagnostic approaches.

A lithography-free procedure for fabricating three-dimensional microchannels using hydrogel molds

We present a lithography-free procedure for fabricating intrinsically three-dimensional smooth-walled microchannels within poly(dimethylsiloxane) (PDMS) elastomer using hydrogel molds. In the fabrication process, small pieces of agarose gel ("wires" or "chips") are embedded in uncured PDMS composite, arranged in the shape of the desired microchannels, and used as molds to form the microchannels. The point of the process is that molds for creating junctions of microchannels such as T-junctions or cross-junctions can be robustly formed by simply grafting gel wires in uncured PDMS composite without using adhesive agents. The technical advantage of this method is that three-dimensional microstructures such as microchannels with circular cross sections, three-dimensionally arranged junctions or interchanges of microchannels can be flexibly designed and fabricated with a straightforward procedure without the need for any specialized equipment or layer-by-layer assemblage processes. This method provides a low-cost, green procedure for fabricating microfluidic devices and promises to make microfluidic processes more accessible and easy to implement in a variety of scientific fields.

Cruise control for segmented flow

Capitalizing on the benefits of microscale segmented flows, e.g., enhanced mixing and reduced sample dispersion, so far requires specialist training and accommodating a few experimental inconveniences. For instance, microscale gas-liquid flows in many current setups take at least 10 min to stabilize and iterative manual adjustments are needed to achieve or maintain desired mixing or residence times. Here, we report a cruise control strategy that overcomes these limitations and allows microscale gas-liquid (bubble) and liquid-liquid (droplet) flow conditions to be rapidly "adjusted" and maintained. Using this strategy we consistently establish bubble and droplet flows with dispersed phase (plug) velocities of 5-300 mm s(-1), plug lengths of 0.6-5 mm and continuous phase (slug) lengths of 0.5-3 mm. The mixing times (1-5 s), mass transfer times (33-250 ms) and residence times (3-300 s) can therefore be directly imposed by dynamically controlling the supply of the dispersed and the continuous liquids either from external pumps or from local pressurized reservoirs. In the latter case, no chip-external pumps, liquid-perfused tubes or valves are necessary while unwanted dead volumes are significantly reduced.

Automated generation of libraries of nL droplets

We demonstrate an integrated system for rapid and automated generation of multiple, chemically distinct populations of ~10(3)-10(4) sub-nanoliter droplets. Generation of these 'libraries of droplets' proceeds in the following automated steps: i) generation of a sequence of micro-liter droplets of individually predetermined composition, ii) injection of these 'parental' droplets onto a chip, iii) transition from a mm- to a μm-scale of the channels and splitting each of the parental drops with a flow-focusing module into thousands of tightly monodisperse daughter drops and iv) separation of such formed homogeneous populations with plugs of a third immiscible fluid. This method is compatible both with aspiration of microliter portions of liquid from a 96-well plate with a robotic station and with automated microfluidic systems that generate (~μL) droplets of preprogrammed compositions. The system that we present bridges the techniques that provide elasticity of protocols executed on microliter droplets with the techniques for high-throughput screening of small (~pL, ~nL) droplet libraries. The method that we describe can be useful in exploiting the synergy between the ability to rapidly screen distinct chemical environments and to perform high-throughput studies of single cells or molecules and in digital droplet PCR systems.

Building droplet-based microfluidic systems for biological analysis

In the present paper, we review and discuss current developments and challenges in the field of droplet-based microfluidics. This discussion includes an assessment of the basic fluid dynamics of segmented flows, material requirements, fundamental unit operations and how integration of functional components can be applied to specific biological problems.

Digital LAMP in a sample self-digitization (SD) chip

This paper describes the realization of digital loop-mediated DNA amplification (dLAMP) in a sample self-digitization (SD) chip. Digital DNA amplification has become an attractive technique to quantify absolute concentrations of DNA in a sample. While digital polymerase chain reaction is still the most widespread implementation, its use in resource-limited settings is impeded by the need for thermal cycling and robust temperature control. In such situations, isothermal protocols that can amplify DNA or RNA without thermal cycling are of great interest. Here, we accomplished the successful amplification of single DNA molecules in a stationary droplet array using isothermal digital loop-mediated DNA amplification. Unlike most (if not all) existing methods for sample discretization, our design allows for automated, loss-less digitization of sample volumes on-chip. We demonstrated accurate quantification of relative and absolute DNA concentrations with sample volumes of less than 2 μl. We assessed the homogeneity of droplet size during sample self-digitization in our device, and verified that the size variation was small enough such that straightforward counting of LAMP-active droplets sufficed for data analysis. We anticipate that the simplicity and robustness of our SD chip make it attractive as an inexpensive and easy-to-operate device for DNA amplification, for example in point-of-care settings.

High throughput single-cell and multiple-cell micro-encapsulation

Microfluidic encapsulation methods have been previously utilized to capture cells in picoliter-scale aqueous, monodisperse drops, providing confinement from a bulk fluid environment with applications in high throughput screening, cytometry, and mass spectrometry. We describe a method to not only encapsulate single cells, but to repeatedly capture a set number of cells (here we demonstrate one- and two-cell encapsulation) to study both isolation and the interactions between cells in groups of controlled sizes. By combining drop generation techniques with cell and particle ordering, we demonstrate controlled encapsulation of cell-sized particles for efficient, continuous encapsulation. Using an aqueous particle suspension and immiscible fluorocarbon oil, we generate aqueous drops in oil with a flow focusing nozzle. The aqueous flow rate is sufficiently high to create ordering of particles which reach the nozzle at integer multiple frequencies of the drop generation frequency, encapsulating a controlled number of cells in each drop. For representative results, 9.9 μm polystyrene particles are used as cell surrogates. This study shows a single-particle encapsulation efficiency P(k=1) of 83.7% and a double-particle encapsulation efficiency P(k=2) of 79.5% as compared to their respective Poisson efficiencies of 39.3% and 33.3%, respectively. The effect of consistent cell and particle concentration is demonstrated to be of major importance for efficient encapsulation, and dripping to jetting transitions are also addressed.

INTRODUCTION

Continuous media aqueous cell suspensions share a common fluid environment which allows cells to interact in parallel and also homogenizes the effects of specific cells in measurements from the media. High-throughput encapsulation of cells into picoliter-scale drops confines the samples to protect drops from cross-contamination, enable a measure of cellular diversity within samples, prevent dilution of reagents and expressed biomarkers, and amplify signals from bioreactor products. Drops also provide the ability to re-merge drops into larger aqueous samples or with other drops for intercellular signaling studies. The reduction in dilution implies stronger detection signals for higher accuracy measurements as well as the ability to reduce potentially costly sample and reagent volumes. Encapsulation of cells in drops has been utilized to improve detection of protein expression, antibodies, enzymes, and metabolic activity for high throughput screening, and could be used to improve high throughput cytometry. Additional studies present applications in bio-electrospraying of cell containing drops for mass spectrometry and targeted surface cell coatings. Some applications, however, have been limited by the lack of ability to control the number of cells encapsulated in drops. Here we present a method of ordered encapsulation which increases the demonstrated encapsulation efficiencies for one and two cells and may be extrapolated for encapsulation of a larger number of cells. To achieve monodisperse drop generation, microfluidic "flow focusing" enables the creation of controllable-size drops of one fluid (an aqueous cell mixture) within another (a continuous oil phase) by using a nozzle at which the streams converge. For a given nozzle geometry, the drop generation frequency f and drop size can be altered by adjusting oil and aqueous flow rates Q(oil) and Q(aq). As the flow rates increase, the flows may transition from drop generation to unstable jetting of aqueous fluid from the nozzle. When the aqueous solution contains suspended particles, particles become encapsulated and isolated from one another at the nozzle. For drop generation using a randomly distributed aqueous cell suspension, the average fraction of drops D(k) containing k cells is dictated by Poisson statistics, where D(k) = λ(k) exp(-λ)/(k!) and λ is the average number of cells per drop. The fraction of cells which end up in the "correctly" encapsulated drops is calculated using P(k) = (k x D(k))/Σ(k' x D(k)'). The subtle difference between the two metrics is that D(k) relates to the utilization of aqueous fluid and the amount of drop sorting that must be completed following encapsulation, and P(k) relates to the utilization of the cell sample. As an example, one could use a dilute cell suspension (low λ) to encapsulate drops where most drops containing cells would contain just one cell. While the efficiency metric P(k) would be high, the majority of drops would be empty (low D(k)), thus requiring a sorting mechanism to remove empty drops, also reducing throughput. Combining drop generation with inertial ordering provides the ability to encapsulate drops with more predictable numbers of cells per drop and higher throughputs than random encapsulation. Inertial focusing was first discovered by Segre and Silberberg and refers to the tendency of finite-sized particles to migrate to lateral equilibrium positions in channel flow. Inertial ordering refers to the tendency of the particles and cells to passively organize into equally spaced, staggered, constant velocity trains. Both focusing and ordering require sufficiently high flow rates (high Reynolds number) and particle sizes (high Particle Reynolds number). Here, the Reynolds number Re =uD(h)/ν and particle Reynolds number Rep =Re(a/D(h))², where u is a characteristic flow velocity, D(h) [=2wh/(w+h)] is the hydraulic diameter, ν is the kinematic viscosity, a is the particle diameter, w is the channel width, and h is the channel height. Empirically, the length required to achieve fully ordered trains decreases as Re and Re(p) increase. Note that the high Re and Re(p) requirements (for this study on the order of 5 and 0.5, respectively) may conflict with the need to keep aqueous flow rates low to avoid jetting at the drop generation nozzle. Additionally, high flow rates lead to higher shear stresses on cells, which are not addressed in this protocol. The previous ordered encapsulation study demonstrated that over 90% of singly encapsulated HL60 cells under similar flow conditions to those in this study maintained cell membrane integrity. However, the effect of the magnitude and time scales of shear stresses will need to be carefully considered when extrapolating to different cell types and flow parameters. The overlapping of the cell ordering, drop generation, and cell viability aqueous flow rate constraints provides an ideal operational regime for controlled encapsulation of single and multiple cells. Because very few studies address inter-particle train spacing, determining the spacing is most easily done empirically and will depend on channel geometry, flow rate, particle size, and particle concentration. Nonetheless, the equal lateral spacing between trains implies that cells arrive at predictable, consistent time intervals. When drop generation occurs at the same rate at which ordered cells arrive at the nozzle, the cells become encapsulated within the drop in a controlled manner. This technique has been utilized to encapsulate single cells with throughputs on the order of 15 kHz, a significant improvement over previous studies reporting encapsulation rates on the order of 60-160 Hz. In the controlled encapsulation work, over 80% of drops contained one and only one cell, a significant efficiency improvement over Poisson (random) statistics, which predicts less than 40% efficiency on average. In previous controlled encapsulation work, the average number of particles per drop λ was tuned to provide single-cell encapsulation. We hypothesize that through tuning of flow rates, we can efficiently encapsulate any number of cells per drop when λ is equal or close to the number of desired cells per drop. While single-cell encapsulation is valuable in determining individual cell responses from stimuli, multiple-cell encapsulation provides information relating to the interaction of controlled numbers and types of cells. Here we present a protocol, representative results using polystyrene microspheres, and discussion for controlled encapsulation of multiple cells using a passive inertial ordering channel and drop generation nozzle.

Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation

One of the benefits of Digital PCR (dPCR) is the potential for unparalleled precision enabling smaller fold change measurements. An example of an assessment that could benefit from such improved precision is the measurement of tumour-associated copy number variation (CNV) in the cell free DNA (cfDNA) fraction of patient blood plasma. To investigate the potential precision of dPCR and compare it with the established technique of quantitative PCR (qPCR), we used breast cancer cell lines to investigate HER2 gene amplification and modelled a range of different CNVs. We showed that, with equal experimental replication, dPCR could measure a smaller CNV than qPCR. As dPCR precision is directly dependent upon both the number of replicate measurements and the template concentration, we also developed a method to assist the design of dPCR experiments for measuring CNV. Using an existing model (based on Poisson and binomial distributions) to derive an expression for the variance inherent in dPCR, we produced a power calculation to define the experimental size required to reliably detect a given fold change at a given template concentration. This work will facilitate any future translation of dPCR to key diagnostic applications, such as cancer diagnostics and analysis of cfDNA.

Mesh-integrated microdroplet array for simultaneous merging and storage of single-cell droplets

We constructed a mesh-grid integrated microwell array which enables easy trapping and consistent addition of droplets. The grid acts as a microchannel structure to guide droplets into the microwells underneath, and also provides open access for additional manipulation in a high-throughput manner. Each droplet in the array forms a stable environment of pico-litre volume to implement a single-cell-based assay.

Single-molecule emulsion PCR in microfluidic droplets

The application of microfluidic droplet PCR for single-molecule amplification and analysis has recently been extensively studied. Microfluidic droplet technology has the advantages of compartmentalizing reactions into discrete volumes, performing highly parallel reactions in monodisperse droplets, reducing cross-contamination between droplets, eliminating PCR bias and nonspecific amplification, as well as enabling fast amplification with rapid thermocycling. Here, we have reviewed the important technical breakthroughs of microfluidic droplet PCR in the past five years and their applications to single-molecule amplification and analysis, such as high-throughput screening, next generation DNA sequencing, and quantitative detection of rare mutations. Although the utilization of microfluidic droplet single-molecule PCR is still in the early stages, its great potential has already been demonstrated and will provide novel solutions to today's biomedical engineering challenges in single-molecule amplification and analysis.