High-throughput injection with microfluidics using picoinjectors

Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions

In vitro evolution methodologies are powerful approaches to identify RNA with new functionalities. While Systematic Evolution of Ligands by Exponential enrichment (SELEX) is an efficient approach to generate new RNA aptamers, it is less suited for the isolation of efficient ribozymes as it does not select directly for the catalysis. In vitro compartmentalization (IVC) in aqueous droplets in emulsions allows catalytic RNAs to be selected under multiple-turnover conditions but suffers severe limitations that can be overcome using the droplet-based microfluidics workflow described in this paper. Using microfluidics, millions of genes in a library can be individually compartmentalized in highly monodisperse aqueous droplets and serial operations performed on them. This allows the different steps of the evolution process (gene amplification, transcription, and phenotypic assay) to be uncoupled, making the method highly flexible, applicable to the selection and evolution of a variety of RNAs, and easily adaptable for evolution of DNA or proteins. To demonstrate the method, we performed cycles of random mutagenesis and selection to evolve the X-motif, a ribozyme which, like many ribozymes selected using SELEX, has limited multiple-turnover activity. This led to the selection of variants, likely to be the optimal ribozymes that can be generated using point mutagenesis alone, with a turnover number under multiple-turnover conditions, k(ss) cat, ∼ 28-fold higher than the original X-motif, primarily due to an increase in the rate of product release, the rate-limiting step in the multiple-turnover reaction.

Low-volume multiplexed proteolytic activity assay and inhibitor analysis through a pico-injector array

Secreted active proteases, from families of enzymes such as matrix metalloproteinases (MMPs) and ADAMs (a disintegrin and metalloproteinases), participate in diverse pathological processes. To simultaneously measure multiple specific protease activities, a series of parallel enzyme reactions combined with a series of inhibitor analyses for proteolytic activity matrix analysis (PrAMA) are essential but limited due to the sample quantity requirements and the complexity of performing multiple reactions. To address these issues, we developed a pico-injector array to generate 72 different reactions in picoliter-volume droplets by controlling the sequence of combinational injections, which allowed simultaneous recording of a wide range of multiple enzyme reactions and measurement of inhibitor effects using small sample volumes (~10 μL). Multiple MMP activities were simultaneously determined by 9 different substrates and 2 inhibitors using injections from a pico-injector array. Due to the advantages of inhibitor analysis, the MMP/ADAM activities of MDA-MB-231, a breast cancer cell line, were characterized with high MMP-2, MMP-3 and ADAM-10 activity. This platform could be customized for a wide range of applications that also require multiple reactions with inhibitor analysis to enhance the sensitivity by encapsulating different chemical sensors.

Microfluidic static droplet array for analyzing microbial communication on a population gradient

Quorum sensing (QS) is a type of cell-cell communication using signal molecules that are released and detected by cells, which respond to changes in their population density. A few studies explain that QS may operate in a density-dependent manner; however, due to experimental challenges, this fundamental hypothesis has never been investigated. Here, we present a microfluidic static droplet array (SDA) that combines a droplet generator with hydrodynamic traps to independently generate a bacterial population gradient into a parallel series of droplets under complete chemical and physical isolation. The SDA independently manipulates both a chemical concentration gradient and a bacterial population density. In addition, the bacterial population gradient in the SDA can be tuned by a simple change in the number of sample plug loading. Finally, the method allows the direct analysis of complicated biological events in an addressable droplet to enable the characterization of bacterial communication in response to the ratio of two microbial populations, including two genetically engineered QS circuits, such as the signal sender for acyl-homoserine lactone (AHL) production and the signal receiver bacteria for green fluorescent protein (GFP) expression induced by AHL. For the first time, we found that the population ratio of the signal sender and receiver indicates a significant and potentially interesting partnership between microbial communities. Therefore, we envision that this simple SDA could be a useful platform in various research fields, including analytical chemistry, combinatorial chemistry, synthetic biology, microbiology, and molecular biology.

Droplet actuation in an electrified microfluidic network

This work demonstrates that liquid droplet emulsions in a microchannel can be deformed, decelerated and/or pinned by applying a suitable electrical potential. By concentrating a potential gradient at the corners, we show that different droplets can be passively binned by size and on demand in a branched microfluidic device. The deformation, deceleration, squeezing and release of droplets in a three-dimensional numerical simulation are qualitatively verified by experiments in a PDMS microfluidic device. The forces required for pinning or binning a droplet provide a delicate balance between hydrodynamics and the electric field, and are obtained using appropriate non-dimensional parameters.

Droplet-based microfluidics at the femtolitre scale

We have built a toolbox of modules for droplet-based microfluidic operations on femtolitre volume droplets. We have demonstrated monodisperse production, sorting, coalescence, splitting, mixing, off-chip incubation and re-injection at high frequencies (up to 3 kHz). We describe the constraints and limitations under which satisfactory performances are obtained, and discuss the physics that controls each operation. For some operations, such as internal mixing, we obtained outstanding performances: for instance, in 75 fL droplets the mixing time was 45 μs, 35-fold faster than previously reported for a droplet microreactor. In practice, in all cases, a level of control comparable to nanolitre or picolitre droplet manipulation was obtained despite the 3 to 6 order of magnitude reduction in droplet volume. Remarkably, all the operations were performed using devices made using standard soft-lithography techniques and PDMS rapid prototyping. We show that femtolitre droplets can be used as microreactors for molecular biology with volumes one billion times smaller than conventional microtitre plate wells: in particular, the Polymerase Chain Reaction (PCR) was shown to work efficiently in 20 fL droplets.

Rapid and continuous magnetic separation in droplet microfluidic devices

We present a droplet microfluidic method to extract molecules of interest from a droplet in a rapid and continuous fashion. We accomplish this by first marginalizing functionalized super-paramagnetic beads within the droplet using a magnetic field, and then splitting the droplet into one droplet containing the majority of magnetic beads and one droplet containing the minority fraction. We quantitatively analysed the factors which affect the efficiency of marginalization and droplet splitting to optimize the enrichment of magnetic beads. We first characterized the interplay between the droplet velocity and the strength of the magnetic field and its effect on marginalization. We found that marginalization is optimal at the midline of the magnet and that marginalization is a good predictor of bead enrichment through splitting at low to moderate droplet velocities. Finally, we focused our efforts on manipulating the splitting profile to improve the enrichment provided by asymmetric splitting. We designed asymmetric splitting forks that employ capillary effects to preferentially extract the bead-rich regions of the droplets. Our strategy represents a framework to optimize magnetic bead enrichment methods tailored to the requirements of specific droplet-based applications. We anticipate that our separation technology is well suited for applications in single-cell genomics and proteomics. In particular, our method could be used to separate mRNA bound to poly-dT functionalized magnetic microparticles from single cell lysates to prepare single-cell cDNA libraries.

A barcode-free combinatorial screening platform for matrix metalloproteinase screening

Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application.

PCR-activated cell sorting for cultivation-free enrichment and sequencing of rare microbes

Microbial systems often exhibit staggering diversity, making the study of rare, interesting species challenging. For example, metagenomic analyses of mixed-cell populations are often dominated by the sequences of the most abundant organisms, while those of rare microbes are detected only at low levels, if at all. To overcome this, selective cultivation or fluorescence-activated cell sorting (FACS) can be used to enrich for the target species prior to sequence analysis; however, since most microbes cannot be grown in the lab, cultivation strategies often fail, while cell sorting requires techniques to uniquely label the cell type of interest, which is often not possible with uncultivable microbes. Here, we introduce a culture-independent strategy for sorting microbial cells based on genomic content, which we term PCR-activated cell sorting (PACS). This technology, which utilizes the power of droplet-based microfluidics, is similar to FACS in that it uses a fluorescent signal to uniquely identify and sort target species. However, PACS differs importantly from FACS in that the signal is generated by performing PCR assays on the cells in microfluidic droplets, allowing target cells to be identified with high specificity with suitable design of PCR primers and TaqMan probes. The PACS assay is general, requires minimal optimization and, unlike antibody methods, can be developed without access to microbial antigens. Compared to non-specific methods in which cells are sorted based on size, granularity, or the ability to take up dye, PACS enables genetic sequence-specific sorting and recovery of the cell genomes. In addition to sorting microbes, PACS can be applied to eukaryotic cells, viruses, and naked nucleic acids.

A journey of trains of droplets in droplet-based microfluidic devices

In this paper, we propose a microfluidic platform toseparate magnetic particles with a constant volumetric flow condition. In order to realize this architecture, three main functions for a droplet manipulation based system are integrated into a single device: synchronization of droplets by matching a location of droplets; lateral electro-coalescence; and magnetic particle manipulation. For an optimized condition of this device, a droplet generation was controlled by varying a droplet size at a fixed flow rate ratio 0.86. The electro-coalescence efficiency and maximum throughput are investigated at a given flow rate condition.

Rapid modulation of droplet composition with pincer microvalves

Single-layer membrane valves are simple to fabricate and to integrate into microfluidic devices. However, due to their rectangular flow channel geometry, they do not fully seal. Here, we show that liquid flow can be reduced by over 3 orders of magnitude, enabling the contents of forming droplets to be dynamically modulated. We use this precision control to perform combinatorial DNA synthesis in the droplets.

Single-cell screening of photosynthetic growth and lactate production by cyanobacteria

BACKGROUND

Photosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible.

RESULTS

We present a method for high-throughput, single-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for l-lactate production, and sort strains with high productivity. We demonstrate the separation of low- and high-producing reference strains, as well as enrichment of a more productive l-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically stalled cells.

CONCLUSIONS

The workflow will facilitate metabolic engineering and directed evolution studies and will be useful in studies of cyanobacteria biochemistry and physiology.

A microfluidic platform for quantitative measurements of effective protein charges and single ion binding in solution

Microfluidic electrophoresis enables the comparison of dry sequence and solvated protein charges, and the detection of protein–ion binding.

Continuous and low error-rate passive synchronization of pre-formed droplets

A microfluidic droplet-handling architecture for the synchronization of asynchronous, mis-matched, pre-formed droplet streams is demonstrated.

On demand nanoliter-scale microfluidic droplet generation, injection, and mixing using a passive microfluidic device

We here present and characterize a programmable nanoliter scale droplet-on-demand device that can be used separately or readily integrated into low cost single layer rapid prototyping microfluidic systems for a wide range of user applications. The passive microfluidic device allows external (off-the-shelf) electronically controlled pinch valves to program the delivery of nanoliter scale aqueous droplets from up to 9 different inputs to a central outlet channel. The inputs can be either continuous aqueous fluid streams or microliter scale aqueous plugs embedded in a carrier fluid, in which case the number of effective input solutions that can be employed in an experiment is no longer strongly constrained (100 s-1000 s). Both nanoliter droplet sequencing output and nanoliter-scale droplet mixing are reported with this device. Optimization of the geometry and pressure relationships in the device was achieved in several hardware iterations with the support of open source microfluidic simulation software and equivalent circuit models. The requisite modular control of pressure relationships within the device is accomplished using hydrodynamic barriers and matched resistance channels with three different channel heights, custom parallel reversible microfluidic I/O connections, low dead-volume pinch valves, and a simply adjustable array of external screw valves. Programmable sequences of droplet mixes or chains of droplets can be achieved with the device at low Hz frequencies, limited by device elasticity, and could be further enhanced by valve integration. The chip has already found use in the characterization of droplet bunching during export and the synthesis of a DNA library.

Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems

Picoinjection is a promising technique to add reagents into pre-formed emulsion droplets on chip however, it is sensitive to pressure fluctuation, making stable operation of the picoinjector challenging. We present a chip architecture using a simple pressure stabilizer for consistent and highly reproducible picoinjection in multi-step biochemical assays with droplets. Incorporation of the stabilizer immediately upstream of a picoinjector or a combination of injectors greatly reduces pressure fluctuations enabling reproducible and effective picoinjection in systems where the pressure varies actively during operation. We demonstrate the effectiveness of the pressure stabilizer for an integrated platform for on-demand encapsulation of bacterial cells followed by picoinjection of reagents for lysing the encapsulated cells. The pressure stabilizer was also used for picoinjection of multiple displacement amplification (MDA) reagents to achieve genomic DNA amplification of lysed bacterial cells.

Acoustofluidic chemical waveform generator and switch

Eliciting a cellular response to a changing chemical microenvironment is central to many biological processes including gene expression, cell migration, differentiation, apoptosis, and intercellular signaling. The nature and scope of the response is highly dependent upon the spatiotemporal characteristics of the stimulus. To date, studies that investigate this phenomenon have been limited to digital (or step) chemical stimulation with little control over the temporal counterparts. Here, we demonstrate an acoustofluidic (i.e., fusion of acoustics and microfluidics) approach for generating programmable chemical waveforms that permits continuous modulation of the signal characteristics including the amplitude (i.e., sample concentration), shape, frequency, and duty cycle, with frequencies reaching up to 30 Hz. Furthermore, we show fast switching between multiple distinct stimuli, wherein the waveform of each stimulus is independently controlled. Using our device, we characterized the frequency-dependent activation and internalization of the β2-adrenergic receptor (β2-AR), a prototypic G-protein coupled receptor (GPCR), using epinephrine. The acoustofluidic-based programmable chemical waveform generation and switching method presented herein is expected to be a powerful tool for the investigation and characterization of the kinetics and other dynamic properties of many biological and biochemical processes.

Generating electric fields in PDMS microfluidic devices with salt water electrodes

Droplet merging and sorting in microfluidic devices usually rely on electric fields generated by solid metal electrodes. We show that simpler and more reliable salt water electrodes, despite their lower conductivity, can perform the same droplet manipulations at the same voltages.

Droplet-based microfluidic washing module for magnetic particle-based assays

In this paper, we propose a continuous flow droplet-based microfluidic platform for magnetic particle-based assays by employing in-droplet washing. The droplet-based washing was implemented by traversing functionalized magnetic particles across a laterally merged droplet from one side (containing sample and reagent) to the other (containing buffer) by an external magnetic field. Consequently, the magnetic particles were extracted to a parallel-synchronized train of washing buffer droplets, and unbound reagents were left in an original train of sample droplets. To realize the droplet-based washing function, the following four procedures were sequentially carried in a droplet-based microfluidic device: parallel synchronization of two trains of droplets by using a ladder-like channel network; lateral electrocoalescence by an electric field; magnetic particle manipulation by a magnetic field; and asymmetrical splitting of merged droplets. For the stable droplet synchronization and electrocoalescence, we optimized droplet generation conditions by varying the flow rate ratio (or droplet size). Image analysis was carried out to determine the fluorescent intensity of reagents before and after the washing step. As a result, the unbound reagents in sample droplets were significantly removed by more than a factor of 25 in the single washing step, while the magnetic particles were successfully extracted into washing buffer droplets. As a proof-of-principle, we demonstrate a magnetic particle-based immunoassay with streptavidin-coated magnetic particles and fluorescently labelled biotin in the proposed continuous flow droplet-based microfluidic platform.

Electrocoalescence based serial dilution of microfluidic droplets

Dilution of microfluidic droplets where the concentration of a reagent is incrementally varied is a key operation in drop-based biological analysis. Here, we present an electrocoalescence based dilution scheme for droplets based on merging between moving and parked drops. We study the effects of fluidic and electrical parameters on the dilution process. Highly consistent coalescence and fine resolution in dilution factor are achieved with an AC signal as low as 10 V even though the electrodes are separated from the fluidic channel by insulator. We find that the amount of material exchange between the droplets per coalescence event is high for low capillary number. We also observe different types of coalescence depending on the flow and electrical parameters and discuss their influence on the rate of dilution. Overall, we find the key parameter governing the rate of dilution is the duration of coalescence between the moving and parked drop. The proposed design is simple incorporating the channel electrodes in the same layer as that of the fluidic channels. Our approach allows on-demand and controlled dilution of droplets and is simple enough to be useful for assays that require serial dilutions. The approach can also be useful for applications where there is a need to replace or wash fluid from stored drops.

Cell-free protein synthesis in a microchamber revealed the presence of an optimum compartment volume for high-order reactions

The application of microelectromechanical systems (MEMS) to chemistry and biochemistry allows various reactions to be performed in microscale compartments. Here, we aimed to use the glass microchamber to study the compartment size dependency of the protein synthesis, one of the most important reactions in the cell. By encapsulating the cell-free protein synthesis system with different reaction orders in femtoliter microchambers, chamber size dependency of the reaction initiated with a constant copy number of DNA was investigated. We were able to observe the properties specific to the high order reactions in microcompartments with high precision and found the presence of an optimum compartment volume for a high-order reaction using real biological molecules.

A new microfluidics-based droplet dispenser for ICPMS

In this work, a novel droplet microfluidic sample introduction system for inductively coupled plasma mass spectrometry (ICPMS) is proposed and characterized. The cheap and disposable microfluidic chip generates droplets of an aqueous sample in a stream of perfluorohexane (PFH), which is also used to eject them as a liquid jet. The aqueous droplets remain intact during the ejection and can be transported into the ICP with >50% efficiency. The transport is realized via a custom-built system, which includes a membrane desolvator necessary for the PFH vapor removal. The introduction system presented here can generate highly monodisperse droplets in the size range of 40–60 μm at frequencies from 90 to 300 Hz. These droplets produced very stable signals with a relative standard deviation (RSD) comparable to the one achieved with a commercial droplet dispenser. Using the current system, samples with a total volume of <1 μL can be analyzed. Moreover, the capabilities of the setup for introduction and quantitative elemental analysis of single cells were described using a test system of bovine red blood cells. In the future, other modules of the modern microfludics can be integrated in the chip, such as on-chip sample pretreatment or parallel introduction of different samples.

Coalescing drops in microfluidic parking networks: A multifunctional platform for drop-based microfluidics

Multiwell plate and pipette systems have revolutionized modern biological analysis; however, they have disadvantages because testing in the submicroliter range is challenging, and increasing the number of samples is expensive. We propose a new microfluidic methodology that delivers the functionality of multiwell plates and pipettes at the nanoliter scale by utilizing drop coalescence and confinement-guided breakup in microfluidic parking networks (MPNs). Highly monodisperse arrays of drops obtained using a hydrodynamic self-rectification process are parked at prescribed locations in the device, and our method allows subsequent drop manipulations such as fine-gradation dilutions, reactant addition, and fluid replacement while retaining microparticles contained in the sample. Our devices operate in a quasistatic regime where drop shapes are determined primarily by the channel geometry. Thus, the behavior of parked drops is insensitive to flow conditions. This insensitivity enables highly parallelized manipulation of drop arrays of different composition, without a need for fine-tuning the flow conditions and other system parameters. We also find that drop coalescence can be switched off above a critical capillary number, enabling individual addressability of drops in complex MPNs. The platform demonstrated here is a promising candidate for conducting multistep biological assays in a highly multiplexed manner, using thousands of submicroliter samples.

The microfluidic jukebox

Music is a form of art interweaving people of all walks of life. Through subtle changes in frequencies, a succession of musical notes forms a melody which is capable of mesmerizing the minds of people. With the advances in technology, we are now able to generate music electronically without relying solely on physical instruments. Here, we demonstrate a musical interpretation of droplet-based microfluidics as a form of novel electronic musical instruments. Using the interplay of electric field and hydrodynamics in microfluidic devices, well controlled frequency patterns corresponding to musical tracks are generated in real time. This high-speed modulation of droplet frequency (and therefore of droplet sizes) may also provide solutions that reconciles high-throughput droplet production and the control of individual droplet at production which is needed for many biochemical or material synthesis applications.

Picoinjection of microfluidic drops without metal electrodes

Existing methods for picoinjecting reagents into microfluidic drops require metal electrodes integrated into the microfluidic chip. The integration of these electrodes adds cumbersome and error-prone steps to the device fabrication process. We have developed a technique that obviates the needs for metal electrodes during picoinjection. Instead, it uses the injection fluid itself as an electrode, since most biological reagents contain dissolved electrolytes and are conductive. By eliminating the electrodes, we reduce device fabrication time and complexity, and make the devices more robust. In addition, with our approach, the injection volume depends on the voltage applied to the picoinjection solution; this allows us to rapidly adjust the volume injected by modulating the applied voltage. We demonstrate that our technique is compatible with reagents incorporating common biological compounds, including buffers, enzymes, and nucleic acids.

Simple and reusable picoinjector for liquid delivery via nanofluidics approach

Precise control of sample volume is one of the most important functions in lab-on-a-chip (LOC) systems, especially for chemical and biological reactions. The common approach used for liquid delivery involves the employment of capillaries and microstructures for generating a droplet which has a volume in the nanoliter or picoliter range. Here, we report a novel approach for constructing a picoinjector which is based on well-controlled electroosmotic (EO) flow to electrokinetically drive sample solutions. This picoinjector comprises an array of interconnected nanochannels for liquid delivery. Such technique for liquid delivery has the advantages of well-controlled sample volume and reusable nanofluidic chip, and it was reported for the first time. In the study of the pumping process for this picoinjector, the EO flow rate was determined by the intensity of the fluorescent probe. The influence of ion concentration in electrolyte solutions over the EO flow rate was also investigated and discussed. The application of this EO-driven picoinjector for chemical reactions was demonstrated by the reaction between Fluo-4 and calcium chloride with the reaction cycle controlled by the applied square waves of different duty cycles. The precision of our device can reach down to picoliter per second, which is much smaller than that of most existing technologies. This new approach, thus, opens further possibilities of adopting nanofluidics for well-controlled chemical reactions with particular applications in nanoparticle synthesis, bimolecular synthesis, drug delivery, and diagnostic testing.

PACS

85.85.+ j; 87.15.hj; 82.39.Wj.

Microfluidic flow-focusing in ac electric fields

We demonstrate the control of droplet sizes by an ac voltage applied across microelectrodes patterned around a flow-focusing junction. The electrodes do not come in contact with the fluids to avoid electrochemical effects. We found several regimes of droplet production in electric fields, controlled by the connection of the chip, the conductivity of the dispersed phase and the frequency of the applied field. A simple electrical modelling of the chip reveals that the effective voltage at the tip of the liquid to be dispersed controls the production mechanism. At low voltages (≲ 600 V), droplets are produced in dripping regime; the droplet size is a function of the ac electric field. The introduction of an effective capillary number that takes into account the Maxwell stress can explain the dependance of droplet size with the applied voltage. At higher voltages (≳ 600 V), jets are observed. The stability of droplet production is a function of the fluid conductivity and applied field frequency reported in a set of flow diagrams.

Synchronized reinjection and coalescence of droplets in microfluidics

Coalescence of two kinds of pre-processed droplets is necessary to perform chemical and biological assays in droplet-based microfluidics. However, a robust technique to accomplish this does not exist. Here we present a microfluidic device to synchronize the reinjection of two different kinds of droplets and coalesce them, using hydrostatic pressure in conjunction with a conventional syringe pump. We use a device consisting of two opposing T-junctions for reinjecting two kinds of droplets and control the flows of the droplets by applying gravity-driven hydrostatic pressure. The hydrostatic-pressure operation facilitates balancing the droplet reinjection rates and allows us to synchronize the reinjection. Furthermore, we present a simple but robust module to coalesce two droplets that sequentially come into the module, regardless of their arrival times. These re-injection and coalescence techniques might be used in lab-on-chip applications requiring droplets with controlled numbers of solid materials, which can be made by coalescing two pre-processed droplets that are formed and sorted in devices.

CotA laccase: high-throughput manipulation and analysis of recombinant enzyme libraries expressed in E. coli using droplet-based microfluidics

A high-throughput cell analysis and sorting platform using droplet-based microfluidics is introduced for directed evolution of recombinant CotA laccase expressed in E. coli.

DNA sequence analysis with droplet-based microfluidics

Droplet-based microfluidic techniques can form and process micrometer scale droplets at thousands per second. Each droplet can house an individual biochemical reaction, allowing millions of reactions to be performed in minutes with small amounts of total reagent. This versatile approach has been used for engineering enzymes, quantifying concentrations of DNA in solution, and screening protein crystallization conditions. Here, we use it to read the sequences of DNA molecules with a FRET-based assay. Using probes of different sequences, we interrogate a target DNA molecule for polymorphisms. With a larger probe set, additional polymorphisms can be interrogated as well as targets of arbitrary sequence.

Combinatorial generation of droplets by controlled assembly and coalescence

We describe a microfluidic system for generating a sequence of liquid droplets of multiple concentrations in a single experimental condition. The series of final droplets has the combination of the compositions varying periodically, with polydispersity of the size less than 8%. By utilizing the design of the microchannel geometry and the passive control of three immiscible fluids (oil, water, and air) including generation, breakup, separation and coalescence of droplets, we can change the system to generate diverse sets of combination of materials. The device can be used for testing different concentration of materials in picoliter volumes and developing a new way to deliver dynamic signals of chemicals with microfluidics.

Ultrahigh-throughput sorting of microfluidic drops with flow cytometry

The detection and sorting of aqueous drops is central to microfluidic workflows for high-throughput biology applications, including directed evolution, digital PCR, and antibody screening. However, high-throughput detection and sorting of drops require optical systems and microfluidic components that are complex, difficult to build, and often yield inadequate sensitivity and throughput. Here, we demonstrate a general method to harness flow cytometry, with its unmatched speed and sensitivity, for droplet-based microfluidic sorting.

High-throughput, multiparameter analysis of single cells

Heterogeneity of cell populations in various biological systems has been widely recognized, and the highly heterogeneous nature of cancer cells has been emerging with clinical relevance. Single-cell analysis using a combination of high-throughput and multiparameter approaches is capable of reflecting cell-to-cell variability, and at the same time of unraveling the complexity and interdependence of cellular processes in the individual cells of a heterogeneous population. In this review, analytical methods and microfluidic tools commonly used for high-throughput, multiparameter single-cell analysis of DNA, RNA, and proteins are discussed. Applications and limitations of currently available technologies for cancer research and diagnostics are reviewed in the light of the ultimate goal to establish clinically applicable assays.

Ultra-high throughput detection of single cell β-galactosidase activity in droplets using micro-optical lens array

We demonstrate the use of a hybrid microfluidic-micro-optical system for the screening of enzymatic activity at the single cell level. Escherichia coli β-galactosidase activity is revealed by a fluorogenic assay in 100 pl droplets. Individual droplets containing cells are screened by measuring their fluorescence signal using a high-speed camera. The measurement is parallelized over 100 channels equipped with microlenses and analyzed by image processing. A reinjection rate of 1 ml of emulsion per minute was reached corresponding to more than 10⁵ droplets per second, an analytical throughput larger than those obtained using flow cytometry.

Real-time image processing for label-free enrichment of Actinobacteria cultivated in picolitre droplets

The majority of today's antimicrobial therapeutics is derived from secondary metabolites produced by Actinobacteria. While it is generally assumed that less than 1% of Actinobacteria species from soil habitats have been cultivated so far, classic screening approaches fail to supply new substances, often due to limited throughput and frequent rediscovery of already known strains. To overcome these restrictions, we implement high-throughput cultivation of soil-derived Actinobacteria in microfluidic pL-droplets by generating more than 600,000 pure cultures per hour from a spore suspension that can subsequently be incubated for days to weeks. Moreover, we introduce triggered imaging with real-time image-based droplet classification as a novel universal method for pL-droplet sorting. Growth-dependent droplet sorting at frequencies above 100 Hz is performed for label-free enrichment and extraction of microcultures. The combination of both cultivation of Actinobacteria in pL-droplets and real-time detection of growing Actinobacteria has great potential in screening for yet unknown species as well as their undiscovered natural products.

Supramolecular hydrogel capsules based on PEG: a step toward degradable biomaterials with rational design

Supramolecular microgel capsules based on polyethylene glycol (PEG) are a promising class of soft particulate scaffolds with tailored properties. An approach to fabricate such particles with exquisite control by droplet-based microfluidics is presented. Linear PEG precursor polymers that carry bipyridine moieties on both chain termini are gelled by complexation to iron(II) ions. To investigate the biocompatibility of the microgels, living mammalian cells are encapsulated within them. The microgel elasticity is controlled by using PEG precursors of different molecular weights at different concentrations and the influence of these parameters on the cell viabilities, which can be optimized to exceed 90% is studied. Reversion of the supramolecular polymer cross-linking allows the microcapsules to be degraded at mild conditions with no effect on the viability of the encapsulated and released cells.

Exploring a direct injection method for microfluidic generation of polymer microgels

Microfluidics (MFs) offers a promising method for the preparation of polymer microgels with exquisite control over their dimensions, shapes and morphologies. A challenging task in this process is the generation of droplets (precursors for microgels) from highly viscous polymer solutions. Spatial separation of MF emulsification and gelation of the precursor droplets on chip can address this challenge. In the present work, we explored the application of the "direct injection" method for the preparation of microgels by adding a highly concentrated polymer solution or a gelling agent directly into the precursor droplets. In the first system, primary droplets were generated from a dilute aqueous solution of agarose, followed by the injection of the concentrated agarose solution directly in the primary droplets. The secondary droplets served as precursors for microgels. In the second system, primary droplets were generated from the low-viscous solution of methyl-β-cyclodextrin and poly(ethylene glycol) end-terminated with octadecyl hydrophobic groups. Addition of surfactant directly into the primary droplets led to the binding of methyl-β-cyclodextrin to the surfactant, thereby releasing hydrophobized poly(ethylene glycol) to form polymer microgels. Our results show that, when optimized, the direct injection method can be used for microgel preparation from highly viscous liquids and thus this method expands the range of polymers used for MF generation of microgels.

Reagent delivery by partial coalescence and noncoalescence of aqueous microdroplets in oil

Reagent delivery constitutes a key step for reaction initiation in droplet-in-oil microfluidic platforms. Currently, this function is performed by complete fusion of a reagent droplet with the reactor droplet. The full coalescence, however, constrains the lower limit of volume delivery because reproducible droplet generation becomes exceedingly difficult as the reagent droplet volume is decreased. Here, we demonstrate fractional volume delivery based on partially coalescent and noncoalescent droplet collisions as a new reagent delivery mechanism. A charged reagent droplet is generated by pulsing a flow carrying needle to high voltage. The charged droplet is directed toward a grounded reactor droplet. Upon collision, the reagent droplet inverts its charge and is pulled away from the reactor droplet prior to full fusion, injecting only a fraction of its volume. The undelivered portion of the reagent drop is then merged with a collector droplet. We demonstrate that a wide range of fractional injections (0.003%-56%) can be reproducibly achieved, providing a means for minute volume delivery without small drop generation.

Controlled dispensing and mixing of pico- to nanoliter volumes using on-demand droplet-based microfluidics

We present an integrated droplet-on-demand microfluidic platform for dispensing, mixing, incubating, extracting and analyzing by mass spectrometry pico- to nanoliter-sized droplets. All of the functional components are successfully integrated for the first time into a monolithic microdevice. Droplet generation is accomplished using computer-controlled pneumatic valves. Controlled actuation of valves for different aqueous streams enables accurate dosing and rapid mixing of reagents within droplets in either the droplet generation area or in a region of widening channel cross-section. Following incubation, which takes place as droplets travel in the oil stream, the droplet contents are extracted to an aqueous channel for subsequent ionization at an integrated nanoelectrospray emitter. Using the integrated platform, rapid enzymatic digestions of a model protein were carried out in droplets and detected on-line by nanoelectrospray ionization mass spectrometry.

Multiplex analysis of enzyme kinetics and inhibition by droplet microfluidics using picoinjectors

Enzyme kinetics and inhibition is important for a wide range of disciplines including pharmacology, medicine and industrial bioprocess technology. We present a novel microdroplet-based device for extensive characterization of the reaction kinetics of enzyme substrate inhibitor systems in a single experiment utilizing an integrated droplet picoinjector for bioanalysis. This device enables the scanning of multiple fluorescently-barcoded inhibitor concentrations and substrate conditions in a single, highly time-resolved experiment yielding the Michaelis constant (Km), the turnover number (kcat) and the enzyme inhibitor dissociation constants (ki, ki'). Using this device we determine Km and kcat for β-galactosidase and the fluorogenic substrate Resorufin β-D-galactopyranoside (RBG) to be 442 μM and 1070 s(-1), respectively. Furthermore, we examine the inhibitory effects of isopropyl-β-D-thiogalactopyranoside (IPTG) on β-galactosidase. This system has a number of potential applications, for example it could be used to screen inhibitors to pharmaceutically relevant enzymes and to characterize engineered enzyme variants for biofuels production, in both cases acquiring detailed information about the enzyme catalysis and enzyme inhibitor interaction at high throughput and low cost.

Droplet-based microfluidic platform for heterogeneous enzymatic assays

Heterogeneous enzymatic reactions are used in many industrial processes including pulp and paper, food, and biofuel production. Industrially-relevant optimization of the enzymes used in these processes requires assaying them with insoluble substrates. However, platforms for high throughput heterogeneous assays do not exist thereby severely increasing the cost and time of enzyme optimization, or leading to the use of assays with soluble substrates for convenient, but non-ideal, optimization. We present an innovative approach to perform heterogeneous reactions in a high throughput fashion using droplet microfluidics. Droplets provide a facile platform for heterogeneous reactions as internal recirculation allows rapid mixing of insoluble substrates with soluble enzymes. Moreover, it is easy to generate hundreds or thousands of picoliter droplets in a small footprint chip allowing many parallel reactions. We validate our approach by screening combinations of cellulases with real-world insoluble substrates, and demonstrate that the chip-based screening is in excellent agreement with the conventional screening methods, while offering advantages of throughput, speed and lower reagent consumption. We believe that our approach, while demonstrated for a biofuel application, provides a generic platform for high throughput monitoring of heterogeneous reactions.

Single-cell analysis and sorting using droplet-based microfluidics

We present a droplet-based microfluidics protocol for high-throughput analysis and sorting of single cells. Compartmentalization of single cells in droplets enables the analysis of proteins released from or secreted by cells, thereby overcoming one of the major limitations of traditional flow cytometry and fluorescence-activated cell sorting. As an example of this approach, we detail a binding assay for detecting antibodies secreted from single mouse hybridoma cells. Secreted antibodies are detected after only 15 min by co-compartmentalizing single mouse hybridoma cells, a fluorescent probe and single beads coated with anti-mouse IgG antibodies in 50-pl droplets. The beads capture the secreted antibodies and, when the captured antibodies bind to the probe, the fluorescence becomes localized on the beads, generating a clearly distinguishable fluorescence signal that enables droplet sorting at ∼200 Hz as well as cell enrichment. The microfluidic system described is easily adapted for screening other intracellular, cell-surface or secreted proteins and for quantifying catalytic or regulatory activities. In order to screen ∼1 million cells, the microfluidic operations require 2-6 h; the entire process, including preparation of microfluidic devices and mammalian cells, requires 5-7 d.

The future is now: single-cell genomics of bacteria and archaea

Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in whole-genome amplification and single-cell manipulation are driving considerable progress in single-cell genomics. Here, the spectrum of applications for single-cell genomics, key advances in the development of the field, and emerging methodology for single-cell genome sequencing are reviewed by example with attention to the diversity of approaches and their unique characteristics. Experimental strategies transcending specific methodologies are identified and organized as a road map for future studies in single-cell genomics of environmental microorganisms. Over the next decade, increasingly powerful tools for single-cell genome sequencing and analysis will play key roles in accessing the genomes of uncultivated organisms, determining the basis of microbial community functions, and fundamental aspects of microbial population biology.

Picoinjection enables digital detection of RNA with droplet rt-PCR

The ability to add reagents to drops in a sequential fashion is necessary for numerous applications of microfluidics in biology. An important method for accomplishing this is picoinjection, a technique in which reagents are injected into aqueous drops using an electric field. While picoinjection has been shown to allow the precise addition of reagents to drops, its compatibility with biological reactions is yet to be thoroughly demonstrated. Here, we investigate the compatibility of picoinjection with digital RT-PCR Taqman assays, reactions that incorporate nucleic acids, enzymes, and other common biological reagents. We find that picoinjection is compatible with this assay and enables the detection of RNA transcripts at rates comparable to workflows not incorporating picoinjection. We also find that picoinjection results in negligible transfer of material between drops and that the drops faithfully retain their compartmentalization.

Small-angle X-ray scattering in droplet-based microfluidics

Small-angle X-ray scattering (SAXS) is a powerful technique to probe nanometer-scale structures; a particularly powerful implementation of SAXS is to apply it to continuously flowing liquid samples in microfluidic devices. This approach has been employed extensively, but virtually all existing studies rely on the use of one-phase microfluidics. We overcome this limitation and present the combination of SAXS with multiphase, droplet-based microfluidics to establish a platform methodology. We focus on the use of two different classes of microfluidic devices in two different approaches. In one approach, we use silicone elastomer devices to form water-in-oil emulsion droplets that contain gold nanoparticles as a model analyte. The emulsion droplets serve as nanoliter-scale compartments that are probed by SAXS off the microfluidic chip. In another approach, we both create and probe the droplets on the same microfluidic chip. In this case, we use a glass microcapillary device that serves to form gold nanoparticles in situ by mixing two aqueous precursor fluids within the drops. Both approaches allow the gold-nanoparticle scattering to be straightforwardly isolated from the raw data; subsequent fitting yields quantitative information on the size, shape, and concentration of the nanoparticles within the compartmentalizing emulsion droplets. In addition, the microfluidic flow parameters scale with the scattering cross-sections in a quantitative fashion. These results foreshadow the utility of this technique for other, more sophisticated tasks such as single-protein analysis or automated assaying.

Quantitative microfluidic biomolecular analysis for systems biology and medicine

In the postgenome era, biology and medicine are rapidly evolving towards quantitative and systems studies of complex biological systems. Emerging breakthroughs in microfluidic technologies and innovative applications are transforming systems biology by offering new capabilities to address the challenges in many areas, such as single-cell genomics, gene regulation networks, and pathology. In this review, we focus on recent progress in microfluidic technology from the perspective of its applications to promoting quantitative and systems biomolecular analysis in biology and medicine.