Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems

Time-resolved single-cell secretion analysis via microfluidics

Revealing how individual cells alter their secretions over time is crucial for understanding their responses to environmental changes. Key questions include: When do cells modify their functions and states? What transitions occur? Insights into the kinetic secretion trajectories of various cell types are essential for unraveling complex biological systems. This review highlights seven microfluidic technologies for time-resolved single-cell secretion analysis: 1. Microwell real-time electrical detection: uses microelectrodes for precise, cell-specific, real-time measurement of secreted molecules. 2. Microwell real-time optical detection: employs advanced optical systems for real-time, multiplexed monitoring of cellular secretions. 3. Microvalve real-time optical detection: dynamically analyzes secretions under controlled in situ stimuli, enabling detailed kinetic studies at the single-cell level. 4. Droplet real-time optical detection: provides superior throughput by generating droplets containing single cells and sensors for high-throughput screening. 5. Microwell time-barcoded optical detection: utilizes sequential barcoding techniques to facilitate scalable assays for tracking multiple secretions over time. 6. Microvalve time-barcoded optical detection: incorporates automated time-barcoding via micro-valves for robust and scalable analysis. 7. Microwell time-barcoded sequencing: captures and labels secretions for sequencing, enabling multidimensional analysis, though currently limited to a few time points and extended intervals. This review specifically addresses the challenges of achieving high-resolution timing measurements with short intervals while maintaining scalability for single-cell screening. Future advancements in microfluidic devices, integrating innovative barcoding technologies, advanced imaging technologies, artificial intelligence-powered decoding and analysis, and automations are anticipated to enable highly sensitive, scalable, high-throughput single-cell dynamic analysis. These developments hold great promise for deepening our understanding of biosystems by exploring single-cell timing responses on a larger scale.

Microfluidics for the biological analysis of atmospheric ice-nucleating particles: Perspectives and challenges

Atmospheric ice-nucleating particles (INPs) make up a vanishingly small proportion of atmospheric aerosol but are key to triggering the freezing of supercooled liquid water droplets, altering the lifetime and radiative properties of clouds and having a substantial impact on weather and climate. However, INPs are notoriously difficult to model due to a lack of information on their global sources, sinks, concentrations, and activity, necessitating the development of new instrumentation for quantifying and characterizing INPs in a rapid and automated manner. Microfluidic technology has been increasingly adopted by ice nucleation research groups in recent years as a means of performing droplet freezing analysis of INPs, enabling the measurement of hundreds or thousands of droplets per experiment at temperatures down to the homogeneous freezing of water. The potential for microfluidics extends far beyond this, with an entire toolbox of bioanalytical separation and detection techniques developed over 30 years for medical applications. Such methods could easily be adapted to biological and biogenic INP analysis to revolutionize the field, for example, in the identification and quantification of ice-nucleating bacteria and fungi. Combined with miniaturized sampling techniques, we can envisage the development and deployment of microfluidic sample-to-answer platforms for automated, user-friendly sampling and analysis of biological INPs in the field that would enable a greater understanding of their global and seasonal activity. Here, we review the various components that such a platform would incorporate to highlight the feasibility, and the challenges, of such an endeavor, from sampling and droplet freezing assays to separations and bioanalysis.

Manipulating the duration of picoinjection controls the injected volume of individual droplets

The ability to add reagents into droplets is required in many microfluidic workflows. Picoinjection can address this need; however, it is unable to control the injection volume for each individual droplet. Here, we present an improved picoinjection method that can inject controlled volumes into individual droplets. We achieve this by adjusting the injection duration for each picoinjection event. This improved picoinjection method can be used to create complex microfluidic workflows that are able to control the biochemical composition of individual droplets.

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.

Droplet Microfluidics Enables Tracing of Target Cells at the Single-Cell Transcriptome Resolution

The rapid promotion of single-cell omics in various fields has begun to help solve many problems encountered in research, including precision medicine, prenatal diagnosis, and embryo development. Meanwhile, single-cell techniques are also constantly updated with increasing demand. For some specific target cells, the workflow from droplet screening to single-cell sequencing is a preferred option and should reduce the impact of operation steps, such as demulsification and cell recovery. We developed an all-in-droplet method integrating cell encapsulation, target sorting, droplet picoinjection, and single-cell transcriptome profiling on chips to achieve labor-saving monitoring of TCR-T cells. As a proof of concept, in this research, TCR-T cells were encapsulated, sorted, and performed single-cell transcriptome sequencing (scRNA-seq) by injecting reagents into droplets. It avoided the tedious operation of droplet breakage and re-encapsulation between droplet sorting and scRNA-seq. Moreover, convenient device operation will accelerate the progress of chip marketization. The strategy achieved an excellent recovery performance of single-cell transcriptome with a median gene number over 4000 and a cross-contamination rate of 8.2 ± 2%. Furthermore, this strategy allows us to develop a device with high integrability to monitor infused TCR-T cells, which will promote the development of adoptive T cell immunotherapy and their clinical application.

Highly flexible and accurate serial picoinjection in droplets by combined pressure and flow rate control

Picoinjection is a robust method for reagent addition into microfluidic droplets and has enabled the implementation of numerous multistep droplet assays. Although serial picoinjectors allow to screen many conditions in one run by injecting different combinations of reagents, their use is limited because it is complex to accurately control each injector independently. Here, we present a novel method for flexible, individual picoinjector control that allows to inject a predefined range of volumes by controlling the flow rate of the injector as well as turning off injection by setting the equilibrium pressure, which resulted in a stable interface of the injector liquid with the main microfluidic channel. Robust setting of the equilibrium pressure of an injector was achieved by applying accurate (R² > 0.94) linear models between the injector and oil pressure in real-time. To illustrate the flexibility of this method, we performed several proof-of-concepts using 1, 2 or 3 picoinjectors loaded with fluorescent dyes. We successfully demonstrated picoinjection approaches using time-invariant settings, in which an injector setting was applied for prolonged times, and time-variant picoinjection, in which the injector settings were continuously varied in order to sweep the injected volumes, both resulting in monodisperse (CV < 3.4%) droplet libraries with different but reproducible fluorescent intensities. To illustrate the potential of the technology for fast compound concentration screenings, we studied the effect of a concentration range of a detergent on single-cell lysis. We anticipate that this robust and versatile methodology will make the serial picoinjection technology more accessible to researchers, allowing its wide implementation in numerous life science applications.

On-Demand Nanoliter Sampling Probe for the Collection of Brain Fluid

Continuous fluidic sampling systems allow collection of brain biomarkers in vivo. Here, we propose a new sequential and intermittent sampling paradigm using droplets, called Droplet on Demand (DoD). It is implemented in a microfabricated neural probe and alternates phases of analyte removal from the tissue and phases of equilibration of the concentration in the tissue. It allows sampling droplets loaded with molecules from the brain extracellular fluid punctually, without the long transient equilibration periods typical of continuous methods. It uses an accurately defined fluidic sequence with controlled timings, volumes, and flow rates, and correct operation is verified by the embedded electrodes and a flow sensor. As a proof of concept, we demonstrated the application of this novel approach in vitro and in vivo, to collect glucose in the brain of mice, with a temporal resolution of 1-2 min and without transient regime. Absolute quantification of the glucose level in the samples was performed by direct infusion nanoelectrospray ionization Fourier transform mass spectrometry (nanoESI-FTMS). By adjusting the diffusion time and the perfusion volume of DoD, the fraction of molecules recovered in the samples can be tuned to mirror the tissue concentration at accurate points in time. Moreover, this makes quantification of biomarkers in the brain possible within acute experiments of only 20-120 min. DoD provides a complementary tool to continuous microdialysis and push-pull sampling probes. Thus, the advances allowed by DoD will benefit quantitative molecular studies in the brain, i.e., for molecules involved in volume transmission or for protein aggregates that form in neurodegenerative diseases over long periods.

Rapid microfluidic platform for screening and enrichment of cells secreting virus neutralizing antibodies

As part of the body's immune response, antibodies (Abs) have the ability to neutralize pathogenic viruses to prevent infection. To screen for neutralizing Abs (nAbs) from the immune repertoire, multiple screening techniques have been developed. However, conventional methods have a trade-off between screening throughput and the ability to screen for nAbs via their functional efficacy. Although droplet microfluidic platforms have the ability to bridge this disparity, the majority of such reported platforms still rely on Ab-binding assays as a proxy for function, which results in irrelevant hits. Herein, we report the multi-module Droplet-based Platform for Effective Antibody RetrievaL (DROP-PEARL) platform, which can achieve high-throughput enrichment of Ab-secreting cells (ASCs) based on the neutralizing activity of secreted nAbs against the a target virus. In this study, in-droplet Chikungunya virus (CHIKV) infection of host cells and neutralization was demonstrated via sequential delivery of viruses and host cells via picoinjection. In addition, we demonstrate the ability of the sorting system to accurately discriminate and isolate uninfected droplets from a mixed population of droplets at a rate of 150 000 cells per hour. As a proof of concept, a single-cell neutralization assay was performed on two populations of cells (nAb-producing and non-Ab producing cells), and up to 2.75-fold enrichment of ASCs was demonstrated. Finally, we demonstrated that DROP-PEARL is able to achieve similar enrichment for low frequency (∼2%) functional nAb-producing cells in a background of excess cells secreting irrelevant antibodies, highlighting its potential prospect as a first round enrichment platform for functional ASCs. We envision that the DROP-PEARL platform could potentially be used to accelerate the discovery of nAbs against other pathogenic viral targets, and we believe it will be a useful in the ongoing fight against biological threats.

Microfluidic active pressure and flow stabiliser

In microfluidics, a well-known challenge is to obtain reproducible results, often constrained by unstable pressures or flow rates. Today, there are existing stabilisers made for low-pressure microfluidics or high-pressure macrofluidics, often consisting of passive membranes, which cannot stabilise long-term fluctuations. In this work, a novel stabilisation method that is able to handle high pressures in microfluidics is presented. It is based on upstream flow capacitance and thermal control of the fluid's viscosity through a PID controlled restrictor-chip. The stabiliser consists of a high-pressure-resistant microfluidic glass chip with integrated thin films, used for resistive heating. Thereby, the stabiliser has no moving parts. The quality of the stabilisation was evaluated with an ISCO pump, an HPLC pump, and a Harvard pump. The stability was greatly improved for all three pumps, with the ISCO reaching the highest relative precision of 0.035% and the best accuracy of 8.0 ppm. Poor accuracy of a pump was compensated for in the control algorithm, as it otherwise reduced the capacity to stabilise longer times. As the dead volume of the stabiliser was only 16 nL, it can be integrated into micro-total-analysis- or other lab-on-a-chip-systems. By this work, a new approach to improve the control of microfluidic systems has been achieved.

Three-dimensional visualization and analysis of flowing droplets in microchannels using real-time quantitative phase microscopy

Recent years have witnessed the development of droplet-based microfluidics as a useful and effective tool for high-throughput analysis in biological, chemical and environmental sciences. Despite the flourishing development of droplet manipulation techniques, only a few methods allow for label-free and quantitative inspection of flowing droplets in microchannels in real-time and in three dimensions (3-D). In this work, we propose and demonstrate the application of a real-time quantitative phase microscopy (RT-QPM) technique for 3-D visualization of droplets, and also for full-field and label-free measurement of analyte concentration distribution in the droplets. The phase imaging system consists of a linear-CCD-based holographic microscopy configuration and an optofluidic phase-shifting element, which can be used for retrieving quantitative phase maps of flowing objects in the microchannels with a temporal resolution only limited to the frame rate of the CCD camera. To demonstrate the capabilities of the proposed imaging technique, we have experimentally validated the 3-D image reconstruction of the droplets generated in squeezing and dripping regimes and quantitatively investigated the volumetric and morphological variation of droplets as well as droplet parameters related to the depth direction under different flow conditions. We also demonstrated the feasibility of using this technique, as a refractive index sensor, for in-line quantitative measurement of carbamide analyte concentration within the flowing droplets.

An ultra high-efficiency droplet microfluidics platform using automatically synchronized droplet pairing and merging

Droplet microfluidics systems hold great promise in their ability to conduct high-throughput assays for a broad range of life science applications. Despite their promise in the field and capability to conduct complex liquid handling steps, currently, most droplet microfluidic systems used for real assays utilize only a few droplet manipulation steps connected in series, and are often not integrated together on a single chip or platform. This is due to the fact that linking multiple sequential droplet functions within a single chip to operate at high efficiency over long periods of time remains technically challenging. Considering sequential manipulation is often required to conduct high-throughput screening assays on large cellular and molecular libraries, advancements in sequential operation and integration are required to advance the field. This current limitation greatly reduces the type of assays that can be realized in a high-throughput droplet format and becomes more prevalent in large library screening applications. Here we present an integrated multi-layer droplet microfluidic platform that can handle large numbers of droplets with high efficiency and minimum error. The platform combines two-photon photolithography-fabricated curved microstructures that allow high-efficiency (99.9%) re-flow of droplets and a unique droplet cleaving that automatically synchronizes paired droplets enabling high-efficiency (99.9%) downstream merging. We demonstrate that this method is applicable to a broad range of droplet sizes, including relatively large droplet sizes (hundreds of micrometers in diameter) that are typically more difficult to manipulate with high efficiency, yet are required in many cell assay applications requiring large organisms or multiple incubation steps. The utility of this highly efficient integrated droplet microfluidic platform was demonstrated by conducting a mock antibiotic screening assay against a bacterial pathogen. The approach and system presented here provides new avenues for the realization of ultra-high-efficiency multi-step droplet microfluidic systems with minimal error.

A Microfluidic Approach for Biosensing DNA within Forensics

Reducing the risk of (cross-)contamination, improving the chain of custody, providing fast analysis times and options of direct analysis at crime scenes: these requirements within forensic DNA analysis can be met upon using microfluidic devices. To become generally applied in forensics, the most important requirements for microfluidic devices are: analysis time, method of DNA detection and biocompatibility of used materials. In this work an overview is provided about biosensing of DNA, by DNA profiling via standard short tandem repeat (STR) analysis or by next generation sequencing. The material of which a forensic microfluidic device is made is crucial: it should for example not inhibit DNA amplification and its thermal conductivity and optical transparency should be suitable for achieving fast analysis. The characteristics of three materials frequently used materials, i.e., glass, silicon and PDMS, are given, in addition to a promising alternative, viz. cyclic olefin copolymer (COC). New experimental findings are presented about the biocompatibility of COC and the use of COC chips for multiple displacement amplification and real-time monitoring of DNA amplification.

High-throughput screening for high-efficiency small-molecule biosynthesis

Systems metabolic engineering faces the formidable task of rewiring microbial metabolism to cost-effectively generate high-value molecules from a variety of inexpensive feedstocks for many different applications. Because these cellular systems are still too complex to model accurately, vast collections of engineered organism variants must be systematically created and evaluated through an enormous trial-and-error process in order to identify a manufacturing-ready strain. The high-throughput screening of strains to optimize their scalable manufacturing potential requires execution of many carefully controlled, parallel, miniature fermentations, followed by high-precision analysis of the resulting complex mixtures. This review discusses strategies for the design of high-throughput, small-scale fermentation models to predict improved strain performance at large commercial scale. Established and promising approaches from industrial and academic groups are presented for both cell culture and analysis, with primary focus on microplate- and microfluidics-based screening systems.

Image-Based Single Cell Sorting Automation in Droplet Microfluidics

The recent boom in single-cell omics has brought researchers one step closer to understanding the biological mechanisms associated with cell heterogeneity. Rare cells that have historically been obscured by bulk measurement techniques are being studied by single cell analysis and providing valuable insight into cell function. To support this progress, novel upstream capabilities are required for single cell preparation for analysis. Presented here is a droplet microfluidic, image-based single-cell sorting technique that is flexible and programmable. The automated system performs real-time dual-camera imaging (brightfield & fluorescent), processing, decision making and sorting verification. To demonstrate capabilities, the system was used to overcome the Poisson loading problem by sorting for droplets containing a single red blood cell with 85% purity. Furthermore, fluorescent imaging and machine learning was used to load single K562 cells amongst clusters based on their instantaneous size and circularity. The presented system aspires to replace manual cell handling techniques by translating expert knowledge into cell sorting automation via machine learning algorithms. This powerful technique finds application in the enrichment of single cells based on their micrographs for further downstream processing and analysis.

High-throughput droplet-based microfluidics for directed evolution of enzymes

Natural enzymes have evolved over millions of years to allow for their effective operation within specific environments. However, it is significant to note that despite their wide structural and chemical diversity, relatively few natural enzymes have been successfully applied to industrial processes. To address this limitation, directed evolution (DE) (a method that mimics the process of natural selection to evolve proteins toward a user‐defined goal) coupled with droplet‐based microfluidics allows the detailed analysis of millions of enzyme variants on ultra‐short timescales, and thus the design of novel enzymes with bespoke properties. In this review, we aim at presenting the development of DE over the last years and highlighting the most important advancements in droplet‐based microfluidics, made in this context towards the high‐throughput demands of enzyme optimization. Specifically, an overview of the range of microfluidic unit operations available for the construction of DE platforms is provided, focusing on their suitability and benefits for cell‐based assays, as in the case of directed evolution experimentations.

Smartphone-based rapid quantification of viable bacteria by single-cell microdroplet turbidity imaging

Standard plate count (SPC) has been recognized as the golden standard for the quantification of viable bacteria. However, SPC usually takes one to several days to grow individual cells into a visible colony, which greatly hampers its application in rapid bacteria enumeration. Here we present a microdroplet turbidity imaging based digital standard plate count (dSPC) method to overcome this hurdle. Instead of cultivating on agar plates, bacteria are encapsulated in monodisperse microdroplets for single-cell cultivation. Proliferation of the encapsulated bacterial cell produced a detectable change in microdroplet turbidity, which allowed, after just a few bacterial doubling cycles (i.e., a few hours), enumeration of viable bacteria by visible-light imaging. Furthermore, a dSPC platform integrating a power-free droplet generator with smartphone-based turbidity imaging was established. As proof-of-concept demonstrations, a series of Gram-negative bacteria (Escherichia coli) and Gram-positive bacteria (Bacillus subtilis) samples were quantified via the smartphone dSPC accurately within 6 hours, representing a detection sensitivity of 100 CFU ml-1 and at least 3 times faster. In addition, Enterobacter sakazakii (E. sakazakii) in infant milk powder as a real sample was enumerated within 6 hours, in contrast to the 24 hours needed in traditional SPC. Results with high accuracy and reproducibility were achieved, with no difference in counts found between dSPC and SPC. By enabling label-free, rapid, portable and low-cost enumeration and cultivation of viable bacteria onsite, smartphone dSPC forms the basis for a temporally and geographically trackable network for surveying live microbes globally where every citizen with a cellphone can contribute anytime and anywhere.

A liquid metal based capacitive soft pressure microsensor

A liquid-metal based capacitive soft pressure microsensor is proposed in this work for measuring pressure in microchannels. To measure the pressure of the target microchannel, a short detection channel is fabricated and connected to the target microchannel. Because the detection channel has only one outlet at the end which is connected to the target microchannel, the fluid in the detection channel will stay still during the measurement and the pressure remains constant inside the detection channel. A segment of reference fluid which is immiscible with the working fluid is sealed inside the detection channel. Because the chip material is soft, the pressure change will lead to the movement of the interface between the reference fluid and working fluid inside the detection channel. A pair of liquid metal electrodes are fabricated on both sides of the detection channel. By measuring the capacitance between these two liquid metal electrodes, the movement of the interface can be detected, and thus the pressure change can be detected as well. To minimize the influence from the environment, two liquid metal shield layers are placed on the top and the bottom of the microchannel layer separately. The microsensor was first tested in a microfluidic system and then utilized to measure the blood pressure of rabbit carotid artery in vivo. The experimental results showed excellent stability and linear correlation between capacitance and the value of fluid pressure. The pressure sensor can achieve a resolution of 7.5 mmHg within a pressure range of 20-300 mmHg. This work provides a promising approach to develop an implantable blood or intraocular pressure-monitoring device for clinical use.

An efficient strategy for a controllable droplet merging system for digital analysis

Droplet merging is an important part of droplet manipulation approaches. Droplet merging methods with expansions inside channels can merge droplets in pairs through simple structures. However, they have a low success rate of merging under unstable fluidic conditions since the one-to-one pairing strategy is sensitive to fluctuation. This study presents a one-to-a-cluster pairing strategy to improve the success rate of merging under fluctuation. The one-to-a-cluster method was suitable for digital analysis and droplet MDA was performed in merged droplets successfully.

Electrically controlled mass transport into microfluidic droplets from nanodroplet carriers with application in controlled nanoparticle flow synthesis

Microfluidic droplets have been applied extensively as reaction vessels in a wide variety of chemical and biological applications. Typically, once the droplets are formed in a flow channel, it is a challenge to add new chemicals to the droplets for subsequent reactions in applications involving multiple processing steps. Here, we present a novel and versatile method that employs a high strength alternating electrical field to tunably transfer chemicals into microfluidic droplets using nanodroplets as chemical carriers. We show that the use of both continuous and cyclic burst square wave signals enables extremely sensitive control over the total amount of chemical added and, equally importantly, the rate of addition of the chemical from the nanodroplet carriers to the microfluidic droplets. An a priori theoretical model was developed to model the mass transport process under the convection-controlled scenario and compared with experimental results. We demonstrate an application of this method in the controlled preparation of gold nanoparticles by reducing chloroauric acid pre-loaded in microfluidic droplets with l-ascorbic acid supplied from miniemulsion nanodroplets. Under different field strengths, l-ascorbic acid is supplied in controllable quantities and addition rates, rendering the particle size and size distribution tunable. Finally, this method also enables multistep synthesis by the stepwise supply of miniemulsions containing different chemical species. We highlight this with a first report of a three-step Au-Pd core-shell nanoparticle synthesis under continuous flow conditions.

Passive Picoinjection Enables Controlled Crystallization in a Droplet Microfluidic Device

Segmented flow microfluidic devices offer an attractive means of studying crystallization processes. However, while they are widely employed for protein crystallization, there are few examples of their use for sparingly soluble compounds due to problems with rapid device fouling and irreproducibility over longer run-times. This article presents a microfluidic device which overcomes these issues, as this is constructed around a novel design of "picoinjector" that facilitates direct injection into flowing droplets. Exploiting a Venturi junction to reduce the pressure within the droplet, it is shown that passive injection of solution from a side-capillary can be achieved in the absence of an applied electric field. The operation of this device is demonstrated for calcium carbonate, where highly reproducible results are obtained over long run-times at high supersaturations. This compares with conventional devices that use a Y-junction to achieve solution loading, where in-channel precipitation of calcium carbonate occurs even at low supersaturations. This work not only opens the door to the use of microfluidics to study the crystallization of low solubility compounds, but the simple design of a passive picoinjector will find wide utility in areas including multistep reactions and investigation of reaction dynamics.

Ultrahigh-Throughput Improvement and Discovery of Enzymes Using Droplet-Based Microfluidic Screening

Enzymes are extremely valuable tools for industrial, environmental, and biotechnological applications and there is a constant need for improving existing biological catalysts and for discovering new ones. Screening microbe or gene libraries is an efficient way of identifying new enzymes. In this view, droplet-based microfluidics appears to be one of the most powerful approaches as it allows inexpensive screenings in well-controlled conditions and an ultrahigh-throughput regime. This review aims to introduce the main microfluidic devices and concepts to be considered for such screening before presenting and discussing the latest successful applications of the technology for enzyme discovery.

K-Channel: A Multifunctional Architecture for Dynamically Reconfigurable Sample Processing in Droplet Microfluidics

By rapidly creating libraries of thousands of unique, miniaturized reactors, droplet microfluidics provides a powerful method for automating high-throughput chemical analysis. In order to engineer in-droplet assays, microfluidic devices must add reagents into droplets, remove fluid from droplets, and perform other necessary operations, each typically provided by a unique, specialized geometry. Unfortunately, modifying device performance or changing operations usually requires re-engineering the device among these specialized geometries, a time-consuming and costly process when optimizing in-droplet assays. To address this challenge in implementing droplet chemistry, we have developed the "K-channel," which couples a cross-channel flow to the segmented droplet flow to enable a range of operations on passing droplets. K-channels perform reagent injection (0-100% of droplet volume), fluid extraction (0-50% of droplet volume), and droplet splitting (1:1-1:5 daughter droplet ratio). Instead of modifying device dimensions or channel configuration, adjusting external conditions, such as applied pressure and electric field, selects the K-channel process and tunes its magnitude. Finally, interfacing a device-embedded magnet allows selective capture of 96% of droplet-encapsulated superparamagnetic beads during 1:1 droplet splitting events at ∼400 Hz. Addition of a second K-channel for injection (after the droplet splitting K-channel) enables integrated washing of magnetic beads within rapidly moving droplets. Ultimately, the K-channel provides an exciting opportunity to perform many useful droplet operations across a range of magnitudes without requiring architectural modifications. Therefore, we envision the K-channel as a versatile, easy to use microfluidic component enabling diverse, in-droplet (bio)chemical manipulations.

Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples

Multiple displacement amplification (MDA) is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples) before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA) technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently, the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet), ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli) compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.

An on-chip microfluidic pressure regulator that facilitates reproducible loading of cells and hydrogels into microphysiological system platforms

Coculturing multiple cell types together in 3-dimensional (3D) cultures better mimics the in vivo microphysiological environment, and has become widely adopted in recent years with the development of organ-on-chip systems. However, a bottleneck in set-up of these devices arises as a result of the delivery of the gel into the microfluidic chip being sensitive to pressure fluctuations, making gel confinement at a specific region challenging, especially when manual operation is performed. In this paper, we present a novel design of an on-chip regulator module with pressure-releasing safety microvalves that can facilitate stable gel delivery into designated microchannel regions while maintaining well-controlled, non-bursting gel interfaces. This pressure regulator design can be integrated into different microfluidic chip designs and is compatible with a wide variety of gel injection apparatuses operated automatically or manually at different flow rates. The sensitivity and working range of this pressure regulator can be adjusted by changing the width of its pressure releasing safety microvalve design. The effectiveness of the design is validated by its incorporation into a microfluidic platform we have developed for generating 3D vascularized micro-organs (VMOs). Reproducible gel loading is demonstrated for both an automatic syringe pump and a manually-operated micropipettor. This design allows for rapid and reproducible loading of hydrogels into microfluidic devices without the risk of bursting gel-air interfaces.

Oligonucleotide Functionalised Microbeads: Indispensable Tools for High-Throughput Aptamer Selection

The functionalisation of microbeads with oligonucleotides has become an indispensable technique for high-throughput aptamer selection in SELEX protocols. In addition to simplifying the separation of binding and non-binding aptamer candidates, microbeads have facilitated the integration of other technologies such as emulsion PCR (ePCR) and Fluorescence Activated Cell Sorting (FACS) to high-throughput selection techniques. Within these systems, monoclonal aptamer microbeads can be individually generated and assayed to assess aptamer candidate fitness thereby helping eliminate stochastic effects which are common to classical SELEX techniques. Such techniques have given rise to aptamers with 1000 times greater binding affinities when compared to traditional SELEX. Another emerging technique is Fluorescence Activated Droplet Sorting (FADS) whereby selection does not rely on binding capture allowing evolution of a greater diversity of aptamer properties such as fluorescence or enzymatic activity. Within this review we explore examples and applications of oligonucleotide functionalised microbeads in aptamer selection and reflect upon new opportunities arising for aptamer science.

Simple Bulk Readout of Digital Nucleic Acid Quantification Assays

Digital assays are powerful methods that enable detection of rare cells and counting of individual nucleic acid molecules. However, digital assays are still not routinely applied, due to the cost and specific equipment associated with commercially available methods. Here we present a simplified method for readout of digital droplet assays using a conventional real-time PCR instrument to measure bulk fluorescence of droplet-based digital assays. We characterize the performance of the bulk readout assay using synthetic droplet mixtures and a droplet digital multiple displacement amplification (MDA) assay. Quantitative MDA particularly benefits from a digital reaction format, but our new method applies to any digital assay. For established digital assay protocols such as digital PCR, this method serves to speed up and simplify assay readout. Our bulk readout methodology brings the advantages of partitioned assays without the need for specialized readout instrumentation. The principal limitations of the bulk readout methodology are reduced dynamic range compared with droplet-counting platforms and the need for a standard sample, although the requirements for this standard are less demanding than for a conventional real-time experiment. Quantitative whole genome amplification (WGA) is used to test for contaminants in WGA reactions and is the most sensitive way to detect the presence of DNA fragments with unknown sequences, giving the method great promise in diverse application areas including pharmaceutical quality control and astrobiology.

Microfluidic plug steering using surface acoustic waves

Digital microfluidic systems, in which isolated droplets are dispersed in a carrier medium, offer a method to study biological assays and chemical reactions highly efficiently. However, it's challenging to manipulate these droplets in closed microchannel devices. Here, we present a method to selectively steer plugs (droplets with diameters larger than the channel's width) at a specially designed Y-junction within a microfluidic chip. The method makes use of surface acoustic waves (SAWs) impinging on a multiphase interface in which an acoustic contrast is present. As a result, the liquid-liquid interface is subjected to acoustic radiation forces. These forces are exploited to steer plugs into selected branches of the Y-junction. Furthermore, the input power can be finely tuned to split a plug into two uneven plugs. The steering of plugs as a whole, based on plug volume and velocity is thoroughly characterized. The results indicate that there is a threshold plug volume after which the steering requires elevated electrical energy input. This plug steering method can easily be integrated to existing lab-on-a-chip devices and it offers a robust and active plug manipulation technique in closed microchannels.