Picoliter Droplets Research Articles

Rapid detection of microbial antibiotic susceptibility via deep learning supported analysis of angle-resolved scattered-light images of picoliter droplet cultivations

The progressive increase in microbial resistance to antibiotics is a global health threat that requires solutions for rapid and reliable determination of antibiotic susceptibility in order to select appropriate antibiotics and dosages prior to treatment. We have established a screening platform that enables the detection of cell growth after just a few cell divisions. Our methodological approach for a robust phenotypic antibiotic susceptibility testing is based on the innovative combination of three cutting-edge technologies: (i) a high-throughput microfluidic platform where individual bacterial cells are encapsulated in picoliter-sized droplets, (ii) a 2D angle-resolved light scattering sensor to perform label-free hourly screening of the droplets, and (iii) a computational image analysis approach based on convolutional neural networks to evaluate the dynamics of microbial growth in droplets. For the gram-positive Staphylococcus aureus and gram-negative Escherichia coli, we demonstrate that microbial growth in droplets can be successfully detected within one to two hours. Furthermore, the potential of this platform for rapid phenotypic antibiotic susceptibility testing is demonstrated as a proof-of-concept with the clinically relevant bacterium S. aureus under various concentrations of the antibiotic tetracycline. Notably, we reach a robust phenotypic decision regarding the sensitivity to this antibiotic within two hours.

Three-dimensional isotropic imaging of live suspension cells enabled by droplet microvortices

Fast, nondestructive three-dimensional (3D) imaging of live suspension cells remains challenging without substrate treatment or fixation, precluding scalable single-cell morphometry with minimal alterations. While optical sectioning techniques achieve 3D live cell imaging, lateral versus depth resolution differences further complicate analysis. We present a scalable microfluidic method capable of 3D fluorescent isotropic imaging of live, nonadherent cells suspended inside picoliter droplets with high-speed single-cell volumetric readout (800 to 1,200 slices in 5 to 8 s) and near-diffraction limit resolution (~216 nm). The platform features a droplet trap array that leverages flow-induced droplet interfacial shear to generate intradroplet microvortices, which rotate single cells on their axis to enable optical projection tomography (OPT)-based imaging. This allows gentle (~1 mPa shear stress) observation of cells encapsulated inside nontoxic isotonic buffer droplets, facilitating scalable OPT acquisition by simultaneous spinning of hundreds of cells. We demonstrate 3D imaging of live myeloid and lymphoid cells in suspension, including K562 cells, as well as naive and activated T cells-small cells prone to movement in their suspended phenotype. Our fully suspended, orientation-independent cell morphometry, driven by isotropic imaging and spherical harmonic analysis, enabled the study of primary T cells across various immunological activation states. This approach unveiled six distinct nuclear content distributions, contrasting with conventional 2D images that typically portray spheroid and bean-like nuclear shapes associated with lymphocytes. Our arrayed-droplet OPT technology is capable of isotropic, single live-cell 3D imaging, with the potential to perform large-scale morphometry of immune cell effector function states while providing compatibility with microfluidic droplet operations.

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes

Bacteria in nature often thrive in fragmented environments, like soil pores, plant roots or plant leaves, leading to smaller isolated habitats, shared with fewer species. This spatial fragmentation can significantly influence bacterial interactions, affecting overall community diversity. To investigate this, we contrast paired bacterial growth in tiny picoliter droplets (1–3 cells per 35 pL up to 3–8 cells per species in 268 pL) with larger, uniform liquid cultures (about 2 million cells per 140 µl). We test four interaction scenarios using different bacterial strains: substrate competition, substrate independence, growth inhibition, and cell killing. In fragmented environments, interaction outcomes are more variable and sometimes even reverse compared to larger uniform cultures. Both experiments and simulations show that these differences stem mostly from variation in initial cell population growth phenotypes and their sizes. These effects are most significant with the smallest starting cell populations and lessen as population size increases. Simulations suggest that slower-growing species might survive competition by increasing growth variability. Our findings reveal how microhabitat fragmentation promotes diverse bacterial interaction outcomes, contributing to greater species diversity under competitive conditions.

Investigation of piezoelectric printing devices for oil-free and on-demand picolitre monodisperse droplet generation

Picolitre monodisperse droplet printing technology has important applications in biochemistry, such as accounting for quantitative analysis and single-cell analysis, and can be used for parallel high-throughput analysis of biomarkers and chemicals. However, commonly used droplet generation devices require complex control systems or customised microfluidic chips, making them costly and difficult for researchers to operate. Additionally, generating picolitre monodisperse droplets with microfluidic devices necessitates the introduction of an oil phase to block and separate the liquid. This requirement can reduce the throughput of the target droplets and cause cell contamination, hindering the adoption of this technology. By employing a common 1-mm-diameter capillary in the laboratory in combination with a piezoelectric transducer, we have achieved on-demand picolitre droplet printing of less than 100 pL in an oil-free environment. The device was found to be biocompatible with K562 cells. This approach is less costly, offers greater operational freedom, and is easier to integrate with other downstream assay modules or even handheld cell-printing devices. This study holds great potential for application in areas such as single-cell analysis, cell sampling, and pharmaceutical analysis.

1-Octanol-assisted ultra-small volume droplet microfluidics with nanoelectrospray ionization mass spectrometry

BackgroundDroplet microfluidics with push-pull and microdialysis sampling from brain slices, cultured cells and engineered tissues produce low volume mass limited samples containing analytes sampled from the extracellular space. This sampling approach coupled to mass spectrometry (MS) detection allows evaluation of time-dependent chemical changes. Our goal is an approach for continuous sampling and segregation of extracellular samples into picoliter droplets followed by the characterization of the droplets using nanoelectrospray ionization (nESI) MS. The main focus here is the optimization of the carrier oil for the microfluidic device that neither affects the stability of picoliter droplets nor compatibility with MS detection of a range of analytes. ResultsWe developed and characterized a 1-octanol-assisted ultra-small volume droplet microfluidic nESI MS system for the analysis of neurotransmitters in distinct samples including cerebrospinal fluid (CSF). The use of a 1-octanol oil phase was effective for generation of aqueous droplets as small as 65 pL and enabled detection of acetylcholine (ACh) and gamma-aminobutyric acid (GABA) in water and artificial CSF. Continuous MS analysis of droplets for extended periods up to 220 min validated the long-term stability of droplet generation and analyte detection by nESI-MS. As an example, ACh response demonstrated a linear working range (R2 = 0.99) between 0.4 μM and 25 μM with a limit of detection of 370 nM (24 amol), enabling its quantitation in rodent CSF. SignificanceThe established droplet microfluidics – nESI MS approach allows the analysis of microenvironments at high spatiotemporal resolution. The approach may allow microsampling and monitoring of spatiotemporal dynamics of neurochemicals and drugs in the brain and spinal cord of live animals.

Discussion: Embracing microfluidics to advance environmental science and technology

Microfluidics, also called lab-on-a-chip, represents an emerging research platform that permits more precise and manipulation of samples at the microscale or even down to the nanoscale (nanofluidic) including picoliter droplets, microparticles, and microbes within miniaturized and highly integrated devices. This groundbreaking technology has made significant strides across multiple disciplines by providing an unprecedented view of physical, chemical, and biological events, fostering a holistic and an in-depth understanding of complex systems. The application of microfluidics to address the challenges in environmental science is likely to contribute to our better understanding, however, it's not yet fully developed. To raise researchers' interest, this discussion first delineates the valuable and underutilized environmental applications of microfluidic technology, ranging from environmental surveillance to acting as microreactors for investigating interfacial dynamic processes, and facilitating high-throughput bioassays. We highlight, with examples, how rationally designed microfluidic devices lead to new insights into the advancement of environmental science and technology. We then critically review the key challenges that hinder the practical adoption of microfluidic technologies. Specifically, we discuss the extent to which microfluidics accurately reflect realistic environmental scenarios, outline the areas to be improved, and propose strategies to overcome bottlenecks that impede the broad application of microfluidics. We also envision new opportunities and future research directions, aiming to provide guidelines for the broader utilization of microfluidics in environmental studies.

Phosphorylation-amplified synchronized droplet microfluidics sensitizes bacterial growth kinetic real-time monitoring

The necessity for rapid and accurate bacterial growth monitoring is imperative across various domains, including healthcare and environmental safety. We introduce the self-synchronized droplet-amplified electrical screening cytometry (SYNC) system, a novel meld of droplet microfluidics and electrochemical amplification tailored for precise bacterial growth kinetic monitoring. SYNC encapsulates single bacteria in picolitre droplets, enabling real-time, fluorescence-free electrochemical monitoring. A specially devised phosphorylation-amplified culture medium translates bacterial metabolic activity into discernible electrical impedance changes. The dual-channel design and a rail-based structure in SYNC facilitate parallel screening and self-synchronization of droplets, addressing the limitations of conventional impedance cytometry. SYNC showcases a 5-fold enhancement in detection sensitivity and reduces 50% of the detection time compared to traditional approaches. Notably, SYNC is pioneering in providing exact initial bacterial concentrations, achieve to 104 bacteria/ml, a capability unmatched by existing real-time techniques measuring electrochemical variations. Along with its robust performance, this earmarks SYNC as a powerful tool for applications such as antibiotic susceptibility testing, food quality monitoring, and real-time water bacteria monitoring, paving the way for enhanced microbial process management and infection control.

Vortexing-generated high throughput single-cell droplets for facile analysis of multiplexed microRNA dynamic secretion

Discriminating secretory phenotypes provides a direct, intact, and dynamic way to evaluate the heterogeneity in cell states and activation, which is significant for dissecting non-genetic heterogeneity for human health studies and disease diagnostics. In particular, secreted microRNAs, soluble signaling molecules released by various cells, are increasingly recognized as a critical mediator for cell-cell communication and the circulating biomarkers for disease diagnosis. However, single-cell analysis of secreted miRNAs is still lacking due to the limited available tools. Herein, we realized three-plexed miRNA secretion analysis over four time points from single cells encapsulated in picoliter droplets with extreme simplicity, coupling vortexing-generated single-cell droplets with multiplexed molecular beacons. Notably, our platform only requires pipetting and vortexing steps to finish the assay setup within 5 min with minimal training, and customized software was developed for automatic data quantification. Applying the platform to human cancer cell lines and primary cells revealed previously undifferentiated heterogeneity and paracrine signaling underlying miRNA secretion. This platform can be used to dissect secretion heterogeneity and cell-cell interactions and has the potential to become a widely used tool in biomedical research.

Understanding Macrophage-Tumor Interactions: Insights from Single-Cell Behavior Monitoring in a Sessile Microdroplet System.

Interaction between tumor-associated macrophages and tumor cells is crucial for tumor development, metastasis, and the related immune process. However, the macrophages are highly heterogeneous spanning from anti-tumorigenic to pro-tumorigenic, which needs to be understood at the single-cell level. Herein, a sessile microdroplet system designed for monitoring cellular behavior and analyzing intercellular interaction, demonstrated with macrophage-tumor cell pairs is presented. An automatic procedure based on the inkjet printing method is utilized for the precise pairing and co-encapsulation of heterotypic cells within picoliter droplets. The sessile nature of microdroplets ensures controlled fusion and provides stable environments conducive to adherent cell culture. The nitric oxide generation and morphological changes over incubation are explored to reveal the complicated interactions from a single-cell perspective. The immune response of macrophages under distinct cellular microenvironments is recorded. The results demonstrate that the tumor microenvironment displays a modulating role in polarizing macrophages from anti-tumorigenic into pro-tumorigenic phenotype. The approach provides a versatile and compatible platform to investigate intercellular interaction at the single-cell level, showing promising potential for advancing single-cell behavior studies.

Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique.

The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, Cand. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.

Dynamics of individual inkjet printed picoliter droplet elucidated by high speed laser speckle imaging.

Inkjet printing is a ubiquitous consumer and industrial process that involves concomitant processes of droplet impact, wetting, evaporation, and imbibement into a substrate as well as consequential substrate rearrangements and remodeling. In this work, we perform a study on the interaction between ink dispersions of different composition on substrates of increasing complexity to disentangle the motion of the liquid from the dynamic response of the substrate. We print three variations of pigmented inks and follow the ensuing dynamics at millisecond and micron time and length scales until complete drying using a multiple scattering technique, laser speckle imaging (LSI). Measurements of the photon transport mean free path, l*, for the printed inks and substrates show that the spatial region of information capture is the entire droplet volume and a depth within the substrate of a few μm beneath the droplet. Within this spatial confinement, LSI is an ideal approach for studying the solid-liquid transition at these small length and time scales by obtaining valid g2 and d2 autocorrelation functions and interpreting these dynamic changes under through kymographs. Our in situ LSI results show that droplets undergo delamination and cracking processes arising during droplet drying, which are confirmed by post mortem SEM imaging.

Droplet microfluidic system for high throughput and passive selection of bacteria producing biosurfactants.

Traditional methods for the enrichment of microorganisms rely on growth in a selective liquid medium or on an agar plate, followed by tedious characterization. Droplet microfluidic techniques have been recently used to cultivate microorganisms and preserve enriched bacterial taxonomic diversity. However, new methods are needed to select droplets comprising not only growing microorganisms but also those exhibiting specific properties, such as the production of value-added compounds. We describe here a droplet microfluidic screening technique for the functional selection of biosurfactant-producing microorganisms, which are of great interest in the bioremediation and biotechnology industries. Single bacterial cells are first encapsulated into picoliter droplets for clonal cultivation and then passively sorted at high throughput based on changes in interfacial tension in individual droplets. Our method expands droplet-based microbial enrichment with a novel approach that reduces the time and resources needed for the selection of surfactant-producing bacteria.

Label-free analysis of bacterial growth and lysis at the single-cell level using droplet microfluidics and object detection-oriented deep learning

Bacteria identification and counting at the small population scale is important to many applications in the food safety industry, the diagnostics of infectious diseases and the study and discovery of novel antimicrobial compounds. There is still a lack of easy to implement, fast and accurate methods to count populations of motile cells at the single-cell level. Here, we report a label-free method to count and localize bacterial cells freely swimming in microfluidic anchored picolitre droplets. We used the object detection oriented YOLOv4 deep learning framework for cell detection from bright-field images obtained with an automated Z-stack setup. The neural network was trained to recognize Escherichia coli cell morphology with an average precision of approximately 84%. This allowed us to accurately identify individual cell division events, enabling the study of stochastic bacterial growth starting from initial populations as low as one cell. This work also demonstrates the ability to study single cell lysis in the presence of T7 lytic bacterial viruses (phages). The high precision in cell numbers facilitated the visualization of bacteria-phage interactions over timescale of hours, paving the way towards deciphering phage life cycles in confined environments.

High frame-rate imaging of the shape oscillations and spreading dynamics of picolitre droplets impacting on a surface

The post-impact dynamics and spreading rates of picolitre liquid droplets on surfaces are critical to many practical and industrial applications, as well as respiratory disease transmission mechanisms. Here we use a high framerate imaging method to explore the shape oscillations and spreading of individual ∼10–180 pl volume droplets (corresponding to ∼30–70 μm in initial droplet diameter) impacting on a surface under ambient conditions with 10 μs temporal resolution. The method allows the surface tension to be accurately extracted from the measured frequency of post-impact shape oscillations for sessile droplets in this size range with surface tensions greater than 40 mN m−1 and viscosities up to at least 3.2 mPa s. The Tanner's law model for predicting sessile droplet spreading rates provides an accurate account of the “steady-state” spreading rate for all droplets with surface tensions in the range 22–73 mN m−1 studied here. However, Tanner's law does not account for the delay in the onset of spreading observed for droplets in this size range, caused by competition between shape oscillations and spreading governing the morphology at short time periods, particularly for surface tensions >22 mN m−1.

Using picoliter droplet deposition to track clonal competition in adherent and organoid cancer cell cultures

Clonal growth and competition underlie processes of key relevance in etiology, progression and therapy response across all cancers. Here, we demonstrate a novel experimental approach, based on multi-color, fluorescent tagging of cell nuclei, in combination with picoliter droplet deposition, to study the clonal dynamics in two- and three-dimensional cell cultures. The method allows for the simultaneous visualization and analysis of multiple clones in individual multi-clonal colonies, providing a powerful tool for studying clonal dynamics and identifying clonal populations with distinct characteristics. Results of our experiments validate the utility of the method in studying clonal dynamics in vitro, and reveal differences in key aspects of clonal behavior of different cancer cell lines in monoculture conditions, as well as in co-cultures with stromal fibroblasts.

Evaporation of alcohol droplets on surfaces in moist air

Droplets of alcohol-based formulations are common in applications from sanitizing sprays to printing inks. However, our understanding of the drying dynamics of these droplets on surfaces and the influence of ambient humidity is still very limited. Here, we report the drying dynamics of picoliter droplets of isopropyl alcohol deposited on a surface under controlled humidity. Condensation of water vapor in the ambient environment onto alcohol droplets leads to unexpectedly complex drying behavior. As relative humidity (RH) increases, we observed a variety of phenomena including enhanced spreading, nonmonotonic changes in the drying time, the formation of pancake-like shapes that suppress the coffee-ring effect, and the formation of water-rich films around an alcohol-rich drop. We developed a lubrication model that accounts for the coupling between the flow field within the drop, the shape of the drop, and the vapor concentration field. The model reproduces many of the experimentally observed morphological and dynamic features, revealing the presence of unusually large spatial compositional gradients within the evaporating droplet and surface-tension-gradient-driven flows arising from water condensation/evaporation at the surface of the droplet. One unexpected feature from the simulation is that water can evaporate and condense concurrently in different parts of the drop, providing fundamental insights that simpler models based on average fluxes lack. We further observed rim instabilities at higher RH that are well-described by a model based on the Rayleigh-Plateau instability. Our findings have implications for the testing and use of alcohol-based disinfectant sprays and printing inks.

Tuning Molecular Orientation Responses of Microfluidic Liquid Crystal Dispersions to Colloid and Polymer Flows.

An important approach to molecular diagnostics is integrating organized substances that provide complex molecular level responses to introduced chemical and biological agents with conditions that optimize and distinguish such responses. In this respect, liquid crystal dispersions are attractive components of molecular diagnostic tools. This paper analyzes a colloid system, containing a nematic liquid crystal as a dispersed phase, and aqueous surfactant and polymer solutions as the continuous phases. We applied a microfluidic approach for tuning orientation of liquid crystal molecules in picoliter droplets immobilized on microchannel walls. Introduction of surfactant to the aqueous phase was found to proportionally increase the order parameter of liquid crystal molecules in microdroplets. Infusion of polymer solutions into surfactant-mediated microfluidic liquid crystal dispersions increased the order parameter at much lower surfactant concentrations, while further infusion of surfactant solutions randomized the orientation of liquid crystal molecules. These effects were correlated with the adsorption of surfactant molecules on surfaces of microdroplets, stabilizing the effect of a polymer matrix on bound surfactant ions and the formation of insoluble polymer-colloid aggregates, respectively. The revealed molecular behavior of liquid crystal dispersions may contribute to optimized synthesis of responsive liquid crystal dispersions for in-flow molecular diagnostics of polymers and colloids, and the development of functional laboratory-on-chip prototypes.

Versatile Product Detection via Coupled Assays for Ultrahigh-Throughput Screening of Carbohydrate-Active Enzymes in Microfluidic Droplets.

Enzyme discovery and directed evolution are the two major contemporary approaches for the improvement of industrial processes by biocatalysis in various fields. Customization of catalysts for improvement of single enzyme reactions or de novo reaction development is often complex and tedious. The success of screening campaigns relies on the fraction of sequence space that can be sampled, whether for evolving a particular enzyme or screening metagenomes. Ultrahigh-throughput screening (uHTS) based on in vitro compartmentalization in water-in-oil emulsion of picoliter droplets generated in microfluidic systems allows screening rates >1 kHz (or >107 per day). Screening for carbohydrate-active enzymes (CAZymes) catalyzing biotechnologically valuable reactions in this format presents an additional challenge because the released carbohydrates are difficult to monitor in high throughput. Activated substrates with large optically active hydrophobic leaving groups provide a generic optical readout, but the molecular recognition properties of sugars will be altered by the incorporation of such fluoro- or chromophores and their typically higher reactivity, as leaving groups with lowered pKa values compared to native substrates make the observation of promiscuous reactions more likely. To overcome these issues, we designed microdroplet assays in which optically inactive carbohydrate products are made visible by specific cascades: the primary reaction of an unlabeled substrate leads to an optical signal downstream. Successfully implementing such assays at the picoliter droplet scale allowed us to detect glucose, xylose, glucuronic acid, and arabinose as final products of complex oligosaccharide degradation by glycoside hydrolases by absorbance measurements. Enabling the use of uHTS for screening CAZyme reactions that have been thus far elusive will chart a route toward faster and easier development of specific and efficient biocatalysts for biovalorization, directing enzyme discovery by challenging catalysts for reaction with natural rather than model substrates.

Chelate complexed multi-elemental printing performance of a small and cost efficient picoliter droplet printing device for micro preparation

We introduce an inexpensive modular picoliter pipetting device using modified commercially available thermal inkjet cartridges. The system is capable of reliable deposition of 65 elements. The printing solutions were modified to prevent the dissolution of Ni from the nozzle head, keeping those at a pH of >9. Loss of cations to the glass surfaces inside the nozzle head is prevented by forming anionic complexes with ethylenediaminetetraacetic acid in basic conditions. For some elements, e.g., Si, additives like tetramethylammonium hydroxide are necessary.The volumes of the droplets were obtained, weighing 30,000–360,000 droplets ejected by the printer using a laboratory scale. The droplet volume was within a range of 142–184 pL, depending on the formulation. The delivered elemental masses and the reproducibility were determined using total reflection X-ray fluorescence analysis and inductively coupled plasma optical emission spectrometry. Delivered masses were in the range of 0.98 pg – 11.9 pg per element and droplet.The shape of deposits of about 31 pg per element was studied using atomic force microscopy, optical microscopy, and confocal laser scanning microscopy. They were mostly spherical and ca. 14 μm in diameter and ca. 2 μm in height. The broad range of printable elements allows for the micro preparation of solid compounds for establishing a grazing incidence X-ray diffraction analysis library. As an example, the MgAl2O4 spinel was synthesized by printing of the formulation and subsequent calcination. Here we show its performance for the preparation of minerals in the context of recycling of critical elements from pyrometallurgical slags.

Droplet-based forward genetic screening of astrocyte-microglia cross-talk.

Cell-cell interactions in the central nervous system play important roles in neurologic diseases. However, little is known about the specific molecular pathways involved, and methods for their systematic identification are limited. Here, we developed a forward genetic screening platform that combines CRISPR-Cas9 perturbations, cell coculture in picoliter droplets, and microfluidic-based fluorescence-activated droplet sorting to identify mechanisms of cell-cell communication. We used SPEAC-seq (systematic perturbation of encapsulated associated cells followed by sequencing), in combination with in vivo genetic perturbations, to identify microglia-produced amphiregulin as a suppressor of disease-promoting astrocyte responses in multiple sclerosis preclinical models and clinical samples. Thus, SPEAC-seq enables the high-throughput systematic identification of cell-cell communication mechanisms.