Accurate microfluidic sorting of droplets at 30 kHz.
Ontology highlight
ABSTRACT:
SUBMITTER: Sciambi A
PROVIDER: S-EPMC4256106 | biostudies-literature | 2015 Jan
REPOSITORIES: biostudies-literature
Publications
Accurate microfluidic sorting of droplets at 30 kHz.
Sciambi Adam A Abate Adam R AR
Lab on a chip 20150101 1
Fluorescence-activated droplet sorting is an important tool for droplet microfluidic workflows, but published approaches are unable to surpass throughputs of a few kilohertz. We present a new geometry that replaces the hard divider separating the outlets with a gapped divider, allowing sorting over ten times faster. ...[more]
Similar Datasets
Project description:Fluorescence-activated droplet sorting (FADS) has become a widely used technique for high-throughput screening applications. However, existing methods are very sensitive to fluctuating flow rates at the sorting junction, which can be caused by the pulsing effects of mechanical pumps, droplet aggregates or the accumulation of precipitates during lengthy biological screening applications. Furthermore, existing sorting devices allow only 2-way sorting. We present here a dielectrophoretic sorting system in which the droplets are sorted along multiple electrode pairs that run parallel to the channels. This enables highly reliable sorting (no errors were detected for more than 2000 sorting events) even when inverting the relative flow rates at a 2-way sorting junction from 80 : 20 to 20 : 80. Furthermore, our toolbox is scalable: we demonstrate on the example of a triple-colour sorting experiment with a total of four decoupled electrodes that multi-way sorting is feasible.
| S-EPMC5544107 | biostudies-literature
Project description:A novel microfluidic calorimeter that measures the enthalpy change of reactions occurring in 100 ?m diameter aqueous droplets in fluoropolymer oil has been developed. The aqueous reactants flow into a microfluidic droplet generation chip in separate fluidic channels, limiting contact between the streams until immediately before they form the droplet. The diffusion-driven mixing of reactants is predominantly restricted to within the droplet. The temperature change in droplets due to the heat of reaction is measured optically by recording the reflectance spectra of encapsulated thermochromic liquid crystals (TLC) that are added to one of the reactant streams. As the droplets travel through the channel, the spectral characteristics of the TLC represent the internal temperature, allowing optical measurement with a precision of ?6 mK. The microfluidic chip and all fluids are temperature controlled, and the reaction heat within droplets raises their temperature until thermal diffusion dissipates the heat into the surrounding oil and chip walls. Position resolved optical temperature measurement of the droplets allows calculation of the heat of reaction by analyzing the droplet temperature profile over time. Channel dimensions, droplet generation rate, droplet size, reactant stream flows and oil flow rate are carefully balanced to provide rapid diffusional mixing of reactants compared to thermal diffusion, while avoiding thermal "quenching" due to contact between the droplets and the chip walls. Compared to conventional microcalorimetry, which has been used in this work to provide reference measurements, this new continuous flow droplet calorimeter has the potential to perform titrations ?1000-fold faster while using ?400-fold less reactants per titration.
| S-EPMC5999407 | biostudies-literature
Project description:Microsphere beads are functionalized with oligonucleotides, antibodies, and other moieties to enable specific detection of analytes. Droplet microfluidics leverages this for single-molecule or -cell analysis by pairing beads and targets in water-in-oil droplets. Pairing is achieved with devices operating in the dripping regime, limiting throughput. Here, we describe a pairing method that uses beads to trigger the breakup of a jet into monodispersed droplets. We use the method to pair 105 Human T cells with polyacrylamide beads ten times faster than methods operating in the dripping regime. Our method improves the throughput of bead-based droplet workflows, enabling analysis of large populations and the detection of rare events.
| S-EPMC6251341 | biostudies-literature
Project description:MotivationWith an increasing number of patient-derived xenograft (PDX) models being created and subsequently sequenced to study tumor heterogeneity and to guide therapy decisions, there is a similarly increasing need for methods to separate reads originating from the graft (human) tumor and reads originating from the host species' (mouse) surrounding tissue. Two kinds of methods are in use: On the one hand, alignment-based tools require that reads are mapped and aligned (by an external mapper/aligner) to the host and graft genomes separately first; the tool itself then processes the resulting alignments and quality metrics (typically BAM files) to assign each read or read pair. On the other hand, alignment-free tools work directly on the raw read data (typically FASTQ files). Recent studies compare different approaches and tools, with varying results.ResultsWe show that alignment-free methods for xenograft sorting are superior concerning CPU time usage and equivalent in accuracy. We improve upon the state of the art sorting by presenting a fast lightweight approach based on three-way bucketed quotiented Cuckoo hashing. Our hash table requires memory comparable to an FM index typically used for read alignment and less than other alignment-free approaches. It allows extremely fast lookups and uses less CPU time than other alignment-free methods and alignment-based methods at similar accuracy. Several engineering steps (e.g., shortcuts for unsuccessful lookups, software prefetching) improve the performance even further.AvailabilityOur software xengsort is available under the MIT license at http://gitlab.com/genomeinformatics/xengsort . It is written in numba-compiled Python and comes with sample Snakemake workflows for hash table construction and dataset processing.
| S-EPMC8017614 | biostudies-literature
Project description:Increasingly, invitro culture of adherent cell types utilizes three-dimensional (3D) scaffolds or aggregate culture strategies to mimic tissue-like, microenvironmental conditions. In parallel, new flow cytometry-based technologies are emerging to accurately analyze the composition and function of these microtissues (i.e., large particles) in a non-invasive and high-throughput way. Lacking, however, is an accessible platform that can be used to effectively sort or purify large particles based on analysis parameters. Here we describe a microfluidic-based, electromechanical approach to sort large particles. Specifically, sheath-less asymmetric curving channels were employed to separate and hydrodynamically focus particles to be analyzed and subsequently sorted. This design was developed and characterized based on wall shear stress, tortuosity of the flow path, vorticity of the fluid in the channel, sorting efficiency and enrichment ratio. The large particle sorting device was capable of purifying fluorescently labelled embryoid bodies (EBs) from unlabelled EBs with an efficiency of 87.3% ± 13.5%, and enrichment ratio of 12.2 ± 8.4 (n = 8), while preserving cell viability, differentiation potential, and long-term function.
| S-EPMC3324260 | biostudies-other
Project description:Microbial interactions are major drivers of microbial community dynamics and functions but remain challenging to identify because of limitations in parallel culturing and absolute abundance quantification of community members across environments and replicates. To this end, we developed Microbial Interaction Network Inference in microdroplets (MINI-Drop). Fluorescence microscopy coupled to computer vision techniques were used to rapidly determine the absolute abundance of each strain in hundreds to thousands of droplets per condition. We showed that MINI-Drop could accurately infer pairwise and higher-order interactions in synthetic consortia. We developed a stochastic model of community assembly to provide insight into the heterogeneity in community states across droplets. Finally, we elucidated the complex web of interactions linking antibiotics and different species in a synthetic consortium. In sum, we demonstrated a robust and generalizable method to infer microbial interaction networks by random encapsulation of sub-communities into microfluidic droplets.
| S-EPMC6763379 | biostudies-literature
Project description:Mechanical properties have emerged as a significant label-free marker for characterizing deformable particles such as cells. Here, we demonstrated the first single-particle-resolved, cytometry-like deformability-activated sorting in the continuous flow on a microfluidic chip. Compared with existing deformability-based sorting techniques, the microfluidic device presented in this work measures the deformability and immediately sorts the particles one-by-one in real time. It integrates the transit-time-based deformability measurement and active hydrodynamic sorting onto a single chip. We identified the critical factors that affect the sorting dynamics by modeling and experimental approaches. We found that the device throughput is determined by the summation of the sensing, buffering, and sorting time. A total time of ~100 ms is used for analyzing and sorting a single particle, leading to a throughput of 600 particles/min. We synthesized poly(ethylene glycol) diacrylate (PEGDA) hydrogel beads as the deformability model for device validation and performance evaluation. A deformability-activated sorting purity of 88% and an average efficiency of 73% were achieved. We anticipate that the ability to actively measure and sort individual particles one-by-one in a continuous flow would find applications in cell-mechanotyping studies such as correlational studies of the cell mechanical phenotype and molecular mechanism.
| S-EPMC8433438 | biostudies-literature
Project description:To advance emulsion droplet technology, we synthesize functional derivatives of Pluronic F127 that can simultaneously act as surfactants and as reactive sites for droplet surface decoration. The amine-, carboxyl-, N-hydroxysuccinimide ester-, maleimide- and biotin-terminated Pluronic F127 allows ligand immobilization on single-emulsion or double-emulsion droplets via electrostatic adsorption, covalent conjugation or site-specific avidin-biotin interaction.
| S-EPMC5328679 | biostudies-literature
Project description:Magnetic nanoparticles (MNPs) are useful for many biomedical applications, but it is challenging to synthetically produce them in large numbers with uniform properties and surface functionalization. Magnetotactic bacteria (MTB) produce magnetosomes with homogenous sizes, shapes, and magnetic properties. Consequently, there is interest in using MTB as biological factories for MNP production. Nonetheless, MTB can only be grown to low yields, and wild-type strains produce low numbers of MNPs/bacterium. There are also limited technologies to facilitate the selection of MTB with different magnetic contents, such as MTB with compromised and enhanced biomineralization ability. Here, we describe a magnetic microfluidic platform combined with transient cold/alkaline treatment to temporarily reduce the rapid flagellar motion of MTB without compromising their long-term proliferation and biomineralization ability for separating MTB on the basis of their magnetic contents. This strategy enables live MTB to be enriched, which, to the best of our knowledge, has not been achieved with another previously described magnetic microfluidic device that makes use of ferrofluid and heat. Our device also facilitates the high-throughput (25,000 cells/min) separation of wild-type Magnetospirillum gryphiswaldense (MSR-1) from nonmagnetic ΔmamAB MSR-1 mutants with a sensitivity of up to 80% and isolation purity of up to 95%, as confirmed with a gold-standard fluorescent-activated cell sorter (FACS) technique. This offers a 25-fold higher throughput than other previously described magnetic microfluidic platforms (1,000 cells/min). The device can also be used to isolate Magnetospirillum magneticum (AMB-1) mutants with different ranges of magnetosome numbers with efficiencies close to theoretical estimates. We believe this technology will facilitate the magnetic characterization of genetically engineered MTB for a variety of applications, including using MTB for large-scale, controlled MNP production.IMPORTANCE Our magnetic microfluidic technology can greatly facilitate biological applications with magnetotactic bacteria, from selection and screening to analysis. This technology will be of interest to microbiologists, chemists, and bioengineers who are interested in the biomineralization and selection of magnetotactic bacteria (MTB) for applications such as directed evolution and magnetogenetics.
| S-EPMC6102981 | biostudies-literature
Project description:Together with droplet creation, fusion and sorting, the incubation of droplets is one of the most important and essential operations for droplet-based microfluidic assays. This manuscript concerns the development of delay-lines, which are necessary to allow incubation of reactions for precise time periods. We analyze the problems associated with creating delay-lines for incubation in the minute to hour time range, which arise from back-pressure and from the dispersion in the incubation time due to the unequal speeds with which droplets pass through the delay-line. We describe delay-line systems which resolve these problems and demonstrate their use to measure reaction kinetics over several minutes in droplets.
| S-EPMC5317046 | biostudies-literature