The single-cell chemostat: an agarose-based, microfluidic device for high-throughput, single-cell studies of bacteria and bacterial communities

Optical microscopy of single bacteria growing on solid agarose support is a powerful method for studying the natural heterogeneity in growth and gene expression. While the material properties of agarose make it an excellent substrate for such studies, the sheer number of exponentially growing cells eventually overwhelms the agarose pad, which fundamentally limits the duration and the throughput of measurements. Here we overcome the limitations of exponential growth by patterning agarose pads on the sub-micron-scale. Linear tracks constrain the growth of bacteria into a high density array of linear micro-colonies. Buffer flow through microfluidic lines washes away excess cells and delivers fresh nutrient buffer. Densely patterned tracks allow us to cultivate and image hundreds of thousands of cells on a single agarose pad over 30-40 generations, which drastically increases single-cell measurement throughput. In addition, we show that patterned agarose can facilitate single-cell measurements within bacterial communities. As a proof-of-principle, we study a community of E. coli auxotrophs that can complement the amino acid deficiencies of one another. We find that the growth rate of colonies of one strain decreases sharply with the distance to colonies of the complementary strain over distances of only a few cell lengths. Because patterned agarose pads maintain cells in a chemostatic environment in which every cell can be imaged, we term our device the single-cell chemostat. High-throughput measurements of single cells growing chemostatically should greatly facilitate the study of a variety of microbial behaviours.     

Synthesis, loading, and application of individual nanocapsules for probing single-cell signaling

This paper describes the synthesis and loading of silica and polystyrene-acrylic based nanocapsules with small molecules. The nanocapsules are used for delivering defined packages of stimuli to single cells with both high spatial and temporal resolutions. To introduce molecules into the capsules, we characterized two approaches. The first approach is based on a base-swell process in which the shell of the capsule is swelled so small molecules can diffuse into the interior of the capsule and be trapped inside once the capsules are de-swelled. The second approach is based on a dry-swell-dry process in which the solution containing the molecules of interest and the nanocapsules is physically dried to promote more molecules to enter into the interior of the capsule. We characterized both methods by monitoring the content of and the release from individual capsules with confocal microscopy and wide-field imaging. To illustrate the biological applications of such nanocapsules, we used optical trapping to position a single carbachol-loaded capsule adjacent to a single CHO cell that has been transfected with muscarinic acetylcholine (M1) receptors, released the carbachol from the capsule with a single 3-ns N2 laser pulse, and then monitored the subsequent intracellular signaling triggered by the binding of carbachol to the M1 receptors.     

A computer-based programmable waveform generator

The programmable waveform generator, which is capable of producing complex voltage—time programs, is based on a PDP-$\text{11}\text{34}$ minicomputer with associated DIGITAL hardware. The desired waveform is obtained by clock-controlled output of a symmetrical triangular voltage sweep. The software can be readily adapted to any computer system. Ramp sections of 1 mV s^-1—50 V s^-1 and potential pulses of 50 μs—500 s can be obtained.     

A high voltage asymmetric waveform generator for FAIMS

High field asymmetric waveform ion mobility spectrometry (FAIMS) has been used increasingly in recent years as an additional method of ion separation and selection before mass spectrometry. The FAIMS electrodes are relatively simple to design and fabricate for laboratories wishing to implement their own FAIMS designs. However, construction of the electronics apparatus needed to produce the required high magnitude asymmetric electric field oscillating at a frequency of several hundred kilohertz is not trivial. Here we present an entirely custom-built electronics setup capable of supplying the required waveforms and voltages. The apparatus is relatively simple and inexpensive to implement. We also present data acquired on this system demonstrating the use of FAIMS as a gas-phase ion filter interface to an ion trap mass spectrometer.     

A scalable microfluidic chip for bacterial suspension culture

Microfluidic systems could, in principle, enable high-throughput breeding and screening of microbial strains for industrial applications, but parallel and scalable culture and detection chips are needed before complete microbial selection systems can be integrated and tested. Here we demonstrate a scalable multi-channel chip that is capable of bacterial suspension culture. The key invention is a multi-layered chip design, which enables a single set of control channels to function as serial peristaltic pumps to drive parallel culture chamber loops. Such design leads to scalability of the culture chip. We demonstrate that E. coli growth in the chip is equivalent or superior to conventional suspension culture on shaking beds. The chip could also be used for suspension culture of other microbes such as Bacillus subtilis, Pseudomonas stutzeri, and Zymomonas mobilis, indicating its general applicability for bacterial suspension culture.     

A high-throughput dielectrophoresis-based cell electrofusion microfluidic device

A high-throughput cell electrofusion microfluidic chip has been designed, fabricated on a silicon-on-insulator wafer and tested for in vitro cell fusion under a low applied voltage. The developed chip consists of six individual straight microchannels with a 40-μm thickness conductive highly doped Si layer as the microchannel wall. In each microchannel, there are 75 pairs of counter protruding microelectrodes, between which the cell electrofusion is performed. The entire highly doped Si layer is covered by a 2-μm thickness aluminum film to maintain a consistent electric field between different protruding microelectrode pairs. A 150-nm thickness SiO? film is subsequently deposited on the top face of each protruding microelectrode for better biocompatibility. Owing to the short distance between two counter protruding microelectrodes, a high electric field can be generated for cell electrofusion with a low voltage imposed across the electrodes. Both mammalian cells and plant protoplasts were used to test the cell electrofusion. About 42-68% cells were aligned to form cell-cell pairs by the dielectrophoretic force. After cell alignment, cell pairs were fused to form hybrid cells under the control of cell electroporation and electrofusion signals. The averaged fusion efficiency in the paired cells is above 40% (the highest was about 60%), which is much higher than the traditional polyethylene glycol method (<5%) and traditional electrofusion methods (～12%). An individual cell electrofusion process could be completed within 10 min, indicating a capability of high throughput.     

A microfluidic flow distributor generating stepwise concentrations for high-throughput biochemical processing

In this paper, we describe a microfluidic device in which solutions with stepwise concentrations can be accurately generated by continuously introducing two kinds of miscible liquids from each inlet, and biochemical processing can be conducted at the various conditions. Introduced liquid flows are geometrically divided into a number of downstream flows through multiple distribution channels, and each divided flow is then mixed with the divided flow of another liquid at a confluent point. The lengths of the precisely designed distribution channels determine the mixing ratio of the two liquids, without the influence of flow rate. In this study, a PDMS microfluidic device able to generate nine different concentrations was fabricated, and the performance of this device was estimated via colorimetric assay. As a biological application of this device, cell cultivation was performed under different concentration conditions. Due to its simplicity of operation, this microfluidic flow distributor will be applied to various kinds of biological analysis and screening systems.     

A high-throughput method for GMO multi-detection using a microfluidic dynamic array

The ever-increasing production of genetically modified crops generates a demand for high-throughput DNA-based methods for the enforcement of genetically modified organisms (GMO) labelling requirements. The application of standard real-time PCR will become increasingly costly with the growth of the number of GMOs that is potentially present in an individual sample. The present work presents the results of an innovative approach in genetically modified crops analysis by DNA based methods, which is the use of a microfluidic dynamic array as a high throughput multi-detection system. In order to evaluate the system, six test samples with an increasing degree of complexity were prepared, preamplified and subsequently analysed in the Fluidigm system. Twenty-eight assays targeting different DNA elements, GM events and species-specific reference genes were used in the experiment. The large majority of the assays tested presented expected results. The power of low level detection was assessed and elements present at concentrations as low as 0.06 % were successfully detected. The approach proposed in this work presents the Fluidigm system as a suitable and promising platform for GMO multi-detection.     

A microfluidic concentration generator for dose-response assays on ion channel pharmacology

We present a microfluidic device to generate either statically spatial or dynamically temporal logarithmic concentrations. The temporal logarithmic concentration generator was also integrated with planar patch-clamp chips for dose-response assays on ion channels. Proposed serial dilution principle controls the flow pattern at each branching point via designing the flow resistance of microchannels. Simple and linear ratios of the flow resistance results in desired logarithmic concentration at outlets, where the concentrations can be dynamically altered by different combination of valve actuations, were demonstrated. Single-cell pharmacology on ion channels was implemented by sequentially applying logarithmic drug concentrations to patched cells. Inhibitory activity of potassium channels of human embryonic kidney cells was examined by tetraethylammonium solutions. Resulted IC(50) and Hill slope reveal excellent agreement with assays from manually prepared drug concentrations showing the practicability and preciseness of the present approach. Applications include cellular analysis under various drugs and/or logarithmic concentrations at the single-cell level.     

A simple microfluidic probe of nanoparticle suspension stability

We describe a simple experimental tool that enables stability of multicomponent nanoparticle suspensions to be readily assessed by establishing a confinement-imposed chemical discontinuity at the interface between co-flowing laminar streams in a microchannel. When applied to examine Al(2)O(3) nanoparticle suspensions, this method readily reveals compositions that are susceptible to aggregation even when conventional bulk measurements (zeta potential, dynamic light scattering, bulk viscosity) suggest only subtle differences between formulations. This microfluidic stability test enables simple and rapid assessment of quality and variability in complex multicomponent mixtures for which few, if any, comparable data exist. The paradoxical ease at which localized aggregation can be triggered in suspensions that would otherwise appear stable also serves as a caution to researchers undertaking tracer-based studies of nanomaterial suspensions.     

Low-cost multi-core inertial microfluidic centrifuge for high-throughput cell concentration

We developed a low-cost multi-core inertial microfluidic centrifuge (IM-centrifuge) to achieve a continuous-flow cell/particle concentration at a throughput of up to 20 mL/min. To lower the cost of our IM-centrifuge, we clamped a disposable multilayer film-based inertial microfluidic (MFIM) chip with two reusable plastic housings. The key MFIM chip was fabricated in low-cost materials by stacking different polymer-film channel layers and double-sided tape. To increase processing throughput, multiplexing spiral inertial microfluidic channels were integrated within an all-in-one MFIM chip, and a novel sample distribution strategy was employed to equally distribute the sample into each channel layer. Then, we characterized the focusing performance in the MFIM chip over a wide flow-rate range. The experimental results showed that our IM-centrifuge was able to focus various-sized particles/cells to achieve volume reduction. The sample distribution strategy also effectively ensured identical focusing and concentration performances in different cores. Finally, our IM-centrifuge was successfully applied to concentrate microalgae cells with irregular shapes and highly polydisperse sizes. Thus, our IM-centrifuge holds the potential to be employed as a low-cost, high-throughput centrifuge for disposable use in low-resource settings.     

Analysis of intercellular calcium signaling using microfluidic adjustable laminar flow for localized chemical stimulation

The propagation of intercellular calcium signals provides a mechanism to coordinate cell population activity, which is essential for regulating cell behavior and organ development. However, existing analytical methods are difficult to realize localized chemical stimulation of a single cell among a population of cells that are in close contact with one another for studying the propagation of calcium wave. In this work, a microfluidic method is presented for the analysis of contact-dependent propagation of intercellular calcium wave induced by extracellular ATP using multiple laminar flows. Adjacent cells were seeded ∼300 μm downstream the intersection of a Y-shaped microchannel with negative pressure pulses. Consequently, the lateral diffusion distance of the chemical at cell locations was limited to ∼26 μm with a total flow rate of 20 μL min⁻¹, which prevented the interference of diffusion-induced cellular responses. Localized stimulation of the target cell with ATP induced the propagation of intercellular calcium wave among the cell population. In addition, studies on the spread of intercellular calcium wave under octanol inhibition allowed us to characterize the gap junction mediated cell–cell communication. Thus, this novel device will provide a versatile platform for intercellular signal transduction studies and high throughput drug screening.     

A microfluidic magnetic bead impact generator for physical stimulation of osteoblast cell

We developed a novel microfluidic cell culture device in which magnetic beads repetitively collide with osteoblast cells, MC3T3‐E1, owing to attractive forces generated by pulsed electromagnetic fields and consequently the cells were physically stimulated by bead impacts. Our device consists of an on‐chip microelectromagnet and a microfluidic channel which were fabricated by a microelectromechanical system technique. The impact forces and stresses acting on a cell were numerically analyzed and experimentally generated with different sizes of bead (4.5, 7.6 and 8.4 μm) and at various pulse frequencies (60 Hz, 1 kHz and 1 MHz). Cells were synchronized at each specific phase of the cell cycle before stimulation in order to determine the most susceptible phase against bead impacts. The cells were stimulated with different sizes of bead at various pulse frequencies for 1 min at G1, S and G2 phases, respectively, and then counted immediately after one doubling time. The growth rate of cells was highly accelerated when they were stimulated with 4.5 μm beads at G1 phase and a pulse frequency of 1 MHz. Almost all of the cells were viable after stimulation, indicating that our cell stimulator did not cause any cellular damage and is suitable for use in new physical stimulus modalities.     

A single-cell encapsulation method based on a microfluidic multi-step droplet splitting system

Single cell analysis is of great significance to understand the physiological activity of organisms.Microfluidic droplet is an ideal analytical platform for single-cell analysis. We developed a microfluidic droplet splitting system integrated with a flow-focusing structure and multi-step splitting structures to form 8-line droplets and encapsulate single cells in the droplets. Droplet generation frequency reached1021 Hz with the aqueous phase flow rate of 1 m L/min and the oil phase flow rate of 15 mL /min. Relative standard deviation of the droplet size was less than 5% in a single channel, while less than 6% in all the8 channels. The system was used for encapsulating human whole blood cells. A single-cell encapsulation efficiency of 31% was obtained with the blood cell concentration of 2.5× 10~4cells/mL, and the multicellular droplet percentage was only 1.3%. The multi-step droplet splitting system for single cell encapsulation featured simple structure and high throughput.     

A modular single-cell pipette microfluidic chip coupling to ETAAS and ICP-MS for single cell analysis

Accurate single-cell capture is a crucial step for single cell biological and chemical analysis. Conventional single-cell capturing often confront operational complexity, limited efficiency, cell damage, large scale but low accuracy, incompetence in the acquirement of nano-upgraded single-cell liquid. Flow cytometry has been widely used in large-scale single-cell detection, while precise single-cell isolation relies on both a precision operating platform and a microscope, which is not only extre...     

Multiparallel microfluidic high-performance liquid chromatography for high-throughput normal-phase chiral analysis

The suitability of the Eksigent Express 800 microfluidic eight-channel HPLC instrument for multiparallel normal-phase chiral analysis in support of high-throughput pharmaceutical process research was investigated. Analysis of test mixtures containing the two enantiomers of benzoin and the closely related (R,S)-dihydrobenzoin, was carried out in a 96-well microplate, affording rapid (<2 h) and accurate assessment of enantiopurity. In a second example, use of the instrument to support high-throughput catalyst screening of the asymmetric hydrogenation of a prochiral unsaturated ester is presented, in which method development (gradient screening of four columns and two eluents, followed by optimization to afford a fast analytical method) and analysis of a 96-well microplate was carried out within a single working day. This represents a considerable improvement over conventional analysis techniques that usually take several days to complete.     

A radial microfluidic concentration gradient generator with high-density channels for cell apoptosis assay

An integrated microfluidic concentration gradient chip was developed for generating stepwise concentrations in high-density channels and applied to high-throughput apoptosis analysis of human uterine cervix cancer (HeLa) cells. The concentration gradient was generated by repeated splitting-and-mixing of the source solutions in a radial channel network which consists of multiple concentric circular channels and an increasing number of branch channels. The gradients were formed over hundreds of branches with predictable concentrations in each branch channel. This configuration brings about some distinctive advantages, e.g., more compact and versatile design, high-density of channels and wide concentration ranges. This concentration gradient generator was used in perfusion culture of HeLa cells and a drug-induced apoptosis assay, demonstrated by investigating the single and combined effects of two model anticancer drugs, 5-fluorouracil and Cyclophosphamide, which were divided into 65 concentrations of the two drugs respectively and 65 of their combinatorial concentrations. The gradient generation, the cell culture/stimulation and staining were performed in a single chip. The present device offers a unique platform to characterize various cellular responses in a high-throughput fashion.     

A high-throughput microfluidic assay to study neurite response to growth factor gradients

Studying neurite guidance by diffusible or substrate bound gradients is challenging with current techniques. In this study, we present the design, fabrication and utility of a microfluidic device to study neurite guidance under chemogradients. Experimental and computational studies demonstrated the establishment of a steep gradient of guidance cue within 30 min and stable for up to 48 h. The gradient was found to be insensitive to external perturbations such as media change and movement of device. The effects of netrin-1 (0.1-10 μg mL(-1)) and brain pulp (0.1 μL mL(-1)) were evaluated for their chemoattractive potential on neurite turning, while slit-2 (62.5 or 250 ng mL(-1)) was studied for its chemorepellant properties. Hippocampal or dorsal root ganglion (DRG) neurons were seeded into a micro-channel and packed onto the surface of a 3D collagen gel. Neurites grew into the matrix in three dimensions, and a gradient of guidance cue was created orthogonal to the direction of neurite growth to impact guidance. The average turning angle of each neurite was measured and averaged across multiple devices cultured under similar conditions to quantify the effect of guidance cue gradient. Significant positive turning towards gradient was measured in the presence of brain pulp and netrin-1 (1 μg mL(-1)), relative to control cultures which received no external guidance cue (p < 0.001). Netrin-1 released from transfected fibroblasts had the most positive turning effect of all the chemoattractive cues tested (p < 0.001). Slit-2 exhibited strong chemorepellant characteristics on both hippocampal and DRG neurite guidance at 250 ng mL(-1) concentration. Slit-2 also showed similar behavior on DRG neuron invasion into 3D collagen gel (p < 0.01 relative to control cultures). Taken together, the results suggest the utility of this microfluidic device to generate stable chemogradients for studying neurobiology, cell migration and proliferation, matrix remodeling and co-cultures with other cell lines, with potential applications in cancer biology, tissue engineering and regenerative medicine.