A modular and reconfigurable open-channel gated device for the electrokinetic extraction of cell-free DNA assays.

The high-efficiency separation and extraction of short fragments of cell-free DNA (cfDNA) remain challenging due to their low abundance and short lengths. This study presents a method for separating short cfDNA fragments, with lengths ranging from about 100 to 200 base pairs, from liquid human plasma samples into separable and extractable bands as solid agarose gel slabs. To achieve this, a novel millimeter-scale fluidic device is used for sample handling, transient isotachophoresis, and extraction. The device features open-to-atmosphere liquid chambers that define and manually actuated (i.e., movable) agarose-made gate valve structures. The agarose gates then define discrete zones for buffers, sample injection, DNA pre-concentration via isotachophoresis, size-based gel separation, and DNA-band extraction. As a demonstration of its efficacy, the device is applied to the enrichment and purification of M. tuberculosis genomic DNA fragments spiked in human plasma samples. This purified cfDNA is analyzed using the quantitative polymerase chain reaction (qPCR) of the IS6110 repetitive sequence in the M. tuberculosis genome. The data from this study demonstrates that high sensitivity can be achieved in cfDNA detection, as shown by the comparison with a typical solid-phase extraction method and buffer spiked with cfDNA. Evidence is presented that suggests plasma peptides generated by treatment of the sample with proteinase K acts as endogenous spacer molecules, which improve the resolution and purification of DNA relative to the marker dye and other contaminants that decrease the signal level in qPCR.

An Integrated Pulsation-Free, Backflow-Free Micropump Using the Analog Waveform-Driven Braille Actuator.

The widespread adoption of long-term organs-on-a-chip culture necessitates both active perfusions that mimic physiological flow conditions and minimization of the complexity of microfluidic system and fluid handling. In particular, flow in microtissue such as microvascular is free of pulsation and backflow. The refreshable Braille actuator-based integrated microfluidic system can be employed with simple microchannels and setups. However, due to high pulsatile flow and backflow, ordinary Braille-driven micropumps generate non-physiological flow conditions. We have described a simple method for creating steady flow employing Braille actuators driven with a high-voltage analog waveform, called "constant flow waveform", without incorporating complicated structures into the microchannel or actuator. We determined the constant flow waveform by measuring volume change of microchannel caused by actuated Braille pins using a conventional fluorescent dye and microscope. Using the constant flow waveform, we demonstrated that a Braille-driven pump reduced pulsating flow by 79% and backflow by 63% compared to conventional Braille-driven pump. Furthermore, we demonstrated that a parallel pair of three-stranded pin pumps effectively eliminated backflow by driving two pumps with the constant flow waveform half-cycle shifted to each other. Moreover, by raising the driving frequency, we could increase the average flow rate to ~2× higher than previously reported flow rate of a typical Braille-driven micropump.

Integrated On-Chip 3D Vascular Network Culture under Hypoxia.

We developed a portable device made of poly(dimethylsiloxane) (PDMS)/polymethylmethacrylate (PMMA) for long-term 3D cell culture of vascular endothelial cells for the development of a vascular network and evaluated the device under different transitions between normoxia and hypoxia with good optical accessibility. The combination of a nested reservoir device and a bicarbonate/ascorbate buffer system accomplished on-chip incubation with 4.91 ± 0.86% pO2 and 5.19 ± 1.70% pCO2 for up to 10 days. Seventy-two hours of normoxic incubation preceding hypoxic culture increased the cell viability, network formation, and size and stability of the resulting lumens compared with those completely maintained in normoxia for the same total duration. We employed different parameters of the network (e.g., total mesh area, total length, number of branches, among others) for the comparison of different oxygen treatments in the device. The differential effect of hypoxic conditions based on the maturity of the vessels may be used as an external factor to improve vascular development in vitro.

Microfluidic Long-Term Gradient Generator with Axon Separation Prototyped by 185 nm Diffused Light Photolithography of SU-8 Photoresist.

We have developed a cast microfluidic chip for concentration gradient generation that contains a thin (~5 µm² cross-sectional area) microchannel. The diffusion of diffused 185 nm ultraviolet (UV) light from an inexpensive low-pressure mercury lamp exposed a layer of the SU-8 photoresist from the backside and successfully patterned durable 2 µm-high microchannel mold features with smooth bell-shaped sidewalls. The thin channel had appropriate flow resistance and simultaneously satisfied both the rapid introduction of test substance and long-term maintenance of gradients. The average height and width at the half height of the channel, defined by a 2 µm-wide line mask pattern, were 2.00 ± 0.19 µm, and 2.14 ± 0.89 µm, respectively. We were able to maintain the concentration gradient of Alexa Fluor 488 fluorescent dye inside or at the exit of the thin microchannel in an H-shaped microfluidic configuration for at least 48 h. We also demonstrated the cultivation of chick embryo dorsal root ganglion neuronal cells for 96 h, and the directional elongation of axons under a nerve growth factor concentration gradient.

Reconfigurable Microfluidic Channel with Pin-discretized Sidewalls.

Microfluidic components need to have various shapes to realize different key microfluidic functions such as mixing, separation, particle trapping, or reactions. A microfluidic channel that deforms even after fabrication while retaining the channel shape enables high spatiotemporal reconfigurability. This reconfigurability is required in such key microfluidic functions that are difficult to achieve in existing "reconfigurable" or "integrated" microfluidic systems. We describe a method for the fabrication of a microfluidic channel with a deformable sidewall consisting of a laterally aligned array of the ends of rectangular pins. Actuating the pins in their longitudinal directions changes the pins' end positions, and thus, the shape of discretized channel sidewalls.Pin gaps can cause unwanted leakage or adhesion to adjacent pins caused by meniscus forces. To close the pin gaps, we have introduced hydrocarbon-fluoropolymer suspension-based gap filler accompanied by an elastomeric barrier. This reconfigurable microfluidic device can generate strong temporal in-channel displacement flow, or can stop the flow in any region of the channel. This feature will facilitate, on demand, the handling of cells, viscous liquids, gas bubbles, and non-fluids, even if their existence or behavior is unknown at the time of fabrication.

Reconfigurable microfluidic device with discretized sidewall.

Various microfluidic features, such as traps, have been used to manipulate flows, cells, and other particles within microfluidic systems. However, these features often become undesirable in subsequent steps requiring different fluidic configurations. To meet the changing needs of various microfluidic configurations, we developed a reconfigurable microfluidic channel with movable sidewalls using mechanically discretized sidewalls of laterally aligned rectangular pins. The user can deform the channel sidewall at any time after fabrication by sliding the pins. We confirmed that the flow resistance of the straight microchannel could be reversibly adjusted in the range of 101-105 Pa s/µl by manually displacing one of the pins comprising the microchannel sidewall. The reconfigurable microchannel also made it possible to manipulate flows and cells by creating a segmented patterned culture of COS-7 cells and a coculture of human umbilical vein endothelial cells (HUVECs) and human lung fibroblasts (hLFs) inside the microchannel. The reconfigurable microfluidic device successfully maintained a culture of COS-7 cells in a log phase throughout the entire period of 216 h. Furthermore, we performed a migration assay of cocultured HUVEC and hLF spheroids within one microchannel and observed their migration toward each other.

Microfluidic device capable of medium recirculation for non-adherent cell culture.

We present a microfluidic device designed for maintenance and culture of non-adherent mammalian cells, which enables both recirculation and refreshing of medium, as well as easy harvesting of cells from the device. We demonstrate fabrication of a novel microfluidic device utilizing Braille perfusion for peristaltic fluid flow to enable switching between recirculation and refresh flow modes. Utilizing fluid flow simulations and the human promyelocytic leukemia cell line, HL-60, non-adherent cells, we demonstrate the utility of this RECIR-REFRESH device. With computer simulations, we profiled fluid flow and concentration gradients of autocrine factors and found that the geometry of the cell culture well plays a key role in cell entrapping and retaining autocrine and soluble factors. We subjected HL-60 cells, in the device, to a treatment regimen of 1.25% dimethylsulfoxide, every other day, to provoke differentiation and measured subsequent expression of CD11b on day 2 and day 4 and tumor necrosis factor-alpha (TNF-α) on day 4. Our findings display perfusion sensitive CD11b expression, but not TNF-α build-up, by day 4 of culture, with a 1:1 ratio of recirculation to refresh flow yielding the greatest increase in CD11b levels. RECIR-REFRESH facilitates programmable levels of cell differentiation in a HL-60 non-adherent cell population and can be expanded to other types of non-adherent cells such as hematopoietic stem cells.

On-chip multi-gas incubation for microfluidic cell cultures under hypoxia.

We developed a simple system that regulates CO2 and O2 levels within a microfluidic chip. This system enables long-term cell culture under hypoxic conditions without the need of a CO2 incubator or a multi-gas incubator. Hypoxic conditions were generated using a miniature water jacket containing dissolved ascorbate as an oxygen scavenger. Formulations of the water jacket were determined that enables both 5% pCO2 and desired pO2 levels ranging from 5 to 15%. We also cultured PC-12 cells and primary neuronal cells from chick embryos under hypoxia and observed hypoxia-induced cell death and inhibition of neurite outgrowth.

Microfluidic cell culture system with on-chip hypoxic conditioning.

We have demonstrated a portable microfluidic cell culture system with multi-gas (CO2 and O2) incubation which we can cultivate under hypoxia without bulky peripheral apparatus such as gas tanks, regulators, and flow controllers. The system contains a chip of 26 mm × 48 mm which is capable to diffuse CO2 and absorb O2 through a gas-permeable wall of nested media reservoir. The media was water-jacketed with aqueous solution containing 0.8 M sodium bicarbonate as CO2 supply and 1 M sodium ascorbate as oxygen scavenger. The partial CO2 pressure (pCO2) in media reservoir stabilized at least 10.2% ± 0.11% for at least 72 hours. The partial O2 pressure (pO2) in the media reservoir decreased to 4.2%. Portable on-chip hypoxic culture of SV40-T2 cells for 72 h was also demonstrated.

A simple microfluidic gradient generator with a soft-lithographically prototyped, high-aspect-ratio, ~2 µm wide microchannel.

We have developed a cast microfluidic chip that contains a thin (~2 µm wide) microchannel that is smoothly connected to thick microfluidics. The thin line features having high aspect ratio for a low-cost photolithography in which an emulsion photomask was used (1:1 ~ 1:3) were fabricated by exposing SU-8 photoresist to diffused 185 nm UV light emitted by a low-cost ozone lamp from the backside of the substrate to ensure sufficient crosslinking of small regions of the SU-8 photoresist. An H-shaped microfluidic configuration was used, in which the thin channel maintained constant diffusion fronts beyond purely static diffusion. We also demonstrated the long-term effects of a gradient of nerve growth factor on axon elongation by primary neurons cultured in the micro channel.

On-chip incubation system for long-term microfluidic cell culture.

We demonstrate the use of a microfluidic cell culture chip with Braille pin-driven pumping, capable of on-chip CO2 incubation that does not require an external chamber or gas supply. The proposed chip consists of a poly(dimethylsiloxane)(PDMS)-made microfluidic chip, flip-mounted on a glass slide, that contains a nested pair of cell culture media reservoirs and water-jacket, insulated by a permeable PDMS wall. By using 0.8 M sodium bicarbonate with 65 mM sodium carbonate as the water-jacket and placing on a 37 °C surface, the chip maintained osmolality shift and the pCO2 in the media reservoir stabilized within < 3 mmol/kg and 5.0% ± 0.2% over at least 24 hours. The incubation capabilities were demonstrated through microfluidic culture of CV-1 epithelial cells under an inverted microscope for at least 12 days.

Acoustically detectable cellular-level lung injury induced by fluid mechanical stresses in microfluidic airway systems.

We describe a microfabricated airway system integrated with computerized air-liquid two-phase microfluidics that enables on-chip engineering of human airway epithelia and precise reproduction of physiologic or pathologic liquid plug flows found in the respiratory system. Using this device, we demonstrate cellular-level lung injury under flow conditions that cause symptoms characteristic of a wide range of pulmonary diseases. Specifically, propagation and rupture of liquid plugs that simulate surfactant-deficient reopening of closed airways lead to significant injury of small airway epithelial cells by generating deleterious fluid mechanical stresses. We also show that the explosive pressure waves produced by plug rupture enable detection of the mechanical cellular injury as crackling sounds.

Small volume low mechanical stress cytometry using computer-controlled Braille display microfluidics.

This paper describes a micro flow cytometer system designed for efficient and non-damaging analysis of samples with small numbers of precious cells. The system utilizes actuation of Braille-display pins for micro-scale fluid manipulation and a fluorescence microscope with a CCD camera for optical detection. The microfluidic chip is fully disposable and is composed of a polydimethylsiloxane (PDMS) slab with microchannel features sealed against a thin deformable PDMS membrane. The channels are designed with diffusers to alleviate pulsatile flow behaviors inherent in pin actuator-based peristaltic pumping schemes to maximize hydrodynamic focusing of samples with minimal disturbances in the laminar streams within the channel. A funnel connected to the microfluidic channel is designed for efficient loading of samples with small number of cells and is also positioned on the chip to prevent physical damages of the samples by the squeezing actions of Braille pins during actuation. The sample loading scheme was characterized by both computational fluidic dynamics (CFD) simulation and experimental observation. A fluorescein solution was first used for flow field investigation, followed by use of fluorescence beads with known relative intensities for optical detection performance calibration. Murine myoblast cells (C2C12) were exploited to investigate cell viability for the sample loading scheme of the device. Furthermore, human promyelocytic leukemia (HL60) cells stained by hypotonic DNA staining buffer were also tested in the system for cell cycle analysis. The ability to efficiently analyze cellular samples where the number of cells is small was demonstrated by analyzing cells from a single embryoid body derived from mouse embryonic stem cells. Consequently, the designed microfluidic device reported in this paper is promising for easy-to-use, small sample size flow cytometric analysis, and has potential to be further integrated with other Braille display-based microfluidic devices to facilitate a multi-functional lab-on-a-chip for mammalian cell manipulations.

Leakage-free bonding of porous membranes into layered microfluidic array systems.

The integration of semiporous membranes into poly(dimethylsiloxane) (PDMS) microfluidic devices is useful for mass transport control. Several methods such as plasma oxidation and manual application of PDMS prepolymer exist to sandwich such membranes into simple channel structures, but these methods are difficult to implement with reliable sealing and no leakage or clogging for devices with intricate channel features. This paper describes a simple but robust strategy to bond semiporous polyester and polycarbonate membranes between layers of PDMS microchannel structures effectively without channel clogging. A thin layer of PDMS prepolymer, spin-coated on a glass slide, is transferred to PDMS substrates with channel features as well as to the edges of the semiporous membrane by stamping. This thin PDMS prepolymer serves as "mortar" to strongly bond the two PDMS layers and seal off the crevices generated from the thickness of the membranes. This bonding method enabled the fabrication of an 8x12 criss-crossing microfluidic channel array with 96 combinations of fluid interactions. The capability of this device for bioanalysis was demonstrated by measuring responses of cells to different color fluorescent reagents.

Characterization and resolution of evaporation-mediated osmolality shifts that constrain microfluidic cell culture in poly(dimethylsiloxane) devices.

Evaporation is a critical problem when handling submicroliter volumes of fluids. This paper characterizes this problem as it applies to microfluidic cell culture in poly(dimethylsiloxane) (PDMS) devices and provides a practical solution. Evaporation-mediated osmolality shifts through PDMS membranes with varying thicknesses (10, 1, 0.2, or 0.1 mm) were measured over 96 h. Even in humidified cell culture incubators, evaporation through PDMS and associated shifts in the osmolality of culture media was significant and prevented mouse embryo and human endothelial cell growth and development. A simple diffusion model, where the measured diffusion coefficient for PDMS matches reported values of approximately 10-9 m2/s, accounts for these evaporation and osmolality shifts. To overcome this problem, a PDMS-parylene-PDMS hybrid membrane was developed that greatly suppresses evaporation and osmolality shifts, yet possesses thinness and the flexibility necessary to interface with deformation-based microfluidic actuation systems, maintains the clarity for optical microscopy, and enables the successful development of single-cell mouse embryos into blastocysts under static conditions and culture of human endothelial cells under dynamic recirculation of submicroliter volumes of media. These insights and methods demonstrated specifically for embryo and endothelial cell studies will be generally useful for understanding and overcoming evaporation-associated effects in microfluidic cell cultures.

Quantitative measurement and control of oxygen levels in microfluidic poly(dimethylsiloxane) bioreactors during cell culture.

Microfluidic bioreactors fabricated from highly gas-permeable poly(dimethylsiloxane) (PDMS) materials have been observed, somewhat unexpectedly, to give rise to heterogeneous long term responses along the length of a perfused mammalian cell culture channel, reminiscent of physiologic tissue zonation that arises at least in part due to oxygen gradients. To develop a more quantitative understanding and enable better control of the physical-chemical mechanisms underlying cell biological events in such PDMS reactors, dissolved oxygen concentrations in the channel system were quantified in real time using fluorescence intensity and lifetime imaging of an oxygen sensitive dye, ruthenium tris(2,2'-dipyridyl) dichloride hexahydrate (RTDP). The data indicate that despite oxygen diffusion through PDMS, uptake of oxygen by cells inside the perfused PDMS microchannels induces an axial oxygen concentration gradient, with lower levels recorded in downstream regions. The oxygen concentration gradient generated by a balance of cellular uptake, convective transport by media flow, and permeation through PDMS in our devices ranged from 0.0003 (mg/l)/mm to 0.7 (mg/l)/mm. The existence of such steep gradients induced by cellular uptake can have important biological consequences. Results are consistent with our mathematical model and give insight into the conditions under which flux of oxygen through PDMS into the microchannels will or will not contribute significantly to oxygen delivery to cells and also provide a design tool to manipulate and control oxygen for cell culture and device engineering. The combination of computerized microfluidics, in situ oxygen sensing, and mathematical models opens new windows for microphysiologic studies utilizing oxygen gradients and low oxygen tensions.

Handheld recirculation system and customized media for microfluidic cell culture.

A palm-sized microfluidic recirculation system and customized media enable simplified long-term culture and imaging of cells. The combination of bare Braille display modules, a leveled monolithic surface for complete chip mounting, and a transparent heater improved portability, mechanical stability and optical accessibility. Modification of basal culture media with Leibovitz's L-15 medium enabled an incubator-free culture of carbonate-dependent cells by eliminating the need for exogenous carbon dioxide. This capability is demonstrated through time-lapse recording of proliferation of C2C12 myoblasts and MC3T3-E1 osteoblasts for over 2 weeks in ambient atmosphere without medium exchange. The method opens up new possibilities for portable cell culture and for long-term continuous visual monitoring of cells.

Computer-controlled microcirculatory support system for endothelial cell culture and shearing.

Endothelial cells (ECs) lining the inner lumen of blood vessels are continuously subjected to hemodynamic shear stress, which is known to modify EC morphology and biological activity. This paper describes a self-contained microcirculatory EC culture system that efficiently studies such effects of shear stress on EC alignment and elongation in vitro. The culture system is composed of elastomeric microfluidic cell shearing chambers interfaced with computer-controlled movement of piezoelectric pins on a refreshable Braille display. The flow rate is varied by design of channels that allow for movement of different volumes of fluid per variable-speed pump stroke. The integrated microfluidic valving and pumping system allowed primary EC seeding and differential shearing in multiple compartments to be performed on a single chip. The microfluidic flows caused ECs to align and elongate significantly in the direction of flow according to their exposed levels of shear stress. This microfluidic system overcomes the small flow rates and the inefficiencies of previously described microfluidic and macroscopic systems respectively to conveniently perform parallel studies of EC response to shear stress.

Computerized microfluidic cell culture using elastomeric channels and Braille displays.

Computer-controlled microfluidics would advance many types of cellular assays and microscale tissue engineering studies wherever spatiotemporal changes in fluidics need to be defined. However, this goal has been elusive because of the limited availability of integrated, programmable pumps and valves. This paper demonstrates how a refreshable Braille display, with its grid of 320 vertically moving pins, can power integrated pumps and valves through localized deformations of channel networks within elastic silicone rubber. The resulting computerized fluidic control is able to switch among: (i) rapid and efficient mixing between streams, (ii) multiple laminar flows with minimal mixing between streams, and (iii) segmented plug-flow of immiscible fluids within the same channel architecture. The same control method is used to precisely seed cells, compartmentalize them into distinct subpopulations through channel reconfiguration, and culture each cell subpopulation for up to 3 weeks under perfusion. These reliable microscale cell cultures showed gradients of cellular behavior from C2C12 myoblasts along channel lengths, as well as differences in cell density of undifferentiated myoblasts and differentiation patterns, both programmable through different flow rates of serum-containing media. This technology will allow future microscale tissue or cell studies to be more accessible, especially for high-throughput, complex, and long-term experiments. The microfluidic actuation method described is versatile and computer programmable, yet simple, well packaged, and portable enough for personal use.