An integrated microfluidic device for influenza and other genetic analyses

Involvement of the open-source community in combating the worldwide COVID-19 pandemic: a review

The ongoing COVID-19 pandemic is unprecedented in the modern age both due to its scale and its disruption to daily life throughout the world. Widespread social isolation and restrictions in the age of modern communicative technology, coupled with some early successes for makers, have united the open-source community towards a common goal in a way not previously seen. Local hospitals and care facilities are turning to makers to print essential consumable parts, such as simple visors, while in the hardest hit areas, critical pieces of medical technology are being fabricated. While important and effective innovations are appearing almost daily, there are also some worrying trends towards hobbyists attempting manufacture of complex medical devices with little understanding of the clinical or scientific rationale behind their design. The nature of the open-source community, an area of intensive innovation, fluidity, and experimentation, jars with the exacting standards of medical device regulation. Here, we review the involvement of rapid prototyping and the open-source community in the key areas of personal protective equipment (PPE), diagnostics, critical care technology, and information acquisition and sharing, highlighting where makers and hackers have clashed with medical device regulations, and areas where the system has worked well to facilitate change.

Microfluidic-Based Single-Cell Study: Current Status and Future Perspective

Investigation of cell behavior under different environments and manual operations can give information in specific cellular processes. Among all cell-based analysis, single-cell study occupies a peculiar position, while it can avoid the interaction effect within cell groups and provide more precise information. Microfluidic devices have played an increasingly important role in the field of single-cell study owing to their advantages: high efficiency, easy operation, and low cost. In this review, the applications of polymer-based microfluidics on cell manipulation, cell treatment, and cell analysis at single-cell level are detailed summarized. Moreover, three mainly types of manufacturing methods, i.e., replication, photodefining, and soft lithography methods for polymer-based microfluidics are also discussed.

Effect of buffer composition on PNA–RNA hybridization studied in the microfluidic microarray chip

Herein, we report that peptide nucleic acid sequences (PNAs) have been used as the probe species for detection of RNA and that a microfluidic microarray (MMA) chip is used as the platform for detection of hybridizations between immobilized PNA probes and RNA targets. The RNA targets used are derived from influenza A sequences. This paper discusses the optimization of two probe technologies used for RNA detection and investigates how the composition of the probe buffer and the content of the hybridization solution can influence the overall results. Our data show that the PNA probe is a better choice than the DNA probe when there is low salt in the probe buffer composition. Furthermore, we show that the absence of salt (NaCl) in the hybridization buffer does not hinder the detection of RNA sequences. The results provide evidence that PNA probes are superior to DNA probes in term of sensitivity and adaptability, as PNA immobilization and PNA–RNA hybridization are less affected by salt content in the reaction buffers unlike DNA probes.

Accurate, predictable, repeatable micro-assembly technology for polymer, microfluidic modules

A method for the design, construction, and assembly of modular, polymer-based, microfluidic devices using simple micro-assembly technology was demonstrated to build an integrated fluidic system consisting of vertically stacked modules for carrying out multi-step molecular assays. As an example of the utility of the modular system, point mutation detection using the ligase detection reaction (LDR) following amplification by the polymerase chain reaction (PCR) was carried out. Fluid interconnects and standoffs ensured that temperatures in the vertically stacked reactors were within ± 0.2 C° at the center of the temperature zones and ± 1.1 C° overall. The vertical spacing between modules was confirmed using finite element models (ANSYS, Inc., Canonsburg, PA) to simulate the steady-state temperature distribution for the assembly. Passive alignment structures, including a hemispherical pin-in-hole, a hemispherical pin-in-slot, and a plate-plate lap joint, were developed using screw theory to enable accurate exactly constrained assembly of the microfluidic reactors, cover sheets, and fluid interconnects to facilitate the modular approach. The mean mismatch between the centers of adjacent through holes was 64 ± 7.7 μm, significantly reducing the dead volume necessary to accommodate manufacturing variation. The microfluidic components were easily assembled by hand and the assembly of several different configurations of microfluidic modules for executing the assay was evaluated. Temperatures were measured in the desired range in each reactor. The biochemical performance was comparable to that obtained with benchtop instruments, but took less than 45 min to execute, half the time.

Gold Nanorod-based Photo-PCR System for One-Step, Rapid Detection of Bacteria

The polymerase chain reaction (PCR) has been an essential tool for diagnosis of infectious diseases, but conventional PCR still has some limitations with respect to applications to point-of-care (POC) diagnostic systems that require rapid detection and miniaturization. Here we report a light-based PCR method, termed as photo-PCR, which enables rapid detection of bacteria in a single step. In the photo-PCR system, poly(enthylene glycol)-modified gold nanorods (PEG-GNRs), used as a heat generator, are added into the PCR mixture, which is subsequently periodically irradiated with a 808-nm laser to create thermal cycling. Photo-PCR was able to significantly reduce overall thermal cycling time by integrating bacterial cell lysis and DNA amplification into a single step. Furthermore, when combined with KAPA2G fast polymerase and cooling system, the entire process of bacterial genomic DNA extraction and amplification was further shortened, highlighting the potential of photo-PCR for use in a portable, POC diagnostic system.

Characterization and analysis of real-time capillary convective PCR toward commercialization

Almost all the reported capillary convective polymerase chain reaction (CCPCR) systems to date are still limited to research use stemming from unresolved issues related to repeatability, reliability, convenience, and sensitivity. To move CCPCR technology forward toward commercialization, a couple of critical strategies and innovations are discussed here. First, single- and dual-end heating strategies are analyzed and compared between each other. Especially, different solutions for dual-end heating are proposed and discussed, and the heat transfer and fluid flow inside the capillary tube with an optimized dual-end heating strategy are analyzed and modeled. Second, real-time CCPCR is implemented with light-emitting diode and photodiode, and the real-time fluorescence detection method is compared with the post-amplification end-point detection method based on a dipstick assay. Thirdly, to reduce the system complexity, e.g., to simplify parameter tuning of the feedback control, an internal-model-control-based proportional-integral-derivative controller is adopted for accurate temperature control. Fourth, as a proof of concept, CCPCR with pre-loaded dry storage of reagent inside the capillary PCR tube is evaluated to better accommodate to point-of-care diagnosis. The critical performances of improved CCPCR, especially with sensitivity, repeatability, and reliability, have been thoroughly analyzed with different experiments using influenza A (H1N1) virus as the detection sample.

Control and automation of multilayered integrated microfluidic device fabrication

Integrated microfluidics is a sophisticated three-dimensional (multi layer) solution for high complexity serial or parallel processes. Fabrication of integrated microfluidic devices requires soft lithography and the stacking of thin-patterned PDMS layers. Precise layer alignment and bonding is crucial. There are no previously reported standards for alignment of the layers, which is mostly performed using uncontrolled processes with very low alignment success. As a result, integrated microfluidics is mostly used in academia rather than in the many potential industrial applications. We have designed and manufactured a semiautomatic Microfluidic Device Assembly System (μDAS) for full device production. μDAS comprises an electrooptic mechanical system consisting of four main parts: optical system, smart media holder (for PDMS), a micropositioning xyzθ system and a macropositioning XY mechanism. The use of the μDAS yielded valuable information regarding PDMS as the material for device fabrication, revealed previously unidentified errors, and enabled optimization of a robust fabrication process. In addition, we have demonstrated the utilization of the μDAS technology for fabrication of a complex 3 layered device with over 12 000 micromechanical valves and an array of 64 × 64 DNA spots on a glass substrate with high yield and high accuracy. We increased fabrication yield from 25% to about 85% with an average layer alignment error of just ∼4 μm. It also increased our protein expression yields from 80% to over 90%, allowing us to investigate more proteins per experiment. The μDAS has great potential to become a valuable tool for both advancing integrated microfluidics in academia and producing and applying microfluidic devices in the industry.

Smartphone-Enabled Detection Strategies for Portable PCR-Based Diagnostics

Incredible progress continues to be made toward development of low-cost nucleic acid-based diagnostic solutions suitable for deployment in resource-limited settings. Detection components play a vitally important role in these systems, but have proven challenging to adapt for operation in a portable format. Here we describe efforts aimed at leveraging the capabilities of consumer-class smartphones as a convenient platform to enable detection of nucleic acid products associated with DNA amplification via the polymerase chain reaction (PCR). First, we show how fluorescence-based detection can be incorporated into a portable convective thermocycling system controlled by a smartphone app. Raw images captured by the phone's camera are processed to yield real-time amplification data comparable to benchtop instruments. Next, we leverage smartphone imaging to achieve label-free detection of PCR products by monitoring changes in electrochemical reactivity of embedded metal electrodes as the target DNA concentration increases during replication. These advancements make it possible to construct rugged inexpensive nucleic acid detection components that can be readily embedded in a variety of portable bioanalysis instruments.

Modified primers for rapid and direct electrochemical analysis of coeliac disease associated HLA alleles

Direct detection of PCR product via hybridisation assay, would facilitate the development of rapid tools for genetic analysis. Here, a PCR primer designed to generate a PCR amplicon tagged with single stranded DNA tails at each end of the duplex, which can be used for direct hybridisation with a surface immobilised probe and an enzyme labelled reporter probe is presented. Four modified sequence specific primers (SSP) pairs were designed for the selective amplification of coeliac disease associated alleles (DQA1*05, DQB1*02, DQB1*03:02 alleles), and human growth hormone (positive control). Multiplex PCR products were electrochemically detected in less than 5 min at 37 °C via direct hybridisation to short probes immobilised on individual electrodes of a genosensor array, and subsequent hybridisation to an enzyme labelled reporter probe. The developed electrochemical genosensor array exploiting the modified primers for the direct detection of PCR products was applied to the genotyping of real patient samples.

Manually operatable on-chip bistable pneumatic microstructures for microfluidic manipulations

Bistable microvalves are of particular interest because of their distinct nature of requiring energy consumption only during the transition between the open and closed states. This characteristic can be highly advantageous in reducing the number of external inputs and the complexity of control circuitries since microfluidic devices as contemporary lab-on-a-chip platforms are transferring from research settings to low-resource environments with high integrability and a small form factor. In this paper, we first present manually operatable, on-chip bistable pneumatic microstructures (BPMs) for microfluidic manipulation. The structural design and operation of the BPM devices can be readily integrated into any pneumatically powered microfluidic network consisting of pneumatic and fluidic channels. It is mainly composed of a vacuum activation chamber (VAC) and a pressure release chamber (PRC), of which users have direct control through finger pressing to switch either to the bistable vacuum state (VS) or the atmospheric state (AS). We have integrated multiple BPM devices into a 4-to-1 microfluidic multiplexor to demonstrate on-chip digital flow switching from different sources. Furthermore, we have shown its clinical relevance in a point-of-care diagnostic chip that processes blood samples to identify the distinct blood types (A/B/O) on-chip.

A droplet microfluidic approach to single-stream nucleic acid isolation and mutation detection

In this work, a droplet microfluidic platform for genetic mutation detection from crude biosample is described. Single-stream integration of nucleic acid isolation and amplification is realized on a simple fluidic cartridge. Subsequent DNA melting curve is employed with signal normalizing algorithm to differentiate heterozygous K-ras codon 12 c.25G>A mutant from the wildtype. This technique showcases an alternative to modular bench-top approaches for genetic mutation screening, which is of interest to decentralized diagnostic platforms.

Recent advances in bioprinting and applications for biosensing

Future biosensing applications will require high performance, including real-time monitoring of physiological events, incorporation of biosensors into feedback-based devices, detection of toxins, and advanced diagnostics. Such functionality will necessitate biosensors with increased sensitivity, specificity, and throughput, as well as the ability to simultaneously detect multiple analytes. While these demands have yet to be fully realized, recent advances in biofabrication may allow sensors to achieve the high spatial sensitivity required, and bring us closer to achieving devices with these capabilities. To this end, we review recent advances in biofabrication techniques that may enable cutting-edge biosensors. In particular, we focus on bioprinting techniques (e.g., microcontact printing, inkjet printing, and laser direct-write) that may prove pivotal to biosensor fabrication and scaling. Recent biosensors have employed these fabrication techniques with success, and further development may enable higher performance, including multiplexing multiple analytes or cell types within a single biosensor. We also review recent advances in 3D bioprinting, and explore their potential to create biosensors with live cells encapsulated in 3D microenvironments. Such advances in biofabrication will expand biosensor utility and availability, with impact realized in many interdisciplinary fields, as well as in the clinic.

Microfluidics and cancer: are we there yet?

More than two decades ago, microfluidics began to show its impact in biological research. Since then, the field of microfluidics has evolving rapidly. Cancer is one of the leading causes of death worldwide. Microfluidics holds great promise in cancer diagnosis and also serves as an emerging tool for understanding cancer biology. Microfluidics can be valuable for cancer investigation due to its high sensitivity, high throughput, less material-consumption, low cost, and enhanced spatio-temporal control. The physical laws on microscale offer an advantage enabling the control of physics, biology, chemistry and physiology at cellular level. Furthermore, microfluidic based platforms are portable and can be easily designed for point-of-care diagnostics. Developing and applying the state of the art microfluidic technologies to address the unmet challenges in cancer can expand the horizons of not only fundamental biology but also the management of disease and patient care. Despite the various microfluidic technologies available in the field, few have been tested clinically, which can be attributed to the various challenges existing in bridging the gap between the emerging technology and real world applications. We present a review of role of microfluidics in cancer research, including the history, recent advances and future directions to explore where the field stand currently in addressing complex clinical challenges and future of it. This review identifies four critical areas in cancer research, in which microfluidics can change the current paradigm. These include cancer cell isolation, molecular diagnostics, tumor biology and high-throughput screening for therapeutics. In addition, some of our lab's current research is presented in the corresponding sections.

DNA mutation detection and analysis using miniaturized microfluidic systems

Identification of genetic sequence variations occurring on a population-wide scale is key to unraveling the complex interactions that are the underlying cause of many medical disorders and diseases. A critical need exists, however, for advanced technology to enable DNA mutation analysis to be performed with significantly higher throughput and at significantly lower cost than is currently attainable. Microfluidic systems offer an attractive platform to address these needs by combining the ability to perform rapid analysis with a simplified device format that can be inexpensively mass-produced. This paper will review recent progress toward developing these next-generation systems and discuss challenges associated with adapting these technologies for routine laboratory use.

Industrial lab-on-a-chip: design, applications and scale-up for drug discovery and delivery

Microfluidics is an emerging and promising interdisciplinary technology which offers powerful platforms for precise production of novel functional materials (e.g., emulsion droplets, microcapsules, and nanoparticles as drug delivery vehicles- and drug molecules) as well as high-throughput analyses (e.g., bioassays, detection, and diagnostics). In particular, multiphase microfluidics is a rapidly growing technology and has beneficial applications in various fields including biomedicals, chemicals, and foods. In this review, we first describe the fundamentals and latest developments in multiphase microfluidics for producing biocompatible materials that are precisely controlled in size, shape, internal morphology and composition. We next describe some microfluidic applications that synthesize drug molecules, handle biological substances and biological units, and imitate biological organs. We also highlight and discuss design, applications and scale up of droplet- and flow-based microfluidic devices used for drug discovery and delivery.

Topography-assisted electromagnetic platform for blood-to-PCR in a droplet

This paper presents an electromagnetically actuated platform for automated sample preparation and detection of nucleic acids. The proposed platform integrates nucleic acid extraction using silica-coated magnetic particles with real-time polymerase chain reaction (PCR) on a single cartridge. Extraction of genomic material was automated by manipulating magnetic particles in droplets using a series of planar coil electromagnets assisted by topographical features, enabling efficient fluidic processing over a variety of buffers and reagents. The functionality of the platform was demonstrated by performing nucleic acid extraction from whole blood, followed by real-time PCR detection of KRAS oncogene. Automated sample processing from whole blood to PCR-ready droplet was performed in 15 min. We took a modular approach of decoupling the modules of magnetic manipulation and optical detection from the device itself, enabling a low-complexity cartridge that operates in tandem with simple external instruments.

Nasal cytokine responses to natural colds in asthmatic children

Background

The mechanisms by which viruses induce asthma exacerbations are not well understood.

Objective

We characterized fluctuations in nasal aspirate cytokines during naturally occurring respiratory viral infections in children with asthma.

Methods

Sixteen children underwent home collections of nasal aspirates when they were without cold symptoms and again during self‐reported respiratory illnesses. The presence of viral infection was ascertained by multiplex PCR. Cytokines were measured using multiplex immune assay. mRNA expression for selected markers of viral infection was measured using RT‐PCR. A cumulative respiratory symptom score was calculated for each day of measurement. Generalized estimated equations were used to evaluate associations between viral infection and marker elevation, and between marker elevation and symptom score.

Results

The 16 patients completed a total of 37 weeks of assessment (15 ‘well’ weeks; 22 self‐assessed ‘sick’ weeks). Viral infections were detected in 3 of the ‘well’ weeks and 17 of the ‘sick’ weeks (10 rhinovirus, three coronavirus, two influenza A, two influenza B, two respiratory syncytial virus, one parainfluenza). Compared to virus‐negative well weeks, nasal aspirate IFN‐γ, CXCL8/IL‐8, CXCL10/IP‐10, CCL5/RANTES, CCL11/eotaxin‐1, CCL2/MCP‐1, CCL4/MIP‐1β, CCL7/MCP‐3, and CCL20/MIP3α protein levels increased during virus‐positive sick weeks. Only a subset of cytokines (IFN‐γ, CXCL8, CCL2, CCL4, CCL5, and CCL20) correlated with self‐reported respiratory tract symptoms. While many aspirates were dilute and showed no mRNA signal, viral infection significantly increased the number of samples that were positive for IFN‐λ1, IFN‐λ2/3, TLR3, RIG‐I, and IRF7 mRNA.

Conclusions and clinical relevance

We conclude that in children with asthma, naturally occurring viral infections apparently induce a robust innate immune response including expression of specific chemokines, IFNs, and IFN‐responsive genes.

Influence of material transition and interfacial area changes on flow and concentration in electro-osmotic flows

This paper presents a numerical study to investigate the effect of geometrical and material transition on the flow and progression of a sample plug in electrokinetic flows. Three cases were investigated: (a) effect of sudden cross-sectional area change (geometrical transition or mismatch) at the interface, (b) effect of only material transition (i.e. varying ζ-potential), and (c) effect of combined material transition and cross-sectional area change at the interface. The geometric transition was quantified based on the ratio of reduced flow area A2 at the mismatch plane to the original cross-sectional area A1. Multiple simulations were performed for varying degrees of area reduction i.e. 0-75% reduction in the available flow area, and the effect of dispersion on the sample plug was quantified by standard metrics. Simulations showed that a 13% combined material and geometrical transition can be tolerated without significant loss of sample resolution. A 6.54% reduction in the flow rates was found between 0% and 75% combined material and geometrical transition.

Microfluidic Paper-Based Analytical Devices (μPADs) and Micro Total Analysis Systems (μTAS): Development, Applications and Future Trends

Microfluidic paper-based analytical devices and micro total analysis systems are relatively new group of analytical tools, capable of analyzing complex biochemical samples containing macromolecules, proteins, nucleic acids, toxins, cells or pathogens. Within one analytical run, fluidic manipulations like transportation, sorting, mixing or separation are available. Recently, microfluidic devices are a subject of extensive research, mostly for fast and non-expensive biochemical analysis but also for screening of medical samples and forensic diagnostics. They are used for neurotransmitter detection, cancer diagnosis and treatment, cell and tissue culture growth and amplification, drug discovery and determination, detection and identification of microorganisms. This review summarizes development history, basic fabrication methods, applications and also future development trends for production of such devices.

Temperature-driven self-actuated microchamber sealing system for highly integrated microfluidic devices

We present here a novel microchamber sealing valve that is self-actuated by a pressure change during the temperature change in the thermal activation of reactions. Actuation of our valve requires only the use of the same heating device as employed for the reactions. A thermoplastic UV-curable polymer is used as a device material; the polymer allows realization of the temperature-driven valve actuation as well as the fabrication of multi-layered devices. The self-actuated valve achieves effective sealing of the microchamber for the polymerase chain reaction (PCR) even at 90 °C, which is essential for developing highly parallel PCR array devices without the need for complicated peripherals to control the valve operation.

A pillar-based microfilter for isolation of white blood cells on elastomeric substrate

Our goal is to design, fabricate, and characterize a pillar-based microfluidic device for size-based separation of human blood cells on an elastomeric substrate with application in the low-cost rapid prototyping of lab-chip devices. The single inlet single outlet device is using parallel U-shape arrays of pillars with cutoff size of 5.5 μm for trapping white blood cells (WBCs) in a pillar chamber with internal dead-volume of less than 1.0 μl. The microstructures are designed to limit the elastomeric deformation against fluid pressures. Numerical analysis showed that at maximum pressure loss of 15 kPa which is lower than the device conformal bonding strength, the pillar elastomeric deformation is less than 5% for flow rates of up to 1.0 ml min(-1). Molding technique was employed for device prototyping using polyurethane methacrylate (PUMA) resin and polydimethylsiloxane (PDMS) mold. Characterization of the dual-layer device with beads and blood samples is performed. Tests with blood injection showed that ∼18%-25% of WBCs are trapped and ∼84%-89% of red blood cells (RBCs) are passed at flow rates of 15-50 μl min(-1) with a slight decrease of WBCs trap and improve of the RBCs pass at higher flow rates. Similar results were obtained by separation of mixed microspheres of different size injected at flow rates of up to 400 μl min(-1). Tests with blood samples stained by fluorescent gel demonstrated that the WBCs are accumulated in the arrays of pillars that later end up to blockage of the device. Filtration results of using elastomeric substrate present a good consistency with the trend of separation efficiencies of the similar silicon-based filters.

Low cost integration of 3D-electrode structures into microfluidic devices by replica molding

We demonstrate a new replica molding method for integrating 3D-composite electrodes into microfluidic devices made from polydimethylsiloxane (PDMS) at low cost. Our process does not require work in a cleanroom, expensive materials, or expensive equipment once a micro mold has been fabricated using standard multilayer SU-8 photolithography. Different device geometries have been fabricated to demonstrate the capabilities and limitations of the method. The electrical properties of the composite electrode material are characterized. Furthermore, a device for concentrating particles via AC-dielectrophoresis is presented as an example for a potential application of the fabrication process.

Pressure driven digital logic in PDMS based microfluidic devices fabricated by multilayer soft lithography

Advances in microfluidics now allow an unprecedented level of parallelization and integration of biochemical reactions. However, one challenge still faced by the field has been the complexity and cost of the control hardware: one external pressure signal has been required for each independently actuated set of valves on chip. Using a simple post-modification to the multilayer soft lithography fabrication process, we present a new implementation of digital fluidic logic fully analogous to electronic logic with significant performance advances over the previous implementations. We demonstrate a novel normally closed static gain valve capable of modulating pressure signals in a fashion analogous to an electronic transistor. We utilize these valves to build complex fluidic logic circuits capable of arbitrary control of flows by processing binary input signals (pressure (1) and atmosphere (0)). We demonstrate logic gates and devices including NOT, NAND and NOR gates, bi-stable flip-flops, gated flip-flops (latches), oscillators, self-driven peristaltic pumps, delay flip-flops, and a 12-bit shift register built using static gain valves. This fluidic logic shows cascade-ability, feedback, programmability, bi-stability, and autonomous control capability. This implementation of fluidic logic yields significantly smaller devices, higher clock rates, simple designs, easy fabrication, and integration into MSL microfluidics.

Genomic DNA extraction from cells by electroporation on an integrated microfluidic platform

The vast majority of genetic analysis of cells involves chemical lysis for release of DNA molecules. However, chemical reagents required in the lysis interfere with downstream molecular biology and often require removal after the step. Electrical lysis based on irreversible electroporation is a promising technique to prepare samples for genetic analysis due to its purely physical nature, fast speed, and simple operation. However, there has been no experimental confirmation on whether electrical lysis extracts genomic DNA from cells in a reproducible and efficient fashion in comparison to chemical lysis, especially for eukaryotic cells that have most of the DNA enclosed in the nucleus. In this work, we construct an integrated microfluidic chip that physically traps a low number of cells, lyses the cells using electrical pulses rapidly, then purifies and concentrates genomic DNA. We demonstrate that electrical lysis offers high efficiency for DNA extraction from both eukaryotic cells (up to ∼36% for Chinese hamster ovary cells) and bacterial cells (up to ∼45% for Salmonella typhimurium) that is comparable to the widely used chemical lysis. The DNA extraction efficiency has dependence on both the electric parameters and relative amount of beads used for DNA adsorption. We envision that electroporation-based DNA extraction will find use in ultrasensitive assays that benefit from minimal dilution and simple procedures.

Lab-on-a-chip pathogen sensors for food safety

There have been a number of cases of foodborne illness among humans that are caused by pathogens such as Escherichia coli O157:H7, Salmonella typhimurium, etc. The current practices to detect such pathogenic agents are cell culturing, immunoassays, or polymerase chain reactions (PCRs). These methods are essentially laboratory-based methods that are not at all real-time and thus unavailable for early-monitoring of such pathogens. They are also very difficult to implement in the field. Lab-on-a-chip biosensors, however, have a strong potential to be used in the field since they can be miniaturized and automated; they are also potentially fast and very sensitive. These lab-on-a-chip biosensors can detect pathogens in farms, packaging/processing facilities, delivery/distribution systems, and at the consumer level. There are still several issues to be resolved before applying these lab-on-a-chip sensors to field applications, including the pre-treatment of a sample, proper storage of reagents, full integration into a battery-powered system, and demonstration of very high sensitivity, which are addressed in this review article. Several different types of lab-on-a-chip biosensors, including immunoassay- and PCR-based, have been developed and tested for detecting foodborne pathogens. Their assay performance, including detection limit and assay time, are also summarized. Finally, the use of optical fibers or optical waveguide is discussed as a means to improve the portability and sensitivity of lab-on-a-chip pathogen sensors.

Asynchronous magnetic bead rotation microviscometer for rapid, sensitive, and label-free studies of bacterial growth and drug sensitivity

The long turnaround time in antimicrobial susceptibility testing (AST) endangers patients and encourages the administration of wide spectrum antibiotics, thus resulting in alarming increases of multidrug resistant pathogens. A method for faster detection of bacterial proliferation presents one avenue toward addressing this global concern. We report on a label-free asynchronous magnetic bead rotation (AMBR) based viscometry method that rapidly detects bacterial growth and determines drug sensitivity by measuring changes in the suspension's viscosity. With this platform, we observed the growth of a uropathogenic Escherichia coli isolate, with an initial concentration of 50 cells per drop, within 20 min; in addition, we determined the gentamicin minimum inhibitory concentration (MIC) of the E. coli isolate within 100 min. We thus demonstrated a label-free, microviscometer platform that can measure bacterial growth and drug susceptibility more rapidly, with lower initial bacterial counts than existing commercial systems, and potentially with any microbial strains.

Divergent dispersion behavior of ssDNA fragments during microchip electrophoresis in pDMA and LPA entangled polymer networks

Resolution of DNA fragments separated by electrophoresis in polymer solutions ("matrices") is determined by both the spacing between peaks and the width of the peaks. Prior research on the development of high-performance separation matrices has been focused primarily on optimizing DNA mobility and matrix selectivity, and gave less attention to peak broadening. Quantitative data are rare for peak broadening in systems in which high electric field strengths are used (>150 V/cm), which is surprising since capillary and microchip-based systems commonly run at these field strengths. Here, we report results for a study of band broadening behavior for ssDNA fragments on a glass microfluidic chip, for electric field strengths up to 320 V/cm. We compare dispersion coefficients obtained in a poly(N,N-dimethylacrylamide) (pDMA) separation matrix that was developed for chip-based DNA sequencing with a commercially available linear polyacrylamide (LPA) matrix commonly used in capillaries. Much larger DNA dispersion coefficients were measured in the LPA matrix as compared to the pDMA matrix, and the dependence of dispersion coefficient on DNA size and electric field strength were found to differ quite starkly in the two matrices. These observations lead us to propose that DNA migration mechanisms differ substantially in our custom pDMA matrix compared to the commercially available LPA matrix. We discuss the implications of these results in terms of developing optimal matrices for specific separation (microchip or capillary) platforms.

Microfluidic chemical analysis systems

The field of microfluidics has exploded in the past decade, particularly in the area of chemical and biochemical analysis systems. Borrowing technology from the solid-state electronics industry and the production of microprocessor chips, researchers working with glass, silicon, and polymer substrates have fabricated macroscale laboratory components in miniaturized formats. These devices pump nanoliter volumes of liquid through micrometer-scale channels and perform complex chemical reactions and separations. The detection of reaction products is typically done fluorescently with off-chip optical components, and the analysis time from start to finish can be significantly shorter than that of conventional techniques. In this review we describe these microfluidic analysis systems, from the original continuous flow systems relying on electroosmotic pumping for liquid motion to the large diversity of microarray chips currently in use to the newer droplet-based devices and segmented flow systems. Although not currently widespread, microfluidic systems have the potential to become ubiquitous.

A miniature gas analyzer made by integrating a chemoresistor with a microchannel

A microfluidic channel is integrated with a tin oxide-based generic gas sensor on a PMMA (polymethyl methacrylate) substrate to fabricate a miniature gas analyzer. The analyte gas diffuses along the air-filled channel to affect the sensor installed in a microcavity positioned at the end of the channel. Analyte diffusion rates, experimentally estimated based on the temporal responses received from the sensor, are connected to the analyte's interactions with the channel walls as well as its diffusivity in air. The analyte-related information is extracted from the recorded responses and used for analyte recognition. A single PMMA channel of 80 μm × 3 mm × 50 mm dimensions facilitates the correct classification of single component contaminants each introduced in a wide concentration range in air. The device is also shown to identify 15 ppm of 2-butanol in air contaminated with 1500 ppm of 1-butanol. The gas analyzer fabricated based on this concept is durable, inexpensive, handheld and suitable for a variety of applications.

Design considerations for electrostatic microvalves with applications in poly(dimethylsiloxane)-based microfluidics

Microvalves are critical in the operation of integrated microfluidic chips for a wide range of applications. In this paper, we present an analytical model to guide the design of electrostatic microvalves that can be integrated into microfluidic chips using standard fabrication processes and can reliably operate at low actuation potentials (<250 V). Based on the analytical model, we identify design guidelines and operational considerations for elastomeric electrostatic microvalves and formulate strategies to minimize their actuation potentials, while maintaining the feasibility of fabrication and integration. We specifically explore the application of the model to design microfluidic microvalves fabricated in poly(dimethylsiloxane), using only soft-lithographic techniques. We discuss the electrostatic actuation in terms of several microscale phenomena, including squeeze-film damping and adhesion-driven microvalve collapse. The actuation potentials predicted by the model are in good agreement with experimental data obtained with a microfabricated array of electrostatic microvalves actuated in air and oil. The model can also be extended to the design of peristaltic pumps for microfluidics and to the prediction of actuation potentials of microvalves in viscous liquid environments. Additionally, due to the compact ancillaries required to generate low potentials, these electrostatic microvalves can potentially be used in portable microfluidic chips.

Silica-on-silicon waveguide integrated polydimethylsiloxane lab-on-a-chip for quantum dot fluorescence bio-detection

Integration of microfluidics and optical components is an essential requirement for the realization of optical detection in lab-on-a-chip (LOC). In this work, a novel hybrid integration of silica-on-silicon (SOS) waveguide and polydymethylsiloxane (PDMS) microfluidics for realizing optical detection based biochip is demonstrated. SOS is a commonly used platform for integrated photonic circuits due to its lower absorption coefficient of silica and the availability of advanced microfabrication technologies for fabricating complicated optical components. However, the fabrication of complex microfluidics circuits on SOS is an expensive process. On the other hand, any complex 3D and high-aspect-ratio microstructures for the microfluidic applications can be easily patterned on PDMS using soft lithography. By exploring the advantages of these two materials, the proposed hybrid integration method greatly simplifies the fabrication of optical LOC. Two simple technologies--namely, diamond machining and soft lithography--were employed for the integration of an optical microfluidic system. Use of PDMS for the fabrication of any complex 3D microfluidics structures, together with the integration of low loss silica-on-silicon photonic waveguides with a straight microfluidic channel, opens up new possibilities to produce low-cost biochips. The performance of SOS-PDMS-integrated hybrid biochip is demonstrated with the detection of laser induced fluorescence of quantum dots. As quantum dots have immense application potential for biodetection, they are used for the demonstration of biodetection.

Integrated continuous flow polymerase chain reaction and micro-capillary electrophoresis system with bioaffinity preconcentration

An integrated and modular DNA analysis system is reported that consists of two modules: (i) A continuous flow polymerase chain reaction (CFPCR) module fabricated in a high T(g) (150°C) polycarbonate substrate in which selected gene fragments were amplified using biotin and fluorescently labeled primers accomplished by continuously shuttling small packets of PCR reagents and template through isothermal zones as opposed to heating and cooling large thermal masses typically performed in batch-type thermal reactors. (ii) μCE (micro-capillary electrophoresis) module fabricated in poly(methylmethacrylate) (PMMA), which utilized a bioaffinity selection and purification bed (2.9  μL) to preconcentrate and purify the PCR products generated from the CFPCR module prior to electrophoretic sorting. Biotin-labeled CFPCR products were hydrostatically pumped through the streptavidin-modified bed, where they were extracted onto the surface of micropillars. The affinity bed was also fabricated in PMMA and was populated with an array of microposts (50  μm width; 100  μm height) yielding a total surface area of ∼117  mm(2). This solid-phase extraction (SPE) process demonstrated high selectivity for biotinylated amplicons and utilized the strong streptavidin/biotin interaction (K(d) = 10(-15)  M) to generate high recoveries. The SPE selected CFPCR products were thermally denatured and single-stranded DNA released for injection into a 7-cm-long μCE channel for size-based separations and fluorescence detection. The utility of the system was demonstrated using Alu DNA typing for gender and ethnicity determinations as a model. Compared with the traditional cross-T injection procedure typically used for μCE, the affinity pre-concentration and injection procedure generated signal enhancements of 17- to 40-fold, critical for CFPCR thermal cyclers due to Taylor dispersion associated with their operation.

Histone modification analysis by chromatin immunoprecipitation from a low number of cells on a microfluidic platform

Histone modifications are important epigenetic mechanisms involved in eukaryotic gene regulation. Chromatin immunoprecipitation (ChIP) assay serves as the primary technique to characterize the genomic locations associated with histone modifications. However, traditional tube-based ChIP assays rely on large numbers of cells as well as laborious and time-consuming procedures. Here we demonstrate a novel microfluidics-based native ChIP assay which dramatically reduces the required cell number and the assay time by conducting cell collection, lysis, chromatin fragmentation, immunoprecipitation, and washing on a microchip. Coupled with real-time PCR, our assay permits the analysis of histone modifications from as few as ~50 cells within 8.5 h. We envision that our method will provide a new approach for the analysis of epigenetic regulations and protein-DNA interactions in general, based on scarce cell samples such as those derived from animals and patients.

A self-contained polymeric cartridge for automated biological sample preparation

Sample preparation is one of the most crucial processes for nucleic acids based disease diagnosis. Several steps are required for nucleic acids extraction, impurity washes, and DNA/RNA elution. Careful sample preparation is vital to the obtaining of reliable diagnosis, especially with low copies of pathogens and cells. This paper describes a low-cost, disposable lab cartridge for automatic sample preparation, which is capable of handling flexible sample volumes of 10 μl to 1 ml. This plastic cartridge contains all the necessary reagents for pathogen and cell lysis, DNA/RNA extraction, impurity washes, DNA/RNA elution and waste processing in a completely sealed cartridge. The entire sample preparation processes are automatically conducted within the cartridge on a desktop unit using a pneumatic fluid manipulation approach. Reagents transportation is achieved with a combination of push and pull forces (with compressed air and vacuum, respectively), which are connected to the pneumatic inlets at the bottom of the cartridge. These pneumatic forces are regulated by pinch valve manifold and two pneumatic syringe pumps within the desktop unit. The performance of this pneumatic reagent delivery method was examined. We have demonstrated the capability of the on-cartridge RNA extraction and cancer-specific gene amplification from 10 copies of MCF-7 breast cancer cells. The on-cartridge DNA recovery efficiency was 54-63%, which was comparable to or better than the conventional manual approach using silica spin column. The lab cartridge would be suitable for integration with lab-chip real-time polymerase chain reaction devices in providing a portable system for decentralized disease diagnosis.

Asynchronous magnetic bead rotation (AMBR) biosensor in microfluidic droplets for rapid bacterial growth and susceptibility measurements

Inappropriate antibiotic use is a major factor contributing to the emergence and spread of antimicrobial resistance. The long turnaround time (over 24 hours) required for clinical antimicrobial susceptibility testing (AST) often results in patients being prescribed empiric therapies, which may be inadequate, inappropriate, or overly broad-spectrum. A reduction in the AST time may enable more appropriate therapies to be prescribed earlier. Here we report on a new diagnostic asynchronous magnetic bead rotation (AMBR) biosensor droplet microfluidic platform that enables single cell and small cell population growth measurements for applications aimed at rapid AST. We demonstrate the ability to rapidly measure bacterial growth, susceptibility, and the minimum inhibitory concentration (MIC) of a small uropathogenic Escherichia coli population that was confined in microfluidic droplets and exposed to concentrations above and below the MIC of gentamicin. Growth was observed below the MIC, and no growth was observed above the MIC. A 52% change in the sensor signal (i.e. rotational period) was observed within 15 minutes, thus allowing AST measurements to be performed potentially within minutes.

Advances in microfluidic PCR for point-of-care infectious disease diagnostics

Global burdens from existing or emerging infectious diseases emphasize the need for point-of-care (POC) diagnostics to enhance timely recognition and intervention. Molecular approaches based on PCR methods have made significant inroads by improving detection time and accuracy but are still largely hampered by resource-intensive processing in centralized laboratories, thereby precluding their routine bedside- or field-use. Microfluidic technologies have enabled miniaturization of PCR processes onto a chip device with potential benefits including speed, cost, portability, throughput, and automation. In this review, we provide an overview of recent advances in microfluidic PCR technologies and discuss practical issues and perspectives related to implementing them into infectious disease diagnostics.

PCR-free digital minisatellite tandem repeat genotyping

We demonstrated a proof-of-concept for novel minisatellite tandem repeat typing, called PCR-free digital VNTR (variable number tandem repeat) typing, which is composed of three steps: a ligation reaction instead of PCR thermal cycling, magnetic bead-based solid-phase capture for purification, and an elongated sample stacking microcapillary electrophoresis (μCE) for sensitive digital coding of repeat number. We designed a 16-bp fluorescently labeled ligation probe which is complementary to a repeat unit of a biotinylated synthetic template mimicking the human D1S80 VNTR locus and is randomly hybridized with the minisatellite tandem repeats. A quick isothermal ligation reaction was followed to link the adjacent ligation probes on the DNA templates, and then the ligated products were purified by streptavidin-coated magnetic beads. After a denaturing step, a large amount of ligated products whose size difference was equivalent to the repeat unit were released and recovered. Through the elongated sample stacking μCE separation on a microdevice, the fluorescence signal of the ligated products was generated in the electropherogram and the peak number was directly counted which was exactly matched with the repeat number of VNTR locus. We could successfully identify the minisatellite tandem repeat number with only 5 fmol of DNA template in 30 min.

Flexible casting of modular self-aligning microfluidic assembly blocks

The recent shift among developers of microfluidic technologies toward modularized "plug and play" construction reflects the steadily increasing realization that, for many would-be users of microfluidic tools, traditional clean-room microfabrication is prohibitively complex and/or expensive. In this work, we present an advanced modular microfluidic construction scheme in which pre-fabricated microfluidic assembly blocks (MABs) can be quickly fashioned, without expertise or specialized facilities, into sophisticated microfluidic devices for a wide range of applications. Specifically, we describe three major advances to the MAB concept: (1) rapid production and extraction of MABs using flexible casting trays, (2) use of pre-coated substrates for simultaneous assembly and bonding, and (3) modification of block design to include automatic alignment and sealing structures. Finally, several exemplary applications of these MABs are demonstrated in chemical gradient synthesis, droplet generation, and total internal reflection fluorescence microscopy.