Showing papers on "Biochip published in 2008"

Polymer microfabrication technologies for microfluidic systems

Abstract: Polymers have assumed the leading role as substrate materials for microfluidic devices in recent years. They offer a broad range of material parameters as well as material and surface chemical properties which enable microscopic design features that cannot be realised by any other class of materials. A similar range of fabrication technologies exist to generate microfluidic devices from these materials. This review will introduce the currently relevant microfabrication technologies such as replication methods like hot embossing, injection molding, microthermoforming and casting as well as photodefining methods like lithography and laser ablation for microfluidic systems and discuss academic and industrial considerations for their use. A section on back-end processing completes the overview.

Chemical Strategies for Generating Protein Biochips

Abstract: Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.

Advances in Giant Magnetoresistance Biosensors With Magnetic Nanoparticle Tags: Review and Outlook

Abstract: We present a review of giant magnetoresistance (GMR) spin valve sensors designed for detection of magnetic nanoparticles as biomolecular labels (nanotags) in magneto-nano biodetection technology. We discuss the intricacy of magneto-nano biosensor design and show that as few as approximately 14 monodisperse 16-nm superparamagnetic nanoparticles can be detected by submicron spin valve sensors at room temperature without resorting to lock-in (narrow band) detection. GMR biosensors and biochips have been successfully applied to the detection of biological events in the form of both protein and DNA assays with great speed, sensitivity, selectivity, and economy. The limit of molecular detection is well below 10 pM in concentration, and the protein or DNA assay time can be under two hours. The technology is highly scalable to deep multiplex detection of biomarkers in a complex disease, and amenable to integration of microfluidics and CMOS electronics for portable applications. On-chip CMOS circuitry makes a sensor density of 0.1-1 million sensors per square centimeter feasible and affordable. The theoretical and experimental results thus far suggest that magneto-nano biochip-based GMR sensor arrays and nanotags hold great promise in biomedicine, particularly for point-of-care molecular diagnostics of cancer, infectious diseases, radiation injury, cardiac diseases, and other diseases.

High-level synthesis of digital microfluidic biochips

Abstract: Microfluidic biochips offer a promising platform for massively parallel DNA analysis, automated drug discovery, and real-time biomolecular recognition. Current techniques for full-custom design of droplet-based “digital” biochips do not scale well for concurrent assays and for next-generation system-on-chip (SOC) designs that are expected to include microfluidic components. We propose a system design methodology that attempts to apply classical high-level synthesis techniques to the design of digital microfluidic biochips. We focus here on the problem of scheduling bioassay functions under resource constraints. We first develop an optimal scheduling strategy based on integer linear programming. However, because the scheduling problem is NP-complete, we also develop two heuristic techniques that scale well for large problem instances. A clinical diagnostic procedure, namely multiplexed in-vitro diagnostics on human physiological fluids, is first used to illustrate and evaluate the proposed method. Next, the synthesis approach is applied to a protein assay, which serves as a more complex bioassay application. The proposed synthesis approach is expected to reduce human effort and design cycle time, and it will facilitate the integration of microfluidic components with microelectronic components in next-generation SOCs.

Broadcast electrode-addressing for pin-constrained multi-functional digital microfluidic biochips

Abstract: Recent advances in digital microfluidics have enabled lab-on-a-chip devices for DNA sequencing, immunoassays, clinical chemistry, and protein crystallization. Basic operations such as droplet dispensing, mixing, dilution, localized heating, and incubation can be carried out using a two-dimensional array of electrodes and nanoliter volumes of liquid. The number of independent input pins used to control the electrodes in such microfluidic "biochips" is an important cost-driver, especially for disposable PCB devices that are being developed for clinical and point-of-care diagnostics. However, most prior work on biochip design-automation has assumed independent control of the electrodes using a large number of input pins. Another limitation of prior work is that the mapping of control pins to electrodes is only applicable for a specific bioassay. We present a broadcast-addressing-based design technique for pin-constrained multi-functional biochips. The proposed method provides high throughput for bioassays and it reduces the number of control pins by identifying and connecting control pins with "compatible" actuation sequences. The proposed method is evaluated using a multifunctional chip designed to execute a set of multiplexed bioassays, the polymerase chain reaction, and a protein dilution assay.

Sample concentration and impedance detection on a microfluidic polymer chip.

Abstract: We present an on-chip microfluidic sample concentrator and detection triggering system for microparticles based on a combination of insulator-based dielectrophoresis (iDEP) and electrical impedance measurement. This platform operates by first using iDEP to selectively concentrate microparticles of interest based on their electrical and physiological characteristics in a primary fluidic channel; the concentrated microparticles are then directed into a side channel configured for particle detection using electrical impedance measurements with embedded electrodes. This is the first study showing iDEP concentration with subsequent sample diversion down an analysis channel and is the first to demonstrate iDEP in the presence of pressure driven flow. Experimental results demonstrating the capabilities of this platform were obtained using polystyrene microspheres and Bacillus subtilis spores. The feasibility of selective iDEP trapping and impedance detection of these particles was demonstrated. The system is intended for use as a front-end unit that can be easily paired with multiple biodetection/bioidentification systems. This platform is envisioned to act as a decision-making component to determine if confirmatory downstream identification assays are required. Without a front end component that triggers downstream analysis only when necessary, bio-identification systems (based on current analytical technologies such as PCR and immunoassays) may incur prohibitively high costs to operate due to continuous consumption of expensive reagents.

A 200-antibody microarray biochip for environmental monitoring: searching for universal microbial biomarkers through immunoprofiling.

Abstract: Environmental biomonitoring approaches require the measurement of either unequivocal biomarkers or specific biological profiles. Antibody microarrays constitute new tools for fast and reliable analysis of up to hundreds of biomarkers simultaneously. Herein we report 150 new polyclonal antibodies against microbial strains and environmental extracts, as well as the construction and validation of an antibody microarray (EMCHIP200, for “Environmental Monitoring Chip”) containing 200 different antibodies. Each antibody was tested against its antigen for its specificity and cross-reactivity by a sandwich microarray immunoassay. The limit of detection was 0.2 ng mL−1 for some proteins and 104−105 cells mL−1 for bacterial cells and spores. Partial biochemical characterization allowed identification of polymeric compounds (proteins and polysaccharides) as some of the targets recognized by the antibodies. We have successfully used the EMCHIP200 for the detection of biological polymers in samples from extreme enviro...

A progressive-ILP based routing algorithm for cross-referencing biochips

Abstract: Due to recent advances in microfluidics technology, digital microfluidic biochips and their associated CAD problems have gained much attention, most of which has been devoted to direct-addressing biochips. In this paper, we solve the droplet routing problem under the more scalable cross-referencing biochip paradigm, which uses row/column addressing scheme to activate electrodes. We propose the first droplet routing algorithm that directly solves the problem of routing in cross-referencing biochips. The main challenge of this type of biochips is the electrode interference which prevents simultaneous movement of multiple droplets. We first present a basic integer linear programming (ILP) formulation to optimally solve the droplet routing problem. Due to its complexity, we also propose a progressive ILP scheme to determine the locations of droplets at each time step. Experimental results demonstrate the efficiency and effectiveness of our progressive ILP scheme on a set of practical bio assays.

Why 3-D? Gel-based microarrays in proteomics

Abstract: Gel-based microarrays (biochips) consisting of nanoliter and sub-nanoliter gel drops on hydrophobic substrate are a versatile technology platform for immobilization of proteins and other biopolymers. Biochips provide a highly hydrophilic environment, which stabilizes immobilized molecules and facilitates their interactions with analytes. The probes are immobilized simultaneously with gel polymerization, evenly distributed throughout individual elements, and are easily accessible because of large pores. Each element is an isolated nanotube. Applications of biochips in the studies of protein interactions with other proteins, nucleic acids, and glycans are described. In particular, biochips are compatible with MALDI-MS. Biochip-based assay of prostate-specific antigen became the first protein microarray approved for clinical use by a national regulatory agency. In this review, 3-D immobilization is compared with mainstream technologies based on surface immobilization.

Gold nanoparticles for one step DNA extraction and real-time PCR of pathogens in a single chamber.

Abstract: The optothermal properties of nanoparticles are of interest for biosensors and highly sensitive biochip applications In this respect, the longitudinal resonance of Au nanorods was used to transform near infrared energy into thermal energy in a microfluidic chip The resulting heat generated effectively caused pathogen lysis Consequently the DNA was extracted out of the cell body and transferred to a PCR system This resulted in the successful demonstration of a one step real-time PCR system for pathogen detection without removal or changing of reagents

Automated, accurate, and inexpensive solution-preparation on a digital microfluidic biochip

Abstract: Solution-preparation is a basic and repetitive step for many biological and chemical experiments in the laboratory. It uses stock solutions of sample, reagents, and diluents to derive various mixed solutions with the required concentration levels. Manual solution-preparation methods are time-consuming, imprecise, and they require large volumes of liquid. We propose an electrowetting-based ldquodigitalrdquo microfluidic biochip design for automated solution-preparation. An efficient solution-preparation algorithm is also presented to generate a preparation plan that lists the intermediate mixing steps needed to generate the target solutions with the required concentrations. It determines the type, concentration, and the number of dispensed droplets of stock solutions. The proposed automated solution-preparation algorithm and biochip platform are evaluated using a protein-crystallization application.

Antibodies and Immunoassays for Detection of Bacterial Pathogens

Abstract: Antibody, also known as immunoglobulin, is normally made in the body in defense of foreign antigen or invading pathogen. Highly specific biorecognition property of antibody with antigen has made antibody as one of the most indispensable molecules for broad application, not only in the diagnosis or detection but also in prevention or curing of diseases. Animals are routinely used for production of both polyclonal and monoclonal antibodies; however, recombinant and phage display technologies are being adopted to improve antibody specificity and to cut cost for antibody production. Available genome sequence of pathogens is also allowing researchers to find and select suitable target antigens for production of antibody with improved specificity. In recent years, however, demand for antibody is even greater as novel biosensor or nanotechnology-based methods continue to utilize antibody for analyte capture and interrogation. Conventional immunoassay methods such as lateral flow and enzyme-linked immunoassays, though lack sensitivity, are available commercially and are widely used. While biosensor-based methods such as time-resolved fluorescence immunoassay, chemiluminescence assay, electrochemical immunoassay, surface plasmon resonance sensor, fiber optic sensor, and microfluidic biochip have, in some cases, demonstrated improved sensitivity, they require further optimization with real-world samples. Furthermore, environmental stress and the growth media are known to affect the physiological state of microorganism and antigen expression, often rendering unsatisfactory signal response from immunoassays. Thus, one must understand the microorganisms’ response to these factors before designing an immunoassay to avoid false results. With the advent of microfluidics and nanotechnology, the adaptation of lab-on-chip concept in immunoassays will soon be a reality for near real-time detection of pathogens from food or clinical specimens.

Combining Self-Assembled Monolayers and Mass Spectrometry for Applications in Biochips

Abstract: Biochip arrays have enabled the massively parallel analysis of genomic DNA and hold great promise for application to the analysis of proteins, carbohydrates, and small molecules. Surface chemistry plays an intrinsic role in the preparation and analysis of biochips by providing functional groups for immobilization of ligands, providing an environment that maintains activity of the immobilized molecules, controlling nonspecific interactions of analytes with the surface, and enabling detection methods. This review describes recent advances in surface chemistry that enable quantitative assays of a broad range of biochemical activities. The discussion emphasizes the use of self-assembled monolayers of alkanethiolates on gold as a structurally well-defined and synthetically flexible platform for controlling the immobilization and activity of molecules in an array. The review also surveys recent methods of performing label-free assays, and emphasizes the use of matrix-assisted laser desorption/ionization mass spectrometry to directly observe molecules attached to the selfassembled monolayers.

Cell-based microfluidic biochip for the electrochemical real-time monitoring of glucose and oxygen

Abstract: We report the fabrication of a microfluidic biochip dedicated to realize a precise and real-time monitoring of the composition and modulation of the cell medium by comparing the rates of glucose and oxygen before and after contact with the cells. The device was composed of specific glucose and oxygen amperometric sensors integrated at the inlet and outlet microchannels of a poly(dimethylsiloxane) (PDMS) cell chamber. The microfluidic device was designed to be compatible with cell cultures and the performances of the integrated sensors in the dynamic conditions of liquid flow during calibration were reported. We show here the compatibility of the developed biochip with cell culture analysis in the case of hepatocytes (HepG2) and put in evidence the good performances of the integrated microsensors in terms of linearity of response and sensitivity of detection during calibration.

Design and optimization of a digital microfluidic biochip for protein crystallization

Abstract: Proteins crystallization is a commonly used technique for protein analysis and subsequent drug design. It predicts the three-dimensional arrangement of the constituent amino acids, which in turn indicates the specific biological function of a protein. Protein crystallization experiments are typically carried out manually on multi-well plates in the laboratory. These experiments are slow, expensive, and error-prone. We present the design of a multi-well plate microfluidic biochip for protein crystallization; this biochip can transfer protein samples, prepare candidate solutions, and carry out crystallization automatically. To reduce the manufacturing cost of such devices, we present an efficient algorithm to generate a pin-assignment plan for the proposed design. The resulting biochip enables control of a large number of on-chip electrodes using only a small number of pins. Based on the pin-constrained chip design, we present an efficient shuttle-passenger-like droplet manipulation method to achieve high-throughput and defect-tolerant well loading.

Integrated droplet routing and defect tolerance in the synthesis of digital microfluidic biochips

Abstract: Microfluidic biochips are revolutionizing high-throughput DNA sequencing, immunoassays, and clinical diagnostics. As high-throughput bioassays are mapped to digital microfluidic platforms, the need for design automation techniques is being increasingly felt. Moreover, as most applications of biochips are safety-critical in nature, defect tolerance is an essential system attribute. Several synthesis tools have recently been proposed for the automated design of biochips from the specifications of laboratory protocols. However, only a few of these tools address the problem of defect tolerance. In addition, most of these methods do not consider the problem of droplet routing in microfluidic arrays. These methods typically rely on postsynthesis droplet routing to implement biochemical protocols. Such an approach is not only time consuming, but also imposes an undue burden on the chip user. Postsynthesis droplet routing does not guarantee that feasible droplet pathways can be found for area-constrained biochip layouts; nonroutable fabricated biochips must be discarded. We present a synthesis tool that integrates defect tolerance and droplet routing in the design flow. Droplet routability, defined as the ease with which droplet pathways can be determined, is estimated and integrated in the synthesis procedure. Presynthesis and postsynthesis defect-tolerance methods are also presented. We use a large-scale protein assay as a case study to evaluate the proposed synthesis method.

A Polymer Microfluidic Chip With Interdigitated Electrodes Arrays for Simultaneous Dielectrophoretic Manipulation and Impedimetric Detection of Microparticles

Abstract: This paper presents the design, fabrication, and characterization of a polymer microfluidic biochip with integrated interdigitated electrodes arrays (IDAs) used to simultaneously separate, manipulate, and detect microparticles using dielectrophoresis (DEP) and electrochemical impedance spectroscopy (EIS) methods. The DEP response of silica microspheres has been characterized, and microspheres of different sizes (1.8 and 3.5 in diameter) have been DEP flow separated and individually trapped in different microchambers by IDAs in a single run. Simultaneously, the impedance change caused by microspheres captured on IDAs has been analyzed for quantification. High-throughput polymer microfabrication techniques such as micro injection molding were used in this work, so that the polymer microfluidic chip can be produced in a low-cost, disposable platform. This low-cost microfluidic chip provides a generic platform for developing multifunctional lab-on-a-chip devices that require the ability to handle and sense microparticles.

A Droplet-Manipulation Method for Achieving High-Throughput in Cross-Referencing-Based Digital Microfluidic Biochips

Abstract: Digital microfluidic biochips are revolutionizing high-throughput DNA, immunoassays, and clinical diagnostics. As high-throughput bioassays are mapped to digital microfluidic platforms, the need for design automation techniques for pin-constrained biochips is being increasingly felt. However, most prior work on biochips computer-aided design has assumed independent control of the underlying electrodes using a large number of (electrical) input pins. We propose a droplet-manipulation method based on a ldquocross-referencingrdquo addressing method that uses ldquorowrdquo and ldquocolumnsrdquo to access electrodes. By mapping the droplet-movement problem on a cross-referenced chip to the clique-partitioning problem from graph theory, the proposed method allows simultaneous movement of a large number of droplets on a microfluidic array. Concurrency is enhanced through the use of an efficient scheduling algorithm that determines the order in which groups of droplets are moved. The proposed design-automation method facilitates high-throughput applications on a pin-constrained biochip, and it is evaluated using random synthetic benchmarks and a set of multiplexed bioassays.

In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water.

Abstract: Pathogen detection tools with high reliability are needed for various applications, including food and water safety and clinical diagnostics. In this study, we designed and validated an in situ-synthesized biochip for detection of 12 microbial pathogens, including a suite of pathogens relevant to water safety. To enhance the reliability of presence/absence calls, probes were designed for multiple virulence and marker genes (VMGs) of each pathogen, and each VMG was targeted by an average of 17 probes. Hybridization of the biochip with amplicon mixtures demonstrated that 95% of the initially designed probes behaved as predicted in terms of positive/negative signals. The probes were further validated using DNA obtained from three different types of water samples and spiked with pathogen genomic DNA at decreasing relative abundance. Excellent specificity for making presence/absence calls was observed by using a cutoff of 0.5 for the positive fraction (i.e., the fraction of probes yielding a positive signal for a given VMG). A split multiplex PCR design for simultaneous amplification of the VMGs resulted in a detection limit of between 0.1 and 0.01% relative abundance, depending on the type of pathogen and the VMG. Thermodynamic analysis of the hybridization patterns obtained with DNA from the different water samples demonstrated that probes with a hybridization Gibbs free energy of approximately -19.3 kcal/mol provided the best trade-off between sensitivity and specificity. The developed biochip may be used to detect the described bacterial pathogens in water samples when parallel and specific detection is required.

On-line cell lysis and DNA extraction on a microfluidic biochip fabricated by microelectromechanical system technology.

Abstract: Integrating cell lysis and DNA purification process into a micrototal analytical system (microTAS) is one critical step for the analysis of nucleic acids. On-chip cell lysis based on a chemical method is realized by sufficient blend of blood sample and the lyzing reagent. In this paper two mixing models, T-type mixing model and sandwich-type mixing model, are proposed and simulation of those models is conducted. Result of simulation shows that the sandwich-type mixing model with coiled channel performs best and this model is further used to construct the microfluidic biochip for on-line cell lysis and DNA extraction. The result of simulation is further verified by experiments. It asserts that more than 80% mixing of blood sample and lyzing reagent which guarantees that completed cell lysis can be achieved near the inlet location when the cell/buffer velocity ratio is less than 1:5. After cell lysis, DNA extraction by means of a solid-phase method is implemented by using porous silicon matrix which is integrated in the biochip. During continuous flow process in the microchip, rapid cell lysis and PCR-amplifiable genomic DNA purification can be achieved within 20 min. The potential of this microfluidic biochip is illustrated by pretreating a whole blood sample, which shows the possibility of integration of sample preparation, PCR, and separation on a single device to work as portable point-of-care medical diagnostic system.

Methods for rapid multiplexed amplification of target nucleic acids

Abstract: A fast, multiplexed PCR system is described that can rapidly generate amplified nucleic acid products, for example, a full STR profile, from a target nucleic acid. Such systems include, for example, microfluidic biochips and a custom built thermal cycler, which are also described. The resulting STR profiles can satisfy forensic guidelines for signal strength, inter-loci peak height balance, heterozygous peak height ratio, incomplete non-template nucleotide addition, and stutter.

Electrically Programmable Surfaces for Configurable Patterning of Cells

Abstract: Microsystems technology provides the ability to precisely control micrometer-scale environments that surround cells in microfluidic devices, small-volume chambers, or biochips. Precise control over the chemical and cellular environment, including interactions with neighboring cells, in microdevices opens doors to new high-throughput and high-content experimental approaches and mechanistic insights into cell behaviors, such as relationships between cell shape and cell growth. Fundamental aspects of complex cell–cell interactions found in living organisms can also be re-created in microsystems for drug and toxicology screening. To create and accurately control the environmental and physiological conditions, surfaces capable of generating micrometer-scale patterns of cells in microsystems are crucial. These surfaces serve for controlling cellular growth factors, engineering tissues, and performing controlled cell-based assays, and could become key components for the development of bioelectronics and portable diagnostic devices useful in clinical settings. In this Communication, we present a newmaterial approach that can be programmed to generate cell patterns on a surface, with the smallest dimension down to the size of single cells. The locations and shapes of the generated cell patterns on a surface can be controlled externally by selectively switching on microelectrode arrays in an engineered microfluidic device. In addition, the method allows one to configure different cell population densities and cell morphologies into generated cell patterns on the same surface by adjusting applied voltage biases on the microelectrodes. Several techniques have demonstrated an ability to immobilize cells on designated regions on a surface. For example, cell patterns have been generated by using microcontact

"Smart" biopolymer for a reversible stimuli-responsive platform in cell-based biochips.

Abstract: The rapid response of a smart material surface to external stimuli is critical for application to cell-based biochips. The sharp and controllable phase transition of elastin-like polypeptide (ELP) ...

Simultaneous analysis of circulating human cytokines using a high-sensitivity cytokine biochip array.

Abstract: Biochip array technology allows the simultaneous measurement of multiple analytes per sample using a single analytical device. This study shows its applicability to the simultaneous measurement of 12 circulating human cytokines with high-sensitivity detection. This application increases their real-time detectability, maintaining a broad concentration range and without compromising the precision. This methodology represents a very applicable tool in cytokine research when simultaneous determination of minute concentrations can be of interest.

Towards fault-tolerant digital microfluidic lab-on-chip: Defects, fault modeling, testing, and reconfiguration

Abstract: Dependability is an important attribute for microfluidic lab-on-chip devices that are being developed for safety-critical applications such as point-of-care health assessment, air-quality monitoring, and food-safety testing. Therefore, these devices must be adequately tested after manufacture and during bioassay operations. This paper presents a survey of early work on fault tolerance in digital microfluidic lab-on-chip systems. Defects are related to logical fault models that can be viewed not only in terms of traditional shorts and opens, but which also target biochip functionality. Based on these fault models, test techniques for lab-on-chip devices and digital microfluidic modules are presented.

Innovative integrated system for real-time measurement of hybridization and melting on standard format microarrays

Abstract: Despite the great popularity and potential of microarrays, their use for research and clinical applications is still hampered by lengthy and costly design and optimization processes, mainly because the technology relies on the end point measurement of hybridization. Thus, the ability to monitor many hybridization events on a standard microarray slide in real time would greatly expand the use and benefit of this technology, as it would give access to better prediction of probe performance and improved optimization of hybridization parameters. Although real-time hybridization and thermal denaturation measurements have been reported, a complete walk-away system compatible with the standard format of microarrays is still unavailable. To address this issue, we have designed a biochip tool that combines a hybridization station with active mixing capability and temperature control together with a fluorescence reader in a single compact benchtop instrument. This integrated live hybridization machine (LHM) allows measuring in real time the hybridization of target DNA to thousands of probes simultaneously and provides excellent levels of detection and superior sequence discrimination. Here we show on an environmental single nucleotide polymorphism (SNP) model system that the LHM enables a variety of experiments unachievable with conventional biochip tools.

Full-automatic biological chips detection system

Abstract: The invention discloses a full automatic biochip detection system belonging to the clinical detection field of multi-marker biochips. The system adopts modular structure and comprises an automatic sample processing module, a reaction washing module, a detection module, a Tip head storage module, a reagent storage module, a biochip storage module, a sample storage module, a system base, an electric control box and a computer, the electric control box and all the modules are operated under the control of software, so as to realize the automatic sampling, the sample adding, the reaction, the washing, the detection and other processes. All the modules can work independently and can also be combined together and matched for work. The full automatic biochip detection system can overcome the shortcomings of the existing biochip detector and reduce the errors caused by human operation, and has stable and reliable detection result and good flexibility, so that the full automatic biochip detection system can not only greatly improve the detection efficiency, but also can be conductive to the accuracy of the detection result; the system has simple operation, therefore, the system is not only applicable to the scientific research and the applications of laboratories and hospitals, but also can be used for large-scale sample screening of large-scale hospitals and blood stations.