Showing papers on "Biochip published in 2010"

Optimization of Dilution and Mixing of Biochemical Samples Using Digital Microfluidic Biochips

Abstract: The recent emergence of lab-on-a-chip (LoC) technology has led to a paradigm shift in many healthcare-related application areas, e.g., point-of-care clinical diagnostics, high-throughput sequencing, and proteomics. A promising category of LoCs is digital microfluidic (DMF)-based biochips, in which nanoliter-volume fluid droplets are manipulated on a 2-D electrode array. A key challenge in designing such chips and mapping lab-bench protocols to a LoC is to carry out the dilution process of biochemical samples efficiently. As an optimization and automation technique, we present a dilution/mixing algorithm that significantly reduces the production of waste droplets. This algorithm takes O(n) time to compute at most n sequential mix/split operations required to achieve any given target concentration with an error in concentration factor less than [1/(2n)]. To implement the algorithm, we design an architectural layout of a DMF-based LoC consisting of two O(n)-size rotary mixers and O(n) storage electrodes. Simulation results show that the proposed technique always yields nonnegative savings in the number of waste droplets and also in the total number of input droplets compared to earlier methods.

Protein Biochips: Oriented Surface Immobilization of Proteins†

Abstract: Substantial progress in biochip technologies has established an efficient and reliable platform for advanced biological and biomedical applications. In particular, the use of protein biochips in high-throughput screens provides high content information. We briefly introduce here recent developments in protein biochip preparation with a special focus on our own work on new methods for protein immobilization and protein microarray fabrication, including the application of the Diels-Alder reaction, Staudinger ligation, 'click' sulfonamide formation, and the photochemical thiol-ene reaction. These chemical methods allow for oriented, site-specific protein conjugation on solid surfaces with high sensitivity and specificity under mild, aqueous conditions.

Integrated control-path design and error recovery in the synthesis of digital microfluidic lab-on-chip

Abstract: Recent advances in digital microfluidics have led to tremendous interest in miniaturized lab-on-chip devices for biochemical analysis Synthesis tools have also emerged for the automated design of lab-on-chip from the specifications of laboratory protocols However, none of these tools consider control flow or address the problem of recovering from fluidic errors that can occur during on-chip bioassay execution We present a synthesis method that incorporates control paths and an error-recovery mechanism in the design of a digital microfluidic lab-on-chip Based on error-propagation estimates, we determine the best locations for fluidic checkpoints during biochip synthesis A microcontroller coordinates the implementation of the control-flow-based bioassay by intercepting the synthesis results that are mapped to the software programs Real-life bioassay applications are used as case studies to evaluate the proposed design method For a representative protein assay, compared to a baseline chip design, the biochip with a control path can reduce the completion time by 30p when errors occur during the implementation of the bioassay

Design Tools for Digital Microfluidic Biochips: Toward Functional Diversification and More Than Moore

Abstract: Microfluidics-based biochips enable the precise control of nanoliter volumes of biochemical samples and reagents. They combine electronics with biology, and they integrate various bioassay operations, such as sample preparation, analysis, separation, and detection. Compared to conventional laboratory procedures, which are cumbersome and expensive, miniaturized biochips offer the advantages of higher sensitivity, lower cost due to smaller sample and reagent volumes, system integration, and less likelihood of human error. This paper first describes the droplet-based “digital” microfluidic technology platform and emerging applications. The physical principles underlying droplet actuation are next described. Finally, the paper presents computer-aided design tools for simulation, synthesis and chip optimization. These tools target modeling and simulation, scheduling, module placement, droplet routing, pin-constrained chip design, and testing.

Digital microfluidic biochips: a vision for functional diversity and more than Moore

Abstract: Advances in droplet-based digital microfluidics have led to the emergence of biochips for automating laboratory procedures in biochemistry and molecular biology. These devices enable the precise control of microliter of nanoliter volumes of biochemical samples and reagents. They combine electronics with biology, and integrate various bioassay operations, such as sample preparation, analysis, separation, and detection. Compared to conventional laboratory procedures, which are cumbersome and expensive, miniaturized digital microfluidic biochips (DMFBs) offer the advantages of higher sensitivity, lower cost, system integration, and less likelihood of human error. This tutorial paper provides an overview of DMFBs and describes emerging computer-aided design (CAD) tools for the automated synthesis and optimization of biochips, from physical modeling to fluidic-level synthesis and then to chip-level design. By efficiently utilizing the electronic design automation (EDA) technique on emerging CAD tools, users can concentrate on the development of nanoscale bioas-says, leaving chip optimization and implementation details to design-automation tools.

Design Automation and Test Solutions for Digital Microfluidic Biochips

Abstract: Microfluidics-based biochips are revolutionizing high-throughput sequencing, parallel immunoassays, blood chemistry for clinical diagnostics, and drug discovery. These devices enable the precise control of nanoliter volumes of biochemical samples and reagents. They combine electronics with biology, and they integrate various bioassay operations, such as sample preparation, analysis, separation, and detection. Compared to conventional laboratory procedures, which are cumbersome and expensive, miniaturized biochips offer the advantages of higher sensitivity, lower cost due to smaller sample and reagent volumes, system integration, and less likelihood of human error. This tutorial paper provides an overview of droplet-based ?digital? microfluidic biochips. It describes emerging computer-aided design (CAD) tools for the automated synthesis and optimization of biochips from bioassay protocols. Recent advances in fluidic-operation scheduling, module placement, droplet routing, pin-constrained chip design, and testing are presented. These CAD techniques allow biochip users to concentrate on the development of nanoscale bioassays, leaving chip optimization and implementation details to design-automation tools.

Defect-Tolerant Design and Optimization of a Digital Microfluidic Biochip for Protein Crystallization

Abstract: Protein crystallization is a commonly used technique for protein analysis and subsequent drug design. It predicts the 3-D arrangement of the constituent amino acids, which in turn indicates the specific biological function of a protein. Protein crystallization experiments are typically carried out in well-plates in the laboratory. As a result, these experiments are slow, expensive, and error-prone due to the need for repeated human intervention. Recently, droplet-based ?digital? microfluidics have been used for executing protein assays on a chip. Protein samples in the form of nanoliter-volume droplets are manipulated using the principle of electrowetting-on-dielectric. 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 and test procedure to achieve high-throughput and defect-tolerant well loading.

Single-cell manipulation on microfluidic chip by dielectrophoretic actuation and impedance detection

Abstract: This paper presents the design, fabrication, and characterization of a microfluidic biochip with integrated actuation electrodes used to manipulate a cell and a microbead by dielectrophoresis and sensing electrodes to detect the trapping by using the impedance detection method. Combining deflective dielectrophoretic barriers with controlled pressure-driven liquid flows allows the accurate control of a cell/microbead in suspensions. The threshold voltage for microbead trapping was experimentally verified at various flow rates. The impedance change caused by the blockage of the electrical conducting path between sensing electrodes with the trapping of an MCF7 cell and a polystyrene microbead was measured. The impedance before the trapping of an MCF7 cell was 10.9 MΩ at 1 kHz and increased to 12 MΩ when the cell was placed between sensing electrodes.

SERS as tool for the analysis of DNA-chips in a microfluidic platform.

Abstract: A sequence-specific detection method of DNA is presented combining a solid chip surface for immobilisation of capture DNAs with a microfluidic platform and a readout of the chip based on SERS. The solid chip surface is used for immobilisation of different capture DNAs, where target strands can be hybridised and unbound surfactants can be washed away. For the detection via SERS, short-labelled oligonucleotides are hybridised to the target strands. This technique is combined with a microfluidic platform that enables a fast and automated preparation process. By applying a chip format, the problems of sequence-specific DNA detection in solution phase by means of SERS can be overcome. With this setup, we are able to distinguish between different complementary and non-complementary target sequences in one sample solution.

Digital Microfluidic Biochips: Design Automation and Optimization

Abstract: Microfluidics-based biochips combine electronics with biochemistry, providing access to new application areas in a wide variety of fields. Continued technological innovations are essential to assuring the future role of these chips in functional diversification in biotech, pharmaceuticals, and other industries.Revolutionary guidance on design, opti

A novel droplet routing algorithm for digital microfluidic biochips

Abstract: One of the recent areas of research interest is the use of microfluidics for building up biochips, the digital microfluidic biochips (DMFB). This paper deals with a challenging problem related to the design of DMFB. Specifically the design problem considered is related to high performance droplet routing, where each droplet has single source location and single target location. The objectives are (i) minimizing the number of electrodes used in the DMFB, and (ii) minimizing the total routing time of all the droplets or arrival time of a droplet that is the last to arrive at its target(latest arrival time). We propose a simple algorithm for concurrent path allocation to multiple droplets, based on the Soukup's routing algorithm [22], together with the use of stalling, and possible detouring of droplets in cases of contentions. Selection of the droplets is based on their respective source to target Manhattan paths. The empirical results are quite encouraging.

Preparation of Biomolecule Microstructures and Microarrays by Thiol–ene Photoimmobilization

Abstract: A mild, fast and flexible method for photoimmobilization of biomolecules based on the light-initiated thiol–ene reaction has been developed. After investigation and optimization of various surface materials, surface chemistries and reaction parameters, microstructures and microarrays of biotin, oligonucleotides, peptides, and MUC1 tandem repeat glycopeptides were prepared with this photoimmobilization method. Furthermore, MUC1 tandem repeat glycopeptide microarrays were successfully used to probe antibodies in mouse serum obtained from vaccinated mice. Dimensions of biomolecule microstructures were shown to be freely controllable through photolithographic techniques, and features down to 5 μm in size covering an area of up to 75×25 mm were created. Use of a confocal laser microscope with a UV laser as UV-light source enabled further reduction of biotin feature size opening access to nanostructured biochips.

Synchronization of washing operations with droplet routing for cross-contamination avoidance in digital microfluidic biochips

Abstract: Digital microfluidic biochips are being utilized in many areas of biochemistry and biomedical sciences. Since cross-contamination between droplets of different biomolecules can lead to erroneous outcomes for bioassays, it is essential to avoid cross-contamination during droplet routing. We propose a wash-operation synchronization method to manipulate wash droplets to clean the residue that is left behind by sample and reagent droplets. We also synchronize wash-droplet routing with sample/reagent droplet-routing steps by controlling the arrival order of droplets at cross-contamination sites. The proposed method minimizes droplet-routing time without cross-contamination, and it is especially effective for tight chip-area constraints. A real-life application is used for evaluation.

Cross-contamination aware design methodology for pin-constrained digital microfluidic biochips

Abstract: Digital microfluidic biochips have emerged as a popular alternative for laboratory experiments. Pin-count reduction and cross-contamination avoidance are key design considerations for practical applications with different droplets being transported and manipulated on highly integrated biochips. We present in this paper the first design automation flow that considers the cross-contamination problems on pin-constrained biochips. We explore the factors that make the problems harder on pin-constrained biochips. To cope with these cross contaminations, we propose (1) early crossing minimization algorithms during placement, and (2) systematic wash droplet scheduling and routing that require only one extra control pin and zero assay completion time overhead for practical bioassays. Experimental results show the effectiveness and scalability of our algorithms for practical bioassays.

CrossRouter: a droplet router for cross-referencing digital microfluidic biochips

Abstract: Digital Microfluidic Biochip (DMFB) has drawn lots of attention today. It offers a promising platform for various kinds of biochemical experiments. DMFB that uses cross-referencing technology to drive droplets movements scales down the control pin number on chip, which not only brings down manufacturing cost but also allows large-scale chip design. However, the cross-referencing scheme that imposes different voltage on rows and columns to activate the cells, might cause severe electrode interference, and hence greatly decreases the degree of parallelism of droplet routing. Most of the previous papers get a direct-addressing result first, and then convert to cross-referencing compatible result. This paper proposes a new method that solves the droplet routing problem on cross-referencing biochip directly. Experimental results on public benchmarks demonstrate the effectiveness and efficiency of our method in comparison with the latest work on this problem.

Biochip System for Rapid and Accurate Identification of Mycobacterial Species from Isolates and Sputum

Abstract: The accurate detection of mycobacterial species from isolates and clinical samples is important for pathogenic diagnosis and treatment and for disease control. There is an urgent need for the development of a rapid, simple, and accurate detection method. We established a biochip assay system, including a biochip, sample preparation apparatus, hybridization instrument, chip washing machine, and laser confocal scanner equipped with interpretation software for automatic diagnosis. The biochip simultaneously identified 17 common mycobacterial species by targeting the differences in the 16S rRNA. The system was assessed with 64 reference strains and 296 Mycobacterium tuberculosis and 243 nontuberculous mycobacterial isolates, as well as 138 other bacteria and 195 sputum samples, and then compared to DNA sequencing. The entire biochip assay took 6 h. The concordance rate between the biochip assay and the DNA sequencing results was 100%. In conclusion, the biochip system provides a simple, rapid, reliable, and highly accurate clinical assay for determination of mycobacterial species in a 6-h procedure, from either culture isolates or sputum samples, allowing earlier pathogen-adapted antimicrobial therapy in patients.

ILP-Based Pin-Count Aware Design Methodology for Microfluidic Biochips

Abstract: Digital microfluidic biochips have emerged as a popular alternative for laboratory experiments. To make the biochip feasible for practical applications, pin-count reduction is a key problem to higher-level integration of reactions on a biochip. Most previous works approach the problem by post-processing the placement and routing solutions to share compatible control signals; however, the quality of such sharing algorithms is inevitably limited by the placement and routing solutions. We present in this paper a comprehensive pin-constrained biochip design flow that addresses the pin-count issue at all design stages. The proposed flow consists of three major stages: 1) pin-count aware stage assignment that partitions the reactions in the given bioassay into execution stages; 2) pin-count aware device assignment that determines a specific device used for each reaction; and 3) guided placement, routing, and pin assignment that utilize the pin-count saving properties from the stage and device assignments to optimize the assay time and pin-count. For both the stage and device assignments, basic integer linear programming formulations and effective solution-space reduction schemes are proposed to minimize the assay time and pin-count. Experimental results show the efficiency of our methods and a 55-57% pin-count reduction over the state-of-the-art algorithms/flow.

Nano-Bio-Technology and Sensing Chips: New Systems for Detection in Personalized Therapies and Cell Biology

Abstract: Further advances in molecular medicine and cell biology also require new electrochemical systems to detect disease biomarkers and therapeutic compounds. Microelectronic technology offers powerful circuits and systems to develop innovative and miniaturized biochips for sensing at the molecular level. However, microelectronic biochips proposed in the literature often do not show the right specificity, sensitivity, and reliability required by biomedical applications. Nanotechnology offers new materials and solutions to improve the surface properties of sensing probes. The aim of the present paper is to review the most recent progress in Nano-Bio-Technology in the area of the development of new electrochemical systems for molecular detection in personalized therapy and cell culture monitoring.

Simultaneous Detection of Seven Staphylococcal Enterotoxins: Development of Hydrogel Biochips for Analytical and Practical Application

Abstract: A method of simultaneous analysis of staphylococcal enterotoxins using hydrogel-based microarrays (biochips) has been developed The method allows simultaneous quantitative detection of seven enterotoxins: A, B, C1, D, E, G, and I in a single sample The development of the method included expression and purification of recombinant toxins, production of panels of monoclonal antibodies (mAbs) against the toxins, and design and manufacturing of an experimental biochip for the screening of mAbs and selection of optimal pairs of primary and secondary antibodies for each toxin The selected mAbs have high affinity toward their targets and no cross-reactivity with unrelated enterotoxins Finally, a diagnostic biochip was designed for quantitative analysis of the toxins, and the analytical protocols were optimized The sensitivity of the detection reached 01-05 ng/mL, depending on the type of enterotoxin The evaluation of the resulting biochip using spiked food samples demonstrated that the sensitivity, specificity, and reproducibility of the proposed test system fully satisfy the requirements for traditional immunoanalytical systems The diagnostic biochips manufactured on reflecting metal-coated surfaces shortened the time of analysis from 17 to 2 h without loss of sensitivity The method was successfully tested on samples of food and biological media

Tabu search-based synthesis of digital microfluidic biochips with dynamically reconfigurable non-rectangular devices

Abstract: Microfluidic biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the necessary functions for biochemical analysis. The "digital" microfluidic biochips are manipulating liquids not as a continuous flow, but as discrete droplets, and hence they are highly reconfigurable and scalable. A digital biochip is composed of a two-dimensional array of cells, together with reservoirs for storing the samples and reagents. Several adjacent cells are dynamically grouped to form a virtual device, on which operations are performed. So far, researchers have assumed that throughout its execution, an operation is performed on a rectangular virtual device, whose position remains fixed. However, during the execution of an operation, the virtual device can be reconfigured to occupy a different group of cells on the array, forming any shape, not necessarily rectangular. In this paper, we present a Tabu Search metaheuristic for the synthesis of digital microfluidic biochips, which, starting from a biochemical application and a given biochip architecture, determines the allocation, resource binding, scheduling and placement of the operations in the application. In our approach, we consider changing the device to which an operation is bound during its execution, to improve the completion time of the biochemical application. Moreover, we devise an analytical method for determining the completion time of an operation on a device of any given shape. The proposed heuristic has been evaluated using a real-life case study and ten synthetic benchmarks.

Ion-Channel Biosensors—Part I: Construction, Operation, and Clinical Studies

Abstract: This paper deals with the construction and operation of a novel biosensor that exploits the molecular switching mechanisms of biological ion channels. The biosensor comprises gramicidin A channels embedded in a synthetic tethered lipid bilayer. It provides a highly sensitive and rapid detection method for a wide variety of analytes. In this paper, we outline the fabrication and principle of operation of the ion-channel switch (ICS) biosensor. The results of a clinical study, in which the ion-channel biosensor is used to detect influenza A in untreated clinical samples, is presented to demonstrate the utility of the technology. Fabrication of biochip arrays using silicon chips decorated with ?ink jet? printing is discussed. We also describe how such biochip arrays can be used for multianalyte sensing. Finally, reproducibility/stability issues of the biosensor are addressed.

Biomolecules Detection Using a Silver-Enhanced Gold Nanoparticle-Based Biochip

Abstract: Silver-enhanced labeling method has been employed in immunochromatographic assays for improving the sensitivity of detecting pathogens. In this paper, we apply the silver enhancement technique for biomolecular signal amplification in a gold nanoparticle-based conductimetric biochip. We show that the response of the silver-enhanced biochip comprises two distinct regions namely: (a) a sub-threshold region where conduction occurs due to electron hopping between silver islands and the electrolyte and (b) an above-threshold region where the conduction is due to a direct flow of electrons. These two regions are characterized by different conduction slopes, and we show that combining the information from both these regions can improve the sensitivity of the biochip. Results from fabricated prototypes show a dynamic range of more than 40 dB and with a detection limit less than 240 pg/mL. The fabrication of the biochip is compatible with standard complementary metal–oxide–semiconductor (CMOS) processes making it ideal for integration in next-generation CMOS biosensors.

Digital Microfluidic Biochips: A Vision for Functional Diversity and More Than Moore

Abstract: Microfluidics-based biochips are revolutionizing high-throughput sequencing, parallel immunoassays, clinical diagnostics, and drug discovery. These devices enable the precise control of nanoliter volumes of biochemical samples and reagents. Compared to conventional laboratory procedures, which are cumbersome and expensive, miniaturized biochips offer the advantages of higher sensitivity, lower cost due to smaller sample and reagent volumes, system integration, and less likelihood of human error. This keynote paper provides an overview of droplet-based “digital” microfluidics and outlines emerging computer-aided design (CAD) tools for the automated synthesis and optimization of biochips from bioassay protocols.

Synchronization of Concurrently-Implemented Fluidic Operations in Pin-Constrained Digital Microfluidic Biochips

Abstract: The implementation of bioassays in pin-constrained biochips may involve pin-actuation conflicts if the concurrently implemented fluidic operations are not carefully synchronized. We propose a two-phase optimization method to identify and synchronize the fluidic operations that can be executed in parallel. The goal is to implement these fluidic operations without pin-actuation conflict, and minimize the duration of implementing the outcome sequence after the synchronization. The effectiveness of the proposed two-phase optimization method is demonstrated for a representative 3-plex assay performed on a fabricated pin-constrained biochip.

Synthesis of biochemical applications on digital microfluidic biochips with operation variability

Abstract: Microfluidic-based biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the necessary functions for biochemical analysis using microfluidics. The digital microfluidic biochips are based on the manipulation of liquids not as a continuous flow, but as discrete droplets. Researchers have presented approaches for the synthesis of digital microfluidic biochips, which, starting from a biochemical application and a given biochip architecture, determine the allocation, resource binding, scheduling and placement of the operations in the application. Existing approaches consider that on-chip operations, such as splitting a droplet of liquid, are perfect. However, these operations have variability margins, which can impact the correctness of the biochemical application.We consider that a split operation, which goes beyond specified variability bounds, is faulty. The fault is detected using on-chip volume sensors. We have proposed an abstract model for a biochemical application, consisting of a sequencing graph, which can capture all the fault scenarios in the application. Starting from this model, we have proposed a synthesis approach that, for a given chip area and number of sensors, can derive a fault-tolerant implementation. Two fault-tolerant scheduling techniques have been proposed and compared. We show that, by taking into account fault-occurrence information, we can derive better quality implementations, which leads to shorter application completion times, even in the case of faults. The proposed synthesis approach under operation variability has been evaluated using several benchmarks.

Digital Microfluidic Logic Gates and Their Application to Built-in Self-Test of Lab-on-Chip

Abstract: Dependability is an important system attribute for microfluidic lab-on-chip. Robust testing methods are therefore needed to ensure correct results. Previously proposed techniques for reading test outcomes and for pulse-sequence analysis are cumbersome and error prone. We present a built-in self-test (BIST) method for digital microfluidic lab-on-chip. This method utilizes digital microfluidic logic gates to implement the BIST architecture; AND, OR and NOT gates are used to compress multiple test-outcome droplets into a single droplet to facilitate detection with low overhead. These approaches obviate the need for capacitive sensing test-outcome circuits for analysis. We also apply the BIST architecture to a pin-constrained biochip design. A multiplexed bioassay protocol is used to evaluate the effectiveness of the proposed test method.