Showing papers on "Biochip published in 2015"

Toward the development of smart and low cost point-of-care biosensors based on screen printed electrodes.

Abstract: Screen printing technology provides a cheap and easy means to fabricate disposable electrochemical devices in bulk quantities which are used for rapid, low-cost, on-site, real-time and recurrent industrial, pharmaceutical or environmental analyses. Recent developments in micro-fabrication and nano-characterization made it possible to screen print reproducible feature on materials including plastics, ceramics and metals. The processed features forms screen-printed disposable biochip (SPDB) upon the application of suitable bio-chemical recognition receptors following appropriate methods. Adequacy of biological and non-biological materials is the key to successful biochip development. We can further improve recognition ability of SPDBs by adopting new screen printed electrode (SPE) configurations. This review covers screen-printing theory with special emphasis on the technical impacts of SPE architectures, surface treatments, operational stability and signal sensitivity. The application of SPE in dif...

Fluorescence-Based Bioassays for the Detection and Evaluation of Food Materials

Abstract: We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials.

An Intelligent Digital Microfluidic Processor for Biomedical Detection

Abstract: An intelligent digital microfluidic processor for biomedical detection is presented. This potential architecture solves lots of traditional development bottlenecks to implement the easy-to-control, easy-to-monitor, system automation and high accuracy for bioassay detection purposes. The proposed processor integrates the functions of microfluidic actuation, droplet location readback and high sensitivity measurement window to demonstrate a novel prototype for personalized medicine. Furthermore, the droplet location map and reaction behaviors are visible on a 2-dimentional (2D) graphical user-interface due to the micro electrode dot array (MEDA) architecture and capacitive sensing technology, and hence system automation is achievable. Fabricated in standard 0.35 μm CMOS process, this work integrates 900 microelectrodes with measurement window in 3.2 mm2, where the high sensitivity capacitive readout circuit occupies only 0.048 mm2. Measurement results show that microdroplet actuation and 2D location map are activated under 1KHz. In addition, the function of digital signal extraction, processing, as well as statistical analysis can be operated under 1 MHz respectively.

Disposable electrochemical sensor prepared using 3D printing for cell and tissue diagnostics

Abstract: In this paper we present a novel electrochemical sensor with a unique 3D architecture allowing for direct measurements on contact, or in close proximity, to biological samples. For biomedical applications, the all-polymer architecture can be mounted on special probes that can access the region under test with no need for biopsy as is done today with the conventional 2D electrodes. The chip consists of a biocompatible substrate comprised of an electrochemical cell with two gold electrodes (working and counter) and an Ag/AgCl quasi-reference electrode. The metal electrodes on the biochip front (sensing) side are fabricated by conventional electroplating and patterning methods. The chip itself is made from PDMS cast from a polymer master fabricated by 3D printing. The electrical communication between the biochip front and backside is enabled by through-hole via-contacts filled with conductive PDMS containing 60 wt% graphite powder. The electroactivity of working electrodes was verified by cyclic voltammetry of ferrocyanide/ferricyanide redox reaction. Amperometric in-vitro detection of the biomarker alkaline phosphatase from three different colon cancer cell lines directly in a cell culture plate while maintaining their biological environment was successfully demonstrated. The sensor exhibit stable voltammetric signatures and significant amperometric response to the enzyme in repeated tests. This approach paves the way to perform direct, non-invasive diagnostics on top of an exposed cell layer for both in-vivo and in-vitro applications.

A General and Exact Routing Methodology for Digital Microfluidic Biochips

Abstract: Advances in microfluidic technologies have led to the emergence of Digital Microfluidic Biochips (DMFBs), which are capable of automating laboratory procedures in biochemistry and molecular biology. During the design and use of these devices, droplet routing represents a particularly critical challenge. Here, various design tasks have to be addressed for which, depending on the corresponding scenario, different solutions are available. However, all these developments eventually result in an "inflation" of different design approaches for routing of DMFBs -- many of them addressing a very dedicated routing task only. In this work, we propose a comprehensive routing methodology which (1) provides one (generic) solution capable of addressing a variety of different design tasks, (2) employs a "push-button"-scheme that requires no (manual) composition of partial results, and (3) guarantees minimality e.g., with respect to the number of timesteps or the number of required control pins. Experimental evaluations demonstrate the benefits of the solution, i.e., the applicability for a wide range of design tasks as well as improvements compared to specialized solutions presented in the past.

Storage and Caching: Synthesis of Flow-Based Microfluidic Biochips

Abstract: This article presents a new concept for designing on-chip storage and cache that will enable efficient management of intermediate fluid samples during transportation and for reuse. By minimizing channel conflicts and recognizing maximum independent sets, storage requirements are efficiently handled jointly by channels as well as by both distributed and dedicated storage cells.

Design and Optimization of a Cyberphysical Digital-Microfluidic Biochip for the Polymerase Chain Reaction

Abstract: The amount of DNA strands available in a biological sample is a major limitation for many genomic bioanalyses. To amplify the traces of DNA strands, polymerase chain reaction (PCR) is widely used for conducting subsequent experiments. Compared to conventional instruments and analyzers, the execution of PCR on a digital microfluidic biochip (DMFB) can achieve short time-to-results, low reagent consumption, rapid heating/cooling rates, and high integration of multiple processing modules. However, the PCR biochip design methods in the literature are oblivious to the inherent randomness and complexity of bioanalyses, and they do not consider the interference among the neighboring devices and the cost of droplet transportation. We present an integrated design solution to optimize the complete PCR procedure, including: 1) DNA amplification and termination control; 2) resource placement that satisfies proximity constraints; and 3) droplet transportation. Based on the sensor feedback data, a statistical model is developed to optimize and control the DNA amplification sequence in real-time on a cyberphysical biochip. Next, we present a geometric algorithm for avoiding device interference and for reducing droplet routing cost. A novel optical sensing system is deployed based on the physical visibility of droplets. Simulation results for three laboratory protocols demonstrate that the proposed design method results in a compact layout and produces an execution sequence for efficient control of PCR operations on a cyberphysical DMFB.

Rapid online fault recovery for cyber-physical digital microfluidic biochips

Abstract: Microfluidic technologies offer benefits to the biological sciences by miniaturizing and automating chemical reactions. Software-controlled laboratories-on-a-chip (LoCs) execute biological protocols (assays) specified using high-level languages. Integrated sensors and video monitoring provide a closed feedback loop between the LoC and its control software, which provide timely information about the progress of an ongoing assay and the overall health of the LoC. This paper introduces a cyber-physical control algorithm that rectifies hard and soft faults that are detected dynamically while executing an assay on a digital microfluidic biochip (DMFB), one specific LoC technology. The approach is scalable (i.e., there is no fixed limit on the number of faults that may occur), and runs efficiently in practice, thereby limiting the performance overhead incurred when a hard or soft fault occurs during assay execution.

Disposable microfluidic immuno-biochip for rapid electrochemical detection of tumor necrosis factor alpha biomarker

Abstract: This paper presents a disposable microfluidic electrochemical immunosensor for rapid, cheap and quantitative detection of biomarkers. Dual screen-printed carbon electrodes were biofunctionalized with specific antibodies and subsequently encapsulated with an all-disposable polymeric microfluidic cell. The electrochemical detection was carried out by means of differential pulse voltammetry (DPV) using a portable potentiostat. One of the two working electrodes was employed as an on-chip integrated negative control. The system was optimized and characterized for the detection of tumor necrosis factor alpha (TNFα), an important inflammation biomarker, with a limit of detection (LOD) of 4.1 ng/mL. Successful experiments in real human serum were also carried out.

Water pollutant monitoring by a whole cell array through lens-free detection on CCD

Abstract: Environmental contamination has become a serious problem to human and environmental health, as exposure to a wide range of possible contaminants continuously increases due to industrial and agricultural activities. Whole cell sensors have been proposed as a powerful tool to detect class-specific toxicants based upon their biological activity and bioavailability. We demonstrated a robust toxicant detection platform based on a bioluminescence whole cell sensor array biochip (LumiChip). LumiChip harbors an integrated temperature control and a 16-member sensor array, as well as a simple but highly efficient luminescence collection setup. On LumiChip, samples were infused in an oxygen-permeable microfluidic flow channel to reach the sensor array. Time-lapse changes in bioluminescence emitted by the array members were measured on a single window-removed linear charge-coupled device (CCD) commonly used in commercial industrial process control or in barcode readers. Removal of the protective window on the linear CCD allowed lens-free direct interfacing of LumiChip to the CCD surface for measurement with high light collection efficiency. Bioluminescence induced by simulated contamination events was detected within 15 to 45 minutes. The portable LumiSense system utilizing the linear CCD in combination with the miniaturized LumiChip is a promising potential platform for on-site environmental monitoring of toxicant contamination.

Scalable One-Pass Synthesis for Digital Microfluidic Biochips

Abstract: This article proposes an automatic design approach, which is based on a one-pass synthesis scheme that integrates scheduling, binding, placement, and routing. Furthermore, it remains scalable and, hence, applicable for larger designs.

Redundancy optimization for error recovery in digital microfluidic biochips

Abstract: Microfluidic-based biochips are replacing the conventional biochemical analyzers, and are able to integrate all the necessary functions for biochemical analysis. The digital microfluidic biochips are based on the manipulation of liquids not as a continuous flow, but as discrete droplets. Researchers have proposed 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, placement and routing of the operations in the application. During the execution of a bioassay, operations could experience transient errors (e.g., erroneous droplet volumes), thus impacting negatively the correctness of the application. Researchers have proposed fault-tolerance approaches, which apply predetermined recovery actions at the moment when errors are detected. In this paper, we propose an online recovery strategy, which decides during the execution of the biochemical application the introduction of the redundancy required for fault-tolerance. We consider both time redundancy, i.e., re-executing erroneous operations, and space redundancy, i.e., creating redundant droplets for fault-tolerance. Error recovery is performed such that the number of transient errors tolerated is maximized and the timing constraints of the biochemical application are satisfied. The proposed redundancy optimization approach has been evaluated using several benchmarks.

Continuous-Flow Biochips: Technology, Physical-Design Methods, and Testing

Abstract: This article is a tutorial on continuous-flow biochips where the basic building blocks are microchannels, and microvalves, and by combining them, more complex units such as mixers, switches, and multiplexers can be built. It also presents the state of the art in flow-based biochip technology and emerging research challenges in the areas of physical design and testing techniques.

Label-Free Detection of Tumor Angiogenesis Biomarker Angiopoietin 2 Using Bloch Surface Waves on One Dimensional Photonic Crystals

Abstract: We describe the design and fabrication of biochips based on 1-D photonic crystals supporting Bloch surface waves for label-free optical biosensing. The optical properties of Bloch surface waves are studied in relation to the geometry of the photonic crystals and on the properties of the dielectric materials used for the fabrication. The planar stacks of the biochips are composed of silica, tantala, and titania that were deposited using plasma-ion-assisted evaporation under high-vacuum conditions. The biochip surfaces were functionalized by silanization, and appropriate fluidic cells were designed to operate in an automated platform. An angularly resolved ellipsometric optical sensing apparatus was assembled to carry out the sensing studies. The angular operation is obtained by a focused laser beam at a fixed wavelength and detection of the angular reflectance spectrum by means of an array detector. The results of the experimental characterization of the physical properties of the fabricated biochips show that their characteristics, in terms of sensitivity and figure of merit, match those expected from the numerical simulations. Practical application of the sensor was demonstrated by detecting a specific glycoprotein, Angio-poietin 2, that is involved in angiogenesis and inflammation processes. The protocol used for the label-free detection of Angiopoietin 2 is described, and the results of an exemplary assay, carried out at a relatively high concentration of 1 μg/ml, are given and confirm that an efficient detection can be achieved. The limit of detection of the biochips for Angiopoietin 2, based on the protocol used, is 1.5 pg/mm2 in buffer solution. The efficiency of the label-free assay is confirmed by independent measurements carried out by means of confocal fluorescence microscopy.

Layout-Aware Mixture Preparation of Biochemical Fluids on Application-Specific Digital Microfluidic Biochips

Abstract: The recent proliferation of digital microfluidic (DMF) biochips has enabled rapid on-chip implementation of many biochemical laboratory assays or protocols. Sample preprocessing, which includes dilution and mixing of reagents, plays an important role in the preparation of assays. The automation of sample preparation on a digital microfluidic platform often mandates the execution of a mixing algorithm, which determines a sequence of droplet mix-split steps (usually represented as a mixing graph). However, the overall cost and performance of on-chip mixture preparation not only depends on the mixing graph but also on the resource allocation and scheduling strategy, for instance, the placement of boundary reservoirs or dispensers, mixer modules, storage units, and physical design of droplet-routing pathways. In this article, we first present a new mixing algorithm based on a number-partitioning technique that determines a layout-aware mixing tree corresponding to a given target ratio of a number of fluids. The mixing graph produced by the proposed method can be implemented on a chip with a fewer number of crossovers among droplet-routing paths as well as with a reduced reservoir-to-mixer transportation distance. Second, we propose a routing-aware resource-allocation scheme that can be used to improve the performance of a given mixing algorithm on a chip layout. The design methodology is evaluated on various test cases to demonstrate its effectiveness in mixture preparation with the help of two representative mixing algorithms. Simulation results show that on average, the proposed scheme can reduce the number of crossovers among droplet-routing paths by 89.7p when used in conjunction with the new mixing algorithm, and by 75.4p when an earlier algorithm [Thies et al. 2008] is used.

A general testing method for digital microfluidic biochips under physical constraints

Abstract: Digital microfluidics is viewed as one of the most promising technologies for biomedical experiments. Digital microfluidic biochips are often used today for applications such as point-of-care health assessment, drug discovery, and air-quality monitoring. Therefore, such devices must be adequately tested after manufacturing to guarantee the correctness of the biomedical experiments. Previous test methods for digital microfluidic biochips are either unable to cover all chip defects or inapplicable for application-specific biochips with arbitrary layouts. Furthermore, previous methods also ignore the fluidic constraints required for droplet routing, which makes the test droplet routing problem much more challenging in realistic test-application scenarios. In this paper, we propose the first test method for digital microfluidic biochips that is not only able to cover all chip defects, but is also applicable for arbitrary chip layouts. Moreover, we propose an optimization technique to route test droplets with minimum test-application time. A polynomial-time scheduling algorithm is also presented to solve the optimization problem in an efficient manner. Experiments demonstrate that the proposed test method requires significantly less test-application time compared to related previous work.

Advances in Design Automation Techniques for Digital-Microfluidic Biochips

Abstract: Due to their emergence as an efficient platform for pointof-care clinical diagnostics, digital-microfluidic biochips (DMFBs) have received considerable attention in recent years. They combine electronics with biology, and they integrate various bioassay operations, such as sample preparation, analysis, separation, and detection. In this chapter, we first present an overview of digital-microfluidic biochips. We next describe emerging computer-aided design (CAD) tools for the automated synthesis and optimization of biochips from bioassay protocols. The chapter includes solutions for fluidic-operation scheduling, module placement, droplet routing, and pin-constrained chip design. We also show how recent advances in the integration of sensors into a DMFB can be exploited to provide cyberphysical system adaptation based on feedback-driven control.

Security implications of cyberphysical digital microfluidic biochips

Abstract: A digital microfluidic biochip (DMFB) is an emerging technology that enables miniaturized analysis systems for point-of-care clinical diagnostics, DNA sequencing, and environmental monitoring. A DMFB reduces the rate of sample and reagent consumption, and automates the analysis of assays. In this paper, we highlight the security vulnerabilities of DMFBs by identifying two potential attacks on a DMFB that performs enzymatic glucose assay on serum. In the first attack, the attacker adjusts the concentration of the glucose sample and thereby modifies the final result. In the second attack, the calibration curve of the assay operation is maliciously modified in order to make it deviate from the nominal/golden calibration curve. We demonstrate these attacks using a digital microluidics synthesis simulator. The results show that the attacks are stealthy as they do not result in any noticeable change in the DMFB synthesis.

Binary DNA hairpin-based colorimetric biochip for simultaneous detection of Pb2+ and Hg2+ in real-world samples

Abstract: A microarray-format colorimetric biochip was constructed on plastic using two specially-designed DNA hairpin strands as binary probes and a binding-induced conformational switching strategy as the signal generation protocol. Coupled with single- or dual-color staining, we were able to simultaneously detect and quantitate the trace amounts of Pb(2+) and Hg(2+) in various real-world samples.

Biomarkers probed in saliva by surface plasmon resonance imaging coupled to matrix-assisted laser desorption/ionization mass spectrometry in array format.

Abstract: Detection of protein biomarkers is of major interest in proteomics. This work reports the analysis of protein biomarkers directly from a biological fluid, human saliva, by surface plasmon resonance imaging coupled to mass spectrometry (SPRi-MS), using a functionalized biochip in an array format enabling multiplex SPR-MS analysis. The SPR biochip presented a gold surface functionalized by a self-assembled monolayer of short poly(ethylene oxide) chains carrying an N-hydroxysuccinimide end-group for the immobilization of antibodies. The experiments were accomplished without any sample pre-purification or spiking with the targeted biomarkers. SPRi monitoring of the interactions, immune capture from the biochip surface, and finally on-chip matrix-assisted laser desorption/ionization-MS structural identification of two protein biomarkers, salivary α-amylase and lysozyme, were successively achieved directly from saliva at the femtomole level. For lysozyme, the on-chip MS identification was completed by a proteomic analysis based on an on-chip proteolysis procedure and a peptide mass fingerprint.

Surface plasmon resonance application in prostate cancer biomarker research

Abstract: Prostate cancer (PCa) diagnostics can be effectively addressed using sensor-based approaches. Proper selection of biomarkers to be included in biosensors for accurate detection becomes the need of the hour. Such biosensor and biochip technologies enable fast and efficient determination of proteins and provide a remarkable insight into the changes in the protein structure, such as aberrant glycosylation, which can increase the performance, sensitivity and specificity of clinic assays. However, for a thorough comprehension of such complex protein modifications, it is crucial to understand their biospecific interactions. Surface plasmon resonance (SPR), one of the most rapidly developing techniques for measuring real-time quantitative binding affinities and kinetics of the interactions of antigens and antibodies, was chosen as an appropriate tool for this purpose. Herein, experiments on the interactions of antibodies specific against different epitopes of free and complexed prostate-specific antigen (PSA), a prominent PCa biomarker, are presented with two main aims: (i) to continue as lectin glycoprofiling studies and; (ii) to be used in microfluidic immunoassay-based platforms for point-of-care devices. Various PSA-specific antibodies were covalently immobilized on the biochip surface via amine coupling, and free or complexed PSA was injected into the dual-flow channels of the SPR device. Kinetic parameters and affinity constants of these interactions, as well as cross-reactivities of the used antibodies were determined. The sandwich assay for PSA determination was developed employing both primary and secondary anti-PSA antibodies. Sensitivity of the assay was 3.63 nM−1, the detection limit was 0.27 nM and the SPR biosensor response towards free PSA was linear up to 25 nM. All these findings are essential for proper design of a selective, sensitive, and highly reliable biosensor for PCa diagnosis as a lab-on-chip device.

Nanotechnologies for biosensor and biochip

Abstract: 1Department of BioNano Technology, Gachon University, 1342 Seongnamdae-ro, Sujeong-gu, Seongnam, Gyeonggi 461-701, Republic of Korea 2Department of Chemistry, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea 3Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA 4College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Xiasha, Hangzhou, Zhejiang 310018, China 5Departement Materiaalkunde (MTM), KU Leuven, Kasteelpark Arenberg 44, Bus 2450, 3001 Leuven, Belgium 6Pivotal Purification Process Development, Amgen, Inc., Cambridge, MA 02142, USA