Showing papers on "Biochip published in 2011"

Improvement of HepG2/C3a cell functions in a microfluidic biochip.

Abstract: Current developments in tissue engineering and microtechnology fields allow the use of microfluidic biochip as microtools for in vitro investigations. In the present study, we describe the behavior of HepG2/C3a cells cultivated in a poly(dimethylsiloxane) (PDMS) microfluidic biochip coupled to a perfusion system. Cell culture in the microfluidic biochip for 96 h including 72 h of perfusion provoked a 24 h delay in cell growth compared to plate cultures. Inside the microfluidic biochip, few apoptosis, and necrosis were detected along the culture and 3D cell organization was observed. Regarding the hepatic metabolism, glucose and glutamine consumptions as well as albumin synthesis were maintained. A transcriptomic analysis performed at 96 h of culture using Affymetrix GeneChip demonstrated that 1,025 genes with a fold change above 1.8 were statistically differentially expressed in the microfluidic biochip cultures compared to plate cultures. Among those genes, phase I enzymes involved in the xenobiotic's metabolism such as the cytochromes P450 (CYP) 1A1/2, 2B6, 3A4, 3A5, and 3A7 were up-regulated. The CYP1A1/2 up-regulation was associated with the appearance of CYP1A1/2's activity evidenced by using EROD biotransformation assay. Several phase II enzymes such as sulfotransferases (SULT1A1 and SULT1A2), UDP-glucuronyltransferase (UGT1A1, UGT2B7) and phase III transporters (such as MDR1, MRP2) were also up-regulated. In conclusion, microfluidic biochip could and provide an important insight to exploring the xenobiotic's metabolism. Altogether, these results suggest that this kind of biochip could be considered as a new pertinent tool for predicting cell toxicity and clearance of xenobiotics in vitro.

Microfluidics-based lab-on-chip systems in DNA-based biosensing: an overview.

Abstract: Microfluidics-based lab-on-chip (LOC) systems are an active research area that is revolutionising high-throughput sequencing for the fast, sensitive and accurate detection of a variety of pathogens. LOCs also serve as portable diagnostic tools. The devices provide optimum control of nanolitre volumes of fluids and integrate various bioassay operations that allow the devices to rapidly sense pathogenic threat agents for environmental monitoring. LOC systems, such as microfluidic biochips, offer advantages compared to conventional identification procedures that are tedious, expensive and time consuming. This paper aims to provide a broad overview of the need for devices that are easy to operate, sensitive, fast, portable and sufficiently reliable to be used as complementary tools for the control of pathogenic agents that damage the environment.

Digital microfluidic biochips: recent research and emerging challenges

Abstract: Microfluidic biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the basic functions for biochemical analysis. The “digital” microfluidic biochips (DM-FBs) are manipulating liquids not as a continuous flow, but as discrete droplets on a two-dimensional array of electrodes. Basic mi-crofluidic operations, such as mixing and dilution, are performed on the array, by routing the corresponding droplets on a series of electrodes. The challenges facing biochips are similar to those faced by microelectronics some decades ago. To meet the challenges of increasing design complexity, computer-aided-design (CAD) tools are being developed for DMFBs. This paper provides an overview of DMFBs and describes emerging CAD tools for the automated synthesis and optimization of DMFB designs, from fluidic-level synthesis and chip-level design to testing. Design automations are expected to alleviate the burden of manual optimization of bioassays, time-consuming chip designs, and costly testing and maintenance procedures. With the assistance of CAD tools, users can concentrate on the development and abstraction of nanoscale bioassays while leaving chip optimization and implementation details to CAD tools.

Digital microfluidic operations on micro-electrode dot array architecture

Abstract: As digital microfluidics-based biochips find more applications, their complexity is expected to increase significantly owing to the trend of multiple and concurrent assays on the chip. There is a pressing need to deliver a top-down design methodology that the biochip designer can leverage the same level of computer-aided design support as the semi-conductor industry now does. Moreover, as microelectronics fabrication technology is scaling up and integrated device performance is improving, it is expected that these microfluidic biochips will be integrated with microelectronic components in next-generation system-on-chip designs. This study presents the analysis and experiments of digital microfluidic operations on a novel electrowetting-on-dielectric-based `micro-electrode dot array architecture` that fosters a development path for hierarchical top-down design approach for digital microfluidics. The proposed architecture allows dynamic configurations and activations of identical basic microfluidic unit called `micro-electrode cells` to design microfluidic components, layouts, routing, microfluidic operations and applications of the biochip hierarchically. Fundamental microfluidic operations have been successfully performed by the architecture. In addition, this novel architecture demonstrates a number of advantages and flexibilities over the conventional digital microfluidics in performing advanced microfluidic operations.

Online monitoring of water toxicity by use of bioluminescent reporter bacterial biochips.

Abstract: We describe a flow-through biosensor for online continuous water toxicity monitoring. At the heart of the device are disposable modular biochips incorporating agar-immobilized bioluminescent recombinant reporter bacteria, the responses of which are probed by single-photon avalanche diode detectors. To demonstrate the biosensor capabilities, we equipped it with biochips harboring both inducible and constitutive reporter strains and exposed it to a continuous water flow for up to 10 days. During these periods we challenged the biosensor with 2-h pulses of water spiked with model compounds representing different classes of potential water pollutants, as well as with a sample of industrial wastewater. The biosensor reporter panel detected all simulated contamination events within 0.5–2.5 h, and its response was indicative of the nature of the contaminating chemicals. We believe that a biosensor of the proposed design can be integrated into future water safety and security networks, as part of an early warning...

Simple One-Step Process for Immobilization of Biomolecules on Polymer Substrates Based on Surface-Attached Polymer Networks

Abstract: For the miniaturization of biological assays, especially for the fabrication of microarrays, immobilization of biomolecules at the surfaces of the chips is the decisive factor. Accordingly, a variety of binding techniques have been developed over the years to immobilize DNA or proteins onto such substrates. Most of them require rather complex fabrication processes and sophisticated surface chemistry. Here, a comparatively simple immobilization technique is presented, which is based on the local generation of small spots of surface attached polymer networks. Immobilization is achieved in a one-step procedure: probe molecules are mixed with a photoactive copolymer in aqueous buffer, spotted onto a solid support, and cross-linked as well as bound to the substrate during brief flood exposure to UV light. The described procedure permits spatially confined surface functionalization and allows reliable binding of biological species to conventional substrates such as glass microscope slides as well as various types of plastic substrates with comparable performance. The latter also permits immobilization on structured, thermoformed substrates resulting in an all-plastic biochip platform, which is simple and cheap and seems to be promising for a variety of microdiagnostic applications.

Waste-aware dilution and mixing of biochemical samples with digital microfluidic biochips

Abstract: A key challenge in design automation of digital microfluidic biochips is to carry out on-chip dilution/mixing of biochemical samples/reagents for achieving a desired concentration factor (CF). In a bioassay, reducing the waste is crucial because the waste droplet handling is cumbersome and the number of waste reservoirs on-chip needs to be minimized to use limited volume of sample and expensive reagents and hence to reduce the cost of a biochip. The existing dilution algorithms attempt to reduce the number of mix/split steps required in the process but focus little on minimization of sample requirement or waste droplets. In this work, we characterize the underlying combinatorial properties of waste generation and identify the inherent limitations of two earlier mixing algorithms (BS algorithm by Thies et al., Natural Computing 2008; DMRW algorithm by Roy et al., IEEE TCAD 2010) in addressing this issue. Based on these properties, we design an improved dilution/mixing algorithm (IDMA) that optimizes the usage of intermediate droplets generated during the dilution process, which in turn, reduces the demand of sample/reagent and production of waste. The algorithm terminates in O(n) steps for producing a target CF with a precision of 1/2n. Based on simulation results for all CF values ranging from 1/1024 to 1023/1024 using a sample (100% concentration) and a buffer solution (0% concentration), we present an integrated scheme of choosing the best waste-aware dilution algorithm among BS, DMRW, and IDMA for any given value of CF. Finally, an architectural layout of a DMF biochip that supports the proposed scheme is designed.

EIS microfluidic chips for flow immunoassay and ultrasensitive cholera toxin detection.

Abstract: A flow-injection impedimetric immunosensor for the sensitive, direct and label-free detection of cholera toxin is reported. A limit of detection smaller than 10 pM was achieved, a value thousands of times lower than the lethal dose. The developed chips fulfil the requirement of low cost and quick reply of the assay and are expected to enable field screening, prompt diagnosis and medical intervention without the need of specialized personnel and expensive equipment, a perspective of special relevance for use in developing countries. Since the chip layout includes two sensing areas each one with a 2 × 2 sensor array, our biochips can allow statistical or (alternatively) multiplex analysis of biorecognition events between antibodies immobilized on each working electrode and different antigens flowing into the chamber.

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. This paper presents the first design automation flow that considers the cross-contamination problems on pin-constrained biochips. The factors that make the problems harder on pin-constrained biochips are explored. To cope with these cross contaminations, this paper proposes: 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.

System-level modeling and synthesis of flow-based microfluidic biochips

Abstract: Microfluidic biochips are replacing the conventional biochemical analyzers and are able to integrate the necessary functions for biochemical analysis on-chip. There are several types of microfluidic biochips, each having its advantages and limitations. In this paper we are interested in flow-based biochips, in which the flow of liquid is manipulated using integrated microvalves. By combining several microvalves, more complex units, such as micropumps, switches, mixers, and multiplexers, can be built. Although researchers have proposed significant work on the system-level synthesis of droplet-based biochips, which manipulate droplets on a two-dimensional array of electrodes, no research on system-level synthesis of flow-based bioch-ips has been reported so far. The focus has been on application modeling and component-level simulation. Therefore, for the first time to our knowledge, we propose a system-level modeling and synthesis approach for flow-based biochips. We have developed a topology graph-based model of the biochip architecture, and we have used a sequencing graph to model the biochemical applications. We consider that the architecture of the biochip is given, and we are interested to synthesize an implementation, consisting of the binding of operations in the application to the functional units of the architecture, the scheduling of operations and the routing and scheduling of the fluid flows, such that the application completion time is minimized. We propose a List Scheduling-based heuristic for solving this problem. The proposed heuristic has been evaluated using two real-life case studies and a set of four synthetic benchmarks.

Reliability-oriented broadcast electrode-addressing for pin-constrained digital microfluidic biochips

Abstract: Designs for pin-constrained digital microfluidic biochips (PDMFBs) are receiving much attention because they simplify chip fabrication and packaging, and reduce product cost. To reduce the pin count, broadcast addressing, by minimally grouping electrode sets with non-conflict signal merging, has emerged as a promising solution. Nevertheless, naive signal merging has the potential to cause excessive electrode actuations, which has been reported to have direct and adverse effect on chip reliability. According to recent studies, reliability is an important attribute for PDMFBs particularly developed for medical applications as it directly affects the final medical decision making. However, no research findings have been reported on the reliability problem in pin-constrained designs. To make PDMFBs more feasible for practical applications, we propose in this paper the first matching-based reliability-oriented broadcast-addressing algorithm for PDMFBs. We identify the factors that affect reliability and incorporate into the design-technique attributes that enhance reliability. Experimental results demonstrate the effectiveness of the proposed algorithm.

Digital microfluidic operations on micro-electrode array architecture

Abstract: As digital microfluidics-based biochips find more applications, their complexity is expected to increase significantly due to the trend of multiple and concurrent assays on the chip. There is a pressing need to deliver a top-down design methodology that the biochip designer can leverage the same level of computer aided design support as the semiconductor industry now does. Moreover, as microelectronics fabrication technology scaling and integrated device performance improving, it is expected that these microfluidic biochips will be integrated with microelectronic components in next-generation system-on-chip designs. This paper presents a novel electrowetting-on-dielectric (EWOD) based “micro-electrode array architecture” that fosters a development path for hierarchical top-down design approach for digital microfluidics, and also allows easy integration of microfluidics and microelectronics on a single chip. In addition, this novel architecture provides a number of advantages and flexibilities over the conventional digital microfluidics such as dynamic activations of variable-sized electrodes and dynamic manipulations of multiple droplets.

Microfabrication of biomedical lab-on-chip devices. A review

Abstract: Lab-on-chip systems are a class of miniaturized analytical devices that integrate fluidics, electronics and various sensorics. They are capable of analysing biochemical liquid samples, like solutions of metabolites, macromolecules, proteins, nucleic acids, or cells and viruses. Supple- mentary to their measuring capabilities, the lab-on-chip devices facilitate fluidic transportation, sorting, mixing, or separation of liquid samples. A type of lab-on-chip devices, named biochip, is devoted specifically to genomic, proteomic and pharmaceutical tests. The significance of such miniaturized devices lies in their potentiality of automating laboratory procedures, which highly reduces the time of biomedical tests and laboratory work. This review summarizes numerous fabrication methods and procedures for producing lab-on-chip devices and also envisages future evolution.

Unitary biochip providing sample-in to results-out processing and methods of manufacture

Abstract: A biochip for the integration of all steps in a complex process from the insertion of a sample to the generation of a result, performed without operator intervention includes microfluidic and macrofluidic features that are acted on by instrument subsystems in a series of scripted processing steps Methods for fabricating these complex biochips of high feature density by injection molding are also provided

Droplet routing in high-level synthesis of configurable digital microfluidic biochips based on microelectrode dot array architecture

Abstract: Droplet-based digital microfluidic lab-on-chips exploiting electrowetting-on-dielectric (EWOD) have been studied over the last decade. With the recent introduction of new highly scalable, reconfigurable and field-programmable microelectrode dot array (MEDA) architecture, there is a compelling need for a new digital microfluidics synthesizer for the new MEDA architecture. Droplet routing is a critical part of the digital microfluidics synthesizer. This paper presents a routing algorithm and the associated performance analysis results. The algorithm is able to route different sizes of reagent and sample droplets simultaneously and also incorporates other characteristics such as diagonal movements and channel-based movements that are specific to the MEDA architecture.

Layout-Aware Solution Preparation for Biochemical Analysis on a Digital Microfluidic Biochip

Abstract: A biochemical analysis is based on several laboratory protocols that require repeated mixing of samples with reagents. Sample preparation and analyte identification steps in such bioassays often involve mixing for solution preparation, i.e., various fluids are to be mixed in a certain volumetric ratio in their resulting mixture. We present an efficient approach for automated mixing of three or more fluids on a droplet based digital micro fluidic biochip and design a layout for implementing this algorithm. The proposed method reduces the droplet transportation time from boundary reservoirs to on chip mixers as well as cross-contamination among overlapping droplet routing paths. Simulation of several example solutions reveals encouraging results.

Integrated Proteomic and Transcriptomic Investigation of the Acetaminophen Toxicity in Liver Microfluidic Biochip

Abstract: Microfluidic bioartificial organs allow the reproduction of in vivo-like properties such as cell culture in a 3D dynamical micro environment. In this work, we established a method and a protocol for performing a toxicogenomic analysis of HepG2/C3A cultivated in a microfluidic biochip. Transcriptomic and proteomic analyses have shown the induction of the NRF2 pathway and the related drug metabolism pathways when the HepG2/C3A cells were cultivated in the biochip. The induction of those pathways in the biochip enhanced the metabolism of the N-acetyl-p-aminophenol drug (acetaminophen-APAP) when compared to Petri cultures. Thus, we observed 50% growth inhibition of cell proliferation at 1 mM in the biochip, which appeared similar to human plasmatic toxic concentrations reported at 2 mM. The metabolic signature of APAP toxicity in the biochip showed similar biomarkers as those reported in vivo, such as the calcium homeostasis, lipid metabolism and reorganization of the cytoskeleton, at the transcriptome and proteome levels (which was not the case in Petri dishes). These results demonstrate a specific molecular signature for acetaminophen at transcriptomic and proteomic levels closed to situations found in vivo. Interestingly, a common component of the signature of the APAP molecule was identified in Petri and biochip cultures via the perturbations of the DNA replication and cell cycle. These findings provide an important insight into the use of microfluidic biochips as new tools in biomarker research in pharmaceutical drug studies and predictive toxicity investigations.

A Nanomembrane-Based Nucleic Acid Sensing Platform for Portable Diagnostics

Abstract: In this perspective article, we introduce a potentially transformative DNA/RNA detection technology that promises to replace DNA microarray and real-time PCR for field applications. It represents a new microfluidic technology that fully exploits the small spatial dimensions of a biochip and some new phenomena unique to the micro- and nanoscales. More specifically, it satisfies all the requisites for portable on-field applications: fast, small, sensitive, selective, robust, label- and reagent-free, economical to produce, and possibly PCR-free. We discuss the mechanisms behind the technology and introduce some preliminary designs, test results, and prototypes.

Broadcast Electrode-Addressing and Scheduling Methods for Pin-Constrained 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 2-D 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 printed circuit board 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. We present a broadcast-addressing-based design technique for pin-constrained multifunctional 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. We also describe two scheduling methods to map fluidic operations on the pin-constrained design, in order to minimize the completion time while avoiding pin-actuation conflicts. The proposed methods are evaluated using multifunctional chips designed to execute a set of multiplexed bioassays, the polymerase chain reaction, and a protein dilution assay.

Rapid microarray detection of DNA and proteins in microliter volumes with surface plasmon resonance imaging measurements.

Abstract: A four-chamber microfluidic biochip is fabricated for the rapid detection of multiple proteins and nucleic acids from microliter volume samples with the technique of surface plasmon resonance imaging (SPRI). The 18 mm × 18 mm biochip consists of four 3 μL microfluidic chambers attached to an SF10 glass substrate, each of which contains three individually addressable SPRI gold thin film microarray elements. The 12-element (4 × 3) SPRI microarray consists of gold thin film spots (1 mm2 area; 45 nm thickness), each in individually addressable 0.5 μL volume microchannels. Microarrays of single-stranded DNA and RNA (ssDNA and ssRNA, respectively) are fabricated by either chemical and/or enzymatic attachment reactions in these microchannels; the SPRI microarrays are then used to detect femtomole amounts (nanomolar concentrations) of DNA and proteins (ssDNA binding protein and thrombin via aptamer−protein bioaffinity interactions). Microarrays of ssRNA microarray elements are also used for the ultrasensitive det...

Co-integrated microfluidic and THz functions for biochip devices

Abstract: TeraHertz (THz) spectroscopy is becoming an alternative way to probe biological interactions in real-time conditions. However, accurate and reproducible THz measurements of aqueous solutions, largely represented in life sciences, remain difficult. A THz microsystem which couples both electromagnetic and microfluidic integrated functions is presented here. Its technological process is accurately detailed and enables easy designs of advanced THz and microfluidic functions. It is composed of the deposition of gold wires on a glass wafer to guide the THz waves. Then, a whole silicon wafer is bonded by using a thermosensitive-polymer thermo-compression. Silicon is deep-etched to create the microchannels which are finally covered with a second glass wafer. This bonding–etching process enables huge freedom and independence for electromagnetic and microfluidic designs. The technological process characterization has shown that the manufactured biochip is compatible with pressures up to 37 bar. First measurements with empty and water-filled channels have been carried out and have shown the ability to perform THz spectroscopy inside the chip. Then, first measurements on proteins have been performed and shown the system ability to probe protein concentration. This kind of microfluidic microsystem, allowing complex design for integrated electronic and microfluidic circuits, defines a true new instrumental way for life science investigations.

Gel-based microarrays in clinical diagnostics in Russia.

Abstract: Immobilization of molecular probes in 3D hydrogel elements provides some essential advantages compared with conventional flat surfaces. In this article, an integrated technology based on the use of low-density microarrays comprised of hemispherical gel elements, developed at the Engelhardt Institute of Molecular Biology (Moscow, Russia) for various applications will be reviewed. The structure of the gel can be adapted for immobilization of virtually any biological molecules in a natural hydrophilic environment. The discrimination between matching and mismatching duplexes of nucleic acids in these conditions is more reliable than on conventional flat surfaces, minimizing the number of elements needed to detect specific sequences. Protein molecules immobilized in hydrogel-based biochips better preserve their biological properties. As described in this article, such biochips were successfully applied for laboratory diagnostics in a wide variety of clinical conditions involving the identification of bacterial and viral pathogens, cancer-related mutations and protein tumor markers.

Design and realization of a microfluidic device devoted to the application of ultra-short pulses of electrical field to living cells

Abstract: In this paper, we present a novel microfluidic system dedicated to the application of ultra short pulses (i.e. nanopulses) on cells and the visualization of their effects. Cell plasma membranes can be rendered permeable by the use of nanosecond pulsed electric field. In conventional macroscopic electroporation chambers, the typical pulse duration is on the order of several hundred microseconds (micropulses), which allows the penetration of genes or other therapeutic molecules inside the cell. Consequently, electroporation pulses can be used in various clinical applications such as skin cancer treatment. A huge interest recently appeared on the use of ultra-short electric pulses (few nanoseconds) for the treatment of cells, as it was shown to enhance the treatment efficacy compared to micropulses. In this paper, the design, fabrication and biological validation of a microfluidic biochip optimized for the nanoporation of cells is detailed. The developed system presents several advantages such as real time monitoring of the effects of nanoporation on cells, single cell analysis, local generation of extremely high strength electrical fields while using reasonably low voltages and the precise control of electrical and fluidic parameters. To achieve the required spatial homogeneity of the electric field within the fluidic channel, the biochip includes thick electroplated gold electrodes (t = 6–30 μm). As demonstrated in the paper, the electrical connections between the chip and the nsPEF generator are of prime importance, as it affects directly the quality of the impedance matching i.e. the transfert of energy between the generator and the cells. A study of the effects of these electrical connections on the biochip impedance is detailed. Nanoporation was achieved on living cells within the proposed chip, and characterized through the measurement of the fluorescence decay of intracellular calcein.