Showing papers on "Biochip published in 2020"
TL;DR: A microfluidic Raman biochip designed to isolate and analyze exosomes in situ was developed and successfully applied in the determination ofExosomes from clinical serum samples and may have potential as a clinical exosome analysis tool for prostate cancer.
Abstract: Tumor-derived exosomes, which contain RNA, DNA, and proteins, are a potentially rich non-invasive source of biomarkers. However, no efficient isolation or detection methods are yet available. Here, we developed a microfluidic Raman biochip designed to isolate and analyze exosomes in situ. Anti-CD63 magnetic nanoparticles were used to enrich exosomes through mixing channels of a staggered triangular pillar array. EpCAM-functionalized Raman-active polymeric nanomaterials (Raman beads) allow rapid analysis of exosome samples within 1 h, with a quantitative signal at 2230 cm-1. The limit of detection of this biochip approaches 1.6 × 102 particles per mL with 20 μL samples. The newly developed biochip assay was successfully applied in the determination of exosomes from clinical serum samples. Thus, this novel device may have potential as a clinical exosome analysis tool for prostate cancer.
64 citations
TL;DR: This study investigates the design and numerical simulation of an integrated microfluidic device, including a cell separation unit for isolating CTCs from a blood sample and a micromixer unit for cell lysis on a rotating disk platform.
Abstract: Separation of circulating tumor cells (CTCs) from blood samples and subsequent DNA extraction from these cells play a crucial role in cancer research and drug discovery. Microfluidics is a versatile technology that has been applied to create niche solutions to biomedical applications, such as cell separation and mixing, droplet generation, bioprinting, and organs on a chip. Centrifugal microfluidic biochips created on compact disks show great potential in processing biological samples for point of care diagnostics. This study investigates the design and numerical simulation of an integrated microfluidic device, including a cell separation unit for isolating CTCs from a blood sample and a micromixer unit for cell lysis on a rotating disk platform. For this purpose, an inertial microfluidic device was designed for the separation of target cells by using contraction–expansion microchannel arrays. Additionally, a micromixer was incorporated to mix separated target cells with the cell lysis chemical reagent to dissolve their membranes to facilitate further assays. Our numerical simulation approach was validated for both cell separation and micromixer units and corroborates existing experimental results. In the first compartment of the proposed device (cell separation unit), several simulations were performed at different angular velocities from 500 rpm to 3000 rpm to find the optimum angular velocity for maximum separation efficiency. By using the proposed inertial separation approach, CTCs, were successfully separated from white blood cells (WBCs) with high efficiency (~90%) at an angular velocity of 2000 rpm. Furthermore, a serpentine channel with rectangular obstacles was designed to achieve a highly efficient micromixer unit with high mixing quality (~98%) for isolated CTCs lysis at 2000 rpm.
37 citations
TL;DR: It is demonstrated that such an optofluidic biochip can measure horseradish peroxidase (HRP)-streptavidin via chromogenic reaction at the concentration level of 0.3 ng mL-1, which is over 2 orders of magnitude better than the ability of current commercial ELISA kits.
Abstract: Optical whispering-gallery-mode (WGM) microcavities offer great promise in ultrasensitive biosensors because of their unique ability to enable resonant recirculation of light to achieve strong light-matter interactions in microscale volumes. However, it remains a challenge to develop cost-effective, high-performance WGM microcavity-based biosensing devices for practical disease diagnosis applications. In this paper, we present an optofluidic chip that is integrated with directly-printed, high-quality-factor (Q) polymer WGM microlaser sensors for ultrasensitive enzyme-linked immunosorbent assay (ELISA). Optical 3D μ-printing technology based on maskless ultraviolet lithography is developed to rapidly fabricate high-Q suspended-disk WGM microcavities. After deposition with a thin layer of optical gain material, low-threshold WGM microlasers are fabricated and then integrated together with optical fibres upon a microfluidic chip to achieve an optofluidic device. With flexible microfluidic technology, on-chip, integrated, WGM microlasers are further modified in situ with biomolecules on surface for highly selective biomarker detection. It is demonstrated that such an optofluidic biochip can measure horseradish peroxidase (HRP)-streptavidin, which is a widely used catalytic molecule in ELISA, via chromogenic reaction at the concentration level of 0.3 ng mL-1. Moreover, it enables on-chip optofluidic ELISA of the disease biomarker vascular endothelial growth factor (VEGF) at the extremely low concentration level of 17.8 fg mL-1, which is over 2 orders of magnitude better than the ability of current commercial ELISA kits.
28 citations
07 Oct 2020
TL;DR: It is envisioned that such a chip has potential applications in single‐cell studies, tumor heterogeneity studies, and perhaps in point‐of‐care cancer diagnostics—especially in developing countries where the cost, limited infrastructures, and limited access to medical technologies are of the utmost importance.
Abstract: Cancers are a complex conglomerate of heterogeneous cell populations with varying genotypes and phenotypes. The intercellular heterogeneity within the same tumor and intratumor heterogeneity within various tumors are the leading causes of resistance to cancer therapies and varied outcomes in different patients. Therefore, performing single-cell analysis is essential to identify and classify cancer cell types and study cellular heterogeneity. Here, the development of a machine learning-assisted nanoparticle-printed biochip for single-cell analysis is reported. The biochip is integrated by combining powerful machine learning techniques with easily accessible inkjet printing and microfluidics technology. The biochip is easily prototype-able, miniaturized, and cost-effective, potentially capable of differentiating a variety of cell types in a label-free manner. n-feature classifiers are established and their performance metrics are evaluated. The biochip's utility to discriminate noncancerous cells from cancerous cells at the single-cell level is demonstrated. The biochip's utility in classifying cancer sub-type cells is also demonstrated. It is envisioned that such a chip has potential applications in single-cell studies, tumor heterogeneity studies, and perhaps in point-of-care cancer diagnostics-especially in developing countries where the cost, limited infrastructures, and limited access to medical technologies are of the utmost importance.
24 citations
TL;DR: This paper forms the first practical timing-driven flow-channel network construction problem for FBMBs and presents a performance-driven placement and routing algorithm for solving this problem.
Abstract: The emergence of flow-based microfluidic biochips (FBMBs) has increased the automation level of biochemical procedures, and these lab-on-a-chip devices are now being used for enzyme-linked immunosorbent assay, point-of-care diagnosis, etc. As fabrication technology advances, the feature size of FBMBs keeps shrinking, thereby introducing a series of knotty challenges to the physical design of FBMBs. In particular, timing-sensitive bioassays, such as forensic DNA typing and chromatin immunoprecipitation, require a highly accurate time-control of fluids within a limited completion time. However, existing work does not consider the real-time requirements of these bioassays. In this paper, we formulate the first practical timing-driven flow-channel network construction problem for FBMBs and present a performance-driven placement and routing algorithm for solving this problem. Given the design specifications of a biochip and its biochemistry application, our goal is to construct a high-quality flow-channel network with minimized timing delay and total cost. The experimental results on 14 benchmarks confirm that our algorithm leads to better timing behavior and lower chip cost.
24 citations
TL;DR: A vertical nanogap architecture with an electrode-insulator-electrode stack structure is proposed, facilitating the generation of strong dielectrophoretic forces at low voltages, to precisely capture and spatiotemporally manipulate nanoparticles and molecular assemblies, including lipid vesicles and amyloid-beta protofibrils/oligomers.
Abstract: Toward the development of surface-sensitive analytical techniques for biosensors and diagnostic biochip assays, a local integration of low-concentration target materials into the sensing region of interest is essential to improve the sensitivity and reliability of the devices. As a result, the dynamic process of sorting and accurate positioning the nanoparticulate biomolecules within pre-defined micro/nanostructures is critical, however, it remains a huge hurdle for the realization of practical surface-sensitive biosensors and biochips. A scalable, massive, and non-destructive trapping methodology based on dielectrophoretic forces is highly demanded for assembling nanoparticles and biosensing tools. Herein, we propose a vertical nanogap architecture with an electrode-insulator-electrode stack structure, facilitating the generation of strong dielectrophoretic forces at low voltages, to precisely capture and spatiotemporally manipulate nanoparticles and molecular assemblies, including lipid vesicles and amyloid-beta protofibrils/oligomers. Our vertical nanogap platform, allowing low-voltage nanoparticle captures on optical metasurface designs, provides new opportunities for constructing advanced surface-sensitive optoelectronic sensors.
23 citations
TL;DR: A PDMS/glass microfluidic biochip integrated with aptamer-modified Ag10NPs nano-biosensors was developed for rapid, simple and specific pathogenic bacteria detection and its potential for the rapid detection of antibiotic-resistant bacteria is demonstrated.
21 citations
TL;DR: This article presents a generic multiple-reactant sample preparation algorithm that exploits the novel fluidic operations on MEDA biochips and proposes an enhanced algorithm that increases the operation-sharing opportunities when multiple target concentrations are needed, and therefore the usage of reactants can be further reduced.
Abstract: Sample preparation, as a key procedure in many biochemical protocols, mixes various samples, and/or reagents into solutions that contain the target concentrations. Digital microfluidic biochips (DMFBs) have been adopted as a platform for sample preparation because they provide automatic procedures that require less reactant consumption and reduce human-induced errors. However, the most existing methods only consider two-reactant sample preparation, and they cannot be used for many biochemical applications that involve multiple reactants. In addition, the existing methods that can be used for multiple-reactant sample preparation were proposed on traditional DMFBs where only the (1:1) mixing model is available. In the (1:1) mixing model, only two droplets of the same volume can be mixed at a time, which results in higher completion time and the wastage of valuable reactants. To overcome this limitation, the micro-electrode-dot-array (MEDA) architecture has been introduced; it provides the flexibility of mixing multiple droplets of different volumes in a single operation. In this article, we present a generic multiple-reactant sample preparation algorithm that exploits the novel fluidic operations on MEDA biochips. We also propose an enhanced algorithm that increases the operation-sharing opportunities when multiple target concentrations are needed, and therefore the usage of reactants can be further reduced. The simulated experiments show that the proposed method outperforms existing methods in terms of saving reactant cost, minimizing the number of operations, and reducing the amount of waste.
15 citations
TL;DR: An unprecedented green-chemistry strategy to produce single-cell capture biochips onto glass surfaces by all-aqueous inkjet printing and enables one to modulate the collagen area available for cell attachment in order to control the number of captured cells per spot.
Abstract: Single-cell microarrays are emerging tools to unravel intrinsic diversity within complex cell populations, opening up new approaches for the in-depth understanding of highly relevant diseases. However, most of the current methods for their fabrication are based on cumbersome patterning approaches, employing organic solvents and/or expensive materials. Here, we demonstrate an unprecedented green-chemistry strategy to produce single-cell capture biochips onto glass surfaces by all-aqueous inkjet printing. At first, a chitosan film is easily inkjet printed and immobilized onto hydroxyl-rich glass surfaces by electrostatic immobilization. In turn, poly(ethylene glycol) diglycidyl ether is grafted on the chitosan film to expose reactive epoxy groups and induce antifouling properties. Subsequently, microscale collagen spots are printed onto the above surface to define the attachment area for single adherent human cancer cells harvesting with high yield. The reported inkjet printing approach enables one to modulate the collagen area available for cell attachment in order to control the number of captured cells per spot, from single-cells up to double- and multiple-cell arrays. Proof-of-principle of the approach includes pharmacological treatment of single-cells by the model drug doxorubicin. The herein presented strategy for single-cell array fabrication can constitute a first step toward an innovative and environmentally friendly generation of aqueous-based inkjet-printed cellular devices.
14 citations
Proceedings Article•
12 Jul 2020TL;DR: It is shown that casting droplet transportation as an RL problem enables the training of deep network policies to capture the underlying health conditions of electrodes and provide reliable fluidic operations.
Abstract: We present and investigate a novel application domain for deep reinforcement learning (RL): droplet routing on digital microfluidic biochips (DMFBs). A DMFB, composed of a twodimensional electrode array, manipulates discrete fluid droplets to automatically execute biochemical protocols such as point-of-care clinical diagnosis. However, a major concern associated with the use of DMFBs is that electrodes in a biochip can degrade over time. Droplet-transportation operations associated with the degraded electrodes can fail, thereby compromising the integrity of the bioassay outcome. We show that casting droplet transportation as an RL problem enables the training of deep network policies to capture the underlying health conditions of electrodes and provide reliable fluidic operations. We propose a new RLbased droplet-routing flow that can be used for various sizes of DMFBs, and demonstrate reliable execution of an epigenetic bioassay with the RL droplet router on a fabricated DMFB. To facilitate further research, we also present a simulation environment based on the OpenAI Gym Interface for RL-guided droplet-routing problems on DMFBs.
13 citations
TL;DR: Roll-to-roll UV nanoimprint lithography has superior advantages for high-throughput manufacturing of micro- or nano-structures on flexible polymer foils with various geometries and configurations and to enhance the light out-coupling thus to improve the system performance, optical structures were integrated into the design.
Abstract: Roll-to-roll UV nanoimprint lithography has superior advantages for high-throughput manufacturing of micro- or nano-structures on flexible polymer foils with various geometries and configurations. Our pilot line provides large-scale structure imprinting for cost-effective polymer biochips (4500 biochips/hour), enabling rapid and multiplexed detections. A complete high-volume process chain of the technology for producing structures like μ-sized, triangular optical out-couplers or capillary channels (width: from 1 μm to 2 mm, height: from 200 nm up to 100 μm) to obtain biochips (width: 25 mm, length: 75 mm, height: 100 μm to 1.5 mm) was described. The imprinting process was performed with custom-developed resins on polymer foils with resin thicknesses ranging between 125–190 μm. The produced chips were tested in a commercial point-of-care diagnostic system for multiplexed DNA analysis of methicillin resistant Staphylococcus aureus (e.g., mecA, mecC gene detections). Specific target DNA capturing was based on hybridisation between surface bound DNA probes and biotinylated targets from the sample. The immobilised biotinylated targets subsequently bind streptavidin–horseradish peroxidase conjugates, which in turn generate light upon incubation with a chemiluminescent substrate. To enhance the light out-coupling thus to improve the system performance, optical structures were integrated into the design. The limits-of-detection of mecA (25 bp) for chips with and without structures were calculated as 0.06 and 0.07 μM, respectively. Further, foil-based chips with fluidic channels were DNA functionalised in our roll-to-roll micro-array spotter following the imprinting. This straightforward approach of sequential imprinting and multiplexed DNA functionalisation on a single foil was also realised for the first time. The corresponding foil-based chips were able to detect mecA gene DNA sequences down to a 0.25 μM concentration.
TL;DR: This article proposes the first artificial neural network (ANN)-based design method for flow-based microfluidic biochips, which accurately generates the customized concentration gradients and validates the accuracy of the proposed neural network model.
Abstract: According to the complexity of human physiology and variability among individuals, e.g., genes, environment, lifestyle exposures, etc., personalized medicine aims to synthesize the specific efficacious drug for each individual patient. For synthesizing personalized medicine, customized solutions with specific concentrations are required. Equipped with the advantages in saving costly reagents and rare samples, microfluidic biochips are promising in generating different concentrations for personalized medicine. On the one hand, digital microfluidic biochips require the programming control for driving the movement of the droplets, which suffer from random errors caused by imbalanced droplet splitting. On the other hand, existing flow-based microfluidic biochips can only generate linear concentration gradients, which cause significant waste for synthesizing personalized medicine. To address the above issues, this article proposes the first artificial neural network (ANN)-based design method for flow-based microfluidic biochips, which accurately generates the customized concentration gradients. According to the required concentration, an initial chip is first selected from the prebuilt database and then fine-tuned by ANN to better match the required concentration. The computational simulation results show that the induced deviations in generated concentrations are generally less than 0.014, which validates the accuracy of the proposed neural network model.
TL;DR: Various types of in vitro model membrane platforms/techniques are introduced and current challenges in the lipid-membrane-assisted surface-sensitive analytical sensors application are discussed.
Abstract: Lipid membranes and their applications in analytical biochip devices represent a great tool for the study of membrane dynamics and the related biological phenomena. Lipid-membrane-assisted surface-sensitive sensors have employed to provide biological information as they improve molecular survivability as well as rule out incorrect signals arising from unwanted nonspecific binding between target molecules with sensor surfaces. To enhance the accuracy of the signal as well as the sensitivity of biochip sensors, a variety of strategies have been employed. Here, we introduce various types of in vitro model membrane platforms/techniques and discuss current challenges in the lipid-membrane-assisted surface-sensitive analytical sensors application.
TL;DR: The proposed microfluidic electrochemical aptasensing system for the detection of gliadin shows promise in its applicability in real-timegliadin detection.
Abstract: Testing gluten content in food, before it reaches the consumer, becomes a major challenge where cross-contamination during processing and transportation is a very common occurrence. In this study, a microfluidic electrochemical aptasensing system for the detection of gliadin has been proposed. The fabrication of the sensor involves its modification by using a combination of 2D nanomaterial molybdenum disulfide (MoS2)/graphene with the addition of gold (Au) nanoparticles. Aptamers, a short string of nucleotide bases that are very specific to gliadin, were used in this sensor as the biomarker. The electrochemical standard reduction potential of the ferro-ferricyanide indicator was found to be ~ 530 mV. This setup was integrated with a unique polydimethylsiloxane (PDMS)-based flexible microfluidic device for sample enrichment and portability. The results of this sensor show that the limit of detection was 7 pM. The total sample assay time was 20 min and a good linear range was observed from 4 to 250 nM with an R2 value of 0.982. Different flour samples sourced from the local market were tested and interfering molecules were added to ensure selectivity. The study shows promise in its applicability in real-time gliadin detection. Graphical abstract
TL;DR: This paper demonstrates a low-cost home-made “sandwich ring” method which was used to measure the TEER of tissue specimens effectively and inspired the subsequent design of a biochip fabricated using standard soft lithography and laser engraving technologies, with which the TEE of pig epithelial tissues was measured.
Abstract: Trans-epithelial electrical resistance (TEER) is a good indicator of the barrier integrity of epithelial tissues and is often employed in biomedical research as an effective tool to assess ion transport and permeability of tight junctions. The Ussing chamber is the gold standard for measuring TEER of tissue specimens, but it has major drawbacks: it is a macroscopic method that requires a careful and labor intensive sample mounting protocol, allows a very limited viability for the mounted sample, has large parasitic components and low throughput as it cannot perform multiple simultaneous measurements, and this sophisticated and delicate apparatus has a relatively high cost. This paper demonstrates a low-cost home-made "sandwich ring" method which was used to measure the TEER of tissue specimens effectively. This method inspired the subsequent design of a biochip fabricated using standard soft lithography and laser engraving technologies, with which the TEER of pig epithelial tissues was measured. Moreover, it was possible to temporarily preserve the tissue specimens for days in the biochip and monitor the TEER continuously. Tissue responses after exposure tests to media of various pH values were also successfully recorded using the biochip. All these demonstrate that this biochip could be an effective, cheaper, and easier to use Ussing chamber substitute that may have relevant applications in clinical practice.
TL;DR: A simple biochip which can be used to trap and rotate a single cell, or to rotate multiple cells relative to each other within a group of individual red blood cells (RBCs), which is crucial for imaging cells in 3D.
TL;DR: New precisely engineered microparticles that achieve electrical multiplexing and adapt this platform for low-cost and label-free multiplexed electrical detection of biomolecules are reported.
Abstract: Rapid, low-cost, and multiplexed biomolecule detection is an important goal in the development of effective molecular diagnostics. Our recent work has demonstrated a microfluidic biochip device that can electrically quantitate a protein target with high sensitivity. This platform detects and quantifies a target analyte by counting and capturing micron-sized beads in response to an immunoassay on the bead surface. Existing microparticles limit the technique to the detection of a single protein target and lack the magnetic properties required for separation of the microparticles for direct measurements from whole blood. Here, we report new precisely engineered microparticles that achieve electrical multiplexing and adapt this platform for low-cost and label-free multiplexed electrical detection of biomolecules. Droplet microfluidic synthesis yielded highly-monodisperse populations of magnetic hydrogel beads (MHBs) with the necessary properties for multiplexing the electrical Coulter counting on chip. Each bead population was designed to contain a different amount of the hydrogel material, resulting in a unique electrical impedance signature during Coulter counting, thereby enabling unique identification of each bead. These monodisperse bead populations span a narrow range of sizes ensuring that all can be captured sensitively and selectively under simultaneously flow. Incorporating these newly synthesized beads, we demonstrate versatile and multiplexed biomolecule detection of proteins or DNA targets. This development of multiplexed beads for the electrical detection of biomolecules, provides a critical advancement towards multiplexing the Coulter counting approach and the development of a low cost point-of-care diagnostic sensor.
02 Nov 2020
TL;DR: This paper proposes a practical synthesis flow called PathDriver for the design automation of microfluidic biochips, integrating the actual fluid manipulations into both high-level synthesis and physical design, which has never been considered in prior work.
Abstract: Continuous-flow microfluidic biochips have attracted high research interest over the past years. Inside such a chip, fluid samples of milliliter volumes are efficiently transported between devices (e.g., mixers, etc.) to automatically perform various laboratory procedures in biology and biochemistry. Each transportation task, however, requires an exclusive flow path composed of multiple contiguous microchannels during its execution period. Excess/waste fluids, in the meantime, should be discarded by independent flow paths connected to waste ports. All these paths are etched in a very tiny chip area using multilayer soft lithography and driven by flow ports connecting with external pressure sources, forming a highly integrated chip architecture that dominates the performance of biochips. In this paper, we propose a practical synthesis flow called PathDriver for the design automation of microfluidic biochips, integrating the actual fluid manipulations into both high-level synthesis and physical design, which has never been considered in prior work. Given the protocols of biochemical applications, PathDriver aims to generate highly efficient chip architectures with a flow-path network that enables the manipulation of actual fluid transportation and removal. Additionally, fluid volume management between devices and flow-path minimization are realized for the first time, thus ensuring the correctness of assay outcomes while reducing the complexity of chip architectures. Experimental results on multiple benchmarks demonstrate the effectiveness of the proposed synthesis flow.
TL;DR: A control-fluidic codesign methodology is proposed in this paper, along with two demonstrative design flows integrating both fluidic design and control design, suitable for designing biochips with sparse electrodes and relatively larger number of droplets.
Abstract: Paper-based digital microfluidic biochips (P-DMFBs) have recently emerged as a promising low-cost and fast-responsive platform for biochemical assays. In P-DMFBs, electrodes and control lines are printed on a piece of photograph paper using an inkjet printer and carbon nanotubes (CNTs) conductive ink. Compared with traditional digital microfluidic biochips (DMFBs), P-DMFBs enjoy significant advantages, such as faster in-place fabrication with printer and ink, lower costs, and better disposability. Since electrodes and CNT control lines are printed on the same side of this paper, a critical design challenge for P-DMFB is to prevent control interference between moving droplets and the voltages on CNT control lines. Control interference may result in unexpected droplet movements and thus incorrect assay outputs. To address this design challenge, a control-fluidic codesign methodology is proposed in this paper, along with two demonstrative design flows integrating both fluidic design and control design, i.e., the droplet-oriented codesign flow and the electrode-oriented codesign flow. The droplet-oriented flow is suitable for designing biochips with sparse electrodes and relatively larger number of droplets, whereas the electrode-oriented flow is suitable for biochips with dense electrodes and smaller number of droplets. The computational simulation results of real-life bioassays demonstrate the effectiveness of the proposed codesign flows.
TL;DR: This work proposes a security mechanism that validates assay execution by reconstructing the sequencing graph from the droplet-location maps and comparing it against the golden sequencing graph, and proves that there is a unique (one-to-one) mapping from the set ofDroplet- location maps (over the duration of the assay) to theSet of possible sequencing graphs.
Abstract: Digital microfluidic biochips (DMFBs) have emerged as a promising platform for DNA sequencing, clinical chemistry, and point-of-care diagnostics. Recent research has shown that DMFBs are susceptible to various types of malicious attacks. Defenses proposed thus far only offer probabilistic guarantees of security due to the limitation of on-chip sensor resources. A micro-electrode-dot-array (MEDA) biochip is a next-generation DMFB that enables the real-time sensing of on-chip droplet locations, which are captured in the form of a droplet-location map. We propose a security mechanism that validates assay execution by reconstructing the sequencing graph (i.e., the assay specification) from the droplet-location maps and comparing it against the golden sequencing graph. We prove that there is a unique (one-to-one) mapping from the set of droplet-location maps (over the duration of the assay) to the set of possible sequencing graphs. Any deviation in the droplet-location maps due to an attack is detected by this countermeasure because the resulting derived sequencing graph is not isomorphic to the original sequencing graph. We highlight the strength of the security mechanism by simulating attacks on real-life bioassays. We also address the concern that the proposed mechanism may raise false alarms when some fluidic operations are executed on MEDA biochips. To avoid such false alarms, we propose an enhanced sensing technique that provides fine-grained sensing for the security mechanism.
TL;DR: A new nanopatterned slide, upon which carved nanotrenches serve as diffusion barriers, enables a more stable and repeatable investigation of real‐time protein–DNA interactions and will serve as a good platform for lab‐on‐a‐chip.
Abstract: DNA curtain is a high-throughput system, integrating a lipid bilayer, fluorescence imaging, and microfluidics to probe protein-DNA interactions in real-time and has provided in-depth understanding of DNA metabolism. Especially, the microfluidic platform of a DNA curtain is highly suitable for a biochip. In the DNA curtain, DNA molecules are aligned along chromium nanobarriers, which are fabricated on a slide surface, and visualized using an intercalating dye, YOYO-1. Although the chromium barriers confer precise geometric alignment of DNA, reuse of the slides is limited by wear of the barriers during cleaning. YOYO-1 is rapidly photobleached and causes photocleavage of DNA under continuous laser illumination, restricting DNA observation to a brief time window. To address these challenges, we developed a new nanopatterned slide, upon which carved nanotrenches serve as diffusion barriers. The nanotrenches were robust under harsh cleaning conditions, facilitating the maintenance of surface cleanliness that is essential to slide reuse. We also stained DNA with a fluorescent protein with a DNA-binding motif, fluorescent protein-DNA binding peptide (FP-DBP). FP-DBP was slowly photobleached and did not cause DNA photocleavage. This new DNA curtain system enables a more stable and repeatable investigation of real-time protein-DNA interactions and will serve as a good platform for lab-on-a-chip.
TL;DR: The experiments with the patient samples demonstrate that the developed microfluidic platform can perform relative measurements and have a potential to monitor the patient response to the applied therapy and to enable personalized dose adjustment.
Abstract: We report a time and cost-efficient microfluidic chip for screening the leukemia cells having three specific antigens. In this method, the target blast cells are double sorted with immunomagnetic beads and captured by the 3rd antibody immobilized on the gold surface in a microfluidic chip. The captured blast cells in the chip were imaged using a bright-field optical microscope and images were analyzed to quantify the cells. First sorting was performed with nano size immunomagnetic beads and followed by 2nd sorting where micron size immunomagnetic beads were used. The low-cost microfluidic platform is made of PMMA and glass including micro size gold pads. The developed microfluidic platform was optimized with cultured B type lymphoblast cells and tested with the samples of leukemia patients. The 8 bone marrow samples of 4 leukemia patients on the initial diagnosis and on the 15th day after the start of the chemotherapy treatment were tested both with the developed microfluidic platform and the flow cytometry. A 99% statistical agreement between the two methods shows that the microfluidic chip is able to monitor the decrease in the number of blast cells due to the chemotherapy. The experiments with the patient samples demonstrate that the developed system can perform relative measurements and have a potential to monitor the patient response to the applied therapy and to enable personalized dose adjustment.
TL;DR: A hardware design that can efficiently activate/de-activated each IDT, and can fully automate an bio-protocol is presented, and a fault-tolerant synthesis technique that allows us to automatically map biomolecular protocols to acoustofluidic biochips is presented.
Abstract: A digital microfluidic biochip (DMB) is an attractive platform for automating laboratory procedures in microbiology. To overcome the problem of cross-contamination due to fouling of the electrode surface in traditional DMBs, a contactless liquid-handling biochip technology, referred to as acoustofluidics, has recently been proposed. A major challenge in operating this platform is the need for a control signal of frequency 24 MHz and voltage range $\pm 10/\pm 20$ V to activate the IDT units in the biochip. In this paper, we present a hardware design that can efficiently activate/de-activated each IDT, and can fully automate an bio-protocol. We also present a fault-tolerant synthesis technique that allows us to automatically map biomolecular protocols to acoustofluidic biochips. We develop and experimentally validate a velocity model, and use it to guide co-optimization for operation scheduling, module placement, and droplet routing in the presence of IDT faults. Simulation results demonstrate the effectiveness of the proposed synthesis method. Our results are expected to open new research directions on design automation of digital acoustofluidic biochips.
TL;DR: The proposed biochip system for detecting and enumerating human lung carcinoma cell flow in the microfluidic channel is simple-to-operate, inexpensive, portable, and exhibits high sensitivity, which are suitable considerations for developing point-of-care applications.
Abstract: Detection and counting of biological living cells in continuous fluidic flows play an essential role in many applications for early diagnosis and treatment of diseases. In this regard, this study highlighted the proposal of a biochip system for detecting and enumerating human lung carcinoma cell flow in the microfluidic channel. The principle of detection was based on the change of impedance between sensing electrodes integrated in the fluidic channel, due to the presence of a biological cell in the sensing region. A compact electronic module was built to sense the unbalanced impedance between the sensing microelectrodes. It consisted of an instrumentation amplifier stage to obtain the difference between the acquired signals, and a lock-in amplifier stage to demodulate the signals at the stimulating frequency as well as to reject noise at other frequencies. The performance of the proposed system was validated through experiments of A549 cells detection as they passed over the microfluidic channel. The experimental results indicated the occurrence of large spikes (up to approximately 180 mV) over the background signal according to the passage of a single A549 cell in the continuous flow. The proposed device is simple-to-operate, inexpensive, portable, and exhibits high sensitivity, which are suitable considerations for developing point-of-care applications.
TL;DR: A pin addressing method based on a support vector machine (SVM) with the reliability constraint algorithm, which can fully consider the electrode addressing method and the reliability of the chip together is proposed.
Abstract: Digital microfluidic biochips (DMFBs) are increasingly important and are used for point-of-care, drug discovery, clinical diagnosis, immunoassays, etc. Pin-constrained DMFBs are an important part of digital microfluidic biochips, and they have gained increasing attention from researchers. However, many previous works have focused on the problem of electrode addressing and aimed to minimize the number of control pins in pin-constrained DMFBs. Although the number of control pins can be effectively redistributed through broadcast addressing technology, the chip reliability will be reduced if the signals are shared arbitrarily. Arbitrary signal sharing can lead to a large number of actuations for many idle electrodes, and as a result, a trapping charge or decreasing contact angle problem could occur for some electrodes, reducing the reliability of the chip. To address this problem, the appropriate electrode matching object should be carefully selected, and the influence of these factors on chip reliability should be fully considered. For this purpose, we aimed to fully consider electrode addressing and the reliability of the chip in improving the reliability of DMFBs. This paper proposed a pin addressing method based on a support vector machine (SVM) with the reliability constraint algorithm, which can fully consider the electrode addressing method and the reliability of the chip together. The proposed method achieved an average maximum number of electrode actuations that was 53.8% and 18.2% smaller than those of the baseline algorithm and the graph-based algorithm, respectively. The simulation experiment results showed that the proposed method can efficiently solve reliability problems during the DMFB design process.
TL;DR: The total number of droplet-sensing operations is reduced to only 0.7%, which prolongs the lifespan of a MEDA biochip by $11\times $ without any impact on bioassay time-to-response.
Abstract: A digital microfluidic biochip (DMFB) enables miniaturization of immunoassays, point-of-care clinical diagnostics, and DNA sequencing. A recent generation of DMFBs uses a micro-electrode-dot-array (MEDA) architecture, which provides fine-grained control of droplets and real-time droplet sensing using the CMOS technology. However, microelectrodes in a MEDA biochip degrade when they are charged and discharged frequently during bioassay execution. In this article, we first make the key observation that the droplet-sensing operations contribute up to 94% of all microelectrode actuation in MEDA. Consequently, to reduce the number of droplet-sensing operations, we present a new microelectrode cell (MC) design as well as a selective-sensing method such that only a small fraction of microelectrodes perform droplet sensing during bioassay execution. The selection of microelectrodes that need to perform the droplet sensing is based on an analysis of experimental data. A comprehensive set of simulation results show that the total number of droplet-sensing operations is reduced to only 0.7%, which prolongs the lifespan of a MEDA biochip by $11\times $ without any impact on bioassay time-to-response.
TL;DR: A multi-target dilution algorithm (MTDA) for continuous-flow-based microfluidic biochips is presented, which to the best of the authors' knowledge is the first of its kind, and a flow-based rotary mixer with a suitable number of segments depending on the target-CF profile, error tolerance, and optimization criteria is designed.
Abstract: Microfluidic technologies enable replacement of time-consuming and complex steps of biochemical laboratory protocols with a tiny chip. Sample preparation (i.e., dilution or mixing of fluids) is one of the primary tasks of any bioprotocol. In real-life applications where several assays need to be executed for different diagnostic purposes, the same sample fluid is often required with different target concentration factors (CFs). Although several multi-target dilution algorithms have been developed for digital microfluidic biochips, they are not efficient for implementation with continuous-flow-based microfluidic chips, which are preferred in the laboratories. In this article, we present a multi-target dilution algorithm (MTDA) for continuous-flow-based microfluidic biochips, which to the best of our knowledge is the first of its kind. We design a flow-based rotary mixer with a suitable number of segments depending on the target-CF profile, error tolerance, and optimization criteria. To schedule several intermediate fluid-mixing tasks, we develop a multi-target scheduling algorithm (MTSA) aiming to minimize the usage of storage units while producing dilutions with multiple CFs. Furthermore, we propose a storage architecture for efficiently loading (storing) of intermediate fluids from (to) the storage units.
01 Jan 2020
TL;DR: The design of an IEEE Std.
Abstract: A digital microfluidic biochip (DMFB) enables miniaturization of immunoassays, point-of-care clinical diagnostics, DNA sequencing, and other laboratory procedures in biochemistry. A recent generation of biochips uses a microelectrode-dot-array (MEDA) architecture, which provides fine-grained control of droplets and seamlessly integrates microelectronics and microfluidics using CMOS technology. To ensure that bioassays are carried out on MEDA biochips efficiently, high-level synthesis algorithms have recently been proposed. However, as in the case of conventional DMFBs, microelectrodes are likely to fail when they are heavily utilized, and previous methods fail to consider reliability issues. In this paper, we present the design of an IEEE Std. 1687 (IJTAG) network and a block-aware high-level synthesis method that can effectively alleviate reliability problems in MEDA biochips. A comprehensive set of simulation results demonstrate the effectiveness of the proposed method.
01 Jun 2020
TL;DR: This work proposes FlowTrojan, the first systematic framework for insertion and detection of Hardware Trojans (HTs) on Flow-based Microfluidic Biochips (FMFBs), and provides a parallel regime of control-value based HT detection as the countermeasure.
Abstract: We propose FlowTrojan, the first systematic framework for insertion and detection of Hardware Trojans (HTs) on Flow-based Microfluidic Biochips (FMFBs). The FMFB is an emerging platform with critical usages in the medical field due to the handling of sensitive information. We discuss the attack model where the malicious foundry aims to compromise the on-chip control circuitry. FlowTrojan is designed to automatically extract the netlist for the control circuitry from the layout and explore the internal independence between regions on FMFBs for partitioning. We demonstrate that HT triggers can feature a low activation probability while placed on the non-critical timing path to stay clandestine during functional and parametric testing. To avoid such attacks, FlowTrojan provides a parallel regime of control-value (CV) based HT detection as the countermeasure. Experimental results corroborate the effectiveness and scalability of the proposed attack and detection schemes.
TL;DR: The fabrication parameters and performance of printable ink consisting of a photoactive hydrogel precursor and antibody mixture for the fabrication of SPRi array biochip is investigated and a high density immobilized probes is obtained which allows high sensitivity, specificity, and surface regeneration.
Abstract: Biochips for multiplex blood typing through surface plasmon resonance imaging (SPRi) readout have been previously reported based on arrays of red blood cell (RBC) specific ABO antibodies (Abs). Although conventional surfaces, such as CM-dextran, are robust and highly specific, they are time and labor intensive to generate and functionalize. This work investigates the fabrication parameters and performance of printable ink consisting of a photoactive hydrogel precursor and antibody mixture for the fabrication of SPRi array biochip. The solid-phase immobilization of commercially available murine IgM ABO Abs on a SPR sensor chip with a multiplex detection of ABO antigens present on the surface membrane of human RBCs is reported. A quick and simple solid phase immobilization of protein on a SPR sensor chip was attained using the photocrosslinking polymer and microarray printing platform. A high density immobilized probes is obtained which allows high sensitivity, specificity, and surface regeneration. A signal to noise ratio of 22:1 and 25:1 at 5% and 10% immobilized-Ab respectively, is obtained with 5% RBC concentration. The sensor surface can be successfully regenerated for repeated use using DI water. Without loss of function, the Ab-printed chips could be stored up to 3 weeks at 4 °C.