Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor

Real-time label-free detection of DNA hybridization using a functionalized graphene field effect transistor: a theoretical study

Detection of DNA hybridization with high sensitivity and accuracy plays a major role in clinical diagnosis and treatment. Despite intense experimental studies of graphene field effect transistor as DNA hybridization detector, the mechanism of detection and changes in the electrical properties of the device is not investigated in detail. To this end, we have investigated an armchair graphene nanoribbon (AGNR) interconnected between gold electrodes as a detector of DNA hybridization. Using non-equilibrium Green's function method and density functional theory, the effect of 1-pyrenebutanoic acid succinimidyl ester (PBASE) linker, probe, and target DNA on the electrical properties of the device has been investigated at zero bias voltage. The results show that, after functionalization of AGNR with PBASE, the conductance of the device increases while functionalization with probe and target DNA leads to a decrease in conductance. The changes in the projected density of states on the AGNR and transmission around Fermi energy are the reason for the change in conductance of the system. In all cases, both charge transfer and electrostatic gating are responsible for the change in the electrical properties of the system. The results show that our device detects DNA hybridization with a sensitivity of 10% at zero bias voltage, and by applying a suitable gate voltage, it can show higher sensitivity.

DNA interfaces with dimensional materials for biomedical applications

DNA interfaces with nano, micro, and macro materials have gained widespread attention for various applications. Such interfaces exhibit distinct functions and properties not only due to the unique properties of interfacing materials but also sequence- and conformation-dependent characteristics of the DNA. Therefore, DNA interfaces with diverse dimensional materials have advanced our understanding of the interaction mechanisms and the properties of such interfaces. The unique interfacial properties of such novel materials have applications in nanotechnology, biophysics, cell biology, biosensing, and bioelectronics. The field is growing rapidly with the frequent emergence of new interfaces carrying remarkable interfacial character. In this review article, we have classified the DNA interfaces into 0D, 1D, 2D, and 3D categories based on the types of dimensional materials. We review the key efforts made in the last five years and focus on types of interfaces, interfacing mechanisms, and their state-of-the-art applications. This review will draw a general interest because of the diversity in the DNA materials science but also the unique applications that will play a cutting-edge role in biomedical and biosensing research.

Sequence-Independent DNA Adsorption on Few-Layered Oxygen-Functionalized Graphene Electrodes: An Electrochemical Study for Biosensing Application

DNA is strongly adsorbed on oxidized graphene surfaces in the presence of divalent cations. Here, we studied the effect of DNA adsorption on electrochemical charge transfer at few-layered, oxygen-functionalized graphene (GO_x) electrodes. DNA adsorption on the inkjet-printed GO_x electrodes caused amplified current response from ferro/ferricyanide redox probe at concentration range 1 aM–10 nM in differential pulse voltammetry. We studied a number of variables that may affect the current response of the interface: sequence type, conformation, concentration, length, and ionic strength. Later, we showed a proof-of-concept DNA biosensing application, which is free from chemical immobilization of the probe and sensitive at attomolar concentration regime. We propose that GO_x electrodes promise a low-cost solution to fabricate a highly sensitive platform for label-free and chemisorption-free DNA biosensing.

Securing Bio-Cyber Interface for the Internet of Bio-Nano Things using Particle Swarm Optimization and Artificial Neural Networks based parameter profiling

Internet of bio-nano things (IoBNT) is a novel communication paradigm where tiny, biocompatible and non-intrusive devices collect and sense biological signals from the environment and send them to data centers for processing through the internet. The concept of the IoBNT has stemmed from the combination of synthetic biology and nanotechnology tools which enable the fabrication of biological computing devices called Bio-nano things. Bio-nano things are nanoscale (1-100 nm) devices that are ideal for in vivo applications, where non-intrusive devices can reach hard-to-access areas of the human body (such as deep inside the tissue) to collect biological information. Bio-nano things work collaboratively in the form of a network called nanonetwork. The interconnection of the biological world and the cyber world of the Internet is made possible by a powerful hybrid device called Bio Cyber Interface. Bio Cyber Interface translates biochemical signals from in-body nanonetworks into electromagnetic signals and vice versa. Bio Cyber Interface can be designed using several technologies. In this paper, we have selected bio field-effect transistor (BioFET) technology, due to its characteristics of being fast, low-cost, and simple The main concern in this work is the security of IoBNT, which must be the preliminary requirement, especially for healthcare applications of IoBNT. Once the human body is accessible through the Internet, there is always a chance that it will be done with malicious intent. To address the issue of security in IoBNT, we propose a framework that utilizes Particle Swarm Optimization (PSO) algorithm to optimize Artificial Neural Networks (ANN) and to detect anomalous activities in the IoBNT transmission. Our proposed PSO-based ANN model was tested for the simulated dataset of BioFET based Bio Cyber Interface communication features. The results show an improved accuracy of 98.9% when compared with Adam based optimization function.

Real-time monitoring of bead-based DNA hybridization in a microfluidic system: study of amplicon hybridization behavior on solid supports

DNA hybridization phenomena occurring on solid supports are not understood as clearly as aqueous phase hybridizations and mathematical models cannot predict some empirically obtained results. Ongoing research has identified important parameters but remains incomplete to accurately account for all interactions. It has previously been shown that the length of the overhanging (dangling) end of the target DNA strand following hybridization to the capture probe is correlated to interactions with the complementary strand in solution which can result in unbinding of the target and its release from the surface. We have developed an instrument for real-time monitoring of DNA hybridization on spherical particles functionalized with oligonucleotide capture probes and arranged in the form of a tightly packed monolayer bead bed inside a microfluidic cartridge. The instrument is equipped with a pneumatic module to mediate displacement of fluid on the cartridge. We compared this system to both conventional (passive) and centrifugally-driven (active) microfluidic microarray hybridization on glass slides to establish performance levels for the detection of single nucleotide polymorphisms. The system was also used to study the effect of the dangling end's length in real-time when the immobilized target DNA is exposed to the complementary strand in solution. Our findings indicate that increasing the length of the dangling end leads to desorption of target amplicons from bead-bound capture probes at a rate approaching that of the initial hybridization process. Finally, bead bed hybridization was performed with Streptococcus agalactiae cfb gene amplicons obtained from randomized clinical samples, which allowed for identification of group B streptococci within 5-15 min. The methodology presented here is useful for investigating competitive hybridization mechanisms on solid supports and to rapidly validate the suitability of microarray capture probes.

Kinetic Microscale Thermophoresis for Simultaneous Measurement of Binding Affinity and Kinetics

Microscale thermophoresis (MST) is a versatile technique to measure binding affinities of binder-ligand systems, based on the directional movement of molecules in a temperature gradient. We extended MST to measure binding kinetics as well as binding affinity in a single experiment by increasing the thermal dissipation of the sample. The kinetic relaxation fingerprints were derived from the fluorescence changes during thermodynamic re-equilibration of the sample after local heating. Using this method, we measured DNA hybridization on-rates and off-rates in the range 10⁴ -10⁶  m^-1  s^-1 and 10^-4 -10^-1  s^-1 , respectively. We observed the expected exponential dependence of the DNA hybridization off-rates on salt concentration, strand length and inverse temperature. The measured on-rates showed a linear dependence on salt concentration and weak dependence on strand length and temperature. For biomolecular interactions with large enthalpic contributions, the kinetic MST technique offers a robust, cost-effective and immobilization-free determination of kinetic rates and binding affinity simultaneously, even in crowded solutions.

Stochastic Time Response and Ultimate Noise Performance of Adsorption-Based Microfluidic Biosensors

In order to improve the interpretation of measurement results and to achieve the optimal performance of microfluidic biosensors, advanced mathematical models of their time response and noise are needed. The random nature of adsorption-desorption and mass transfer (MT) processes that generate the sensor response makes the sensor output signal inherently stochastic and necessitates the use of a stochastic approach in sensor response analysis. We present a stochastic model of the sensor time response, which takes into account the coupling of adsorption-desorption and MT processes. It is used for the analysis of response kinetics and ultimate noise performance of protein biosensors. We show that slow MT not only decelerates the response kinetics, but also increases the noise and decreases the sensor's maximal achievable signal-to-noise ratio, thus degrading the ultimate sensor performance, including the minimal detectable/quantifiable analyte concentration. The results illustrate the significance of the presented model for the correct interpretation of measurement data, for the estimation of sensors' noise performance metrics important for reliable analyte detection/quantification, as well as for sensor optimization in terms of the lower detection/quantification limit. They are also incentives for the further investigation of the MT influence in nanoscale sensors, as a possible cause of false-negative results in analyte detection experiments.

Graphene Oxide Normal (GO + Mn2+) and Ultrapure: Short-Term Impact on Selected Antioxidant Stress Markers and Cytokines in NHDF and A549 Cell Lines

Since biological applications and toxicity of graphene-based materials are structure dependent, studying their interactions with the biological systems is very timely and important. We studied short-term (1, 24, and 48 h) effects of ultrapure (GO) and Mn²⁺-contaminated (GOS) graphene oxide on normal human dermal fibroblasts (NHDF) and adenocarcinomic human alveolar basal epithelial cells (A549) using selected oxidative stress markers and cytokines: glutathione reductase (GR) and catalase (CAT) activity, total antioxidative capacity (TAC), and malondialdehyde (MDA) concentration, levels of vascular endothelial growing factor (VEGF), tumor necrosis factor-alpha (TNF-α), platelet-derived growth factor-BB (PDGF-BB), and eotaxin. GOS induced higher levels of oxidative stress, measured with CAT activity, TAC, and MDA concentration than GO in both cell lines when compared to control cells. GR activity decreased in time in NHDF cells but increased in A549 cells. The levels of cytokines were related to the exposure time and graphene oxide type in both analyzed cell lines and their levels comparably increased over time. We observed higher TNF-α levels in NHDF and higher levels of VEGF and eotaxin in the A549 cell line. Both types of cells showed similar susceptibility to GO and GOS. We concluded that the short-time exposure to GOS induced the stronger response of oxidative stress markers without collapsing the antioxidative systems of analysed cells. Increased levels of inflammatory cytokines after GO and GOS exposure were similar both in NHDF and A549 cells.

Printable graphene BioFETs for DNA quantification in Lab-on-PCB microsystems

Lab-on-Chip is a technology that aims to transform the Point-of-Care (PoC) diagnostics field; nonetheless a commercial production compatible technology is yet to be established. Lab-on-Printed Circuit Board (Lab-on-PCB) is currently considered as a promising candidate technology for cost-aware but simultaneously high specification applications, requiring multi-component microsystem implementations, due to its inherent compatibility with electronics and the long-standing industrial manufacturing basis. In this work, we demonstrate the first electrolyte gated field-effect transistor (FET) DNA biosensor implemented on commercially fabricated PCB in a planar layout. Graphene ink was drop-casted to form the transistor channel and PNA probes were immobilized on the graphene channel, enabling label-free DNA detection. It is shown that the sensor can selectively detect the complementary DNA sequence, following a fully inkjet-printing compatible manufacturing process. The results demonstrate the potential for the effortless integration of FET sensors into Lab-on-PCB diagnostic platforms, paving the way for even higher sensitivity quantification than the current Lab-on-PCB state-of-the-art of passive electrode electrochemical sensing. The substitution of such biosensors with our presented FET structures, promises further reduction of the time-to-result in microsystems combining sequential DNA amplification and detection modules to few minutes, since much fewer amplification cycles are required even for low-abundance nucleic acid targets.

Wafer-scalable chemical modification of amino groups on graphene biosensors

Graphene's remarkable attributes make it suitable for application to biosensors for biomolecular recognition. Specific and precise target detection is realized by designing robust methods for immobilization of probe molecules, such as oligonucleotides, antibodies, receptors, and sugar chains, to a device surface. In this research, we developed a chemical modification method with a plasma treatment of amino groups on natural defects of graphene, which is compatible with a wafer-scalable semiconductor process, to prevent deterioration of the carrier mobility. The plasma treatment was optimized in terms of the efficiency of the amino radical generation, length of the mean free path, and reaction energy on graphene. The density of the modified amino groups on graphene was approximately 0.065 groups/nm², and the change in the ΔI_d/ΔV_g characteristic of the graphene field-effect transistor (FET) was negligible. DNA probes were then attached to the amino groups on the graphene FET. The target complementary DNA was detected at 1 nM after hybridization using the graphene FET devices. The plasma-assisted modification of the amino groups on the graphene surface was developed for immobilization of the DNA probes, and hybridization with the target DNA was demonstrated without deterioration of the carrier mobility.

An optic-fiber graphene field effect transistor biosensor for the detection of single-stranded DNA

Herein, a graphene field effect transistor (GFET) was constructed on an optic fiber end face to develop an integrated optical/electrical double read-out biosensor, which was used to detect target single-stranded DNA (tDNA). Two isolated Au electrodes were, respectively, prepared as the drain and source at the ends of an optic fiber and coated with a graphene film to construct a field effect transistor (FET). Probe aptamers modified with fluorophore 6'-carboxy-fluorescein (6'-FAM) were immobilized on the graphene for specific capture of tDNA. Graphene oxide (GO) was introduced to quench 6'-FAM and construct a fluorescence biosensor. Thus, a dual GFET and fluorescence biosensor was integrated on the end-face of an optic fiber. Following synchronous detection by fluorescence and FET methods, results showed satisfactory sensitivity for DNA detection. Compared with conventional biosensors using a single sensing technology, these dual sensing integrated biosensors significantly improved the reliability and accuracy of DNA detection. Furthermore, this proposed technique provides both a new biosensor for single-stranded DNA detection and a strategy for designing multi-sensing integrated biosensors.

De Novo Development of a Universal Biosensing Platform by Rapid Direct Native Protein Modification

An innovative biosensing assay was developed for simplified, cost-effective, and sensitive detection. By rapid, direct treatment of target proteins with iron porphyrin (TPPFe) in situ, a carboxyl group of amino acid conjugates with an Fe atom of the TPPFe molecule, forming a stable protein complex. We have shown that this complex not only maintains the integrity and functions of original proteins but also acquires peroxidase activity that can turn TMB to a comparably visible signal like that in ELISA. This study is unique since such conversion is difficult to achieve with standard chemical modification or molecular biology methods. In addition, the proposed immunoassay is superior to traditional ELISA as it eliminates an expensive and complicated cross-linking process of an enzyme-labeled antibody. From a practical point of view, we extended this assay to rapid detection of clinically relevant proteins and glucose in blood samples. The results show that this simple immunoassay provides clinical diagnosis, food safety, and environmental monitoring in an easy-to-implement manner.

The C-terminus of the mu opioid receptor is critical in G-protein interaction as demonstrated by a novel graphene biosensor

Several water-soluble variants of the human mu opioid receptor (wsMORs) have been designed and expressed, which enables the detection of opioids in the nM to pM range using biosensing platforms. The tools previously developed allowed us to investigate MOR and G-protein interactions in a lipid free system to demonstrate that the lipid bilayer might not be essential for the G-protein recognition and binding. In this study, we are able to investigate G-protein interactions with MOR by using graphene enabled technology, in a lipid free system, with a high sensitivity in a real time manner. A new wsMOR with the native C-terminus was designed, expressed and then immobilized on the surfaces of scalable graphene field effect transistor (GFET)-based biosensors, enabling the recording of wsMOR/G-protein interaction with an electronic readout. G-protein only interacts with the wsMOR in the presence of the native MOR C-terminus with a K_A of 32.3±11.1 pM. The electronic readout of such interaction is highly reproducible with little variance across 50 devices in one biosensor array. For devices with receptors that do not have the native C-terminus, no significant electronic response was observed in the presence of G-protein, indicating an absence of interaction. These findings reveal that lipid environment is not essential for the G-protein interaction with MOR, however, the C-terminus of MOR is essential for G-protein recognition and high affinity binding. A system to detect MOR-G protein interaction is developed. wsMOR-G2_Cter provides a novel tool to investigate the role of C terminus in the signaling pathway.

Modeling Effects of Surface Properties and Probe Density for Nanoscale Biosensor Design: A Case Study of DNA Hybridization near Surfaces

Electrochemical biosensors have extremely robust applications while offering ease of preparation, miniaturization, and tunability. By adjusting the arrangement and properties of immobilized probes on the sensor surface to optimize target-probe association, one can design highly sensitive and efficient sensors. In electrochemical nucleic acid biosensors, a self-assembled monolayer (SAM) is widely used as a tunable surface with inserted DNA or RNA probes to detect target sequences. The effects of inhomogeneous probe distribution across surfaces are difficult to study experimentally due to inadequate resolution. Regions of high probe density may inhibit hybridization with targets, and the magnitude of the effect may vary depending on the hybridization mechanism on a given surface. Another fundamental question concerns diffusion and hybridization of DNA taking place on surfaces and whether it speeds up or hinders molecular recognition. We used all-atom Brownian dynamics simulations to help answer these questions by simulating the hybridization process of single-stranded DNA (ssDNA) targets with a ssDNA probe on polar, nonpolar, and anionic SAMs at three different probe surface densities. Moreover, we simulated three tightly packed probe clusters by modeling clusters with different interprobe spacing on two different surfaces. Our results indicate that hybridization efficiency depends strongly on finding a balance that allows attractive forces to steer target DNA toward probes without anchoring it to the surface. Furthermore, we found that the hybridization rate becomes severely hindered when interprobe spacing is less than or equal to the target DNA length, proving the need for a careful design to both enhance target-probe association and avoid steric hindrance. We developed a general kinetic model to predict hybridization times and found that it works accurately for typical probe densities. These findings elucidate basic features of nanoscale biosensors, which can aid in rational design efforts and help explain trends in experimental hybridization rates at different probe densities.

Bio-Separated and Gate-Free 2D MoS2 Biosensor Array for Ultrasensitive Detection of BRCA1

2D molybdenum disulfide (MoS₂)-based thin film transistors are widely used in biosensing, and many efforts have been made to improve the detection limit and linear range. However, in addition to the complexity of device technology and biological modification, the compatibility of the physical device with biological solutions and device reusability have rarely been considered. Herein, we designed and synthesized an array of MoS₂ by employing a simple-patterned chemical vapor deposition growth method and meanwhile exploited a one-step biomodification in a sensing pad based on DNA tetrahedron probes to form a bio-separated sensing part. This solves the signal interference, solution erosion, and instability of semiconductor-based biosensors after contacting biological solutions, and also allows physical devices to be reused. Furthermore, the gate-free detection structure that we first proposed for DNA (BRCA1) detection demonstrates ultrasensitive detection over a broad range of 1 fM to 1 μM with a good linear response of R² = 0.98. Our findings provide a practical solution for high-performance, low-cost, biocompatible, reusable, and bio-separated biosensor platforms.

Detection of an IL-6 Biomarker Using a GFET Platform Developed with a Facile Organic Solvent-Free Aptamer Immobilization Approach

Aptamer-immobilized graphene field-effect transistors (GFETs) have become a well-known detection platform in the field of biosensing with various biomarkers such as proteins, bacteria, virus, as well as chemicals. A conventional aptamer immobilization technique on graphene involves a two-step crosslinking process. In the first step, a pyrene derivative is anchored onto the surface of graphene and, in the second step, an amine-terminated aptamer is crosslinked to the pyrene backbone with EDC/NHS (1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride/N-hydroxysuccinimide) chemistry. However, this process often requires the use of organic solvents such as dimethyl formamide (DMF) or dimethyl sulfoxide (DMSO) which are typically polar aprotic solvents and hence dissolves both polar and nonpolar compounds. The use of such solvents can be especially problematic in the fabrication of lab-on-a-chip or point-of-care diagnostic platforms as they can attack vulnerable materials such as polymers, passivation layers and microfluidic tubing leading to device damage and fluid leakage. To remedy such challenges, in this work, we demonstrate the use of pyrene-tagged DNA aptamers (PTDA) for performing a one-step aptamer immobilization technique to implement a GFET-based biosensor for the detection of Interleukin-6 (IL-6) protein biomarker. In this approach, the aptamer terminal is pre-tagged with a pyrene group which becomes soluble in aqueous solution. This obviates the need for using organic solvents, thereby enhancing the device integrity. In addition, an external electric field is applied during the functionalization step to increase the efficiency of aptamer immobilization and hence improved coverage and density. The results from this work could potentially open up new avenues for the use of GFET-based BioMEMS platforms by broadening the choice of materials used for device fabrication and integration.

Reduced graphene oxide coating enhances osteogenic differentiation of human mesenchymal stem cells on Ti surfaces

BACKGROUND

Titanium (Ti) has been utilized as hard tissue replacement owing to its superior mechanical and bioinert property, however, lack in tissue compatibility and biofunctionality has limited its clinical use. Reduced graphene oxide (rGO) is one of the graphene derivatives that possess extraordinary biofunctionality and are known to induce osseointegration in vitro and in vivo. In this study, rGO was uniformly coated by meniscus-dragging deposition (MDD) technique to fabricate rGO-Ti substrate for orthopedic and dental implant application.

METHODS

The physicochemical characteristics of rGO-coated Ti (rGO-Ti) substrates were evaluated by atomic force microscopy, water contact angle, and Raman spectroscopy. Furthermore, human mesenchymal stem cells (hMSCs) were cultured on the rGO-Ti substrate, and then their cellular behaviors such as growth and osteogenic differentiation were determined by a cell counting kit-8 assay, alkaline phosphatase (ALP) activity assay, and alizarin red S staining.

RESULTS

rGO was coated uniformly on Ti substrates by MDD process, which allowed a decrease in the surface roughness and contact angle of Ti substrates. While rGO-Ti substrates significantly increased cell proliferation after 7 days of incubation, they significantly promoted ALP activity and matrix mineralization, which are early and late differentiation markers, respectively.

CONCLUSION

It is suggested that rGO-Ti substrates can be effectively utilized as dental and orthopedic bone substitutes since these graphene derivatives have potent effects on stimulating the osteogenic differentiation of hMSCs and showed superior bioactivity and osteogenic potential.

Graphene field effect transistor scaling for ultra-low-noise sensors

The discovery of the field effect in graphene initiated the development of graphene field effect transistor (FET) sensors, wherein high mobility surface conduction is readily modulated by surface adsorption. For all graphene transistor sensors, low-frequency 1/f noise determines sensor resolution, and the absolute measure of 1/f noise is thus a crucial performance metric for sensor applications. Here we report a simple method for reducing 1/f noise by scaling the active area of graphene FET sensors. We measured 1/f noise in graphene FETs with size 5 μm × 5 μm to 5.12 mm × 5.12 mm, observing more than five orders of magnitude reduction in 1/f noise. We report the lowest normalized graphene 1/f noise parameter observed to date, 5 × 10^-13, and we demonstrate a sulfate ion sensor with a record resolution of 1.2 × 10^-3 log molar concentration units. Our work highlights the importance of area scaling in graphene FET sensor design, wherein increased channel area improves sensor resolution.

Hard template synthesis of 2D porous Co3O4 nanosheets with graphene oxide for H2O2 sensing

In this work, we used graphene oxide (GO) as a template that was removed by calcination to finally successfully prepare Co₃O₄ with 2D porous nanostructure. The results show that 2D porous structure Co₃O₄ nanosheets were only prepared at pH = 2. After electrochemical tests, the as-prepared Co₃O₄ nanosheets showed electrochemical properties that are highly suitable for H₂O₂ detection, such as high current response, short response time (less than 3 s), wide linear range (0.388-44.156 mM), low limit of detection (2.33 μM) and high sensitivity (0.0891 mA mM^-1 cm^-2). These excellent properties are mainly due to GO, as a 2D template, which connects Co₃O₄ nanoparticles to each other on a 2D plane, preventing the agglomeration of Co₃O₄ nanoparticles. The abundant pores between Co₃O₄ nanoparticles can greatly increase the reaction between the nanoparticles and H₂O₂ molecules.

Graphene field effect transistor for ultrasensitive label-free detection of ATP and Adenosine

Because of unique electrical and structural properties, graphene has attracted widespread attention in biosensing applications. In this paper, a single layer of graphene was grown by chemical vapor deposition (CVD). Using graphene as the electric channel, a graphene field effect transistor (G-FET) biosensor was fabricated and used to detect adenosine triphosphate (ATP) and adenosine. Compared with traditional methods, the G-FET biosensor has the advantages of higher sensitivity and better stability. The sensor showed high performance and achieved a detection limit down to 0.5 pM for both ATP and adenosine. Moreover, the G-FET biosensor showed an excellent linear electrical response to ATP concentrations in a broad range from 0.5 pM to 50 μM. The developed graphene biosensor has high sensitivity, simple operation, and fast analysis speed, which may provide a new feasible direction to detect ATP and adenosine. Healthy sexually mature male laboratory Wistar rats, weighing 180-200 gr (“FSUE “Nursery of laboratory animals “Rappolovo”) and having been placed under quarantine not less than for 14 days, were selected for the experiment.

An accurate, high-speed, portable bifunctional electrical detector for COVID-19

Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has rapidly spread and caused a severe global pandemic. Because no specific drugs are available for COVID-19 and few vaccines are available for SARS-CoV-2, accurate and rapid diagnosis of COVID-19 has been the most crucial measure to control this pandemic. Here, we developed a portable bifunctional electrical detector based on graphene fieldeffect transistors for SARS-CoV-2 through either nucleic acid hybridization or antigen-antibody protein interaction, with ultra-low limits of detection of ~0.1 and ~1 fg mL^-1 in phosphate buffer saline, respectively. We validated our method by assessment of RNA extracts from the oropharyngeal swabs of ten COVID-19 patients and eight healthy subjects, and the IgM/IgG antibodies from serum specimens of six COVID-19 patients and three healthy subjects. Here we show that the diagnostic results are in excellent agreement with the findings of polymerase chain reaction-based optical methods; they also exhibit rapid detection speed (~10 min for nucleic acid detection and ~5 min for immunoassay). Therefore, our assay provides an efficient, accurate tool for high-throughput point-of-care testing.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material is available in the online version of this article at 10.1007/s40843-020-1577-y.

Click Chemistry Enabling Covalent and Non-Covalent Modifications of Graphene with (Poly)saccharides

Graphene is a material with outstanding properties and numerous potential applications in a wide range of research and technology areas, spanning from electronics, energy materials, sensors, and actuators to life-science and many more. However, the insolubility and poor dispersibility of graphene are two major problems hampering its use in certain applications. Tethering mono-, di-, or even poly-saccharides on graphene through click-chemistry is gaining more and more attention as a key modification approach leading to new graphene-based materials (GBM) with improved hydrophilicity and substantial dispersibility in polar solvents, e.g., water. The attachment of (poly)saccharides on graphene further renders the final GBMs biocompatible and could open new routes to novel biomedical and environmental applications. In this review, recent modifications of graphene and other carbon rich materials (CRMs) through click chemistry are reviewed.

Rapid, Ultrasensitive, and Quantitative Detection of SARS-CoV-2 Using Antisense Oligonucleotides Directed Electrochemical Biosensor Chip

A large-scale diagnosis of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is essential to downregulate its spread within as well as across communities and mitigate the current outbreak of the pandemic novel coronavirus disease 2019 (COVID-19). Herein, we report the development of a rapid (less than 5 min), low-cost, easy-to-implement, and quantitative paper-based electrochemical sensor chip to enable the digital detection of SARS-CoV-2 genetic material. The biosensor uses gold nanoparticles (AuNPs), capped with highly specific antisense oligonucleotides (ssDNA) targeting viral nucleocapsid phosphoprotein (N-gene). The sensing probes are immobilized on a paper-based electrochemical platform to yield a nucleic-acid-testing device with a readout that can be recorded with a simple hand-held reader. The biosensor chip has been tested using samples collected from Vero cells infected with SARS-CoV-2 virus and clinical samples. The sensor provides a significant improvement in output signal only in the presence of its target-SARS-CoV-2 RNA-within less than 5 min of incubation time, with a sensitivity of 231 (copies μL-1)-1 and limit of detection of 6.9 copies/μL without the need for any further amplification. The sensor chip performance has been tested using clinical samples from 22 COVID-19 positive patients and 26 healthy asymptomatic subjects confirmed using the FDA-approved RT-PCR COVID-19 diagnostic kit. The sensor successfully distinguishes the positive COVID-19 samples from the negative ones with almost 100% accuracy, sensitivity, and specificity and exhibits an insignificant change in output signal for the samples lacking a SARS-CoV-2 viral target segment (e.g., SARS-CoV, MERS-CoV, or negative COVID-19 samples collected from healthy subjects). The feasibility of the sensor even during the genomic mutation of the virus is also ensured from the design of the ssDNA-conjugated AuNPs that simultaneously target two separate regions of the same SARS-CoV-2 N-gene.

A Point-of-Care Immunosensor Based on a Quartz Crystal Microbalance with Graphene Biointerface for Antibody Assay

We present a sensitive and low-cost immunoassay, based on a customized open-source quartz crystal microbalance coupled with graphene biointerface sensors (G-QCM), to quantify antibodies in undiluted patient serum. We demonstrate its efficacy for a specific antibody against the phospholipase A2 receptor (anti-PLA2R), which is a biomarker in primary membranous nephropathy. A novel graphene-protein biointerface was constructed by adsorbing a low concentration of denatured bovine serum albumin (dBSA) on the reduced graphene oxide (rGO) sensor surface. The dBSA film prevents the denaturation of the protein receptor on the rGO surface and serves as the cross-linker for immobilization of the receptor for anti-PLA2R antibodies on the surface. The detection limit and selectivity of this G-QCM biosensor was compared with a commercial QCM system. The G-QCM immunoassay exhibited good specificity and high sensitivity toward the target, with an order of magnitude better detection limit (of 100 ng/mL) compared to the commercial system, at a fraction of the cost and with considerable time saving. The results obtained from patient sera compared favorably with those from enzyme-linked immunosorbent assay, validating the feasibility of use in clinical applications. The multifunctional dBSA-rGO platform provides a promising biofunctionalization method for universal immunoassay and biosensors. With the advantages of inexpensive, rapid, and sensitive detection, the G-QCM sensor and instrument form an effective autoimmune disease screening tool.

Avidin-Biotin Technology in Gold Nanoparticle-Decorated Graphene Field Effect Transistors for Detection of Biotinylated Macromolecules with Ultrahigh Sensitivity and Specificity

The strong and specific noncovalent interaction between avidin and biotin is widely exploited in different types of enzyme-linked immunosorbent assay kits, labeled immunosensors, and polymer-based sensing devices for the detection of different biomarkers specific to different diseases such as cancer and influenza. Here, we employed the avidin-biotin technology in a novel gold nanoparticle-decorated graphene field-effect transistor (AuNP-GFET) and demonstrated the specific detection of the biotinylated macromolecules such as biotinylated proteins and nucleotides in the sub-picomolar (pM) range. The AuNP-GFET was constructed by fabricating six pairs of interdigital electrodes on graphene transferred on a SiO2/Si substrate. The sensing performance of AuNP-GFET was characterized by the real-time two-terminal electrical current measurement upon injection of the analyte solution into a silicone pool preattached onto the electrodes. Avidin, a tetrameric biotin-binding protein with strong affinity and specificity, immobilized on AuNP-decorated single-layer graphene, was used as the sensing platform and transduced the electrical signal upon binding to the analyte macromolecules. The sensing capability of the AuNP-GFET was tested with the biotinylated protein A. Sensitivity of the present biosensor was estimated to be ∼0.4 pM. The specificity and applicability of the biosensor were confirmed using both synthetic and real samples. Because the biotin label can retain its binding capability to avidin with strong affinity and specificity even after conjugating with varieties of proteins and nucleotides, the present AuNP-GFET biosensor is expected to promote the research in developing different biosensors.

Field-effect transistor bioassay for ultrasensitive detection of folate receptor 1 by ligand-protein interaction

A miniaturized and integrated bioassay was developed based on molybdenum disulfide (MoS₂) field-effect transistor (FET) functionalized with bovine serum albumin-folic acid (BSA-FA) for monitoring FOLR1. We performed the electrical test of FOLR1 within the range 100 fg/mL to 10 ng/mL, and the limit of detection was 0.057 pg/mL. The ultrahigh sensitivity of the bioassay was realized by ligand-protein interaction between FA and FOLR1, with a ligand-protein binding ratio of 3:1. The formation of FA-FOLR1 was confirmed with ELISA. The binding affinity dissociation constant K_D was 12 ± 6 pg/mL. This device can work well for FOLR1 detection in human serum, which presents its promising application in point-of-care diagnosis. This study supports the future applications of such ligand-protein-based bioassays in the clinical practices. Graphical abstract MoS₂-based FET device for detecting folate receptor 1 (FOLR1) was fabricated. The molecular folic acid as a probe can specifically bound to FOLR1 with a high affinity.

Integrated Micropillar Polydimethylsiloxane Accurate CRISPR Detection System for Viral DNA Sensing

A fully Integrated Micropillar Polydimethylsiloxane Accurate CRISPR deTection (IMPACT) system is developed for viral DNA detection. This powerful system is patterned with high-aspect-ratio micropillars to enhance reporter probe binding. After surface modification and probe immobilization, the CRISPR-Cas12a/crRNA complex is injected into the fully enclosed microchannel. With the presence of a double-stranded DNA target, the CRISPR enzyme is activated and denatures the single-stranded DNA reporters from the micropillars. This collateral cleavage releases fluorescence reporters into the assay, and the intensity is linearly proportional to the target DNA concentration ranging from 0.1 to 10 nM. Importantly, this system does not rely on the traditional dye-quencher-labeled probe, thus reducing the fluorescence background presented in the assay. Furthermore, our one-step detection protocol is performed on-chip at isothermal conditions (37 °C) without using complicated and time-consuming off-chip probe hybridization and denaturation. This miniaturized and fully packed IMPACT chip demonstrates sensitive and accurate DNA detection within 120 min and paves ways to the next-generation point-of-care diagnostics, responding to emerging and deadly pathogen outbreaks.

Lighting up single-nucleotide variation in situ in single cells and tissues

The ability to 'see' genetic information directly in single cells can provide invaluable insights into complex biological systems. In this review, we discuss recent advances of in situ imaging technologies for visualizing the subtlest sequence alteration, single-nucleotide variation (SNV), at single-cell level. The mechanism of recently developed methods for SNV discrimination are summarized in detail. With recent developments, single-cell SNV imaging methods have opened a new door for studying the heterogenous and stochastic genetic information in individual cells. Furthermore, SNV imaging can be used on morphologically preserved tissue, which can provide information on histological context for gene expression profiling in basic research and genetic diagnosis. Moreover, the ability to visualize SNVs in situ can be further developed into in situ sequencing technology. We expect this review to inspire more research work into in situ SNV imaging technologies for investigating cellular phenotypes and gene regulation at single-nucleotide resolution, and developing new clinical and biomedical applications.

Faradaic effects in electrochemically gated graphene sensors in the presence of redox active molecules

Field-effect transistors (FETs) based on graphene are promising devices for the direct sensing of a range of analytes in solution. We show here that the presence of redox active molecules in the analyte solution leads to the occurrence of heterogeneous electron transfer with graphene generating a Faradaic current (electron transfer) in a FET configuration resulting in shifts of the Dirac point. Such a shift occurs if the Faradaic current is significantly high, e.g. due to a large graphene area. Furthermore, the redox shift based on the Faradaic current, reminiscent of a doping-like effect, is found to be non-Nernstian and dependent on parameters known from electrode kinetics in potentiodynamic methods, such as the electrode area, the standard potential of the redox probes and the scan rate of the gate voltage modulation. This behavior clearly differentiates this effect from other transduction mechanisms based on electrostatic interactions or molecular charge transfer doping effects, which are usually behind a shift of the Dirac point. These observations suggest that large-area unmodified/pristine graphene in field-effect sensors behaves as a non-polarized electrode in liquid. Strategies for ensuring a polarized interface are discussed.

Graphene transistors for real-time monitoring molecular self-assembly dynamics

Mastering the dynamics of molecular assembly on surfaces enables the engineering of predictable structural motifs to bestow programmable properties upon target substrates. Yet, monitoring self-assembly in real time on technologically relevant interfaces between a substrate and a solution is challenging, due to experimental complexity of disentangling interfacial from bulk phenomena. Here, we show that graphene devices can be used as highly sensitive detectors to read out the dynamics of molecular self-assembly at the solid/liquid interface in-situ. Irradiation of a photochromic molecule is used to trigger the formation of a metastable self-assembled adlayer on graphene and the dynamics of this process are monitored by tracking the current in the device over time. In perspective, the electrical readout in graphene devices is a diagnostic and highly sensitive means to resolve molecular ensemble dynamics occurring down to the nanosecond time scale, thereby providing a practical and powerful tool to investigate molecular self-organization in 2D.

Molecular self-assembly provides the desired functions to substrates, but investigation and control of its dynamics is challenging for the large area over which it must be detected. Here the authors report the use of graphene field effect devices to monitor with sub-second time resolution the photoinduced supramolecular assembly of a spiropyran derivative on graphene, covering an area of 100 × 100 μm².

CVD-Bi2Te3 as a saturable absorber for various solitons in a mode-locked Er-doped fiber laser

In this work, we report about high energy and various solitons' operation by using high-efficiency topological insulator bismuth telluride (Bi₂Te₃) nanofilms as broadband saturable absorbers in the passively mode-locked Er-doped fiber laser. The Bi₂Te₃ film was successfully synthesized by chemical vapor deposition (CVD). Excellent characteristics of the dark-bright pulse pairs, bright pulses, and multiharmonics have been investigated experimentally by adjusting the polarization state. At the same time, the maximum average output power was 40.18 mW, and the single-pulse energy was 20.91 nJ. As we all know, it is the various solitons of the first generation with large pulse energy in an Er-doped fiber laser with Bi₂Te₃ as saturable absorber. The experimental results show that CVD Bi₂Te₃ can be used as an excellent candidate in mode-locked fiber lasers.

Detecting DNA and RNA and Differentiating Single-Nucleotide Variations via Field-Effect Transistors

We detect short oligonucleotides and distinguish between sequences that differ by a single base, using label-free, electronic field-effect transistors (FETs). Our sensing platform utilizes ultrathin-film indium oxide FETs chemically functionalized with single-stranded DNA (ssDNA). The ssDNA-functionalized semiconducting channels in FETs detect fully complementary DNA sequences and differentiate these sequences from those having different types and locations of single base-pair mismatches. Changes in charge associated with surface-bound ssDNA vs double-stranded DNA (dsDNA) alter FET channel conductance to enable detection due to differences in DNA duplex stability. We illustrate the capability of ssDNA-FETs to detect complementary RNA sequences and to distinguish from RNA sequences with single nucleotide variations. The development and implementation of electronic biosensors that rapidly and sensitively detect and differentiate oligonucleotides present new opportunities in the fields of disease diagnostics and precision medicine.

Opportunities and Challenges for Biosensors and Nanoscale Analytical Tools for Pandemics: COVID-19

Biosensors and nanoscale analytical tools have shown huge growth in literature in the past 20 years, with a large number of reports on the topic of 'ultrasensitive', 'cost-effective', and 'early detection' tools with a potential of 'mass-production' cited on the web of science. Yet none of these tools are commercially available in the market or practically viable for mass production and use in pandemic diseases such as coronavirus disease 2019 (COVID-19). In this context, we review the technological challenges and opportunities of current bio/chemical sensors and analytical tools by critically analyzing the bottlenecks which have hindered the implementation of advanced sensing technologies in pandemic diseases. We also describe in brief COVID-19 by comparing it with other pandemic strains such as that of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) for the identification of features that enable biosensing. Moreover, we discuss visualization and characterization tools that can potentially be used not only for sensing applications but also to assist in speeding up the drug discovery and vaccine development process. Furthermore, we discuss the emerging monitoring mechanism, namely wastewater-based epidemiology, for early warning of the outbreak, focusing on sensors for rapid and on-site analysis of SARS-CoV2 in sewage. To conclude, we provide holistic insights into challenges associated with the quick translation of sensing technologies, policies, ethical issues, technology adoption, and an overall outlook of the role of the sensing technologies in pandemics.

Graphene Templated DNA Arrays and Biotin-Streptavidin Sensitive Bio-Transistors Patterned by Dynamic Self-Assembly of Polymeric Films Confined within a Roll-on-Plate Geometry

Patterning of surfaces with a simple strategy provides insights into the functional interfaces by suitable modification of the surface by novel techniques. Especially, highly ordered structural topographies and chemical features from the wide range of interfaces have been considered as important characteristics to understand the complex relationship between the surface chemistries and biological systems. Here, we report a simple fabrication method to create patterned surfaces over large areas using evaporative self-assembly that is designed to produce a sacrificial template and lithographic etch masks of polymeric stripe patterns, ranging from micrometer to nanoscale. By facilitating a roll-on-plate geometry, the periodically patterned surface structures formed by repetitive slip-stick motions were thoroughly examined to be used for the deposition of the Au nanoparticles decorated graphene oxide (i.e., AuNPs, ~21 nm) and the formation of conductive graphene channels. The fluorescently labeled thiol-modified DNA was applied on the patterned arrays of graphene oxide (GO)/AuNPs, and biotin-streptavidin sensitive devices built with graphene-based transistors (GFETs, effective mobility of ~320 cm² V^-1 s^-1) were demonstrated as examples of the platform for the next-generation biosensors with the high sensing response up to ~1 nM of target analyte (i.e., streptavidin). Our strategy suggests that the stripe patterned arrays of polymer films as sacrificial templates can be a simple route to creating highly sensitive biointerfaces and highlighting the development of new chemically patterned surfaces composed of graphene-based nanomaterials.

Inter-particle biomolecular reactivity tuned by surface crowders

The rate at which colloidal particles can form biomolecular bonds controls the kinetics of applications such as particle-based biosensing, targeted drug delivery and directed colloidal assembly. Here we study how the reactivity of the particle surface depends on its molecular composition, quantified by the inter-particle rate of aggregation in an optomagnetic cluster experiment. Particles were functionalized with DNA or with proteins for specific binding, and with polyethylene glycol as a passive surface crowder. The data show that the inter-particle binding kinetics are dominated by specific interactions, which surprisingly can be tuned by the passive crowder molecules for both the DNA and the protein system. The experimental results are interpreted using model simulations, which show that the crowder-induced decrease of the particle surface reactivity can be described as a reduced reactivity of the specific binder molecules on the particle surface.

An integrated microfluidic platform for selective and real-time detection of thrombin biomarkers using a graphene FET

Lab-on-a-chip technology offers an ideal platform for low-cost, reliable, and easy-to-use diagnostics of key biomarkers needed for early screening of diseases and other health concerns. In this work, a graphene field-effect transistor (GFET) functionalized with target-binding aptamers is used as a biosensor for the detection of thrombin protein biomarker. Furthermore, this GFET is integrated with a microfluidic device for enhanced sensing performances in terms of detection limit, sensitivity, and continuous monitoring. Under this platform, a picomolar limit of detection was achieved for measuring thrombin; in our experiment measured as low as 2.6 pM. FTIR, Raman and UV-Vis spectroscopy measurements were performed to confirm the device functionalization steps. Based on the concentration-dependent calibration curve, a dissociation constant of KD = 375.8 pM was obtained. Continuous real-time measurements were also conducted under a constant gate voltage (VGS) to observe the transient response of the sensor when analyte was introduced to the device. The target selectivity of the sensor platform was evaluated and confirmed by challenging the GFET biosensor with various concentrations of lysozyme protein. The results suggest that this device technology has the potential to be used as a general diagnostic platform for measuring clinically relevant biomarkers for point-of-care applications.

Kinetic Exclusion Assay of Biomolecules by Aptamer Capture

DNA aptamers are short nucleotide oligomers selected to bind a target ligand with affinity and specificity rivaling that of antibodies. These remarkable features recommend aptamers as candidates for analytical and therapeutic applications that traditionally use antibodies as biorecognition elements. Numerous traditional and emerging analytical techniques have been proposed and successfully implemented to utilize aptamers for sensing purposes. In this work, we exploited the analytical capabilities offered by the kinetic exclusion assay technology to measure the affinity of fluorescent aptamers for their thrombin target and quantify the concentration of analyte in solution. Standard binding curves constructed by using equilibrated mixtures of aptamers titrated with thrombin were fitted with a 1:1 binding model and provided an effective Kd of the binding in the sub-nanomolar range. However, our experimental results suggest that this simple model does not satisfactorily describe the binding process; therefore, the possibility that the aptamer is composed of a mixture of two or more distinct Kd populations is discussed. The same standard curves, together with a four-parameter logistic equation, were used to determine "unknown" concentrations of thrombin in mock samples. The ability to identify and characterize complex binding stoichiometry, together with the determination of target analyte concentrations in the pM-nM range, supports the adoption of this technology for kinetics, equilibrium, and analytical purposes by employing aptamers as biorecognition elements.

Metasurface with metallic nanoantennas and graphene nanoslits for sensing of protein monolayers and sub-monolayers

Biomolecule sensing plays an important role in both fundamental biological studies and medical diagnostic applications. Infrared (IR) spectroscopy presents opportunities for sensing biomolecules as it allows their fingerprints to be determined by directly measuring their absorption spectra. However, the detection of biomolecules at low concentrations is difficult with conventional IR spectroscopy due to signal-to-noise considerations. This has led to recent interest on the use of nanostructured surfaces to boost the signals from biomolecules in a method termed surface enhanced infrared spectroscopy. So far, efforts have largely involved the use of metallic nanoantennas (which produce large field enhancement) or graphene nanostructures (which produce strong field confinement and provide electrical tunability). Here, we propose a nanostructured surface that combines the large field enhancement of metallic nanoantennas with the strong field confinement and electrical tunability of graphene plasmons. Our device consists of an array of plasmonic nanoantennas and graphene nanoslits on a resonant substrate. We perform systematic electromagnetic simulations to quantify the sensing performance of the proposed device and show that it outperforms designs in which only plasmons from metallic nanoantennas or plasmons from graphene are utilized. These investigations consider the model system of a representative protein-goat anti-mouse immunoglobulin G (IgG) - in monolayer or sub-monolayer form. Our findings provide guidance for future biosensors for the sensitive quantification and identification of biomolecules.

Graphene field-effect transistor biosensor for detection of biotin with ultrahigh sensitivity and specificity

Because avidin and biotin molecules exhibit the most specific and strongest non-covalent interaction, avidin-biotin technology is widely used in ELISA (enzyme-linked immunosorbent assay) kits for the detection of different bio-macromolecules linked to different diseases including cancer and influenza. Combining the outstanding electrical conductivity (200,000 cm²V^-1s^-1) of graphene with the unique avidin and biotin interaction, we demonstrate a novel graphene field-effect transistor (GFET) biosensor for the quantitative detection of bio-macromolecules. The GFET consists of six pairs of interdigital Cr/Au electrodes supported on Si/SiO₂ substrate with an avidin immobilized single layer graphene channel as the sensing platform. By monitoring the real time current change upon the addition of biotin solution in bovine serum albumin (BSA) in the silicone pool preformed onto the GFET, the lowest detectable biotin concentration is estimated to be 90 fg/ml (0.37 pM). The specificity of the GFET is confirmed both by controlled and real sample measurements. From the magnitude of current change upon the addition of different concentrations of biotin solutions, the dissociation constant K_d is estimated to be 1.6 × 10^-11 M. Since biotin is capable of conjugating with proteins, nucleotides and other bio-macromolecules without altering their properties, the present GFET sensor with its ultra-high sensitivity (0.37 pM) and specificity can be tailored to the rapid point-of-care detection of different types of desired biomolecules at very low concentration level through biotinylation as well as the exogenous biotin in blood serum.

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Combining the outstanding electrical conductivity of graphene with the unique interaction between avidin and biotin, a novel graphene field-effect transistor (GFET) biosensor for quantitative detection of bio-macromolecules is demonstrated.

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The present biosensor is capable of detecting the biotin with the sensitivity of 90 fg/ml (~0.37 pM) and high specificity.

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Since the biotin is capable of conjugating with protein, nucleotide and other bio-macromolecules without affecting their properties, the present GFET sensor can be tailored to various medical applications.

TMAVA, a Metabolite of Intestinal Microbes, Is Increased in Plasma From Patients With Liver Steatosis, Inhibits γ-Butyrobetaine Hydroxylase, and Exacerbates Fatty Liver in Mice

BACKGROUND & AIMS

Nonalcoholic fatty liver disease is characterized by excessive hepatic accumulation of triglycerides. We aimed to identify metabolites that differ in plasma of patients with liver steatosis vs healthy individuals (controls) and investigate the mechanisms by which these might contribute to fatty liver in mice.

METHODS

We obtained blood samples from 15 patients with liver steatosis and 15 controls from a single center in China (discovery cohort). We performed untargeted liquid chromatography with mass spectrometry analysis of plasma to identify analytes associated with liver steatosis. We then performed targeted metabolomic analysis of blood samples from 2 independent cohorts of individuals who underwent annual health examinations in China (1157 subjects with or without diabetes and 767 subjects with or without liver steatosis; replication cohorts). We performed mass spectrometry analysis of plasma from C57BL/6J mice, germ-free, and mice given antibiotics. C57BL/6J mice were given 0.325% (m/v) N,N,N-trimethyl-5-aminovaleric acid (TMAVA) in their drinking water and placed on a 45% high-fat diet (HFD) for 2 months. Plasma, liver tissues, and fecal samples were collected; fecal samples were analyzed by 16S ribosomal RNA gene sequencing. C57BL/6J mice with CRISPR-mediated disruption of the gene encoding γ-butyrobetaine hydroxylase (BBOX-knockout mice) were also placed on a 45% HFD for 2 months. Hepatic fatty acid oxidation (FAO) in liver tissues was determined by measuring liberation of ³H₂O from [³H] palmitic acid. Liver tissues were analyzed by electron microscopy, to view mitochondria, and proteomic analyses. We used surface plasmon resonance analysis to quantify the affinity of TMAVA for BBOX.

RESULTS

Levels of TMAVA, believed to be a metabolite of intestinal microbes, were increased in plasma from subjects with liver steatosis compared with controls, in the discovery and replication cohorts. In 1 replication cohort, the odds ratio for fatty liver in subjects with increased liver plasma levels of TMAVA was 1.82 (95% confidence interval [CI], 1.14-2.90; P = .012). Plasma from mice given antibiotics or germ-free mice had significant reductions in TMAVA compared with control mice. We found the intestinal bacteria Enterococcus faecalis and Pseudomonas aeruginosa to metabolize trimethyllysine to TMAVA; levels of trimethyllysine were significantly higher in plasma from patients with steatosis than controls. We found TMAVA to bind and inhibit BBOX, reducing synthesis of carnitine. Mice given TMAVA had alterations in their fecal microbiomes and reduced cold tolerance; their plasma and liver tissue had significant reductions in levels of carnitine and acyl-carnitine and their hepatocytes had reduced mitochondrial FAO compared with mice given only an HFD. Mice given TMAVA on an HFD developed liver steatosis, which was reduced by carnitine supplementation. BBOX-knockout mice had carnitine deficiency and decreased FAO, increasing uptake and liver accumulation of free fatty acids and exacerbating HFD-induced fatty liver.

CONCLUSIONS

Levels of TMAVA are increased in plasma from subjects with liver steatosis. In mice, intestinal microbes metabolize trimethyllysine to TMAVA, which reduces carnitine synthesis and FAO to promote steatosis.

Dual-Functional Plasmonic Photothermal Biosensors for Highly Accurate Severe Acute Respiratory Syndrome Coronavirus 2 Detection

The ongoing outbreak of the novel coronavirus disease (COVID-19) has spread globally and poses a threat to public health in more than 200 countries. Reliable laboratory diagnosis of the disease has been one of the foremost priorities for promoting public health interventions. The routinely used reverse transcription polymerase chain reaction (RT-PCR) is currently the reference method for COVID-19 diagnosis. However, it also reported a number of false-positive or -negative cases, especially in the early stages of the novel virus outbreak. In this work, a dual-functional plasmonic biosensor combining the plasmonic photothermal (PPT) effect and localized surface plasmon resonance (LSPR) sensing transduction provides an alternative and promising solution for the clinical COVID-19 diagnosis. The two-dimensional gold nanoislands (AuNIs) functionalized with complementary DNA receptors can perform a sensitive detection of the selected sequences from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through nucleic acid hybridization. For better sensing performance, the thermoplasmonic heat is generated on the same AuNIs chip when illuminated at their plasmonic resonance frequency. The localized PPT heat is capable to elevate the in situ hybridization temperature and facilitate the accurate discrimination of two similar gene sequences. Our dual-functional LSPR biosensor exhibits a high sensitivity toward the selected SARS-CoV-2 sequences with a lower detection limit down to the concentration of 0.22 pM and allows precise detection of the specific target in a multigene mixture. This study gains insight into the thermoplasmonic enhancement and its applicability in the nucleic acid tests and viral disease diagnosis.

Dual-Functional Plasmonic Photothermal Biosensors for Highly Accurate Severe Acute Respiratory Syndrome Coronavirus 2 Detection

The ongoing outbreak of the novel coronavirus disease (COVID-19) has spread globally and poses a threat to public health in more than 200 countries. Reliable laboratory diagnosis of the disease has been one of the foremost priorities for promoting public health interventions. The routinely used reverse transcription polymerase chain reaction (RT-PCR) is currently the reference method for COVID-19 diagnosis. However, it also reported a number of false-positive or -negative cases, especially in the early stages of the novel virus outbreak. In this work, a dual-functional plasmonic biosensor combining the plasmonic photothermal (PPT) effect and localized surface plasmon resonance (LSPR) sensing transduction provides an alternative and promising solution for the clinical COVID-19 diagnosis. The two-dimensional gold nanoislands (AuNIs) functionalized with complementary DNA receptors can perform a sensitive detection of the selected sequences from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through nucleic acid hybridization. For better sensing performance, the thermoplasmonic heat is generated on the same AuNIs chip when illuminated at their plasmonic resonance frequency. The localized PPT heat is capable to elevate the in situ hybridization temperature and facilitate the accurate discrimination of two similar gene sequences. Our dual-functional LSPR biosensor exhibits a high sensitivity toward the selected SARS-CoV-2 sequences with a lower detection limit down to the concentration of 0.22 pM and allows precise detection of the specific target in a multigene mixture. This study gains insight into the thermoplasmonic enhancement and its applicability in the nucleic acid tests and viral disease diagnosis.

Protein Detection using Quadratic Fit Analysis Near Dirac Point of Graphene Field Effect Biosensors

Although graphene-based biosensors provid extreme sensitivity for the detection of atoms, gases, and biomolecules, the specificity of graphene biosensors to the target molecules requires surface decoration of graphene with bifunctional linkers such pyrene derivatives. Here, we demonstrate that the pyrene functionalization influences graphene's electrical properties by yielding partial formation of bilayer graphene which was confirmed by Raman 2D spectrum. Based on this observation, we introduce quadratic fit analysis of the nonlinear electrical behavior of pyrene-functionalized graphene near the Dirac point. Compared to the conventional linear fit analysis of the transconductance at a distance from the Dirac point, the quadratic fit analysis of the nonlinear transconductance near the Dirac point increased the overall protein detection sensitivity by a factor of 5. Furthermore, we show that both pyrene linkers and gating voltage near the Dirac point play critical roles in sensitive and reliable detection of proteins' biological activities with the graphene biosensors.

Gold and silver nanoparticles used for SERS detection of S. aureus and E. coli

Surface enhanced Raman scattering (SERS) is emerging as a robust analytical method used in sensing applications in chemical as well as biological systems. SERS has been reported to be used in fast detection of micro-organisms up to the specificity of strain identification. However, use of SERS is tricky because of difficulties involved in selection of SERS active substrate so as to give uniform, sensitive as well as reproducible results. We have synthesized silver and gold nanoparticles using chemical, electrochemical and microwave-assisted methods followed by their characterization. Uses of these nanoparticles in association with micro-organisms such as S. aureus and E. coli have been analyzed using SERS to generate signature spectra. This demonstrates use of so synthesized gold and silver nanoparticles as SERS active substrates for rapid detection of micro-organisms which pave way to find applications in disease diagnostics.