Multiplex label-free biosensor for detection of autoantibodies in human serum: Tool for new kinetics-based diagnostics of autoimmune diseases

Enhanced Analytical Performance in CYFRA 21-1 Detection Using Lateral Flow Assay with Magnetic Bioconjugates: Integration and Comparison of Magnetic and Optical Registration

A novel approach to developing lateral flow assays (LFAs) for the detection of CYFRA 21-1 (cytokeratin 19 fragment, a molecular biomarker for epithelial-origin cancers) is proposed. Magnetic bioconjugates (MBCs) were employed in combination with advanced optical and magnetic tools to optimize assay conditions. The approach integrates such techniques as label-free spectral-phase interferometry, colorimetric detection, and ultrasensitive magnetometry using the magnetic particle quantification (MPQ) technique. For the first time in LFA applications, the MPQ-based and colorimetry-based detection methods were compared side by side, and superior analytical performance was demonstrated. The limit of detection (LOD) of 0.9 pg/mL was achieved using MPQ, and 2.9 pg/mL with optical detection. This study has demonstrated that MPQ provides elimination of signal saturation, higher sensitivity (slope of the calibration curve), and a 19-fold wider dynamic range of detected signals. Both optical and magnetic detection results are comparable to the best laboratory-based tests with the added benefits of a 20-min assay duration and the LFA format convenience. The assay effectiveness was validated in human serum and artificial saliva, and high recovery rates were observed. The proposed approach offers rapid and reliable detection of molecular biomarkers and holds significant potential for point-of-care diagnostics, particularly in resource-limited settings.

Early diagnosis of autoimmune diseases through electrochemical biosensing using a modified plastic chip electrode

Detecting chronic autoimmune disorders (ADs) early reduces the risk of morbidity, disability, and mortality and offers the possibility of significant therapeutic action in a timely manner. Developing low-cost, reliable, and sensitive sensors for ADs can ensure the efficient utilization of healthcare resources at earlier stages. Here, we report on the development of an electrochemical biosensor for sensing CXCL10, a chemokine protein that serves as a biomarker for autoimmune diseases. A self-assembly strategy is used for the immobilization of biorecognition elements on a plastic chip electrode (PCE). A homemade PCE offers a versatile and cost-effective scaffold for sensing applications. Gold nanoparticles were electrochemically deposited on the electrode via the reduction of gold ions on the PCE galvanostatically. The CXCL10 antibody and recognition elements were immobilized on the gold-deposited PCE. The attachment of recognition molecules was confirmed by energy-dispersive scanning electron microscopy, atomic force microscopy, infrared spectroscopy, and electrochemical techniques. Electrochemical impedance spectroscopy (EIS) was used for the detection of CXCL10 within a concentration range spanning from pico- to micro-molar levels. The sensor exhibited remarkable linearity in both buffer and plasma solutions, with a limit of detection (LOD) of up to 0.72 pg mL-1.

Surface plasmonic biosensors: principles, designs and applications

Recently, surface plasmon resonance (SPR) biosensors have been widely used in environmental monitoring, food contamination detection and diagnosing medical conditions due to their superior sensitivity, label-free detection and rapid analysis speed. This paper briefly elaborates on the development history of SPR technology and introduces SPR signal sensing principles. A summary of recent applications of SPR sensors in different fields is highlighted, including their figures of merit and limitations. Finally, the personal perspectives and future development trends about sensor preparation and design are discussed in detail, which may be critical for improving the performance of SPR sensors.

A novel tunable metal-clad planar waveguide with 0.62PMN-0.38PT material for detection of cancer cells

A dynamically tunable metal clad planar waveguide having 0.62PMN-0.38PT material is simulated and optimized for detection of cancer cells. Angular interrogation of the TE0 mode of waveguide shows that critical angle increases greater than the resonance angle with increasing of cover refractive index, which limits the detection range of waveguide. To overcome this limitation, proposed waveguide applies a potential on the PMN-PT adlayer. Although a sensitivity of 105.42 degree/RIU was achieved at 70 Volts in testing the proposed waveguide, it was found that the optimal performance parameters were obtained at 60 Volts. At this voltage, the waveguide demonstrated detection range 1.3330-1.5030, a detection accuracy 2393.33, and a figure of merit 2243.59 RIU-1 , which enabled the detection of the entire range of the targeted cancer cells. Therefore, it is recommended to apply a potential of 60 Volts to achieve the best performance from the proposed waveguide.

Immunosensors for Autoimmune-Disease-Related Biomarkers: A Literature Review

Immunosensors are a special class of biosensors that employ specific antibodies for biorecognition of the target analyte. Immunosensors that target disease biomarkers may be exploited as tools for disease diagnosis and/or follow-up, offering several advantages over conventional analytical techniques, such as rapid and easy analysis of patients' samples at the point-of-care. Autoimmune diseases have been increasingly prevalent worldwide in recent years, while the COVID-19 pandemic has also been associated with autoimmunity. Consequently, demand for tools enabling the early and reliable diagnosis of autoimmune diseases is expected to increase in the near future. To this end, interest in immunosensors targeting autoimmune disease biomarkers, mainly, various autoantibodies and specific pro-inflammatory proteins (e.g., specific cytokines), has been rekindled. This review article presents most of the immunosensors proposed to date as potential tools for the diagnosis of various autoimmune diseases, such as type 1 diabetes, rheumatoid arthritis, and multiple sclerosis. The signal transduction and the immunoassay principles of each immunosensor have been suitably classified and are briefly presented along with certain sensor elements, e.g., special nano-sized materials used in the construction of the immunosensing surface. The main concluding remarks are presented and future perspectives of the field are also briefly discussed.

The convergence of traditional and digital biomarkers through AI-assisted biosensing: A new era in translational diagnostics?

Advances in consumer electronics, alongside the fields of microfluidics and nanotechnology have brought to the fore low-cost wearable/portable smart devices. Although numerous smart devices that track digital biomarkers have been successfully translated from bench-to-bedside, only a few follow the same fate when it comes to track traditional biomarkers. Current practices still involve laboratory-based tests, followed by blood collection, conducted in a clinical setting as they require trained personnel and specialized equipment. In fact, real-time, passive/active and robust sensing of physiological and behavioural data from patients that can feed artificial intelligence (AI)-based models can significantly improve decision-making, diagnosis and treatment at the point-of-procedure, by circumventing conventional methods of sampling, and in person investigation by expert pathologists, who are scarce in developing countries. This review brings together conventional and digital biomarker sensing through portable and autonomous miniaturized devices. We first summarise the technological advances in each field vs the current clinical practices and we conclude by merging the two worlds of traditional and digital biomarkers through AI/ML technologies to improve patient diagnosis and treatment. The fundamental role, limitations and prospects of AI in realizing this potential and enhancing the existing technologies to facilitate the development and clinical translation of "point-of-care" (POC) diagnostics is finally showcased.

Polysaccharide-based C-dots and polysaccharide/C-dot nanocomposites: fabrication strategies and applications

C-dots are a new class of materials with vast applications. The synthesis of bio-based C-dots has attracted increasing attention in recent years. Polysaccharides being the most abundant natural materials with high biodegradability and no toxicity have been the focus of researchers for the synthesis of C-dots. C-dots obtained from polysaccharides are generally fabricated via thermal procedures, carbonization, and microwave pyrolysis. Small size, photo-induced electron transfer (PET), and highly adjustable luminosity behavior are the most important physical and chemical properties of C-dots. However, C-dot/polysaccharide composites can be introduced as a new generation of composites that combine the features of both C-dots and polysaccharides having a wide range of applications in biomedicines, biosensors, drug delivery systems, etc. This review demonstrates the features, raw materials, and methods used for the fabrication of C-dots derived from different polysaccharides. Furthermore, the properties, applications, and synthesis conditions of various C-dot/polysaccharide composites are discussed in detail.

Kinetic Analysis of Prostate-Specific Antigen Interaction with Monoclonal Antibodies for Development of a Magnetic Immunoassay Based on Nontransparent Fiber Structures

Prostate cancer is the second most common cancer diagnosed in men worldwide. Measuring the prostate-specific antigen (PSA) is regarded as essential during prostate cancer screening. Early diagnosis of this disease relapse after radical prostatectomy requires extremely sensitive methods. This research presents an approach to development of an ultrasensitive magnetic sandwich immunoassay, which demonstrates the limit of PSA detection in human serum of 19 pg/mL at a dynamic range exceeding 3.5 orders of concentration. Such attractive performance stems, inter alia, from the kinetic analysis of monoclonal antibodies (mAbs) against free PSA to select the mAbs exhibiting best kinetic characteristics and specificity. The analysis is carried out with a label-free multiplex spectral-correlation interferometry compatible with inexpensive single-use glass sensor chips. The high sensitivity of developed PSA immunoassay is due to electronic quantification of magnetic nanolabels functionalized by the selected mAbs and three-dimension porous filters used as an extended solid phase. The assay is promising for PSA monitoring after radical prostatectomy. The proposed versatile approach can be applied for the rational design of highly sensitive tests for detection of other analytes in many fields, including in vitro diagnostics, veterinary, food safety, etc.

Measurements of SARS-CoV-2 antibody dissociation rate constant by chaotrope-free biolayer interferometry in serum of COVID-19 convalescent patients

Kinetics measurements of antigen-antibody binding interactions are critical to understanding the functional efficiency of SARS-CoV-2 antibodies. Previously reported chaotrope-based avidity assays that rely on artificial disruption of binding do not reflect the natural binding kinetics. This study developed a chaotrope- and label-free biolayer interferometry (BLI) assay for the real-time monitoring of receptor binding domain (RBD) binding kinetics with SARS-CoV-2 spike protein in convalescent COVID-19 patients. An improved conjugation biosensor probe coated with streptavidin-polysaccharide (SA-PS) led to a six-fold increase of signal intensities and two-fold reduction of non-specific binding (NSB) compared to streptavidin only probe. Furthermore, by utilizing a separate reference probe and biotin-human serum albumin (B-HSA) blocking process to subtracted NSB signal in serum, this BLI biosensor can measure a wide range of the dissociation rate constant (koff), which can be measured without knowledge of the specific antibody concentrations. The clinical utility of this improved BLI kinetics assay was demonstrated by analyzing the koff values in sera of 24 pediatric (≤18 years old) and 63 adult (>18 years old) COVID-19 convalescent patients. Lower koff values for SARS-CoV-2 serum antibodies binding to RBD were measured in samples from children. This rapid, easy to operate and chaotrope-free BLI assay is suitable for clinical use and can be readily adapted to characterize SARS-CoV-2 antibodies developed by COVID-19 patients and vaccines.

Express high-sensitive detection of ochratoxin A in food by a lateral flow immunoassay based on magnetic biolabels

We present an easy-to-use lateral flow immunoassay for rapid, precise and sensitive quantification of one of the most hazardous mycotoxins - ochratoxin A (OTA), which is widely present in food and agricultural commodities. The achieved limit of detection during the 20-min OTA registration is 11 pg/mL. The assay provides accurate results in both low- and high-concentration ranges. That is due to the extraordinary steepness of the linear calibration plot: 5-order dynamic range of concentrations causes almost a 1000-fold change in the signal obtained by electronic detection of magnetic biolabels using their non-linear magnetization. High specificity, repeatability, and reproducibility of the assay have been verified, including measuring OTA in real samples of contaminated corn flour. The developed assay is a promising analytical tool for food and feed safety control; it may become an express, convenient and high-precision alternative to the traditional sophisticated laboratory techniques based on liquid chromatography.

Multiplex Label-Free Kinetic Characterization of Antibodies for Rapid Sensitive Cardiac Troponin I Detection Based on Functionalized Magnetic Nanotags

Express and highly sensitive immunoassays for the quantitative registration of cardiac troponin I (cTnI) are in high demand for early point-of-care differential diagnosis of acute myocardial infarction. The selection of antibodies that feature rapid and tight binding with antigens is crucial for immunoassay rate and sensitivity. A method is presented for the selection of the most promising clones for advanced immunoassays via simultaneous characterization of interaction kinetics of different monoclonal antibodies (mAb) using a direct label-free method of multiplex spectral correlation interferometry. mAb-cTnI interactions were real-time registered on an epoxy-modified microarray glass sensor chip that did not require activation. The covalent immobilization of mAb microdots on its surface provided versatility, convenience, and virtually unlimited multiplexing potential. The kinetics of tracer antibody interaction with the “cTnI—capture antibody” complex was characterized. Algorithms are shown for excluding mutual competition of the tracer/capture antibodies and selecting the optimal pairs for different assay formats. Using the selected mAbs, a lateral flow assay was developed for rapid quantitative cTnI determination based on electronic detection of functionalized magnetic nanoparticles applied as labels (detection limit—0.08 ng/mL, dynamic range > 3 orders). The method can be extended to other molecular biomarkers for high-throughput screening of mAbs and rational development of immunoassays.

Nanoplasmonic multiplex biosensing for COVID-19 vaccines

The ongoing emergence of severe acute respiratory syndrome caused by the new coronavirus (SARS-CoV-2) variants requires swift actions in identifying specific antigens and optimizing vaccine development to maximize the humoral response of the patient. Measuring the specificity and the amount of antibody produced by the host immune system with high throughput and accuracy is critical to develop timely diagnostics and therapeutic strategies. Motivated by finding an easy-to-use and cost-effective alternative to existing serological methodologies for multiplex analysis, we develop a proof-of-concept multiplex nanoplasmonic biosensor to capture the humoral response in serums against multiple antigens. Nanoplasmonic sensing relies on the wavelength shift of the localized surface plasmon resonance (LSPR) peak of gold nanostructures upon binding interactions between the antibodies and the immobilized antigens. Here the antigens are first immobilized on different sensing areas by using a mono-biotinylation system based on the high affinity interaction between biotin and streptavidin. We then validate the multiplex platform by detecting the presence of 3 monoclonal antibodies against 3 antigens (2 different hemagglutinins (HAs) from influenza viruses, and the SARS-CoV-2 Spike RBD (receptor binding domain)). We also measure the humoral response in murine sera collected before and after its immunization with the SARS-CoV-2 Spike protein, in good agreement with the results obtained by the ELISA assay. Our nanoplasmonic assays have successfully demonstrated multiple serum antibody profiling, which can be further integrated with microfluidics as an effective high throughput screening platform in future studies for the ongoing SARS-CoV-2 vaccine development.

Double-Resonant Nanostructured Gold Surface for Multiplexed Detection

A novel double-resonant plasmonic substrate for fluorescence amplification in a chip-based apta-immunoassay is herein reported. The amplification mechanism relies on plasmon-enhanced fluorescence (PEF) effect. The substrate consists of an assembly of plasmon-coupled and plasmon-uncoupled gold nanoparticles (AuNPs) immobilized onto a glass slide. Plasmon-coupled AuNPs are hexagonally arranged along branch patterns whose resonance lies in the red band (∼675 nm). Plasmon-uncoupled AuNPs are sprinkled onto the substrate, and they exhibit a narrow resonance at 524 nm. Numerical simulations of the plasmonic response of the substrate through the finite-difference time-domain (FDTD) method reveal the presence of electromagnetic hot spots mainly confined in the interparticle junctions. In order to realize a PEF-based device for potential multiplexing applications, the plasmon resonances are coupled with the emission peak of 5-carboxyfluorescein (5-FAM) fluorophore and with the excitation/emission peaks of cyanine 5 (Cy5). The substrate is implemented in a malaria apta-immunoassay to detect Plasmodium falciparum lactate dehydrogenase (PfLDH) in human whole blood. Antibodies against Plasmodium biomarkers constitute the capture layer, whereas fluorescently labeled aptamers recognizing PfLDH are adopted as the top layer. The fluorescence emitted by 5-FAM and Cy5 fluorophores are linearly correlated (logarithm scale) to the PfLDH concentration over five decades. The limits of detection are 50 pM (1.6 ng/mL) with the 5-FAM probe and 260 fM (8.6 pg./mL) with the Cy5 probe. No sample preconcentration and complex pretreatments are required. Average fluorescence amplifications of 160 and 4500 are measured in the 5-FAM and Cy5 channel, respectively. These results are reasonably consistent with those worked out by FDTD simulations. The implementation of the proposed approach in multiwell-plate-based bioassays would lead to either signal redundancy (two dyes for a single analyte) or to a simultaneous detection of two analytes by different dyes, the latter being a key step toward high-throughput analysis.

Advances in surface plasmon resonance-based biosensor technologies for cancer biomarker detection

Surface plasmon resonance approach is a highly useful option to offer optical and label-free detection of target bioanalytes with numerous advantages (e.g., low-cost fabrication, appreciable sensitivity, label-free detection, and outstanding accuracy). As such, it allows early diagnosis of cancer biomarkers to monitor tumor progression and to prevent the recurrence of oncogenic tumors. This work highlights the recent progress in SPR biosensing technology for the diagnosis of various cancer types (e.g., lung, breast, prostate, and ovarian). Further, the performance of various SPR biosensors is also evaluated in terms of the basic quality assurance criteria (e.g., limit of detection (LOD), selectivity, sensor response time, and reusability). Finally, the limitations and future challenges associated with SPR biosensors are also discussed with respect to cancer biomarker detection.

Evolution of "On-Barcode" Luminescence Oxygen Channeling Immunoassay by Exploring the Barcode Structure and the Assay System

The multiplexed luminescence oxygen channeling immunoassay (multi-LOCI) platform we developed recently that combines conventional LOCI and suspension array technology is capable of realizing facile "mix-and-measure" multiplexed assays without tedious washing steps. However, previous work lacks comprehensive studies of the structure-performance relationship of the host-guest-structured barcode, which may obstruct the evolution and further translation of this exciting new technology to practical applications. Accordingly, this work revealed that polyelectrolyte interlayers played a crucial role in tuning the packing density of guest acceptor beads (ABs). More interestingly, we noticed that "sparse" barcodes (barcodes with low ABs packing density) exhibited comparable assay performance with "compact" ones (barcodes with high ABs packing density). The high robustness of barcodes allows for multi-LOCI to be a more universal and flexible assay platform. Furthermore, through optimization of the assay system including the laser power, as well as the concentrations of donor beads and biotinylated detection antibodies, the multi-LOCI platform showed a significant improvement in sensitivity compared with our previous work, with the limit of detection decreasing to as low as ca. 1 pg/mL. Impressively, multi-LOCI that enabled simultaneous detection of multiple analytes exhibited comparable sensitivity with the classical single-plexed LOCI, due to the ingenious structural design of the multi-LOCI barcode and the unique "on-barcode" assay format.

Antibodies as Biosensors' Key Components: State-of-the-Art in Russia 2020-2021

The recognition of biomolecules is crucial in key areas such as the timely diagnosis of somatic and infectious diseases, food quality control, and environmental monitoring. This determines the need to develop highly sensitive display devices based on the achievements of modern science and technology, characterized by high selectivity, high speed, low cost, availability, and small size. Such requirements are met by biosensor systems—devices for reagent-free analysis of compounds that consist of a biologically sensitive element (receptor), a transducer, and a working solution. The diversity of biological material and methods for its immobilization on the surface or in the volume of the transducer and the use of nanotechnologies have led to the appearance of an avalanche-like number of different biosensors, which, depending on the type of biologically sensitive element, can be divided into three groups: enzyme, affinity, and cellular/tissue. Affinity biosensors are one of the rapidly developing areas in immunoassay, where the key point is to register the formation of an antigen–antibody complex. This review analyzes the latest work by Russian researchers concerning the production of molecules used in various immunoassay formats as well as new fundamental scientific data obtained as a result of their use.

One-Step, Wash-free, Nanoparticle Clustering-Based Magnetic Particle Spectroscopy Bioassay Method for Detection of SARS-CoV-2 Spike and Nucleocapsid Proteins in the Liquid Phase

With the ongoing global pandemic of coronavirus disease 2019 (COVID-19), there is an increasing quest for more accessible, easy-to-use, rapid, inexpensive, and high-accuracy diagnostic tools. Traditional disease diagnostic methods such as qRT-PCR (quantitative reverse transcription-PCR) and ELISA (enzyme-linked immunosorbent assay) require multiple steps, trained technicians, and long turnaround time that may worsen the disease surveillance and pandemic control. In sight of this situation, a rapid, one-step, easy-to-use, and high-accuracy diagnostic platform will be valuable for future epidemic control, especially for regions with scarce medical resources. Herein, we report a magnetic particle spectroscopy (MPS) platform for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) biomarkers: spike and nucleocapsid proteins. This technique monitors the dynamic magnetic responses of magnetic nanoparticles (MNPs) and uses their higher harmonics as a measure of the nanoparticles' binding states. By anchoring polyclonal antibodies (pAbs) onto MNP surfaces, these nanoparticles function as nanoprobes to specifically bind to target analytes (SARS-CoV-2 spike and nucleocapsid proteins in this work) and form nanoparticle clusters. This binding event causes detectable changes in higher harmonics and allows for quantitative and qualitative detection of target analytes in the liquid phase. We have achieved detection limits of 1.56 nM (equivalent to 125 fmole) and 12.5 nM (equivalent to 1 pmole) for detecting SARS-CoV-2 spike and nucleocapsid proteins, respectively. This MPS platform combined with the one-step, wash-free, nanoparticle clustering-based assay method is intrinsically versatile and allows for the detection of a variety of other disease biomarkers by simply changing the surface functional groups on MNPs.

The Pathological Mechanism and Potential Application of IL-38 in Autoimmune Diseases

Interleukin-38 (IL-38), a new cytokine of interleukin-1 family (IL-1F), is expressed in the human heart, kidney, skin, etc. Recently, new evidence indicated that IL-38 is involved in the process of different autoimmune diseases. Autoimmune diseases are a cluster of diseases accompanied with tissue damage caused by autoimmune reactions, including rheumatoid arthritis (RA), psoriasis, etc. This review summarized the links between IL-38 and autoimmune diseases, as well as the latest knowledge about the function and regulatory mechanism of IL-38 in autoimmune diseases. Especially, this review focused on the differentiation of immune cells and explore future prospects, such as the application of IL-38 in new technologies. Understanding the function of IL-38 is helpful to shed light on the progress of autoimmune diseases.

Nanobiosensing based on optically selected antibodies and superparamagnetic labels for rapid and highly sensitive quantification of polyvalent hepatitis B surface antigen

Hepatitis B surface antigen (HBsAg) is the most clinically relevant serological marker of hepatitis B virus (HBV) infection. Its detection in blood is extremely important for identification of asymptomatic individuals or chronic HBV carriers, screening blood donors, and early seroconversion. Rapid point-of-care HBsAg tests are predominantly qualitative, and their analytical sensitivity does not meet the requirements of regulatory agencies. We present a highly sensitive lateral flow assay based on superparamagnetic nanoparticles for rapid quantification (within 30 min) of polyvalent HBsAg in serum. The demonstrated limit of detection (LOD) of 80 pg mL^-1 in human serum is better than both the FDA recommendations for HBsAg assays (which is 0.5 ng mL^-1) and the sensitivity of traditional laboratory-based methods such as enzyme linked immunosorbent assays. Along with the attractive LOD at lower concentrations and the wide linear dynamic range of more than 2.5 orders, the assay features rapidity, user-friendliness, on-site operation and effective performance in the complex biological medium. These are due to the combination of the immunochromatographic approach with a highly sensitive electronic registration of superparamagnetic nanolabels over the entire volume of a 3D test structure by their non-linear magnetization and selection of optimal antibodies by original optical label-free methods. The developed cost-efficient bioanalytical technology can be used in many socially important fields such as out-of-lab screening and diagnosis of HBV infection at a point-of-demand, especially in hard-to-reach or sparsely populated areas, as well as highly endemic regions.

Rapid and Easy-to-Use Method for Accurate Characterization of Target Binding and Kinetics of Magnetic Particle Bioconjugates for Biosensing

The ever-increasing use of magnetic particle bioconjugates (MPB) in biosensors calls for methods of comprehensive characterization of their interaction with targets. Label-free optical sensors commonly used for studying inter-molecular interactions have limited potential for MPB because of their large size and multi-component non-transparent structure. We present an easy-to-use method that requires only three 20-min express measurements to determine the key parameters for selection of optimal MPB for a biosensor: kinetic and equilibrium characteristics, and a fraction of biomolecules on the MPB surface that are capable of active targeting. The method also provides a prognostic dependence of MPB targeting efficiency upon interaction duration and sample volume. These features are possible due to joining a magnetic lateral flow assay, a highly sensitive sensor for MPB detection by the magnetic particle quantification technique, and a novel mathematical model that explicitly describes the MPB-target interactions and does not comprise parameters to be fitted additionally. The method was demonstrated by experiments on MPB targeting of cardiac troponin I and staphylococcal enterotoxin B. The validation by an independent label-free technique of spectral-correlation interferometry showed good correlation between the results obtained by both methods. The presented method can be applied to other targets for faster development and selection of MPB for affinity sensors, analytical technologies, and realization of novel concepts of MPB-based biosensing in vivo.

High-performance method for identification of super enhancers from ChIP-Seq data with configurable cloud virtual machines

A universal method for rapid identifying super-enhancers which are large domains of multiple closely-spaced enhancers is proposed. The method applies configurable cloud virtual machines (cVMs) and the rank-ordering of super-enhancers (ROSE) algorithm. To identify super-enhancers a сVM-based analysis of the ChIP-seq binding patterns of the active enhancer-associated mark is employed. The use of the proposed method is described step-by-step: configuration of cVM; ChIP-seq data alignment; peak calling; ROSE algorithm; interpretation of the results on a client machine. The method was validated for the search of super-enhancers using the H3K27ac mark in the sample datasets of a cell line (human MCF-7), mouse tissue (heart), and human tissue (adrenal gland). The total analysis cycle time of raw ChIP-seq data ranges from 15 to 48 min, depending on the number of initial short reads. Depending on the data processing step and availability of multi-threading, a cVM can be scaled up to a multi-CPU configuration with large amount of RAM. An important feature of the method is that it can run on a client machine that has low-performance with virtually any OS. The proposed method allows for simultaneous and independent processing of different sample datasets on multiple clones of a single cVM.•

Cloud VMs were used for rapid processing of ChIP-seq data to identify super-enhancers.

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The method can use a low-performance computer with virtually any OS on it.

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It can be scaled up for parallel processing of individual sample datasets on their own VMs for rapid high-throughput processing.

Peptide-based electrochemical biosensors utilized for protein detection

Proteins are generally detected as biomarkers for tracing or determining various disorders in organisms. Biomarker proteins can be tracked in samples with various origins and in different concentrations, revealing whether an organism is in a healthy or unhealthy state. In regard to detection, electrochemical biosensors are a potential fusion of electronics, chemistry, and biology, allowing for fast and early point-of-care detection from a biological sample with the advantages of high sensitivity, simple construction, and easy operation. Peptides present a promising approach as a biorecognition element when connected with electrochemical biosensors. The benefits of short peptides lie mainly in their good stability and selective affinity to a target analyte. Therefore, peptide-based electrochemical biosensors (PBEBs) represent an alternative approach for the detection of different protein biomarkers. This review provides a summary of the past decade of recently proposed PBEBs designed for protein detection, dividing them according to different protein types: (i) enzyme detection, including proteases and kinases; (ii) antibody detection; and (iii) other protein detection. According to these protein types, different sensing mechanisms are discussed, such as the peptide cleavage by a proteases, phosphorylation by kinases, presence of antibodies, and exploiting of affinities; furthermore, measurements are obtained by different electrochemical methods. A discussion and comparison of various constructions, modifications, immobilization strategies and different sensing techniques in terms of high sensitivity, selectivity, repeatability, and potential for practical application are presented.

Spectral-Phase Interferometry Detection of Ochratoxin A via Aptamer-Functionalized Graphene Coated Glass

In this work, we report a novel method of label-free detection of small molecules based on direct observation of interferometric signal change in graphene-modified glasses. The interferometric sensor chips are fabricated via a conventional wet transfer method of CVD-grown graphene onto the glass coverslips, lowering the device cost and allowing for upscaling the sensor fabrication. For the first time, we report the use of graphene functionalized by the aptamer as the bioreceptor, in conjunction with Spectral-Phase Interferometry (SPI) for detection of ochratoxin A (OTA). In a direct assay with an OTA-specific aptamer, we demonstrated a quick and significant change of the optical signal in response to the maximum tolerable level of OTA concentration. The sensor regeneration is possible in urea solution. The developed platform enables a direct method of kinetic analysis of small molecules using a low-cost optical chip with a graphene-aptamer sensing layer.

Label-Free Optical Resonator-Based Biosensors

The demand for biosensor technology has grown drastically over the last few decades, mainly in disease diagnosis, drug development, and environmental health and safety. Optical resonator-based biosensors have been widely exploited to achieve highly sensitive, rapid, and label-free detection of biological analytes. The advancements in microfluidic and micro/nanofabrication technologies allow them to be miniaturized and simultaneously detect various analytes in a small sample volume. By virtue of these advantages and advancements, the optical resonator-based biosensor is considered a promising platform not only for general medical diagnostics but also for point-of-care applications. This review aims to provide an overview of recent progresses in label-free optical resonator-based biosensors published mostly over the last 5 years. We categorized them into Fabry-Perot interferometer-based and whispering gallery mode-based biosensors. The principles behind each biosensor are concisely introduced, and recent progresses in configurations, materials, test setup, and light confinement methods are described. Finally, the current challenges and future research topics of the optical resonator-based biosensor are discussed.

Data on characterization of glass biochips and validation of the label-free biosensor for detection of autoantibodies in human serum

The data represent in-depth characterization of a novel method for highly sensitive simultaneous measuring in human serum of both critical parameters of autoantibodies: concentration and native kinetics. The latter refers to autoantibody interaction with free, not immobilized, antigen. The method and related biosensors are based on the spectral-correlation and spectral-phase interferometry. The data cover: multi-factor optimization and quantitative characterization of the developed affordable single-used biochips, including X-ray photoelectron spectroscopy (XPS) control of chemical modifications of the surface during fabrication; antibody screening; optimization and verification of protocols for label-free biosensing in human serum; mathematical model for fitting experimental data and calculation of kinetic constants of interaction of autoantibodies with free antigen; comprehensive verification of the method specificity; correlation between the data obtained with the developed biosensor and with enzyme linked immunosorbent assay (ELISA); comparison of analytical characteristics of the developed biosensor with the most advanced label-based methods. The data importance is confirmed by a companion paper (DOI 10.1016/j.bios.2020.112187), which shows that the combination of mentioned autoantibody parameters is promising for more accurate criteria for early diagnostics and efficient therapy of autoimmune disorders. The obtained data can be used in development of a wide range of biosensors, both label-free and based on various labels.

Nanomagnetic lateral flow assay for high-precision quantification of diagnostically relevant concentrations of serum TSH

Thyroid stimulating hormone (TSH) is the first-line marker for initial evaluation of the thyroid gland function. We present a lateral flow immunoassay based on superparamagnetic nanolabels for rapid (<25 min) quantitative determination of TSH at a point of care. The demonstrated limit of detection (LOD) of 0.017 μIU/mL in human serum is on the level of third-generation TSH laboratory tests. The wide linear dynamic range of more than 3 orders covers the whole range of clinically relevant TSH concentrations for confident quantitative diagnostics of the gland function from hyper- to hypothyroidism, and different states in-between. The attractive values of LOD and linear dynamic range are due to counting of the superparamagnetic nanolabels over the whole reaction volume by their non-linear magnetization at two frequencies of an alternating magnetic field and detecting the response at combinatorial frequencies. The developed cost-efficient and user-friendly immunoassay can be used for express in vitro diagnostics and long-term quantitative monitoring of thyroid dysfunctions, especially in distant regions, developing countries, and sparsely populated areas.