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Graphene-based materials are actively being investigated as sensing elements for the detection of different analytes. Both graphene grown by chemical vapor deposition (CVD) and graphene oxide (GO) produced by the modified Hummers’ method are actively used in the development of biosensors. The production costs of CVD graphene- and GO-based sensors are similar; however, the question remains regarding the most efficient graphene-based material for the construction of point-of-care diagnostic devices. To this end, in this work, we compare CVD graphene aptasensors with the aptasensors based on reduced GO (rGO) for their capabilities in the detection of NT-proBNP, which serves as the gold standard biomarker for heart failure. Both types of aptasensors were developed using commercial gold interdigitated electrodes (IDEs) with either CVD graphene or GO formed on top as a channel of liquid-gated field-effect transistor (FET), yielding GFET and rGO-FET sensors, respectively. The functional properties of the two types of aptasensors were compared. Both demonstrate good dynamic range from 10 fg/mL to 100 pg/mL. The limit of detection for NT-proBNP in artificial saliva was 100 fg/mL and 1 pg/mL for rGO-FET- and GFET-based aptasensors, respectively. While CVD GFET demonstrates less variations in parameters, higher sensitivity was demonstrated by the rGO-FET due to its higher roughness and larger bandgap. The demonstrated low cost and scalability of technology for both types of graphene-based aptasensors may be applicable for the development of different graphene-based biosensors for rapid, stable, on-site, and highly sensitive detection of diverse biochemical markers.

Super-enhancers (SEs) are regions of the genome that play a crucial regulatory role in gene expression by promoting large-scale transcriptional responses in various cell types and tissues. Recent research suggests that alterations in super-enhancer activity can contribute to the development and progression of various disorders. The aim of this research is to explore the multifaceted roles of super-enhancers in gene regulation and their significant implications for understanding and treating complex diseases. Here, we study and summarise the classification of super-enhancer constituents, their possible modes of interaction, and cross-regulation, including super-enhancer RNAs (seRNAs). We try to investigate the opportunity of SE dynamics prediction based on the hierarchy of enhancer single elements (enhancers) and their aggregated action. To further our understanding, we conducted an in silico experiment to compare and differentiate between super-enhancers and locus-control regions (LCRs), shedding light on the enigmatic relationship between LCRs and SEs within the human genome. Particular attention is paid to the classification of specific mechanisms and their diversity, exemplified by various oncological, cardiovascular, and immunological diseases, as well as an overview of several anti-SE therapies. Overall, the work presents a comprehensive analysis of super-enhancers across different diseases, aiming to provide insights into their regulatory roles and may act as a rationale for future clinical interventions targeting these regulatory elements.

Magnetite nanoparticles (MNPs) are highly favored materials for a wide range of applications, from smart composite materials and biosensors to targeted drug delivery. These multifunctional applications typically require the biofunctional coating of MNPs that involves various conjugation techniques to form stable MNP–biomolecule complexes. In this study, a cost-effective method is developed for the chlorostannate modification of MNP surfaces that provides efficient one-step conjugation with biomolecules. The proposed method was validated using MNPs obtained via an optimized co-precipitation technique that included the use of degassed water, argon atmosphere, and the pre-filtering of FeCl2 and FeCl3 solutions followed by MNP surface modification using stannous chloride. The resulting chlorostannated nanoparticles were comprehensively characterized, and their efficiency was compared with both carboxylate-modified and unmodified MNPs. The biorecognition performance of MNPs was verified via magnetic immunochromatography. Mouse monoclonal antibodies to folic acid served as model biomolecules conjugated with the MNP to produce nanobioconjugates, while folic acid–gelatin conjugates were immobilized on the test lines of immunochromatography lateral flow test strips. The specific trapping of the obtained nanobioconjugates via antibody–antigen interactions was registered via the highly sensitive magnetic particle quantification technique. The developed chlorostannate modification of MNPs is a versatile, rapid, and convenient tool for creating multifunctional nanobioconjugates with applications that span in vitro diagnostics, magnetic separation, and potential in vivo uses.

In this study, we present a novel and ultrasensitive magnetic lateral flow immunoassay (LFIA) tailored for the precise detection of zearalenone, a mycotoxin with significant implications for human and animal health. A versatile and straightforward method for creating non-covalent magnetic labels is proposed and comprehensively compared with a covalent immobilization strategy. We employ the magnetic particle quantification (MPQ) technique for precise detection of the labels and characterization of their functionality, including measuring the antibody sorption density on the particle surface. Through kinetic studies using the label-free spectral phase interferometry, the rate and equilibrium constants for the binding of monoclonal antibodies with free (not bound with carrier protein) zearalenone were determined to be kon = 3.42 × 105 M−1s−1, koff = 7.05 × 10−4 s−1, and KD = 2.06 × 10−9 M. The proposed MPQ-LFIA method exhibits detection limits of 2.3 pg/mL and 7.6 pg/mL when employing magnetic labels based on covalent immobilization and non-covalent sorption, with dynamic ranges of 5.5 and 5 orders, correspondingly. We have successfully demonstrated the effective determination of zearalenone in barley flour samples contaminated with Fusarium graminearum. The ease of use and effectiveness of developed test systems further enhances their value as practical tools for addressing mycotoxin contamination challenges.

Magnetite nanoparticles (MNPs) are a preferable material for different bioassays because of their quite low toxicity both for cells and for mammals, and they have a big variety of surface functionalization approaches. We have synthesized MNPs via a simple and convenient co-precipitation method with preliminary filtration of FeCl2 and FeCl3 solution, under argon atmosphere and non-magnetic stirring. MNPs were citrate-stabilized and then modified stage by stage with tetraethoxysilane (TEOS), (3-Aminopropyl)triethoxysilane (APTES) and acylated with succinic anhydride, resulting in carboxylated MNPs. Carboxylated MNPs were covalently bounded with folic acid antibody (FA-1) via 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). MNP-EDC-FA-1 were passed through a test-stripe with the line consisting of folic acid–gelatin conjugate. The conjugation of MNP-EDC-FA-1 with folic acid was observed visually, and the magnetic signal distribution was scanned through the test-stripe with the magnetic particle quantification technique (MPQ) developed earlier. Visually, the line with folic acid–gelatin conjugate on the test-stripe turned dark, with color intensity strongly depending on the MNP-EDC-FA-1 concentration. MPQ has shown that the great majority of MNP-EDC-FA-1 was bound with the acid–gelatin conjugate. The MPQ technique allowed quantification down to 5 ng of MNP-EDC-FA-1 in this experiment with MNPs synthesized, with a strong peak at the acid–conjugate line.

Super-enhancers (SEs) are cis-regulatory elements of the human genome that have been widely discussed since the discovery and origin of the term. Super-enhancers have been shown to be strongly associated with the expression of genes crucial for cell differentiation, cell stability maintenance, and tumorigenesis. Our goal was to systematize research studies dedicated to the investigation of structure and functions of super-enhancers as well as to define further perspectives of the field in various applications, such as drug development and clinical use. We overviewed the fundamental studies which provided experimental data on various pathologies and their associations with particular super-enhancers. The analysis of mainstream approaches for SE search and prediction allowed us to accumulate existing data and propose directions for further algorithmic improvements of SEs’ reliability levels and efficiency. Thus, here we provide the description of the most robust algorithms such as ROSE, imPROSE, and DEEPSEN and suggest their further use for various research and development tasks. The most promising research direction, which is based on topic and number of published studies, are cancer-associated super-enhancers and prospective SE-targeted therapy strategies, most of which are discussed in this review.

The therapeutic potential of short interfering RNA (siRNA) to treat many diseases that are incurable with traditional preparations is limited by the extensive metabolism of serum nucleases, low permeability through biological membrane barriers because of a negative charge, and endosomal trapping. Effective delivery vectors are required to overcome these challenges without causing unwanted side effects. Here, we present a relatively simple synthetic protocol to obtain positively charged gold nanoparticles (AuNPs) with narrow size distribution and the surface modified with Tat-related cell-penetrating peptide. The AuNPs were characterized using TEM and the localized surface plasmon resonance technique. The synthesized AuNPs showed low toxicity in experiments in vitro and were able to effectively form complexes with double-stranded siRNA. The obtained delivery vehicles were used for intracellular delivery of siRNA in an ARPE-19 cell line transfected with secreted embryonic alkaline phosphatase (SEAP). The delivered oligonucleotide remained intact and caused a significant knockdown effect on SEAP cell production. The developed material could be useful for delivery of negatively charged macromolecules, such as antisense oligonucleotides and various RNAs, particularly for retinal pigment epithelial cell drug delivery.

Development of rapid and sensitive immunoassays is a task of great importance in a variety of fields ranging from clinical practice and urgent diagnostics to food quality control and environmental monitoring. High attention of researches is paid to methods of screening, selection, and kinetic characterization of antibodies that enable fast, specific, and effective formation of immunocomplexes. Herein, we present a method for direct investigation of kinetics of immunoreagents during developments of express high sensitive lateral flow assays. As model biomolecules to be detected, the following substances were tested: ochratoxin A (OTA), which is one of the most dangerous mycotoxins naturally present in many vegetable raw materials; and heart fatty acids binding protein (hFABP), which is a cardiac marker used in differential diagnosis of acute myocardial infarction. The kinetic constants of association (kon) and dissociation (koff) with monoclonal antibodies are determined along with the corresponding equilibrium constants (KA and KD). The obtained values are as follows: for the anti-OTA antibodies – kon = 4.54*103 M−1s−1; koff = 3.32*10−4 s−1; KA = 1.37*107 M−1; KD = 7.31*10−8 M; and for the anti-hFABP antibodies – kon = 7.28*103 M−1s−1; koff = 1.97*10−4 s−1; KA = 3.70*107 M−1; KD = 2.70*10−8 M. The proposed method can be employed in combination with the immunochromatographic assays based on magnetic biolabels. • Investigation of immunoreagent kinetics for development of express high sensitive lateral flow assays • Kinetic characterization of monoclonal antibodies against OTA and hFABP for their rapid and sensitive detection • Both kinetic and equilibrium constants of association and dissociation are determined

Folic acid (FA) and its other forms known as folates are small molecules vital for humans. The high demand for increasingly sensitive methods of measuring folate concentrations is due to the fact that abnormal levels of FA cause severe health disorders. Besides, folates are used as recognition molecules in targeted drug delivery. The majority of FA measuring techniques are rather expensive, laborious, sometimes not sufficiently sensitive and specific, and often employ consumables that are too costly to be single-use for routine medical diagnostics. Here, we present a procedure for transformation of a simple microscope cover glass slip without deposition of any metal or dielectric films into a cost-efficient chemosensor chip interrogated by spectral correlation interferometry for highly sensitive measurements of the concentration of small molecules, as well as a feasibility study of long-term monitoring of such molecules in a flow mode. The obtained chips were tested for folate detection. The highly specific and sensitive measurements can be performed in real-time in a wide dynamic range of 0.9–220,000 pM. The developed method and single-use consumables are promising for concentration measurements of low molecular weight substances in pharmaceuticals and in vitro diagnostics.

A novel photochemical technological route for one-step functionalization of a graphene surface with an azide-modified DNA aptamer for biomarkers is developed. The methodology is demonstrated for the functionalization of a DNA aptamer for an N-terminal B-type natriuretic peptide (NT-proBNP) heart failure biomarker on the surface of a graphene channel within a system based on a liquid-gated graphene field effect transistor (GFET). The limit of detection (LOD) of the aptamer-functionalized sensor is 0.01 pg/mL with short response time (75 s) for clinically relevant concentrations of the cardiac biomarker, which could be of relevance for point-of-care (POC) applications. The novel methodology could be applicable for the development of different graphene-based biosensors for fast, stable, real-time, and highly sensitive detection of disease markers.

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.

Extracellular vesicles (EVs) are promising agents for liquid biopsy—a non-invasive approach for the diagnosis of cancer and evaluation of therapy response. However, EV potential is limited by the lack of sufficiently sensitive, time-, and cost-efficient methods for their registration. This research aimed at developing a highly sensitive and easy-to-use immunochromatographic tool based on magnetic nanoparticles for EV quantification. The tool is demonstrated by detection of EVs isolated from cell culture supernatants and various body fluids using characteristic biomarkers, CD9 and CD81, and a tumor-associated marker—epithelial cell adhesion molecules. The detection limit of 3.7 × 105 EV/µL is one to two orders better than the most sensitive traditional lateral flow system and commercial ELISA kits. The detection specificity is ensured by an isotype control line on the test strip. The tool’s advantages are due to the spatial quantification of EV-bound magnetic nanolabels within the strip volume by an original electronic technique. The inexpensive tool, promising for liquid biopsy in daily clinical routines, can be extended to other relevant biomarkers.

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.

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. • The method can use a low-performance computer with virtually any OS on it. • It can be scaled up for parallel processing of individual sample datasets on their own VMs for rapid high-throughput processing.

The reaction of β-diketophosphazene with the europium (III) salt synthesized the corresponding metal complex which was structured with (3-aminopropyl)triethoxysilane and treated with dibenzoylmethane for additional coordination of europium atoms. The polymer thus obtained exhibits luminescence with a maximum of 615 nm, which is characteristic of europium. The polymer is thermally stable up to 300 °C, the coating based on it has a contact angle of 101°, and the adhesive strength of the coating to non-finished glass (according to ISO 2409: 2013) is 1 point.

This work is devoted to the influence of phosphazene modifiers with different substituents on the curing process, thermal properties and flammability of benzoxazine resin. Novel catalysts with m-toluidine substituents were introduced. The catalytic activity of studied phosphazene compounds decreased in the row: hexachlorocyclotriphosphazene (HCP) > tetra m-toluidine substituted phosphazene PN-mt (4) > hexa m-toluidine substituted phosphazene PN-mt (6) > hexaphenoxycyclotriphosphazene (HPP), where HPP is totally inactive. Two types of catalysis: basic and acid were proposed. A brief study of resulting properties of polybenzoxazines was presented. The addition of any studied modifier caused the decrease of glass transition temperature and thermal stability of polymers. The morphology of cured compositions was characterized by matrix-dispersion phase structure. All phosphazene containing polybenzoxazines demonstrated the improved flame resistance.

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.

A novel type of phosphazene containing an additive that acts both as a catalyst and as a flame retardant for benzoxazine binders is presented in this study. The synthesis of a derivative of hexachlorocyclotriphosphazene (HCP) and meta-toluidine was carried out in the medium of the latter, which made it possible to achieve the complete substitution of chlorine atoms in the initial HCP. Thermal and flammability characteristics of modified compositions were investigated. The modifier catalyzes the process of curing and shifts the beginning of reaction from 222.0 °C for pure benzoxazine to 205.9 °C for composition with 10 phr of modifier. The additive decreases the glass transition temperature of compositions. Achievement of the highest category of flame resistance (V-0 in accordance with UL-94) is ensured both by increasing the content of phenyl residues in the composition and by the synergistic effect of phosphorus and nitrogen. A brief study of the curing kinetics disclosed the complex nature of the reaction. An accurate two-step model is obtained using the extended Prout–Tompkins equation for both steps.

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.