Surface plasmon resonance: a versatile technique for biosensor applications

Vaccinomics to Design a Multiepitope Vaccine against Legionella pneumophila

Legionella pneumophila is found in the natural aquatic environment and can resist a wide range of environmental conditions. There are around fifty species of Legionella, at least twenty-four of which are directly linked to infections in humans. L. pneumophila is the cause of Legionnaires' disease, a potentially lethal form of pneumonia. By blocking phagosome-lysosome fusion, L. pneumophila lives and proliferates inside macrophages. For this disease, there is presently no authorized multiepitope vaccine available. For the multi-epitope-based vaccine (MEBV), the best antigenic candidates were identified using immunoinformatics and subtractive proteomic techniques. Several immunoinformatics methods were utilized to predict B and T cell epitopes from vaccine candidate proteins. To construct an in silico vaccine, epitopes (07 CTL, 03 HTL, and 07 LBL) were carefully selected and docked with MHC molecules (MHC-I and MHC-II) and human TLR4 molecules. To increase the immunological response, the vaccine was combined with a 50S ribosomal adjuvant. To maximize vaccine protein expression, MEBV was cloned and reverse-translated in Escherichia coli. To prove the MEBV's efficacy, more experimental validation is required. After its development, the resulting vaccine is greatly hoped to aid in the prevention of L. pneumophila infections.

Spoon-shaped polymer waveguides to excite multiple plasmonic phenomena: A multisensor based on antibody and molecularly imprinted nanoparticles to detect albumin concentrations over eight orders of magnitude

A polymeric multimode waveguide, characterized by a pioneering spoon-shaped geometry, was herein proposed for the first time to devise Surface Plasmon Resonance (SPR) biochemical sensors. The plasmon excitation was enabled by layering a gold nanofilm of ∼60 nm onto the spoon-waveguide. As a consequence of the waveguide's extra-ordinary geometry, two distinct sensing regions were identified: a planar one, located on the spoon's neck, and a concave one on the bowl, with angled surfaces. The bulk sensitivity (S_n) is correlated both to the way the light was launched in/collected from the sensor (parallel or orthogonal to the main axis of the waveguide) and to the sensing area interrogated (planar-neck or angled-bowl), indicating that the sensor's performance can be conveniently tuned, depending on the chosen measuring configuration. The SPR sensor's characterization showed S_n equal to 750 nm/RIU for the neck and to 950 nm/RIU for the bowl. To further inspect the peculiar sensing-features and assess the application niches, the spoon-shaped waveguide was functionalized with two kinds of receptors, both specific for human serum albumin (HSA): an antibody on the bowl region (high S_n); molecularly imprinted nanoparticles (nanoMIPs) on the neck region (low S_n). The experimental results showed a limit of detection (LOD) for the immune-sensor of 280 pM and an LOD for the nanoMIP-sensor of 4.16 fM. The overall response of the HSA multi-sensor encompassed eight orders of magnitude, suggesting that the spoon-shaped waveguide's provides multi-scale detection and holds potential to devise multi-analyte sensing platforms.

Biomedical Applications of an Ultra-Sensitive Surface Plasmon Resonance Biosensor Based on Smart MXene Quantum Dots (SMQDs)

In today's world, the use of biosensors occupies a special place in a variety of fields such as agriculture and industry. New biosensor technologies can identify biological compounds accurately and quickly. One of these technologies is the phenomenon of surface plasmon resonance (SPR) in the development of biosensors based on their optical properties, which allow for very sensitive and specific measurements of biomolecules without time delay. Therefore, various nanomaterials have been introduced for the development of SPR biosensors to achieve a high degree of selectivity and sensitivity. The diagnosis of deadly diseases such as cancer depends on the use of nanotechnology. Smart MXene quantum dots (SMQDs), a new class of nanomaterials that are developing at a rapid pace, are perfect for the development of SPR biosensors due to their many advantageous properties. Moreover, SMQDs are two-dimensional (2D) inorganic segments with a limited number of atomic layers that exhibit excellent properties such as high conductivity, plasmonic, and optical properties. Therefore, SMQDs, with their unique properties, are promising contenders for biomedicine, including cancer diagnosis/treatment, biological sensing/imaging, antigen detection, etc. In this review, SPR biosensors based on SMQDs applied in biomedical applications are discussed. To achieve this goal, an introduction to SPR, SPR biosensors, and SMQDs (including their structure, surface functional groups, synthesis, and properties) is given first; then, the fabrication of hybrid nanoparticles (NPs) based on SMQDs and the biomedical applications of SMQDs are discussed. In the next step, SPR biosensors based on SMQDs and advanced 2D SMQDs-based nanobiosensors as ultrasensitive detection tools are presented. This review proposes the use of SMQDs for the improvement of SPR biosensors with high selectivity and sensitivity for biomedical applications.

Hemocompatibility challenge of membrane oxygenator for artificial lung technology

The artificial lung (AL) technology is one of the membrane-based artificial organs that partly augments lung functions, i.e. blood oxygenation and CO₂ removal. It is generally employed as an extracorporeal membrane oxygenation (ECMO) device to treat acute and chronic lung-failure patients, and the recent outbreak of the COVID-19 pandemic has re-emphasized the importance of this technology. The principal component in AL is the polymeric membrane oxygenator that facilitates the O₂/CO₂ exchange with the blood. Despite the considerable improvement in anti-thrombogenic biomaterials in other applications (e.g., stents), AL research has not advanced at the same rate. This is partly because AL research requires interdisciplinary knowledge in biomaterials and membrane technology. Some of the promising biomaterials with reasonable hemocompatibility - such as emerging fluoropolymers of extremely low surface energy - must first be fabricated into membranes to exhibit effective gas exchange performance. As AL membranes must also demonstrate high hemocompatibility in tandem, it is essential to test the membranes using in-vitro hemocompatibility experiments before in-vivo test. Hence, it is vital to have a reliable in-vitro experimental protocol that can be reasonably correlated with the in-vivo results. However, current in-vitro AL studies are unsystematic to allow a consistent comparison with in-vivo results. More specifically, current literature on AL biomaterial in-vitro hemocompatibility data are not quantitatively comparable due to the use of unstandardized and unreliable protocols. Such a wide gap has been the main bottleneck in the improvement of AL research, preventing promising biomaterials from reaching clinical trials. This review summarizes the current state-of-the-art and status of AL technology from membrane researcher perspectives. Particularly, most of the reported in-vitro experiments to assess AL membrane hemocompatibility are compiled and critically compared to suggest the most reliable method suitable for AL biomaterial research. Also, a brief review of current approaches to improve AL hemocompatibility is summarized. STATEMENT OF SIGNIFICANCE: The importance of Artificial Lung (AL) technology has been re-emphasized in the time of the COVID-19 pandemic. The utmost bottleneck in the current AL technology is the poor hemocompatibility of the polymer membrane used for O₂/CO₂ gas exchange, limiting its use in the long-term. Unfortunately, most of the in-vitro AL experiments are unsystematic, irreproducible, and unreliable. There are no standardized in-vitro hemocompatibility characterization protocols for quantitative comparison between AL biomaterials. In this review, we tackled this bottleneck by compiling the scattered in-vitro data and suggesting the most suitable experimental protocol to obtain reliable and comparable hemocompatibility results. To the best of our knowledge, this is the first review paper focusing on the hemocompatibility challenge of AL technology.

The AIRE G228W mutation disturbs the interaction of AIRE with its partner molecule SIRT1

The autoimmune regulator (AIRE) protein functions as a tetramer, interacting with partner proteins to form the “AIRE complex,” which relieves RNA Pol II stalling in the chromatin of medullary thymic epithelial cells (mTECs). AIRE is the primary mTEC transcriptional controller, promoting the expression of a large set of peripheral tissue antigen genes implicated in the negative selection of self-reactive thymocytes. Under normal conditions, the SIRT1 protein temporarily interacts with AIRE and deacetylates K residues of the AIRE SAND domain. Once the AIRE SAND domain is deacetylated, the binding with SIRT1 is undone, allowing the AIRE complex to proceed downstream with the RNA Pol II to the elongation phase of transcription. Considering that the in silico and in vitro binding of the AIRE SAND domain with SIRT1 provides a powerful model system for studying the dominant SAND G228W mutation mechanism, which causes the autoimmune polyglandular syndrome-1, we integrated computational molecular modeling, docking, dynamics between the whole SAND domain with SIRT1, and surface plasmon resonance using a peptide harboring the 211 to 230 residues of the SAND domain, to compare the structure and energetics of binding/release between AIRE G228 (wild-type) and W228 (mutant) SAND domain to SIRT1. We observed that the G228W mutation in the SAND domain negatively influences the AIRE-SIRT1 interaction. The disturbed interaction might cause a disruption in the binding of the AIRE SAND domain with the SIRT1 catalytic site, impairing the AIRE complex to proceed downstream with RNA Pol II.

Evaluating the immunogenicity of heparin and heparin derivatives by measuring their binding to platelet factor 4 using biolayer interferometry

Heparin (HP) is a polysaccharide that is widely used in the clinic as an anticoagulant. A major side effect associated with HP is the heparin-induced thrombocytopenia (HIT), which is initiated by the immune response to complex formed by HP and platelet factor 4 (PF4). Low molecular weight heparins (LMWHs) are the depolymerized version of HP, which have reduced risks of inducing HIT. However, it is still necessary to evaluate the immunogenicity of LMWHs to ensure their drug safety. Since HIT involves very complicated processes, the evaluation of HP and LMWH immunogenicity requires experiments from multiple aspects, of which the binding affinity between HP and PF4 is a key property to be monitored. Herein, we developed a novel competitive biolayer interferometry (BLI) method to investigate the binding affinity between HP and PF4. The influence of different domains in HP on its immunogenicity was compared for better understanding of the molecular mechanism of HP immunogenicity. Furthermore, the half maximal inhibitory concentration (IC50) of HP and LMWH can be measured by competitive combination, which is important for the quality control during the developing and manufacturing of HP and LMWH drugs.

Enhanced graphene surface plasmonics through incorporation into metallic nanostructures

A methodology for enhancing the surface plasmon polariton (SPP) resonance associated with graphene, through nanoscale metal-dielectric-metal (MDM) gaps, is proposed. The modulation of the resonances, in the range of 0.7 µm to 1 µm was done through tuning the carrier density in graphene and has been shown to be of potential utility for surface analyte sensing. It was shown, from finite element simulations in the frequency domain, that the related hybrid SPP modes could be clearly delineated in far field spectroscopy.

Chemical Sensor Nanotechnology in Pharmaceutical Drug Research

The increase in demand for pharmaceutical treatments due to pandemic-related illnesses has created a need for improved quality control in drug manufacturing. Understanding the physical, biological, and chemical properties of APIs is an important area of health-related research. As such, research into enhanced chemical sensing and analysis of pharmaceutical ingredients (APIs) for drug development, delivery and monitoring has become immensely popular in the nanotechnology space. Nanomaterial-based chemical sensors have been used to detect and analyze APIs related to the treatment of various illnesses pre and post administration. Furthermore, electrical and optical techniques are often coupled with nano-chemical sensors to produce data for various applications which relate to the efficiencies of the APIs. In this review, we focus on the latest nanotechnology applied to probing the chemical and biochemical properties of pharmaceutical drugs, placing specific interest on several types of nanomaterial-based chemical sensors, their characteristics, detection methods, and applications. This study offers insight into the progress in drug development and monitoring research for designing improved quality control methods for pharmaceutical and health-related research.

An LSPR Sensor Integrated with VCSEL and Microfluidic Chip

The work introduces a localized surface plasmon resonance (LSPR) sensor chip integrated with vertical-cavity surface-emitting lasers (VCSELs). Using VCSEL as the light source, the hexagonal gold nanoparticle array was integrated with anodic aluminum oxide (AAO) as the mask on the light-emitting end face. The sensitivity sensing test of the refractive index solution was realized, combined with microfluidic technology. At the same time, the finite-difference time- domain (FDTD) algorithm was applied to model and simulate the gold nanostructures. The experimental results showed that the output power of the sensor was related to the refractive index of the sucrose solution. The maximum sensitivity of the sensor was 1.65 × 106 nW/RIU, which gives it great application potential in the field of biomolecular detection.

Enhancement of lattice dynamics by an azimuthal surface plasmon on the femtosecond time scale in multi-walled carbon nanotubes

Plasmon-enhanced light-matter interactions have been widely investigated in the past decades. Here, we report surface plasmon-enhanced structural dynamics in multi-walled carbon nanotubes. The optical polarization dependent dynamic properties of multi-walled carbon nanotubes are investigated using ultrafast transmission electron microscopy. Lattice contractions in the femtosecond time regime are observed upon excitation of the azimuthal plasmon by light polarized perpendicular to the tubular axis. The polarization dependence of the plasmon near field was examined using photon-induced near-field electron microscopy. The lattice changes resulting from the azimuthal plasmon enhance ultrafast alterations in both localized evanescent fields and the collective charge excitation, which play critical roles governing the light-matter interaction. These results suggest that the ultrafast responses of lattice degrees of freedom in nanomaterials could be essential for understanding the mechanism of surface plasmon enhanced effects.

Biodetection Techniques for Quantification of Chemokines

Chemokines are a class of cytokine whose special properties, together with their involvement and relevant role in various diseases, make them a restricted group of biomarkers suitable for diagnosis and monitoring. Despite their importance, biodetection techniques dedicated to the selective determination of one or more chemokines are very scarce. For some years now, the critical diagnosis of inflammatory diseases by detecting both cytokine and chemokine biomarkers, has had a strong impact on the development of multiple detection platforms. However, it would be desirable to implement methodologies with a higher degree of selectivity for chemokines, in order to provide more precise information. In addition, better development of biosensor technology applied to this specific field would make it possible to address the main challenges of detection methods for several diseases with a high incidence in the population, avoiding high costs and low sensitivity. Taking this into account, this review aims to present the state of the art of chemokine biodetection techniques and emphasize the role of these systems in the prevention, monitoring and treatment of various diseases associated with chemokines as a starting point for future developments that are also analyzed throughout the article.

Network Pharmacology and Experimental Validation to Explore the Mechanism of Qing-Jin-Hua-Tan-Decoction Against Acute Lung Injury

Qing-Jin-Hua-Tan-Decoction (QJHTD), a classic famous Chinese ancient prescription, has been used for treatment of pulmonary diseases since Ming Dynasty. A total of 22 prototype compounds of QJHTD absorbed into rat blood were chosen as candidates for the pharmacological network analysis and molecular docking. The targets from the intersection of compound target and ALI disease targets were used for GO and KEGG enrichment analyses. Molecular docking was adopted to further verify the interactions between 22 components and the top 20 targets with higher degree values in the component–target–pathway network. In vitro experiments were performed to verify the results of network pharmacology using SPR experiments, Western blot experiments, and the PMA-induced neutrophils to produce neutrophil extracellular trap (NET) model. The compound–target–pathway network includes 176 targets and 20 signaling pathways in which the degree of MAPK14, CDK2, EGFR, F2, SRC, and AKT1 is higher than that of other targets and which may be potential disease targets. The biological processes in QJHTD for ALI mainly included protein phosphorylation, response to wounding, response to bacterium, regulation of inflammatory response, and so on. KEGG enrichment analyses revealed multiple signaling pathways, including lipid and atherosclerosis, HIF-1 signaling pathway, renin–angiotensin system, and neutrophil extracellular trap formation. The molecular docking results showed that baicalin, oroxylin A-7-glucuronide, hispidulin-7-O-β-D-glucuronide, wogonoside, baicalein, wogonin, tianshic acid, and mangiferin can be combined with most of the targets, which might be the core components of QJHTD in treatment of ALI. Direct binding ability of baicalein, wogonin, and baicalin to thrombin protein was all micromolar, and their K_D values were 11.92 μM, 1.303 μM, and 1.146 μM, respectively, revealed by SPR experiments, and QJHTD could inhibit Src phosphorylation in LPS-activated neutrophils by Western blot experiments. The experimental results of PMA-induced neutrophils to produce NETs indicated that QJHTD could inhibit the production of NETs. This study revealed the active compounds, effective targets, and potential pharmacological mechanisms of QJHTD acting on ALI.

"Plasmonic Nanomaterials": An emerging avenue in biomedical and biomedical engineering opportunities

BACKGROUND

Plasmonic nanomaterials asnoble metal-based materials have unique optical characteristic upon exposure to incident light with an appropriate wavelength. Today, generated plasmon by nanoparticles has receivedincreasingattention in nanomedicine; from diagnosis, tissue and tumor imaging to therapeutic and biomedical engineering.

AIM OF REVIEW

Due to rapid growing of knowledge in the inorganic nanomaterial field, this paper aims to be a comprehensive and authoritative, critical, and broad interest to the scientific community. Here, we introduce basic physicochemical properties of plasmonic nanoparticles and their applications in biomedical and tissue engineering The first part of each division explain the basic physico-chemical properties of each nanomaterial with a graphical abstract. In the second part, concepts by describing classic examples taken from the biomedical and biomedical engineering literature are illustrated. The selected case studies are intended to give an overview of the different systems and mechanisms utilized in nanomedicine.

KEY SCIENTIFIC CONCEPTS OF REVIEW

In this communication, we have tried to introduce the needed concepts of plasmonic nanomaterials and their implication in a particular part of biomedical over the last 20 years. Moreover, in each part with insist on limitations, a perspective is presented which can guide a researcher how they can develop or modify new scaffolds for biomedical engineering.

Emerging Biosensing Technologies for the Diagnostics of Viral Infectious Diseases

Several viral infectious diseases appear limitless since the beginning of the 21^st century, expanding into pandemic lengths. Thus, there are extensive efforts to provide more efficient means of diagnosis, a better understanding of acquired immunity, and improved monitoring of inflammatory biomarkers, as these are all crucial for controlling the spread of infection while aiding in vaccine development and improving patient outcomes. In this regard, various biosensors have been developed recently to streamline pathogen and immune response detection by addressing the limitations of traditional methods, including isothermal amplification-based systems and lateral flow assays. This review explores state-of-the-art biosensors for detecting viral pathogens, serological assays, and inflammatory biomarkers from the material perspective, by discussing their advantages, limitations, and further potential regarding their analytical performance, clinical utility, and point-of-care adaptability. Additionally, next-generation biosensing technologies that offer better sensitivity and selectivity, and easy handling for end-users are highlighted. An emerging example of these next-generation biosensors are those powered by novel synthetic biology tools, such as clustered regularly interspaced short palindromic repeats (CRISPR) with CRISPR-associated proteins (Cas), in combination with integrated point-of-care devices. Lastly, the current challenges are discussed and a roadmap for furthering these advanced biosensing technologies to manage future pandemics is provided.

Highly Sensitive Plasmonic Waveguide Biosensor Based on Phase Singularity-Enhanced Goos-Hänchen Shift

The detection for small molecules with low concentrations is known to be challenging for current chemical and biological sensors. In this work, we designed a highly sensitive plasmonic biosensor based on the symmetric metal cladding plasmonic waveguide (SMCW) structure for the detection of biomolecules. By precisely designing the configuration and tuning the thickness of the guiding layer, ultra-high order modes can be excited, which generates a steep phase change and a large position shift from the Goos−Hänchen effect (with respect to refractive index changes). This position shift is related to the sharpness of the optical phase change from the reflected signal of the SPR sensing substrate and can be directly measured by a position sensor. Based on our knowledge, this is the first experimental study done using this configuration. Experimental results showed a lateral position signal change > 90 µm for glycerol with a sensitivity figure-of-merit of 2.33 × 104 µm/RIU and more than 15 µm for 10−4 M biotin, which is a low molecular weight biomolecule (less than 400 Da) and difficult to be detected with traditional SPR sensing techniques. Through integrating the waveguide with a guiding layer, a strong improvement in the electric field, as well as sensitivity have been achieved. The lateral position shift has been further improved from 14.17 µm to 284 µm compared with conventional SPR substrate with 50 nm gold on single side. The as-reported sensing technique allows for the detection of ultra-small biological molecules and will play an important role in biomedical and clinical diagnostics.

Exogenous human α-Synuclein acts in vitro as a mild platelet antiaggregant inhibiting α-thrombin-induced platelet activation

α-Synuclein (αSyn) is a small disordered protein, highly conserved in vertebrates and involved in the pathogenesis of Parkinson’s disease (PD). Indeed, αSyn amyloid aggregates are present in the brain of patients with PD. Although the pathogenic role of αSyn is widely accepted, the physiological function of this protein remains elusive. Beyond the central nervous system, αSyn is expressed in hematopoietic tissue and blood, where platelets are a major cellular host of αSyn. Platelets play a key role in hemostasis and are potently activated by thrombin (αT) through the cleavage of protease-activated receptors. Furthermore, both αT and αSyn could be found in the same spatial environment, i.e. the platelet membrane, as αT binds to and activates platelets that can release αSyn from α-granules and microvesicles. Here, we investigated the possibility that exogenous αSyn could interfere with platelet activation induced by different agonists in vitro. Data obtained from distinct experimental techniques (i.e. multiple electrode aggregometry, rotational thromboelastometry, immunofluorescence microscopy, surface plasmon resonance, and steady-state fluorescence spectroscopy) on whole blood and platelet-rich plasma indicate that exogenous αSyn has mild platelet antiaggregating properties in vitro, acting as a negative regulator of αT-mediated platelet activation by preferentially inhibiting P-selectin expression on platelet surface. We have also shown that both exogenous and endogenous (i.e. cytoplasmic) αSyn preferentially bind to the outer surface of activated platelets. Starting from these findings, a coherent model of the antiplatelet function of αSyn is proposed.

Colorimetric Kit for Rapid Porcine Circovirus 2 (PCV-2) Diagnosis

The aim of the current study is to present a low-cost and easy-to-interpret colorimetric kit used to diagnose porcine circovirus 2 (PCV-2) to the naked eye, without any specific equipment. The aforementioned kit used as base hybrid nanoparticles resulting from the merge of surface active maghemite nanoparticles and gold nanoparticles, based on the deposition of specific PCV-2 antibodies on their surface through covalent bonds. In total, 10 negative and 40 positive samples (≥102 DNA copies/µL of serum) confirmed by qPCR technique were tested. PCV-1 virus, adenovirus, and parvovirus samples were tested as interferents to rule out likely false-positive results. Positive samples showed purple color when they were added to the complex, whereas negative samples showed red color; they were visible to the naked eye. The entire color-change process took place approximately 1 min after the analyzed samples were added to the complex. They were tested at different dilutions, namely pure, 1:10, 1:100, 1:1000, and 1:10,000. Localized surface plasmon resonance (LSPR) and transmission electron microscopy (TEM) images were generated to validate the experiment. This new real-time PCV-2 diagnostic methodology emerged as simple and economic alternative to traditional tests since the final price of the kit is USD 4.00.

Chimeric Peptide-Based Biomolecular Constructs for Versatile Nucleic Acid Biosensing

Nucleic acid biomarkers hold great potential as key indicators for the diagnosis and monitoring of diseases. Herein we design and implement bifunctional chimeric biomolecules composed of a solid-binding peptide (SBP) domain that specifically adsorbs onto solid sensor surfaces and a peptide nucleic acid (PNA) moiety that facilitates anchoring of antisense oligonucleotide (ASO) probes for the detection of nucleic acid targets. A gold-binding peptide, AuBP1, previously selected by directed evolution to specifically bind to gold, served as the basis for immobilizing nucleic acid probes onto gold substrates. Using surface plasmon resonance (SPR) spectroscopy and quartz crystal microbalance (QCM) analyses, we demonstrate the sequential biomolecular assembly of the heterofunctional solid-binding peptide-antisense oligomer (SBP-ASO) construct onto a sensor surface and the subsequent detection of DNA in an aqueous environment. The effect of steric hindrance on optimal probe assembly is observed, establishing that less packing density results in greater target capture efficacy. In addition, an adsorbed layer of chimeric solid-binding peptide-peptide nucleic acid (SBP-PNA) undergoes viscoelastic changes at the solid-liquid interface upon probe immobilization and DNA target capture, whereby the rigid biofunctional layer becomes more flexible. The dual nature of the chimeric construct is highly amenable to a variety of platforms allowing for both specific recognition and probe immobilization on the sensor surface, while the modular design of the solid-binding peptide-antisense oligonucleotide provides facile functionalization of a wide diversity of solid substrates.

Research on optimization of magnetic field sensing characteristics of PCF sensor based on SPR

A photonic crystal fiber utilizing surface plasmon resonance (PCF-SPR) sensor based on refractive index (RI) control of magnetic fluid (MF) is designed. The air holes of the sensor are arranged in a hexagonal shape, and the optical field transmission channels on both sides of the central air hole can effectively confine the energy of the optical field. We use MF as the sensing medium, and coat the inner wall of the central air hole with gold. It can effectively stimulate the SPR effect to achieve the purpose of magneto-refractive modulation. We study the sensing characteristics of the proposed sensor by finite element analysis. The results show that the highest refractive index sensitivity reaches 19520 nm/RIU in the RI range of 1.42-1.435 and the maximum figure of merit (FOM) is 374.3 RIU^-1. In addition, the magnetic field and the temperature response characteristics of the designed sensor are also investigated. In the magnetic field range of 50-130 Oe, the magnetic field sensitivity is 590 pm/Oe. In the temperature range of 24.3-144.3 °C, the temperature sensitivity is only -29.7 pm/℃. The proposed sensor has significant advantages such as stable structure, high sensitivity, easy integration, resistance to electromagnetic interference and can be used for weak magnetic magnitude detection. It has wide application prospects in industrial production, military, and medical equipment.

Recent Advances in Fluorescence Recovery after Photobleaching for Decoupling Transport and Kinetics of Biomacromolecules in Cellular Physiology

Among the new molecular tools available to scientists and engineers, some of the most useful include fluorescently tagged biomolecules. Tools, such as green fluorescence protein (GFP), have been applied to perform semi-quantitative studies on biological signal transduction and cellular structural dynamics involved in the physiology of healthy and disease states. Such studies focus on drug pharmacokinetics, receptor-mediated endocytosis, nuclear mechanobiology, viral infections, and cancer metastasis. In 1976, fluorescence recovery after photobleaching (FRAP), which involves the monitoring of fluorescence emission recovery within a photobleached spot, was developed. FRAP allowed investigators to probe two-dimensional (2D) diffusion of fluorescently-labelled biomolecules. Since then, FRAP has been refined through the advancements of optics, charged-coupled-device (CCD) cameras, confocal microscopes, and molecular probes. FRAP is now a highly quantitative tool used for transport and kinetic studies in the cytosol, organelles, and membrane of a cell. In this work, the authors intend to provide a review of recent advances in FRAP. The authors include epifluorescence spot FRAP, total internal reflection (TIR)/FRAP, and confocal microscope-based FRAP. The underlying mathematical models are also described. Finally, our understanding of coupled transport and kinetics as determined by FRAP will be discussed and the potential for future advances suggested.

Proteome-wide prediction and analysis of the Cryptosporidium parvum protein-protein interaction network through integrative methods

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By combining a sequence embedding technique (i.e., Doc2Vec) and a di-peptide composition representation to convert protein sequences into feature vectors, we proposed an RF classifier trained on the Plasmodium falciparum dataset for predicting Cryptosporidium parvum PPIs.

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A high-confidence Cryptosporidium parvum PPI network was identified by conjoining interolog mapping, domain-domain interaction-based inference, and the RF classifier.

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Some detected hub proteins and functional modules provided clues for an in-depth biological understanding of Cryptosporidium parvum.

As one of the most studied Apicomplexan parasite Cryptosporidium, Cryptosporidium parvum (C. parvum) causes worldwide serious diarrhea disease cryptosporidiosis, which can be deadly to immunodeficiency individuals, newly born children, and animals. Proteome-wide identification of protein–protein interactions (PPIs) has proven valuable in the systematic understanding of the genome-phenome relationship. However, the PPIs of C. parvum are largely unknown because of the limited experimental studies carried out. Therefore, we took full advantage of three bioinformatics methods, i.e., interolog mapping (IM), domain-domain interaction (DDI)-based inference, and machine learning (ML) method, to jointly predict PPIs of C. parvum. Due to the lack of experimental PPIs of C. parvum, we used the PPI data of Plasmodium falciparum (P. falciparum), which owned the largest number of PPIs in Apicomplexa, to train an ML model to infer C. parvum PPIs. We utilized consistent results of these three methods as the predicted high-confidence PPI network, which contains 4,578 PPIs covering 554 proteins. To further explore the biological significance of the constructed PPI network, we also conducted essential network and protein functional analysis, mainly focusing on hub proteins and functional modules. We anticipate the constructed PPI network can become an important data resource to accelerate the functional genomics studies of C. parvum as well as offer new hints to the target discovery in developing drugs/vaccines.

High-Resolution Native Mass Spectrometry

Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of─among others─biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein-ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.

Accurate Correction of the "Bulk Response" in Surface Plasmon Resonance Sensing Provides New Insights on Interactions Involving Lysozyme and Poly(ethylene glycol)

Surface plasmon resonance is a very well-established surface sensitive technique for label-free analysis of biomolecular interactions, generating thousands of publications each year. An inconvenient effect that complicates interpretation of SPR results is the “bulk response” from molecules in solution, which generate signals without really binding to the surface. Here we present a physical model for determining the bulk response contribution and verify its accuracy. Our method does not require a reference channel or a separate surface region. We show that proper subtraction of the bulk response reveals an interaction between poly(ethylene glycol) brushes and the protein lysozyme at physiological conditions. Importantly, we also show that the bulk response correction method implemented in commercial instruments is not generally accurate. Using our method, the equilibrium affinity between polymer and protein is determined to be K_D = 200 μM. One reason for the weak affinity is that the interaction is relatively short-lived (1/k_off < 30 s). Furthermore, we show that the bulk response correction also reveals the dynamics of self-interactions between lysozyme molecules on surfaces. Besides providing new insights on important biomolecular interactions, our method can be widely applied to improve the accuracy of SPR data generated by instruments worldwide.

Graphene-Based Biosensors for Molecular Chronic Inflammatory Disease Biomarker Detection

Chronic inflammatory diseases, such as cancer, diabetes mellitus, stroke, ischemic heart diseases, neurodegenerative conditions, and COVID-19 have had a high number of deaths worldwide in recent years. The accurate detection of the biomarkers for chronic inflammatory diseases can significantly improve diagnosis, as well as therapy and clinical care in patients. Graphene derivative materials (GDMs), such as pristine graphene (G), graphene oxide (GO), and reduced graphene oxide (rGO), have shown tremendous benefits for biosensing and in the development of novel biosensor devices. GDMs exhibit excellent chemical, electrical and mechanical properties, good biocompatibility, and the facility of surface modification for biomolecular recognition, opening new opportunities for simple, accurate, and sensitive detection of biomarkers. This review shows the recent advances, properties, and potentialities of GDMs for developing robust biosensors. We show the main electrochemical and optical-sensing methods based on GDMs, as well as their design and manufacture in order to integrate them into robust, wearable, remote, and smart biosensors devices. We also describe the current application of such methods and technologies for the biosensing of chronic disease biomarkers. We also describe the current application of such methods and technologies for the biosensing of chronic disease biomarkers with improved sensitivity, reaching limits of detection from the nano to atto range concentration.

Binding Specificity of ASHH2 CW Domain Toward H3K4me1 Ligand Is Coupled to Its Structural Stability Through Its α1-Helix

The CW domain binds to histone tail modifications found in different protein families involved in epigenetic regulation and chromatin remodeling. CW domains recognize the methylation state of the fourth lysine on histone 3 and could, therefore, be viewed as a reader of epigenetic information. The specificity toward different methylation states such as me1, me2, or me3 depends on the particular CW subtype. For example, the CW domain of ASHH2 methyltransferase binds preferentially to H3K4me1, and MORC3 binds to both H3K4me2 and me3 modifications, while ZCWPW1 is more specific to H3K4me3. The structural basis for these preferential bindings is not well understood, and recent research suggests that a more complete picture will emerge if dynamical and energetic assessments are included in the analysis of interactions. This study uses fold assessment by NMR in combination with mutagenesis, ITC affinity measurements, and thermal denaturation studies to investigate possible couplings between ASHH2 CW selectivity toward H3K4me1 and the stabilization of the domain and loops implicated in binding. The key elements of the binding site—the two tryptophans and the α1-helix form and maintain the binding pocket— were perturbed by mutagenesis and investigated. Results show that the α1-helix maintains the overall stability of the fold via the I915 and L919 residues and that the correct binding consolidates the loops designated as η1 and η3, as well as the C-terminal. This consolidation is incomplete for H3K4me3 binding to CW, which experiences a decrease in overall thermal stability on binding. Loop mutations not directly involved in the binding site, nonetheless, affect the equilibrium positions of the key residues.

Developing a Biosensor-Based Immunoassay to Detect HPV E6 Oncoprotein in the Saliva Rinse Fluid of Oral Cancer Patients

Transmission of Human papillomavirus (HPVs) is faithfully associated with carcinogenesis of oral cavity and oropharyngeal cancers. Therefore, clinical researchers may need to generate customized antibodies for the upcoming ELISA-based analysis to discover rare but valuable biomarkers. The aim of study was to develop and generate a biosensor-based immunoassay for early screening HPV-related oral cancer via saliva rinse fluid analysis. A peptide fragment of high-risk HPV subtype 16/18 protein, E6 protein (HP-1 protein sequence 48–66), was designed and synthesized, followed by the generation of polyclonal antibodies (anti-HP1 IgY) in our university-based laboratories. The titer and specificity of antibodies were determined by enzyme-linked immunosorbent assay (ELISA), and the Surface Plasmon Resonance (SPR) biosensor-based method was developed. Kinetic analyses by SPR confirmed that this designed peptide showed a high affinity with its generated polyclonal antibodies. Saliva fluid samples of thirty oral cancer patients and 13 healthy subjects were analyzed. SPR indicated that 26.8% of oral cancer patients had higher resonance unit (ΔRU) values than normal subjects. In conclusion, we developed a biosensor-based immunoassay to detect HPV E6 oncoprotein in the saliva rinse fluid for early screening and discrimination of HPV-related oral cancer patients.

Interferon-γ detection in point of care diagnostics: Short review

Interferon (IFN)-γ is a cytokine secreted by immune cells. The elevated levels of IFN-γ are an early indicator of multiple diseases such as tuberculosis and autoimmune diseases. This short review focuses on different sensing methods based on optical, electrochemical, and mechanical principles. We explain how specific biorecognition molecules such as antibodies and aptamers are employed in the sensing methods. We also compare different surface functionalization methods and their details. Although the review gives an overview of only IFN-γ sensing, the same strategies can be applied to sensing other analytes with appropriate modifications.

Polydopamine-Coated Magnetic Iron Oxide Nanoparticles: From Design to Applications

Magnetic iron oxide nanoparticles have been extensively investigated due to their applications in various fields such as biomedicine, sensing, and environmental remediation. However, they need to be coated with a suitable material in order to make them biocompatible and to add new functionalities on their surface. This review is intended to give a comprehensive overview of recent advantages and applications of iron oxide nanoparticles coated by polydopamine film. The synthesis method of magnetic nanoparticles, their functionalization with bioinspired materials and (in particular) with polydopamine are discussed. Finally, some interesting applications of polydopamine-coated magnetic iron oxide nanoparticles will be pointed out.

Applications of Surface Plasmon Resonance and Biolayer Interferometry for Virus–Ligand Binding

Surface plasmon resonance and biolayer interferometry are two common real-time and label-free assays that quantify binding events by providing kinetic parameters. There is increased interest in using these techniques to characterize whole virus-ligand interactions, as the methods allow for more accurate characterization than that of a viral subunit-ligand interaction. This review aims to summarize and evaluate the uses of these technologies specifically in virus–ligand and virus-like particle–ligand binding cases to guide the field towards studies that apply these robust methods for whole virus-based studies.

Methods for the Discovery and Identification of Small Molecules Targeting Oxidative Stress-Related Protein–Protein Interactions: An Update

The oxidative stress response pathway is one of the hotspots of current pharmaceutical research. Many proteins involved in these pathways work through protein–protein interactions (PPIs). Hence, targeting PPI to develop drugs for an oxidative stress response is a promising strategy. In recent years, small molecules targeting protein–protein interactions (PPIs), which provide efficient methods for drug discovery, are being investigated by an increasing number of studies. However, unlike the enzyme–ligand binding mode, PPIs usually exhibit large and dynamic binding interfaces, which raise additional challenges for the discovery and optimization of small molecules and for the biochemical techniques used to screen compounds and study structure–activity relationships (SARs). Currently, multiple types of PPIs have been clustered into different classes, which make it difficult to design stationary methods for small molecules. Deficient experimental methods are plaguing medicinal chemists and are becoming a major challenge in the discovery of PPI inhibitors. In this review, we present current methods that are specifically used in the discovery and identification of small molecules that target oxidative stress-related PPIs, including proximity-based, affinity-based, competition-based, structure-guided, and function-based methods. Our aim is to introduce feasible methods and their characteristics that are implemented in the discovery of small molecules for different types of PPIs. For each of these methods, we highlight successful examples of PPI inhibitors associated with oxidative stress to illustrate the strategies and provide insights for further design.

Recent Advances in Surface Plasmon Resonance Sensors for Sensitive Optical Detection of Pathogens

The advancement of science and technology has led to the recent development of highly sensitive pathogen biosensing techniques. The effective treatment of pathogen infections requires sensing technologies to not only be sensitive but also render results in real-time. This review thus summarises the recent advances in optical surface plasmon resonance (SPR) sensor technology, which possesses the aforementioned advantages. Specifically, this technology allows for the detection of specific pathogens by applying nano-sized materials. This review focuses on various nanomaterials that are used to ensure the performance and high selectivity of SPR sensors. This review will undoubtedly accelerate the development of optical biosensing technology, thus allowing for real-time diagnosis and the timely delivery of appropriate treatments as well as preventing the spread of highly contagious pathogens.

Current Advances in Immunoassays for the Detection of β2-Agonists

β2-agonists are a group of synthetic phenylethanolamine compounds which are traditionally used for treating bronchospasm. These compounds can also increase skeletal muscle mass and decrease body fat. The illegal use of β2-agonists in food-producing animals results in residue of β2-agonists in edible tissues and causes adverse health effects in humans. Thus, the detection of β2-agonists at trace level in complex sample matrices is of great importance for monitoring the abuse of β2-agonists. Many methods have been developed to detect β2-agonists. Among them, a variety of antigen–antibody interaction-based techniques have been established to detect β2-agonists in various samples, including animal feed, urine, serum, milk, tissues and hair. In this review, we summarized current achievement in the extraction of β2-agonists from testing samples and detection of β2-agonists using immunological techniques. Future perspectives were briefly discussed.

A Novel Modulator of the Renin–Angiotensin System, Benzoylaconitine, Attenuates Hypertension by Targeting ACE/ACE2 in Enhancing Vasodilation and Alleviating Vascular Inflammation

The monoester alkaloids in Aconitum carmichaelii, including benzoylaconitine (BAC), benzoylmesaconine, and benzoylhypaconitine, were found to have anti-hypertensive effects in spontaneously hypertension rats (SHRs), of which BAC is the strongest. However, its antihypertensive target and underlying molecular mechanisms remain unclear. In this study, first, we screened the antihypertensive targets of BAC by using the CVDPlatform (www.cbligand.org/CVD) and found that ACE/ACE2 are the most possible targets. Then, we verified the effect of BAC on ACE/ACE2 by virtual docking, SPR, enzyme activity assay, and HUVECs cell experiment. We found that BAC could bind with ACE/ACE2, inhibit ACE activity and protein expression, and activate ACE2 enzyme activity. Using vascular function test in vitro, we found that BAC could target ACE/ACE2 to enhance endothelium-dependent vasorelaxation. In BAC-treated SHRs, the levels of ACE and AngII in serum were reduced while Ang (1–7) was increased significantly, and the expression of ACE was reduced, which suggested that BAC can inhibit ACE and activate ACE2 to inhibit AngI to AngII and promote AngII to Ang (1–7) to inhibit vasoconstriction and finally attenuate hypertension. Furthermore, the signaling pathways with regard to vasorelaxation and vascular inflammation were investigated. The results showed that BAC could significantly activate Akt/eNOS, increase NO production, and promote endothelial-related vasodilation; BAC could also reduce inflammatory factors TNF-α and IL6, inhibition of COX-2 expression, and IKB-α phosphorylation to reduce vascular inflammation in SHRs. In brief, BAC targets ACE/ACE2 to enhance endothelium-dependent vasorelaxation and reduce vascular inflammation to attenuate hypertension as a potential modulator of the renin–angiotensin system.

Revealing protein binding affinity on metal surfaces: an electrochemical approach

Revealing the binding affinity between viruses and surfaces of environmental matrices is crucial to evaluate the bioactivity of an immobilized virus and accompanying indirect virus-related infection pathways. The understanding for SARS-CoV-2 remaining infective for even days on stainless steel but only hours on copper is still unclear. Electrochemical chronoamperometry, ultrasensitive to interfacial capacitance on surface species, was used to investigate the binding affinity of SARS-CoV-2 on metal surfaces. S_RBD, the surrogate of SARS-CoV-2, shows the highest adsorption capacity on a gold surface, followed by Cu, but lowest on a stainless steel surface. The strong binding of S_RBD on copper is a result of the naturally grown Cu₂O under ambient conditions. Measurement of electrochemical capacitance provides a simple strategy to explore and evaluate the potential risk of an indirect virus-related infection pathway through conductive environmental matrices.

Catch, Modify and Analyze: Methods of Chemoselective Modification of Cysteine-Containing Peptides

One effective solution in the analysis of complex mixtures, including protein or cell hydrolysates, is based on chemoselective derivatization of a selected group of compounds by using selective tags to facilitate detection. Another method is based on the capture of the desired compounds by properly designed solid supports, resulting in sample enrichment. Cysteine is one of the rarest amino acids, but at least one cysteine residue is present in more than 91% of human proteins, which clearly confirms its important role in biological systems. Some cysteine-containing peptides may serve as significant molecular biomarkers, which may emerge as key indices in the management of patients with particular diseases. In the current review, we describe recent advances in the development of cysteine-containing peptide modification techniques based on solution and solid phase derivatization and enrichment strategies.

Nanostructured Carbons: towards Soft-Bioelectronics, Biosensing and Theraputic Applications

Recently, nanostructured carbon-based soft bioelectronics and biosensors have received tremendous attention due to their outstanding physical and chemical properties. The ultrahigh specific surface area, high flexibility, lightweight, high electrical conductivity, and biocompatibility of 1D and 2D nanocarbons, such as carbon nanotubes (CNT) and graphene, are advantageous for bioelectronics applications. These materials improve human life by delivering therapeutic advancements in gene, tumor, chemo, photothermal, immune, radio, and precision therapies. They are also utilized in biosensing platforms, including optical and electrochemical biosensors to detect cholesterol, glucose, pathogenic bacteria (e. g., coronavirus), and avian leucosis virus. This review summarizes the most recent advancements in bioelectronics and biosensors by exploiting the outstanding characteristics of nanocarbon materials. The synthesis and biocompatibility of nanocarbon materials are briefly discussed. In the following sections, applications of graphene and CNTs for different therapies and biosensing are elaborated. Finally, the key challenges and future perspectives of nanocarbon materials for biomedical applications are highlighted.

Surface plasmon resonance: A promising approach for label-free early cancer diagnosis

Cancer is the second leading cause of death worldwide after cardiovascular disease. The major cause of high mortality is delayed detection. Therefore, detection at an early stage followed by early treatment can mitigate morbidity as well as mortality. The utilization of biomarker-based detection tools helps in early-stage recognition. Fortunately, biomarkers indicating disease status can be released in to the circulation. These include traditional marker proteins as well as exosomes, micro-RNA (miRNA) and circulating tumor DNA (ct-DNA). Biosensors are biological and chemical reaction devices that generate signals based on analyte concentration. Due to analyte binding, these devices demonstrate high sensitivity and specificity. This review examines the use of surface plasmon resonance (SPR)-based sensors in the diagnosis of various cancer including those of the breast, prostate, lung, ovary, cervix and pancreas. SPR is a label-free, real-time and non-invasive optical biosensing technology representing a novel diagnostic tool in cancer detection.

Stimuli-responsive DNA-based hydrogels for biosensing applications

The base sequences of DNA are endowed with the rich structural and functional information and are available for the precise construction of the 2D and 3D macro products. The hydrogels formed by DNA are biocompatible, stable, tunable and biologically versatile, thus, these have a wide range of promising applications in bioanalysis and biomedicine. In particular, the stimuli-responsive DNA hydrogels (smart DNA hydrogels), which exhibit a reversible and switchable hydrogel to sol transition under different triggers, have emerged as smart materials for sensing. Thus far, the combination of the stimuli-responsive DNA hydrogels and multiple sensing platforms is considered as biocompatible and is useful as the flexible recognition components. A review of the stimuli-responsive DNA hydrogels and their biosensing applications has been presented in this study. The synthesis methods to prepare the DNA hydrogels have been introduced. Subsequently, the current status of the stimuli-responsive DNA hydrogels in biosensing has been described. The analytical mechanisms are further elaborated by the combination of the stimuli-responsive DNA hydrogels with the optical, electrochemical, point-of-care testing (POCT) and other detection platforms. In addition, the prospects of the application of the stimuli-responsive DNA hydrogels in biosensing are presented.

Surface Plasmon Resonance, a Novel Technique for Sensing Cancer Biomarker: Folate Receptor and Nanoparticles Interface

Despite advances in healthcare technology, the early detection biomarker and treatment remain one of the biggest challenges in humanity. Thus, developing a biosensor for timely diagnosis is well-justified to improve the prospect of remission of cancer patients. Surface plasmon resonance (SPR), a biosensor, is of interest that monitors many cancer biomarkers with high sensitivity and rapidity. For various cancers, nanoparticle (NP)-based targeted drug/gene delivery has been widely employed as it directs mainly the receptors expressed specifically on the cell membrane of the cancer cell. Folate Receptor 1 (FOLR1) or FOLRα, predominantly expressed on epithelial cells, remains a principal target for drug discovery in several cancers, including prostate or ovarian. Therefore, conjugation of folic acid to the NPs precisely targeting the biomarkers on the tumor cells allows the detection and helps in the treatment of various cancers. In the present study, we discuss the folate receptor as of diagnostic interest and focus on the use of the targeted planetary ball milled nanoparticles (PBM-NPs) and its formulation, emphasizing the approach using sensor chips in the Open SPR system for cancer biomarker detection.

Penetration of the SARS-CoV-2 Spike Protein across the Blood–Brain Barrier, as Revealed by a Combination of a Human Cell Culture Model System and Optical Biosensing

Since the outbreak of the global pandemic caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), several clinical aspects of the disease have come into attention. Besides its primary route of infection through the respiratory system, SARS-CoV-2 is known to have neuroinvasive capacity, causing multiple neurological symptoms with increased neuroinflammation and blood–brain barrier (BBB) damage. The viral spike protein disseminates via circulation during infection, and when reaching the brain could possibly cross the BBB, which was demonstrated in mice. Therefore, its medical relevance is of high importance. The aim of this study was to evaluate the barrier penetration of the S1 subunit of spike protein in model systems of human organs highly exposed to the infection. For this purpose, in vitro human BBB and intestinal barrier cell–culture systems were investigated by an optical biosensing method. We found that spike protein crossed the human brain endothelial cell barrier effectively. Additionally, spike protein passage was found in a lower amount for the intestinal barrier cell layer. These observations were corroborated with parallel specific ELISAs. The findings on the BBB model could provide a further basis for studies focusing on the mechanism and consequences of spike protein penetration across the BBB to the brain.